cobot-io-0.1.4.3: test/PDB/BondsRestoring/ALA_3.mae
{
s_m_m2io_version
:::
2.0.0
}
f_m_ct {
s_m_title
s_m_entry_name
i_m_stars
s_m_entry_id
s_m_job_name
r_mmod_Potential_Energy-OPLS-2005
s_pdb_PDB_TITLE
s_pdb_PDB_ID
r_pdb_PDB_CRYST1_a
r_pdb_PDB_CRYST1_b
r_pdb_PDB_CRYST1_c
r_pdb_PDB_CRYST1_alpha
r_pdb_PDB_CRYST1_beta
r_pdb_PDB_CRYST1_gamma
s_pdb_PDB_CRYST1_Space_Group
i_pdb_PDB_CRYST1_z
s_pdb_PDB_CLASSIFICATION
s_pdb_PDB_DEPOSITION_DATE
s_pdb_PDB_format_version
r_pdb_PDB_R
r_pdb_PDB_Rfree
r_pdb_PDB_RESOLUTION
s_pdb_PDB_EXPDTA
r_pdb_PDB_EXPDTA_TEMPERATURE
r_pdb_PDB_EXPDTA_PH
s_pdb_PDB_REMARK_350_Biomolecule_1_Chains
s_pdb_PDB_REMARK_350_Biomolecule_1_Transformation_1
s_pdb_PDB_REMARK_350_Biomolecule_2_Chains
s_pdb_PDB_REMARK_350_Biomolecule_2_Transformation_1
s_ppw_entry_id_backup
b_ppw_prepared
b_ppw_assigned_bond_orders
b_ppw_added_hydrogens
b_ppw_treated_metals
b_ppw_created_disulfur
b_ppw_deleted_far_waters
s_m_Source_Path
s_m_Source_File
i_m_Source_File_Index
s_st_Chirality_1
b_psp_distorted_structure
i_psp_model_num
r_psp_Prime_Coulomb
r_psp_Prime_Covalent
r_psp_Prime_vdW
r_psp_Prime_Solv_GB
r_psp_Prime_Lipo
r_psp_Prime_Energy
r_psp_Prime_Hbond
r_psp_Prime_Packing
r_psp_Prime_SelfCont
r_i_target_temperature
b_ppw_ran_impref
b_ppw_ran_protassign
i_m_source_file_index
i_lp_mmshare_version
r_epik_Ionization_Penalty
r_epik_Ionization_Penalty_Charging
r_epik_Ionization_Penalty_Neutral
r_epik_State_Penalty
i_epik_Tot_Q
s_st_Chirality_2
s_st_Chirality_3
b_mmod_Minimization_Converged-OPLS-2005
r_mmod_RMS_Derivative-OPLS-2005
i_mmod_Times_Found-OPLS-2005
r_mmod_Relative_Potential_Energy-OPLS-2005
b_mmod_Chiralities_Consistent-OPLS-2005
i_mmod_Conformation-OPLS-2005
i_mmod_Serial_Number-OPLS-2005
:::
Structure
Structure
0
272
ligprep_2
25.4914207458496
"CRYSTAL STRUCTURE OF EGFR KINASE DOMAIN T790M MUTATION IN COMPEX WITH HKI-272"
2JIV
56.087
98.989
73.326
90
109.94
90
"P 1 21 1"
4
TRANSFERASE
02-JUL-07
3.30
0.250999987125397
0.284000009298325
3.5
"X-RAY DIFFRACTION"
100
7.5
A
"1.000000 0.000000 0.000000 0.000000;0.000000 1.000000 0.000000 0.000000;0.000000 0.000000 1.000000 0.000000"
B
"1.000000 0.000000 0.000000 0.000000;0.000000 1.000000 0.000000 0.000000;0.000000 0.000000 1.000000 0.000000"
254
1
1
1
1
1
1
/home/shehovtsov/ownCloud/SchResults/ChemNext/OPLSCrack.prj
2jiv.pdb
1
4_S_3_5_2_22
0
0
-15228.2951610052
8844.27158380025
50916082887.1437
-4025.5362735107
-3537.76289714321
50916068618.8497
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32018
0.1225
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0.1115
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7_S_6_8_10_24
12_S_11_13_15_29
1
0.00200419803149998
1
0
1
1
1
m_depend[17] {
# First column is dependency index #
i_m_depend_dependency
s_m_depend_property
:::
1 30 s_m_job_name
2 20 r_mmod_Potential_Energy-OPLS-2005
3 10 s_st_Chirality_1
4 10 r_epik_Ionization_Penalty
5 10 r_epik_Ionization_Penalty_Charging
6 10 r_epik_Ionization_Penalty_Neutral
7 10 r_epik_State_Penalty
8 10 i_epik_Tot_Q
9 10 s_st_Chirality_2
10 10 s_st_Chirality_3
11 20 b_mmod_Minimization_Converged-OPLS-2005
12 20 r_mmod_RMS_Derivative-OPLS-2005
13 20 i_mmod_Times_Found-OPLS-2005
14 20 r_mmod_Relative_Potential_Energy-OPLS-2005
15 20 b_mmod_Chiralities_Consistent-OPLS-2005
16 20 i_mmod_Conformation-OPLS-2005
17 10 i_mmod_Serial_Number-OPLS-2005
:::
}
m_atom[33] {
# First column is atom index #
i_m_mmod_type
r_m_x_coord
r_m_y_coord
r_m_z_coord
i_m_residue_number
s_m_mmod_res
s_m_chain_name
i_m_color
r_m_charge1
r_m_charge2
s_m_pdb_residue_name
s_m_pdb_atom_name
s_m_grow_name
i_m_atomic_number
i_m_formal_charge
i_m_representation
i_m_visibility
s_m_color_rgb
s_m_atom_name
i_m_secondary_structure
s_m_label_format
i_m_label_color
s_m_label_user_text
r_m_pdb_occupancy
r_m_pdb_tfactor
r_psp_Prime_Coulomb
r_psp_Prime_Covalent
r_psp_Prime_Energy
r_psp_Prime_Hbond
r_psp_Prime_Lipo
r_psp_Prime_Packing
r_psp_Prime_SelfCont
r_psp_Prime_Solv_GB
r_psp_Prime_Solv_SA
r_psp_Prime_vdW
r_psp_atom_born_radius
r_psp_atom_partial_charge
r_psp_atom_sgb_radius
r_psp_atom_vdw_radius
r_psp_ffld_partial_charge
r_psp_solvent_exposed_surface_area
i_i_constraint
i_i_internal_atom_index
i_m_Hcount
i_pa_atomindex
i_pdb_PDB_serial
i_pdb_seqres_chain
i_pdb_seqres_index
i_zob_match_atom_index
i_zob_match_atom_type
r_epik_H2O_pKa
r_epik_H2O_pKa_uncertainty
:::
1 15 14.990554 -6.772408 3.076800 702 A A 75 -0.50000 -0.50000 "ALA " " O " " " 8 0 3 1 FF5757 "" 0 "" 75 "" 1 38.22 -52.863 0.002 -4.166 -0.053 0 0 0 43.242 0 5.505 4.286 -0.5 1.678 1.48 -0.5 2.293 0 6 0 6 18 1 3 1 -1 <> <>
2 3 17.248524 -5.500628 1.114095 702 A A 10 -0.18000 -0.18000 "ALA " " CB " " " 6 0 3 1 1EE11E "" 0 "" 10 "" 1 38.67 -16.454 0.566 -2.916 0 -2.086 0 0 14.912 0 0.145 4.195 -0.18 1.975 1.75 -0.18 1.496 0 7 3 7 19 1 3 2 -1 <> <>
3 32 17.252295 -5.273120 3.576736 702 A A 43 -0.30000 -0.30000 "ALA " " N " " " 7 1 3 1 5757FF "" 0 "" 38 "" 1 39.05 -44.236 0.556 -8.041 -0.03 0 0 0 35.782 0 -0.114 4.721 -0.5 1.92 1.625 -0.5 0 0 8 3 8 15 1 3 3 -1 <> <>
4 3 16.468061 -5.032000 2.351712 702 A A 10 0.25000 0.25000 "ALA " " CA " " " 6 0 3 1 1EE11E "" 0 "" 10 "" 1 38.59 11.935 0.574 3.991 0 -1.399 0 0 -6.836 0 -0.283 4.771 0.14 1.975 1.75 0.14 0 0 9 1 9 16 1 3 4 -1 <> <>
5 2 15.106278 -5.729636 2.433057 702 A A 10 0.50000 0.50000 "ALA " " C " " " 6 0 3 1 1EE11E "" 0 "" 10 "" 1 38.18 40.757 0.733 3.047 0 0 0 0 -46.947 0 8.503 5.367 0.5 2.112 1.875 0.5 0 0 10 0 10 17 1 3 5 -1 <> <>
6 25 14.093802 -5.132405 1.779119 703 A A 38 -0.50000 -0.50000 "ALA " " N " " c1" 7 0 3 1 2F2FFF "N12" -1 "" 38 "" <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> 0 12 1 12 <> <> <> 6 -1 <> <>
7 3 12.691092 -5.556884 1.686621 703 A A 10 0.14000 0.14000 "ALA " " CA " " g0" 6 0 3 1 1EE11E "C13" -1 "" 10 "" <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> 0 13 1 13 <> <> <> 7 -1 <> <>
8 2 11.838035 -5.066554 2.867123 703 A A 10 0.50000 0.50000 "ALA " " C " " n1" 6 0 3 1 1EE11E "C14" -1 "" 10 "" <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> 0 14 0 14 <> <> <> 8 -1 <> <>
9 15 12.356370 -4.855328 3.963740 703 A A 75 -0.50000 -0.50000 "ALA " " O " " " 8 0 3 1 FF5757 "O15" -1 "" 75 "" <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> 0 15 0 15 <> <> <> 9 -1 -1.677 0.746
10 3 12.515299 -7.054765 1.364177 703 A A 10 -0.18000 -0.18000 "ALA " " CB " " g1" 6 0 3 1 1EE11E "C16" -1 "" 10 "" <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> 0 16 3 16 <> <> <> 10 -1 <> <>
11 25 10.529949 -4.890188 2.610446 704 A A 38 -0.50000 -0.50000 "ALA " " N " " c1" 7 0 3 1 2F2FFF "N22" -1 "" 38 "" <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> 0 22 1 22 <> <> <> 11 -1 <> <>
12 3 9.475121 -4.435355 3.520735 704 A A 10 0.04000 0.04000 "ALA " " CA " " g0" 6 0 3 1 1EE11E "C23" -1 "" 10 "" <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> 0 23 1 23 <> <> <> 12 -1 <> <>
13 2 9.393844 -2.904178 3.567672 704 A A 10 0.70000 0.70000 "ALA " " C " " n1" 6 0 3 1 1EE11E "C24" -1 "" 10 "" <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> 0 24 0 24 <> <> <> 13 -1 <> <>
14 15 8.706856 -2.346088 2.683930 704 A A 75 -0.80000 -0.80000 "ALA " " O " " " 8 0 3 1 FF5757 "O25" -1 "" 75 "" <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> 0 25 0 25 <> <> <> 14 -1 <> <>
15 3 9.479252 -5.139179 4.894444 704 A A 10 -0.18000 -0.18000 "ALA " " CB " " g1" 6 0 3 1 1EE11E "C26" -1 "" 10 "" <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> 0 26 3 26 <> <> <> 15 -1 <> <>
16 18 10.030686 -2.315400 4.468878 704 X A 70 -0.80000 -0.80000 "ALA " "OXT " " n2" 8 -1 3 1 FF2F2F "O27" -1 "%UT" 75 "" <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> 0 32 0 27 <> <> <> 16 -1 3.647 0.775
17 41 16.692080 -5.303613 0.196715 702 A A 21 0.06000 0.06000 "ALA " " HB1" " " 1 0 3 0 FFFFFF "" -1 "" 21 "" <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> 0 <> <> <> <> 17 -1 <> <>
18 41 18.203449 -4.980567 1.031668 702 A A 21 0.06000 0.06000 "ALA " " HB2" " " 1 0 3 0 FFFFFF "" -1 "" 21 "" <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> 0 <> <> <> <> 18 -1 <> <>
19 41 17.455921 -6.571126 1.151605 702 A A 21 0.06000 0.06000 "ALA " " HB3" " " 1 0 3 0 FFFFFF "" -1 "" 21 "" <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> 0 <> <> <> <> 19 -1 <> <>
20 44 16.736538 -4.927325 4.373555 702 A A 21 0.33000 0.33000 "ALA " " H1 " " " 1 0 3 1 FFFFFF "" -1 "" 21 "" <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> 0 <> <> <> <> 20 -1 7.641 0.791
21 44 17.394087 -6.267655 3.683649 702 A A 21 0.33000 0.33000 "ALA " " H2 " " " 1 0 3 1 FFFFFF "" -1 "" 21 "" <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> 0 <> <> <> <> 21 -1 7.641 0.791
22 41 16.304340 -3.955510 2.281420 702 A A 21 0.06000 0.06000 "ALA " " HA " " " 1 0 3 0 FFFFFF "" -1 "" 21 "" <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> 0 <> <> <> <> 22 -1 <> <>
23 43 14.311194 -4.272661 1.296478 703 A A 21 0.30000 0.30000 "ALA " " H " " " 1 0 3 1 FFFFFF "" -1 "" 21 "" <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> 0 <> <> <> <> 23 -1 10.426 0.746
24 41 12.319997 -5.017059 0.814122 703 A A 21 0.06000 0.06000 "ALA " " HA " " " 1 0 3 0 FFFFFF "" -1 "" 21 "" <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> 0 <> <> <> <> 24 -1 <> <>
25 41 11.480911 -7.275798 1.099127 703 A A 21 0.06000 0.06000 "ALA " " HB1" " " 1 0 3 0 FFFFFF "" -1 "" 21 "" <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> 0 <> <> <> <> 25 -1 <> <>
26 41 13.137289 -7.352938 0.519739 703 A A 21 0.06000 0.06000 "ALA " " HB2" " " 1 0 3 0 FFFFFF "" -1 "" 21 "" <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> 0 <> <> <> <> 26 -1 <> <>
27 41 12.768546 -7.690979 2.212181 703 A A 21 0.06000 0.06000 "ALA " " HB3" " " 1 0 3 0 FFFFFF "" -1 "" 21 "" <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> 0 <> <> <> <> 27 -1 <> <>
28 43 10.225854 -5.076323 1.666369 704 A A 21 0.30000 0.30000 "ALA " " H " " " 1 0 3 1 FFFFFF "" -1 "" 21 "" <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> 0 <> <> <> <> 28 -1 12.322 0.746
29 41 8.551949 -4.757203 3.036779 704 A A 21 0.06000 0.06000 "ALA " " HA " " " 1 0 3 0 FFFFFF "" -1 "" 21 "" <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> 0 <> <> <> <> 29 -1 <> <>
30 41 8.580047 -4.887228 5.457279 704 A A 21 0.06000 0.06000 "ALA " " HB1" " " 1 0 3 0 FFFFFF "" -1 "" 21 "" <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> 0 <> <> <> <> 30 -1 <> <>
31 41 9.501137 -6.223250 4.781251 704 A A 21 0.06000 0.06000 "ALA " " HB2" " " 1 0 3 0 FFFFFF "" -1 "" 21 "" <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> 0 <> <> <> <> 31 -1 <> <>
32 41 10.330791 -4.847720 5.508967 704 A A 21 0.06000 0.06000 "ALA " " HB3" " " 1 0 3 0 FFFFFF "" -1 "" 21 "" <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> 0 <> <> <> <> 32 -1 <> <>
33 44 18.143618 -4.802897 3.515682 702 A A 21 0.33000 0.33000 "ALA " " H3 " " " 1 0 0 1 FFFFFF "" -1 "" 1 "" <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> <> 0 <> <> <> <> <> <> 7.641 0.791
:::
}
m_bond[32] {
# First column is bond index #
i_m_from
i_m_to
i_m_order
i_m_from_rep
i_m_to_rep
:::
1 1 5 2 3 3
2 2 4 1 3 3
3 2 17 1 3 3
4 2 18 1 3 3
5 2 19 1 3 3
6 3 4 1 3 3
7 3 20 1 3 3
8 3 21 1 3 3
9 3 33 1 1 1
10 4 5 1 3 3
11 4 22 1 3 3
12 5 6 1 3 3
13 6 7 1 3 3
14 6 23 1 3 3
15 7 8 1 3 3
16 7 10 1 3 3
17 7 24 1 3 3
18 8 9 2 3 3
19 8 11 1 3 3
20 10 25 1 3 3
21 10 26 1 3 3
22 10 27 1 3 3
23 11 12 1 3 3
24 11 28 1 3 3
25 12 13 1 3 3
26 12 15 1 3 3
27 12 29 1 3 3
28 13 14 2 3 3
29 13 16 1 3 3
30 15 30 1 3 3
31 15 31 1 3 3
32 15 32 1 3 3
:::
}
}