# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 15:55:57 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: 6-[(2-hydroxybenzyl)amino]pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1ccc(NCc2ccccc2O)nc1
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 4GM  4GM  6-[(2-hydroxybenzyl)amino]pyridine-3-carboxamide  ligand  31  18  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4GM
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 4GM  C8   C  CR16  0  -0.273   5.0218   1.1093   0.8074
 4GM  C9   C  CR16  0  -0.251   5.5016  -0.1561   0.5039
 4GM  C2   C  CR16  0  -0.151  -2.8070   0.6158  -0.9895
 4GM  C7   C  CR16  0  -0.282   3.7110   1.4308   0.4796
 4GM  C10  C  CR16  0  -0.377   4.6821  -1.0869  -0.1181
 4GM  C3   C  CR16  0  -0.401  -1.4427   0.7272  -0.8950
 4GM  C12  C  CR16  0  -0.072  -2.8128  -0.4962   1.0998
 4GM  C1   C  CR6   0  -0.166  -3.5448  -0.0149   0.0187
 4GM  C6   C  CR6   0  -0.028   2.8712   0.5176  -0.1457
 4GM  C11  C  CR6   0   0.340   3.3689  -0.7569  -0.4415
 4GM  C4   C  CR6   0   0.520  -0.8028   0.1870   0.2407
 4GM  C5   C  CH2   0  -0.320   1.4558   0.8853  -0.4884
 4GM  N2   N  N     0  -0.464  -1.5015  -0.4063   1.2182
 4GM  N    N  NH2   0  -0.829  -5.6899  -0.7861   0.8276
 4GM  N1   N  NH1   0  -0.643   0.5303   0.2303   0.4090
 4GM  O    O  O     0  -0.494  -5.5952   0.4159  -1.0677
 4GM  O1   O  OH1   0  -0.621   2.5372  -1.6268  -1.0456
 4GM  H1   H  HCR6  0   0.254   5.6569   1.8386   1.2917
 4GM  H2   H  HCR6  0   0.261   6.5200  -0.4268   0.7504
 4GM  H3   H  HCR6  0   0.268  -3.3146   1.0240  -1.8530
 4GM  H4   H  HCR6  0   0.255   3.3269   2.4174   0.7109
 4GM  H5   H  HCR6  0   0.270   5.0652  -2.0732  -0.3551
 4GM  H6   H  HCR6  0   0.277  -0.8841   1.2239  -1.6752
 4GM  H7   H  HCR6  0   0.247  -3.3014  -0.9839   1.9375
 4GM  H8   H  HCH2  0   0.253   1.3445   1.9739  -0.4395
 4GM  H9   H  HCH2  0   0.254   1.2339   0.5947  -1.5183
 4GM  H10  H  HNH2  0   0.410  -5.2494  -1.2411   1.6060
 4GM  H11  H  HNH2  0   0.403  -6.6924  -0.8549   0.7701
 4GM  H12  H  HNH1  0   0.390   0.8798  -0.1005   1.2943
 4GM  H13  H  HOH1  0   0.476   2.9916  -2.4591  -1.2180
 4GM  C    C  C     0   0.493  -5.0198  -0.1084  -0.1195

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 4GM  C10  C9   aromatic  1.387  0.020  1.387
 4GM  C10  C11  aromatic  1.392  0.020  1.392
 4GM  C9   C8   aromatic  1.387  0.020  1.387
 4GM  O1   C11  single    1.347  0.020  1.347
 4GM  C11  C6   aromatic  1.400  0.020  1.400
 4GM  C8   C7   aromatic  1.389  0.020  1.389
 4GM  C6   C7   aromatic  1.389  0.020  1.389
 4GM  C6   C5   single    1.502  0.020  1.502
 4GM  C5   N1   single    1.446  0.020  1.446
 4GM  N1   C4   single    1.344  0.020  1.344
 4GM  C3   C4   aromatic  1.411  0.020  1.411
 4GM  C3   C2   aromatic  1.372  0.020  1.372
 4GM  C4   N2   aromatic  1.340  0.020  1.340
 4GM  C2   C1   aromatic  1.400  0.020  1.400
 4GM  N2   C12  aromatic  1.320  0.020  1.320
 4GM  C1   C12  aromatic  1.392  0.020  1.392
 4GM  C1   C    single    1.484  0.020  1.484
 4GM  C    O    double    1.227  0.020  1.227
 4GM  C    N    single    1.344  0.020  1.344
 4GM  C8   H1   single    0.930  0.020  1.080
 4GM  C9   H2   single    0.930  0.020  1.080
 4GM  C2   H3   single    0.930  0.020  1.080
 4GM  C7   H4   single    0.930  0.020  1.080
 4GM  C10  H5   single    0.930  0.020  1.080
 4GM  C3   H6   single    0.930  0.020  1.080
 4GM  C12  H7   single    0.930  0.020  1.080
 4GM  C5   H8   single    0.970  0.020  1.090
 4GM  C5   H9   single    0.970  0.020  1.090
 4GM  N    H10  single    0.860  0.020  1.020
 4GM  N    H11  single    0.860  0.020  1.020
 4GM  N1   H12  single    0.860  0.020  1.020
 4GM  O1   H13  single    0.850  0.020  0.980

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 4GM  H1   C8   C7   120.25  3.000
 4GM  H1   C8   C9   120.66  3.000
 4GM  C7   C8   C9   119.08  3.000
 4GM  H2   C9   C10  119.35  3.000
 4GM  H2   C9   C8   120.26  3.000
 4GM  C10  C9   C8   120.39  3.000
 4GM  H3   C2   C1   119.85  3.000
 4GM  H3   C2   C3   119.41  3.000
 4GM  C1   C2   C3   120.74  3.000
 4GM  H4   C7   C6   118.70  3.000
 4GM  H4   C7   C8   119.66  3.000
 4GM  C6   C7   C8   121.64  3.000
 4GM  H5   C10  C11  119.87  3.000
 4GM  H5   C10  C9   119.98  3.000
 4GM  C11  C10  C9   120.15  3.000
 4GM  H6   C3   C4   121.51  3.000
 4GM  H6   C3   C2   120.11  3.000
 4GM  C4   C3   C2   118.38  3.000
 4GM  H7   C12  N2   114.11  3.000
 4GM  H7   C12  C1   121.21  3.000
 4GM  N2   C12  C1   124.67  3.000
 4GM  C    C1   C12  124.98  3.000
 4GM  C    C1   C2   119.03  3.000
 4GM  C12  C1   C2   115.99  3.000
 4GM  C5   C6   C11  120.64  3.000
 4GM  C5   C6   C7   120.76  3.000
 4GM  C11  C6   C7   118.60  3.000
 4GM  O1   C11  C6   117.60  3.000
 4GM  C6   C11  C10  120.14  3.000
 4GM  O1   C11  C10  122.26  3.000
 4GM  N1   C4   N2   116.10  3.000
 4GM  N2   C4   C3   121.34  3.000
 4GM  N1   C4   C3   122.56  3.000
 4GM  H9   C5   H8   106.60  3.000
 4GM  H9   C5   N1   109.54  3.000
 4GM  H8   C5   N1   110.94  3.000
 4GM  H9   C5   C6   109.95  3.000
 4GM  H8   C5   C6   109.19  3.000
 4GM  N1   C5   C6   110.52  3.000
 4GM  C4   N2   C12  118.87  3.000
 4GM  H11  N    H10  116.78  3.000
 4GM  H11  N    C    119.40  3.000
 4GM  H10  N    C    123.82  3.000
 4GM  H12  N1   C5   118.17  3.000
 4GM  H12  N1   C4   116.32  3.000
 4GM  C5   N1   C4   124.86  3.000
 4GM  H13  O1   C11  110.29  3.000
 4GM  O    C    N    121.77  3.000
 4GM  N    C    C1   117.50  3.000
 4GM  O    C    C1   120.73  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 4GM  CONST_01  C11  C10  C9   C8      0.00   0.0  0
 4GM  CONST_02  C11  C6   C7   C8      0.00   0.0  0
 4GM  CONST_03  C6   C11  C10  C9      0.00   0.0  0
 4GM  CONST_04  C6   C7   C8   C9      0.00   0.0  0
 4GM  CONST_05  N2   C4   C3   C2      0.00   0.0  0
 4GM  CONST_06  N2   C12  C1   C2      0.00   0.0  0
 4GM  CONST_07  C10  C9   C8   C7      0.00   0.0  0
 4GM  CONST_08  C10  C11  C6   C7      0.00   0.0  0
 4GM  CONST_09  C12  N2   C4   C3      0.00   0.0  0
 4GM  CONST_10  C12  C1   C2   C3      0.00   0.0  0
 4GM  CONST_11  C4   C3   C2   C1      0.00   0.0  0
 4GM  CONST_12  C4   N2   C12  C1      0.00   0.0  0
 4GM  CONST_13  C5   C6   C7   C8    180.00   0.0  0
 4GM  CONST_14  O1   C11  C10  C9    180.00   0.0  0
 4GM  CONST_15  N1   C4   C3   C2    180.00   0.0  0
 4GM  CONST_16  O1   C11  C6   C7    180.00   0.0  0
 4GM  CONST_17  C5   C6   C11  C10   180.00   0.0  0
 4GM  CONST_18  C    C1   C2   C3    180.00   0.0  0
 4GM  CONST_19  N1   C4   N2   C12   180.00   0.0  0
 4GM  CONST_20  N2   C12  C1   C     180.00   0.0  0
 4GM  CONST_21  H5   C10  C9   C8    180.00   0.0  0
 4GM  CONST_22  H4   C7   C8   C9    180.00   0.0  0
 4GM  CONST_23  H7   C12  C1   C2    180.00   0.0  0
 4GM  CONST_24  H2   C9   C8   C7    180.00   0.0  0
 4GM  CONST_25  H1   C8   C9   C10   180.00   0.0  0
 4GM  CONST_26  H3   C2   C1   C12   180.00   0.0  0
 4GM  CONST_27  H6   C3   C2   C1    180.00   0.0  0
 4GM  CONST_28  C5   N1   C4   C3      0.00   0.0  0
 4GM  CONST_29  N2   C4   N1   C5    180.00   0.0  0
 4GM  CONST_30  H12  N1   C4   C3    180.00   0.0  0
 4GM  CONST_31  H10  N    C    C1      0.00   0.0  0
 4GM  CONST_32  H11  N    C    C1    180.00   0.0  0
 4GM  Var_01    O    C    C1   C2     -3.61  30.0  2
 4GM  Var_02    N1   C5   C6   C7   -106.31  30.0  2
 4GM  Var_03    C4   N1   C5   C6   -169.15  30.0  3

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 4GM  plan-1  C8   0.020
 4GM  plan-1  C9   0.020
 4GM  plan-1  C7   0.020
 4GM  plan-1  C10  0.020
 4GM  plan-1  C6   0.020
 4GM  plan-1  C11  0.020
 4GM  plan-1  C5   0.020
 4GM  plan-1  O1   0.020
 4GM  plan-1  H1   0.020
 4GM  plan-1  H2   0.020
 4GM  plan-1  H4   0.020
 4GM  plan-1  H5   0.020
 4GM  plan-2  C2   0.020
 4GM  plan-2  C3   0.020
 4GM  plan-2  C12  0.020
 4GM  plan-2  C1   0.020
 4GM  plan-2  C4   0.020
 4GM  plan-2  N2   0.020
 4GM  plan-2  N1   0.020
 4GM  plan-2  H3   0.020
 4GM  plan-2  H6   0.020
 4GM  plan-2  H7   0.020
 4GM  plan-2  C    0.020
 4GM  plan-3  C1   0.020
 4GM  plan-3  N    0.020
 4GM  plan-3  O    0.020
 4GM  plan-3  H10  0.020
 4GM  plan-3  H11  0.020
 4GM  plan-3  C    0.020
 4GM  plan-4  C4   0.020
 4GM  plan-4  C5   0.020
 4GM  plan-4  N1   0.020
 4GM  plan-4  H12  0.020

