# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 15:30:13 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: 6-[(3-hydroxybenzyl)amino]pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1ccc(NCc2cccc(O)c2)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
 4G3  4G3  6-[(3-hydroxybenzyl)amino]pyridine-3-carboxamide  ligand  31  18  .  2021-08-04  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_4G3
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
 4G3  C8   C  CR16  0  -0.230   4.6849   1.4011  -0.9662
 4G3  C2   C  CR16  0  -0.151  -2.9514   0.5560   1.0482
 4G3  C7   C  CR16  0  -0.323   3.3701   1.6091  -0.5661
 4G3  C9   C  CR16  0  -0.344   5.3662   0.2543  -0.5965
 4G3  C3   C  CR16  0  -0.398  -1.5836   0.6541   0.9912
 4G3  C11  C  CR16  0  -0.413   3.4097  -0.5003   0.5909
 4G3  C12  C  CR16  0  -0.071  -2.8923  -0.7350  -0.9358
 4G3  C1   C  CR6   0  -0.166  -3.6580  -0.1493   0.0677
 4G3  C6   C  CR6   0   0.081   2.7319   0.6574   0.2189
 4G3  C10  C  CR6   0   0.372   4.7253  -0.7050   0.1872
 4G3  C4   C  CR6   0   0.517  -0.9111   0.0226  -0.0754
 4G3  C5   C  CH2   0  -0.339   1.3013   0.8500   0.6396
 4G3  N2   N  N     0  -0.463  -1.5768  -0.6602  -1.0157
 4G3  N    N  NH2   0  -0.829  -5.7911  -0.8612  -0.8244
 4G3  N1   N  NH1   0  -0.646   0.4289   0.0616  -0.2036
 4G3  O    O  O     0  -0.492  -5.7299   0.2671   1.1176
 4G3  O1   O  OH1   0  -0.632   5.4248  -1.8064   0.5233
 4G3  H1   H  HCR6  0   0.260   5.1864   2.1424  -1.5747
 4G3  H2   H  HCR6  0   0.269  -3.4855   1.0318   1.8596
 4G3  H3   H  HCR6  0   0.252   2.8463   2.5092  -0.8624
 4G3  H4   H  HCR6  0   0.265   6.3910   0.0957  -0.9083
 4G3  H5   H  HCR6  0   0.279  -1.0450   1.2040   1.7498
 4G3  H6   H  HCR6  0   0.269   2.9075  -1.2430   1.2033
 4G3  H7   H  HCR6  0   0.248  -3.3548  -1.3083  -1.7330
 4G3  H8   H  HCH2  0   0.256   1.1804   0.5459   1.6835
 4G3  H9   H  HCH2  0   0.254   1.0403   1.9124   0.5864
 4G3  H10  H  HNH2  0   0.410  -5.3444  -1.2062  -1.6545
 4G3  H11  H  HNH2  0   0.403  -6.7970  -0.8951  -0.8069
 4G3  H12  H  HNH1  0   0.392   0.8085  -0.3296  -1.0510
 4G3  H13  H  HOH1  0   0.475   4.8887  -2.3940   1.0673
 4G3  C    C  C     0   0.494  -5.1377  -0.2265   0.1638

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
 4G3  C9   C8   aromatic  1.384  0.020  1.384
 4G3  C9   C10  aromatic  1.395  0.020  1.395
 4G3  C8   C7   aromatic  1.390  0.020  1.390
 4G3  O1   C10  single    1.347  0.020  1.347
 4G3  C10  C11  aromatic  1.391  0.020  1.391
 4G3  C7   C6   aromatic  1.389  0.020  1.389
 4G3  C11  C6   aromatic  1.392  0.020  1.392
 4G3  C6   C5   single    1.504  0.020  1.504
 4G3  C5   N1   single    1.447  0.020  1.447
 4G3  N1   C4   single    1.347  0.020  1.347
 4G3  C3   C4   aromatic  1.410  0.020  1.410
 4G3  C3   C2   aromatic  1.372  0.020  1.372
 4G3  C4   N2   aromatic  1.339  0.020  1.339
 4G3  C2   C1   aromatic  1.399  0.020  1.399
 4G3  N2   C12  aromatic  1.320  0.020  1.320
 4G3  C1   C12  aromatic  1.391  0.020  1.391
 4G3  C1   C    single    1.485  0.020  1.485
 4G3  C    O    double    1.226  0.020  1.226
 4G3  C    N    single    1.344  0.020  1.344
 4G3  C8   H1   single    0.930  0.020  1.080
 4G3  C2   H2   single    0.930  0.020  1.080
 4G3  C7   H3   single    0.930  0.020  1.080
 4G3  C9   H4   single    0.930  0.020  1.080
 4G3  C3   H5   single    0.930  0.020  1.080
 4G3  C11  H6   single    0.930  0.020  1.080
 4G3  C12  H7   single    0.930  0.020  1.080
 4G3  C5   H8   single    0.970  0.020  1.090
 4G3  C5   H9   single    0.970  0.020  1.090
 4G3  N    H10  single    0.860  0.020  1.020
 4G3  N    H11  single    0.860  0.020  1.020
 4G3  N1   H12  single    0.860  0.020  1.020
 4G3  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
 4G3  H1   C8   C9   119.31  3.000
 4G3  H1   C8   C7   119.84  3.000
 4G3  C9   C8   C7   120.84  3.000
 4G3  H2   C2   C1   119.87  3.000
 4G3  H2   C2   C3   119.46  3.000
 4G3  C1   C2   C3   120.67  3.000
 4G3  H3   C7   C6   120.13  3.000
 4G3  H3   C7   C8   120.21  3.000
 4G3  C6   C7   C8   119.65  3.000
 4G3  H4   C9   C10  119.73  3.000
 4G3  H4   C9   C8   120.68  3.000
 4G3  C10  C9   C8   119.59  3.000
 4G3  H5   C3   C4   121.40  3.000
 4G3  H5   C3   C2   120.25  3.000
 4G3  C4   C3   C2   118.34  3.000
 4G3  H6   C11  C10  120.02  3.000
 4G3  H6   C11  C6   119.63  3.000
 4G3  C10  C11  C6   120.35  3.000
 4G3  H7   C12  N2   114.21  3.000
 4G3  H7   C12  C1   121.17  3.000
 4G3  N2   C12  C1   124.62  3.000
 4G3  C    C1   C12  124.97  3.000
 4G3  C    C1   C2   118.95  3.000
 4G3  C12  C1   C2   116.08  3.000
 4G3  C5   C6   C11  119.67  3.000
 4G3  C5   C6   C7   120.50  3.000
 4G3  C11  C6   C7   119.81  3.000
 4G3  O1   C10  C11  122.60  3.000
 4G3  C11  C10  C9   119.75  3.000
 4G3  O1   C10  C9   117.64  3.000
 4G3  N1   C4   N2   116.26  3.000
 4G3  N2   C4   C3   121.49  3.000
 4G3  N1   C4   C3   122.25  3.000
 4G3  H9   C5   H8   106.83  3.000
 4G3  H9   C5   N1   110.88  3.000
 4G3  H8   C5   N1   109.76  3.000
 4G3  H9   C5   C6   109.72  3.000
 4G3  H8   C5   C6   109.66  3.000
 4G3  N1   C5   C6   109.93  3.000
 4G3  C4   N2   C12  118.80  3.000
 4G3  H11  N    H10  116.58  3.000
 4G3  H11  N    C    119.27  3.000
 4G3  H10  N    C    123.64  3.000
 4G3  H12  N1   C5   118.32  3.000
 4G3  H12  N1   C4   116.34  3.000
 4G3  C5   N1   C4   124.07  3.000
 4G3  H13  O1   C10  110.51  3.000
 4G3  O    C    N    121.81  3.000
 4G3  N    C    C1   117.48  3.000
 4G3  O    C    C1   120.70  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
 4G3  CONST_01  C11  C10  C9   C8     0.00   0.0  0
 4G3  CONST_02  C11  C6   C7   C8     0.00   0.0  0
 4G3  CONST_03  N2   C4   C3   C2     0.00   0.0  0
 4G3  CONST_04  N2   C12  C1   C2     0.00   0.0  0
 4G3  CONST_05  C10  C9   C8   C7     0.00   0.0  0
 4G3  CONST_06  C10  C11  C6   C7     0.00   0.0  0
 4G3  CONST_07  C6   C7   C8   C9     0.00   0.0  0
 4G3  CONST_08  C6   C11  C10  C9     0.00   0.0  0
 4G3  CONST_09  C12  N2   C4   C3     0.00   0.0  0
 4G3  CONST_10  C12  C1   C2   C3     0.00   0.0  0
 4G3  CONST_11  C4   C3   C2   C1     0.00   0.0  0
 4G3  CONST_12  C4   N2   C12  C1     0.00   0.0  0
 4G3  CONST_13  O1   C10  C9   C8   180.00   0.0  0
 4G3  CONST_14  C5   C6   C7   C8   180.00   0.0  0
 4G3  CONST_15  N1   C4   C3   C2   180.00   0.0  0
 4G3  CONST_16  C    C1   C2   C3   180.00   0.0  0
 4G3  CONST_17  N1   C4   N2   C12  180.00   0.0  0
 4G3  CONST_18  O1   C10  C11  C6   180.00   0.0  0
 4G3  CONST_19  C5   C6   C11  C10  180.00   0.0  0
 4G3  CONST_20  N2   C12  C1   C    180.00   0.0  0
 4G3  CONST_21  H7   C12  C1   C2   180.00   0.0  0
 4G3  CONST_22  H4   C9   C8   C7   180.00   0.0  0
 4G3  CONST_23  H6   C11  C6   C7   180.00   0.0  0
 4G3  CONST_24  H3   C7   C8   C9   180.00   0.0  0
 4G3  CONST_25  H2   C2   C1   C12  180.00   0.0  0
 4G3  CONST_26  H5   C3   C2   C1   180.00   0.0  0
 4G3  CONST_27  H1   C8   C7   C6   180.00   0.0  0
 4G3  CONST_28  C5   N1   C4   C3     0.00   0.0  0
 4G3  CONST_29  N2   C4   N1   C5   180.00   0.0  0
 4G3  CONST_30  H12  N1   C4   C3   180.00   0.0  0
 4G3  CONST_31  H10  N    C    C1     0.00   0.0  0
 4G3  CONST_32  H11  N    C    C1   180.00   0.0  0
 4G3  Var_01    O    C    C1   C2    -3.25  30.0  2
 4G3  Var_02    N1   C5   C6   C7   100.53  30.0  2
 4G3  Var_03    C4   N1   C5   C6   179.98  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
 4G3  plan-1  C8   0.020
 4G3  plan-1  C7   0.020
 4G3  plan-1  C9   0.020
 4G3  plan-1  C11  0.020
 4G3  plan-1  C6   0.020
 4G3  plan-1  C10  0.020
 4G3  plan-1  C5   0.020
 4G3  plan-1  O1   0.020
 4G3  plan-1  H1   0.020
 4G3  plan-1  H3   0.020
 4G3  plan-1  H4   0.020
 4G3  plan-1  H6   0.020
 4G3  plan-2  C2   0.020
 4G3  plan-2  C3   0.020
 4G3  plan-2  C12  0.020
 4G3  plan-2  C1   0.020
 4G3  plan-2  C4   0.020
 4G3  plan-2  N2   0.020
 4G3  plan-2  N1   0.020
 4G3  plan-2  H2   0.020
 4G3  plan-2  H5   0.020
 4G3  plan-2  H7   0.020
 4G3  plan-2  C    0.020
 4G3  plan-3  C1   0.020
 4G3  plan-3  N    0.020
 4G3  plan-3  O    0.020
 4G3  plan-3  H10  0.020
 4G3  plan-3  H11  0.020
 4G3  plan-3  C    0.020
 4G3  plan-4  C4   0.020
 4G3  plan-4  C5   0.020
 4G3  plan-4  N1   0.020
 4G3  plan-4  H12  0.020

