# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 20:44:41 2021
#   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  31  18  .  2022-03-23  2022-11-17
;
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  -0.400   9.3831  23.9843   3.0320
 S1J  N3   N  NH2   0  -0.871  15.4746  23.8823  -0.7672
 S1J  C4   C  CR16  0  -0.097  10.4033  23.1727   2.7830
 S1J  C5   C  CR16  0  -0.074   9.5509  25.2799   2.7965
 S1J  C7   C  CR6   0   0.353  13.2849  22.9856  -0.2822
 S1J  C8   C  CR16  0  -0.322  12.0247  22.5802  -0.7284
 S1J  C10  C  CR6   0  -0.111  12.5774  23.1798  -2.9947
 S1J  C13  C  C     0   0.518  12.2590  23.3151  -4.4239
 S1J  C1   C  CR16  0  -0.317  10.7337  25.8102   2.3026
 S1J  C11  C  CR16  0  -0.334  13.8539  23.5566  -2.5579
 S1J  C12  C  CR6   0   0.218  14.2227  23.4663  -1.2322
 S1J  C2   C  CR16  0  -0.173  11.7920  24.9520   2.0507
 S1J  C3   C  CR6   0  -0.009  11.6369  23.5946   2.2998
 S1J  C9   C  CR16  0  -0.278  11.6743  22.6748  -2.0649
 S1J  N2   N  NH1   0  -0.679  13.6685  22.9184   1.0271
 S1J  O1   O  OH1   0  -0.602  11.0243  22.9236  -4.7303
 S1J  O2   O  O     0  -0.457  13.0290  23.7390  -5.2586
 S1J  H1   H  HNH2  0   0.374  15.9714  23.1612  -0.2593
 S1J  H2   H  HNH2  0   0.378  16.0712  24.2186  -1.5092
 S1J  H3   H  HCR6  0   0.258  10.2338  22.1161   2.9714
 S1J  H4   H  HCR6  0   0.263   8.7057  25.9266   3.0054
 S1J  H5   H  HCH2  0   0.259  12.3353  21.6030   1.9377
 S1J  H6   H  HCH2  0   0.291  13.3492  22.5332   3.0065
 S1J  H7   H  HCR6  0   0.265  11.2942  22.2022  -0.0262
 S1J  H8   H  HCR6  0   0.271  10.8201  26.8725   2.1193
 S1J  H9   H  HCR6  0   0.258  14.5778  23.9254  -3.2751
 S1J  H10  H  HCR6  0   0.263  12.7250  25.3393   1.6601
 S1J  H11  H  HCR6  0   0.257  10.6851  22.3565  -2.3624
 S1J  H12  H  HNH1  0   0.390  14.4584  23.4913   1.2791
 S1J  H13  H  HOH1  0   0.482  10.8763  23.0332  -5.6807
 S1J  C6   C  CH2   0  -0.375  12.7573  22.6000   2.0922

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  double    1.212  0.020  1.212
 S1J  O1   C13  single    1.331  0.020  1.331
 S1J  C13  C10  single    1.471  0.020  1.471
 S1J  C10  C11  aromatic  1.401  0.020  1.401
 S1J  C10  C9   aromatic  1.391  0.020  1.391
 S1J  C11  C12  aromatic  1.379  0.020  1.379
 S1J  C9   C8   aromatic  1.385  0.020  1.385
 S1J  C12  N3   single    1.399  0.020  1.399
 S1J  C12  C7   aromatic  1.419  0.020  1.419
 S1J  C8   C7   aromatic  1.397  0.020  1.397
 S1J  C7   N2   single    1.366  0.020  1.366
 S1J  N2   C6   single    1.437  0.020  1.437
 S1J  C6   C3   single    1.512  0.020  1.512
 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  1.327  0.020  1.327
 S1J  C1   C5   aromatic  1.387  0.020  1.387
 S1J  N1   C5   aromatic  1.328  0.020  1.328
 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
 S1J  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
 S1J  C5   N1   C4   117.80  3.000
 S1J  H2   N3   H1   108.42  3.000
 S1J  H2   N3   C12  112.56  3.000
 S1J  H1   N3   C12  113.21  3.000
 S1J  H3   C4   C3   119.59  3.000
 S1J  H3   C4   N1   116.24  3.000
 S1J  C3   C4   N1   124.17  3.000
 S1J  H4   C5   C1   120.34  3.000
 S1J  H4   C5   N1   116.70  3.000
 S1J  C1   C5   N1   122.96  3.000
 S1J  N2   C7   C12  118.21  3.000
 S1J  N2   C7   C8   123.04  3.000
 S1J  C12  C7   C8   118.73  3.000
 S1J  H7   C8   C9   118.66  3.000
 S1J  H7   C8   C7   120.22  3.000
 S1J  C9   C8   C7   121.11  3.000
 S1J  C9   C10  C11  118.74  3.000
 S1J  C9   C10  C13  122.85  3.000
 S1J  C11  C10  C13  118.40  3.000
 S1J  O2   C13  O1   122.26  3.000
 S1J  O1   C13  C10  113.42  3.000
 S1J  O2   C13  C10  124.32  3.000
 S1J  H8   C1   C2   121.10  3.000
 S1J  H8   C1   C5   120.27  3.000
 S1J  C2   C1   C5   118.63  3.000
 S1J  H9   C11  C12  118.67  3.000
 S1J  H9   C11  C10  119.60  3.000
 S1J  C12  C11  C10  121.73  3.000
 S1J  C11  C12  C7   119.28  3.000
 S1J  C7   C12  N3   118.02  3.000
 S1J  C11  C12  N3   122.65  3.000
 S1J  H10  C2   C3   120.69  3.000
 S1J  H10  C2   C1   120.13  3.000
 S1J  C3   C2   C1   119.18  3.000
 S1J  C2   C3   C6   122.37  3.000
 S1J  C2   C3   C4   117.26  3.000
 S1J  C6   C3   C4   120.36  3.000
 S1J  H11  C9   C10  121.14  3.000
 S1J  H11  C9   C8   118.49  3.000
 S1J  C10  C9   C8   120.37  3.000
 S1J  H12  N2   C7   115.58  3.000
 S1J  H12  N2   C6   115.95  3.000
 S1J  C7   N2   C6   122.89  3.000
 S1J  H13  O1   C13  109.54  3.000
 S1J  H6   C6   H5   105.78  3.000
 S1J  H6   C6   N2   106.89  3.000
 S1J  H5   C6   N2   109.99  3.000
 S1J  H6   C6   C3   109.09  3.000
 S1J  H5   C6   C3   109.46  3.000
 S1J  N2   C6   C3   115.19  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  CONST_33  H13  O1   C13  C10  180.00   0.0  0
 S1J  Var_01    N2   C6   C3   C4   149.39  30.0  2
 S1J  Var_02    C3   C6   N2   C7   -63.42  30.0  3
 S1J  Var_03    O2   C13  C10  C11   -0.31  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
 S1J  plan-5  H13  0.020

