# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 15:32:45 2022
#   Inital geometry file: a 83 line input string
#   Ligand name: 3-azanyl-4-(pyridin-3-ylmethylamino)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cc(ccc1NCc2cccnc2)C(O)=O
#
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
 S1J  S1J  '3-azanyl-4-(pyridin-3-ylmethylamino)benzoic acid'  ligand  30  18  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_S1J
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
 S1J  N1   N  N      0  -0.397   9.3632  24.0024   2.9313
 S1J  N3   N  NH2    0  -0.869  15.4193  23.9081  -0.7580
 S1J  C4   C  CR16   0  -0.100  10.3667  23.1676   2.6895
 S1J  C5   C  CR16   0  -0.074   9.5908  25.3015   2.7814
 S1J  C7   C  CR6    0   0.311  13.2590  22.9357  -0.2839
 S1J  C8   C  CR16   0  -0.322  12.0099  22.5160  -0.7376
 S1J  C10  C  CR6    0  -0.120  12.5314  23.1868  -3.0040
 S1J  C13  C  C      0   0.383  12.1466  23.3378  -4.4677
 S1J  C1   C  CR16   0  -0.315  10.8181  25.8120   2.3843
 S1J  C11  C  CR16   0  -0.365  13.7912  23.5823  -2.5505
 S1J  C12  C  CR6    0   0.209  14.1709  23.4659  -1.2235
 S1J  C2   C  CR16   0  -0.180  11.8565  24.9285   2.1373
 S1J  C3   C  CR6    0   0.000  11.6396  23.5654   2.2961
 S1J  C9   C  CR16   0  -0.312  11.6555  22.6393  -2.0761
 S1J  N2   N  NH1    0  -0.677  13.6705  22.8293   1.0333
 S1J  O1   O  OC    -1  -0.596  10.9998  22.9629  -4.7860
 S1J  O2   O  O      0  -0.595  13.0075  23.8237  -5.2303
 S1J  H1   H  HNH2   0   0.365  15.9356  23.1893  -0.2664
 S1J  H2   H  HNH2   0   0.370  16.0023  24.2612  -1.5034
 S1J  H3   H  HCR6   0   0.255  10.1505  22.1094   2.8099
 S1J  H4   H  HCR6   0   0.260   8.7591  25.9680   2.9822
 S1J  H5   H  HCH2   0   0.254  12.2857  21.5592   1.9285
 S1J  H6   H  HCH2   0   0.279  13.3140  22.4542   3.0114
 S1J  H7   H  HCR6   0   0.251  11.2920  22.0974  -0.0438
 S1J  H8   H  HCR6   0   0.268  10.9532  26.8791   2.2711
 S1J  H9   H  HCR6   0   0.233  14.5010  23.9914  -3.2604
 S1J  H10  H  HCR6   0   0.263  12.8238  25.3012   1.8213
 S1J  H11  H  HCR6   0   0.227  10.6748  22.3099  -2.3934
 S1J  H12  H  HNH1   0   0.377  14.3901  23.4917   1.2836
 S1J  C6   C  CH2    0  -0.382  12.7360  22.5425   2.0891

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
 S1J  O2   C13  deloc     1.249  0.020  1.249
 S1J  O1   C13  deloc     1.248  0.020  1.248
 S1J  C13  C10  single    1.521  0.020  1.521
 S1J  C10  C11  aromatic  1.396  0.020  1.396
 S1J  C10  C9   aromatic  1.389  0.020  1.389
 S1J  C11  C12  aromatic  1.385  0.020  1.385
 S1J  C9   C8   aromatic  1.390  0.020  1.390
 S1J  C12  N3   single    1.404  0.020  1.404
 S1J  C12  C7   aromatic  1.413  0.020  1.413
 S1J  C8   C7   aromatic  1.394  0.020  1.394
 S1J  C7   N2   single    1.384  0.020  1.384
 S1J  N2   C6   single    1.439  0.020  1.439
 S1J  C6   C3   single    1.514  0.020  1.514
 S1J  C3   C2   aromatic  1.389  0.020  1.389
 S1J  C3   C4   aromatic  1.390  0.020  1.390
 S1J  C2   C1   aromatic  1.386  0.020  1.386
 S1J  C4   N1   aromatic  1.328  0.020  1.328
 S1J  C1   C5   aromatic  1.387  0.020  1.387
 S1J  N1   C5   aromatic  1.327  0.020  1.327
 S1J  N3   H1   single    0.890  0.020  1.040
 S1J  N3   H2   single    0.890  0.020  1.040
 S1J  C4   H3   single    0.930  0.020  1.080
 S1J  C5   H4   single    0.930  0.020  1.080
 S1J  C6   H5   single    0.970  0.020  1.090
 S1J  C6   H6   single    0.970  0.020  1.090
 S1J  C8   H7   single    0.930  0.020  1.080
 S1J  C1   H8   single    0.930  0.020  1.080
 S1J  C11  H9   single    0.930  0.020  1.080
 S1J  C2   H10  single    0.930  0.020  1.080
 S1J  C9   H11  single    0.930  0.020  1.080
 S1J  N2   H12  single    0.890  0.020  1.040

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
 S1J  C5   N1   C4   117.73  3.000
 S1J  H2   N3   H1   108.19  3.000
 S1J  H2   N3   C12  112.26  3.000
 S1J  H1   N3   C12  113.01  3.000
 S1J  H3   C4   C3   119.48  3.000
 S1J  H3   C4   N1   116.22  3.000
 S1J  C3   C4   N1   124.31  3.000
 S1J  H4   C5   C1   120.35  3.000
 S1J  H4   C5   N1   116.68  3.000
 S1J  C1   C5   N1   122.97  3.000
 S1J  N2   C7   C12  118.03  3.000
 S1J  N2   C7   C8   123.58  3.000
 S1J  C12  C7   C8   118.37  3.000
 S1J  H7   C8   C9   118.83  3.000
 S1J  H7   C8   C7   120.15  3.000
 S1J  C9   C8   C7   121.01  3.000
 S1J  C9   C10  C11  117.64  3.000
 S1J  C9   C10  C13  121.51  3.000
 S1J  C11  C10  C13  120.85  3.000
 S1J  O2   C13  O1   126.50  3.000
 S1J  O1   C13  C10  116.63  3.000
 S1J  O2   C13  C10  116.87  3.000
 S1J  H8   C1   C2   121.12  3.000
 S1J  H8   C1   C5   120.24  3.000
 S1J  C2   C1   C5   118.65  3.000
 S1J  H9   C11  C12  118.66  3.000
 S1J  H9   C11  C10  119.02  3.000
 S1J  C12  C11  C10  122.32  3.000
 S1J  C11  C12  C7   119.46  3.000
 S1J  C7   C12  N3   118.15  3.000
 S1J  C11  C12  N3   122.34  3.000
 S1J  H10  C2   C3   120.67  3.000
 S1J  H10  C2   C1   120.11  3.000
 S1J  C3   C2   C1   119.22  3.000
 S1J  C2   C3   C6   122.29  3.000
 S1J  C2   C3   C4   117.13  3.000
 S1J  C6   C3   C4   120.56  3.000
 S1J  H11  C9   C10  119.72  3.000
 S1J  H11  C9   C8   119.11  3.000
 S1J  C10  C9   C8   121.17  3.000
 S1J  H12  N2   C7   113.41  3.000
 S1J  H12  N2   C6   114.32  3.000
 S1J  C7   N2   C6   121.37  3.000
 S1J  H6   C6   H5   105.63  3.000
 S1J  H6   C6   N2   106.98  3.000
 S1J  H5   C6   N2   109.81  3.000
 S1J  H6   C6   C3   108.82  3.000
 S1J  H5   C6   C3   109.24  3.000
 S1J  N2   C6   C3   115.86  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
 S1J  CONST_01  C2   C3   C4   N1     0.00   0.0  0
 S1J  CONST_02  C2   C1   C5   N1     0.00   0.0  0
 S1J  CONST_03  C1   C2   C3   C4     0.00   0.0  0
 S1J  CONST_04  C1   C5   N1   C4     0.00   0.0  0
 S1J  CONST_05  C3   C2   C1   C5     0.00   0.0  0
 S1J  CONST_06  C3   C4   N1   C5     0.00   0.0  0
 S1J  CONST_07  C10  C11  C12  C7     0.00   0.0  0
 S1J  CONST_08  C10  C9   C8   C7     0.00   0.0  0
 S1J  CONST_09  C11  C10  C9   C8     0.00   0.0  0
 S1J  CONST_10  C11  C12  C7   C8     0.00   0.0  0
 S1J  CONST_11  C9   C10  C11  C12    0.00   0.0  0
 S1J  CONST_12  C9   C8   C7   C12    0.00   0.0  0
 S1J  CONST_13  C6   C3   C4   N1   180.00   0.0  0
 S1J  CONST_14  C10  C11  C12  N3   180.00   0.0  0
 S1J  CONST_15  C8   C7   C12  N3   180.00   0.0  0
 S1J  CONST_16  C1   C2   C3   C6   180.00   0.0  0
 S1J  CONST_17  C13  C10  C9   C8   180.00   0.0  0
 S1J  CONST_18  C12  C11  C10  C13  180.00   0.0  0
 S1J  CONST_19  N2   C7   C12  C11  180.00   0.0  0
 S1J  CONST_20  N2   C7   C8   C9   180.00   0.0  0
 S1J  CONST_21  H8   C1   C5   N1   180.00   0.0  0
 S1J  CONST_22  H10  C2   C3   C4   180.00   0.0  0
 S1J  CONST_23  H4   C5   N1   C4   180.00   0.0  0
 S1J  CONST_24  H3   C4   N1   C5   180.00   0.0  0
 S1J  CONST_25  H9   C11  C12  C7   180.00   0.0  0
 S1J  CONST_26  H11  C9   C8   C7   180.00   0.0  0
 S1J  CONST_27  H7   C8   C9   C10  180.00   0.0  0
 S1J  CONST_28  C12  C7   N2   C6   180.00   0.0  0
 S1J  CONST_29  C8   C7   N2   C6     0.00   0.0  0
 S1J  CONST_31  H2   N3   C12  C7   180.00   0.0  0
 S1J  Var_01    N2   C6   C3   C4   145.36  30.0  2
 S1J  Var_02    C3   C6   N2   C7   -61.70  30.0  3
 S1J  Var_03    O2   C13  C10  C11    0.21  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
 S1J  plan-1  N3   0.020
 S1J  plan-1  C7   0.020
 S1J  plan-1  C8   0.020
 S1J  plan-1  C10  0.020
 S1J  plan-1  C13  0.020
 S1J  plan-1  C11  0.020
 S1J  plan-1  C12  0.020
 S1J  plan-1  C9   0.020
 S1J  plan-1  N2   0.020
 S1J  plan-1  H7   0.020
 S1J  plan-1  H9   0.020
 S1J  plan-1  H11  0.020
 S1J  plan-2  N1   0.020
 S1J  plan-2  C4   0.020
 S1J  plan-2  C5   0.020
 S1J  plan-2  C1   0.020
 S1J  plan-2  C2   0.020
 S1J  plan-2  C3   0.020
 S1J  plan-2  H3   0.020
 S1J  plan-2  H4   0.020
 S1J  plan-2  H8   0.020
 S1J  plan-2  H10  0.020
 S1J  plan-2  C6   0.020
 S1J  plan-3  N3   0.020
 S1J  plan-3  C12  0.020
 S1J  plan-3  H1   0.020
 S1J  plan-3  H2   0.020
 S1J  plan-4  C7   0.020
 S1J  plan-4  N2   0.020
 S1J  plan-4  H12  0.020
 S1J  plan-4  C6   0.020
 S1J  plan-5  C10  0.020
 S1J  plan-5  C13  0.020
 S1J  plan-5  O1   0.020
 S1J  plan-5  O2   0.020

