# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 19:48:01 2021
#   Inital geometry file: a 68 line input string
#   Ligand name: ~{N}2-pyridin-2-ylbenzene-1,2-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccccc1Nc2ccccn2
#
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
 S4V  S4V  ~{N}2-pyridin-2-ylbenzene-1,2-diamine  ligand  25  14  .  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_S4V
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
 S4V  N1   N  NH1   0  -0.735  -28.3320  100.5584  135.3347
 S4V  C4   C  CR6   0   0.277  -26.6323  100.0241  133.6798
 S4V  C5   C  CR16  0  -0.333  -26.1101  100.2240  132.3964
 S4V  C6   C  CR6   0   0.459  -27.8292  101.1234  136.4792
 S4V  C7   C  CR16  0  -0.373  -26.5942  101.7907  136.5058
 S4V  C8   C  CR16  0  -0.155  -26.1579  102.3060  137.7085
 S4V  C10  C  CR16  0  -0.069  -28.1429  101.4919  138.7133
 S4V  N    N  NH2   0  -0.845  -26.0206   99.1756  134.5737
 S4V  C    C  CR16  0  -0.252  -26.7138  101.0981  131.5085
 S4V  C1   C  CR16  0  -0.293  -27.8539  101.8038  131.8737
 S4V  C2   C  CR16  0  -0.281  -28.3690  101.6290  133.1496
 S4V  C3   C  CR6   0   0.207  -27.7751  100.7546  134.0516
 S4V  C9   C  CR16  0  -0.359  -26.9391  102.1581  138.8514
 S4V  N2   N  N     0  -0.461  -28.5840  100.9856  137.5674
 S4V  H1   H  HNH1  0   0.386  -29.3118  100.3221  135.3813
 S4V  H2   H  HCR6  0   0.257  -25.2275   99.6724  132.0941
 S4V  H3   H  HCR6  0   0.271  -26.0060  101.9094  135.6070
 S4V  H4   H  HCR6  0   0.267  -25.2102  102.8274  137.7546
 S4V  H5   H  HCR6  0   0.256  -28.7929  101.3566  139.5713
 S4V  H6   H  HNH2  0   0.379  -26.6261   98.7944  135.2850
 S4V  H7   H  HNH2  0   0.380  -25.4340   98.4678  134.1609
 S4V  H8   H  HCR6  0   0.253  -26.2915  101.2226  130.5195
 S4V  H9   H  HCR6  0   0.249  -28.3291  102.4848  131.1808
 S4V  H10  H  HCR6  0   0.257  -29.2522  102.1741  133.4610
 S4V  H11  H  HCR6  0   0.259  -26.6285  102.5491  139.8097

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
 S4V  C    C5   aromatic  1.384  0.020  1.384
 S4V  C    C1   aromatic  1.390  0.020  1.390
 S4V  C5   C4   aromatic  1.400  0.020  1.400
 S4V  C1   C2   aromatic  1.387  0.020  1.387
 S4V  C4   N    single    1.376  0.020  1.376
 S4V  C4   C3   aromatic  1.406  0.020  1.406
 S4V  C2   C3   aromatic  1.390  0.020  1.390
 S4V  C3   N1   single    1.412  0.020  1.412
 S4V  N1   C6   single    1.372  0.020  1.372
 S4V  C7   C6   aromatic  1.404  0.020  1.404
 S4V  C7   C8   aromatic  1.379  0.020  1.379
 S4V  C6   N2   aromatic  1.332  0.020  1.332
 S4V  C8   C9   aromatic  1.392  0.020  1.392
 S4V  N2   C10  aromatic  1.328  0.020  1.328
 S4V  C10  C9   aromatic  1.383  0.020  1.383
 S4V  N1   H1   single    0.890  0.020  1.040
 S4V  C5   H2   single    0.930  0.020  1.080
 S4V  C7   H3   single    0.930  0.020  1.080
 S4V  C8   H4   single    0.930  0.020  1.080
 S4V  C10  H5   single    0.930  0.020  1.080
 S4V  N    H6   single    0.890  0.020  1.040
 S4V  N    H7   single    0.890  0.020  1.040
 S4V  C    H8   single    0.930  0.020  1.080
 S4V  C1   H9   single    0.930  0.020  1.080
 S4V  C2   H10  single    0.930  0.020  1.080
 S4V  C9   H11  single    0.930  0.020  1.080

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
 S4V  H1   N1   C3   117.21  3.000
 S4V  H1   N1   C6   114.45  3.000
 S4V  C3   N1   C6   123.79  3.000
 S4V  C3   C4   N    120.65  3.000
 S4V  C3   C4   C5   118.12  3.000
 S4V  N    C4   C5   121.19  3.000
 S4V  H2   C5   C    119.84  3.000
 S4V  H2   C5   C4   119.13  3.000
 S4V  C    C5   C4   121.03  3.000
 S4V  N2   C6   C7   122.16  3.000
 S4V  N2   C6   N1   115.56  3.000
 S4V  C7   C6   N1   122.27  3.000
 S4V  H3   C7   C8   120.80  3.000
 S4V  H3   C7   C6   121.01  3.000
 S4V  C8   C7   C6   118.19  3.000
 S4V  H4   C8   C9   120.49  3.000
 S4V  H4   C8   C7   119.60  3.000
 S4V  C9   C8   C7   119.91  3.000
 S4V  H5   C10  N2   115.84  3.000
 S4V  H5   C10  C9   120.18  3.000
 S4V  N2   C10  C9   123.99  3.000
 S4V  H7   N    H6   111.89  3.000
 S4V  H7   N    C4   115.20  3.000
 S4V  H6   N    C4   115.10  3.000
 S4V  H8   C    C1   120.10  3.000
 S4V  H8   C    C5   119.24  3.000
 S4V  C1   C    C5   120.65  3.000
 S4V  H9   C1   C2   120.37  3.000
 S4V  H9   C1   C    120.79  3.000
 S4V  C2   C1   C    118.84  3.000
 S4V  H10  C2   C3   118.58  3.000
 S4V  H10  C2   C1   120.24  3.000
 S4V  C3   C2   C1   121.18  3.000
 S4V  C2   C3   C4   120.17  3.000
 S4V  C2   C3   N1   120.57  3.000
 S4V  C4   C3   N1   119.23  3.000
 S4V  H11  C9   C10  120.87  3.000
 S4V  H11  C9   C8   121.89  3.000
 S4V  C10  C9   C8   117.24  3.000
 S4V  C10  N2   C6   118.52  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
 S4V  CONST_01  C1   C    C5  C4    0.00   0.0  0
 S4V  CONST_02  C1   C2   C3  C4    0.00   0.0  0
 S4V  CONST_03  C2   C1   C   C5    0.00   0.0  0
 S4V  CONST_04  C2   C3   C4  C5    0.00   0.0  0
 S4V  CONST_05  C9   C8   C7  C6    0.00   0.0  0
 S4V  CONST_06  C9   C10  N2  C6    0.00   0.0  0
 S4V  CONST_07  C10  N2   C6  C7    0.00   0.0  0
 S4V  CONST_08  C10  C9   C8  C7    0.00   0.0  0
 S4V  CONST_09  N2   C6   C7  C8    0.00   0.0  0
 S4V  CONST_10  N2   C10  C9  C8    0.00   0.0  0
 S4V  CONST_11  C3   C4   C5  C     0.00   0.0  0
 S4V  CONST_12  C3   C2   C1  C     0.00   0.0  0
 S4V  CONST_13  C5   C4   C3  N1  180.00   0.0  0
 S4V  CONST_14  C1   C2   C3  N1  180.00   0.0  0
 S4V  CONST_15  C8   C7   C6  N1  180.00   0.0  0
 S4V  CONST_16  C10  N2   C6  N1  180.00   0.0  0
 S4V  CONST_17  C    C5   C4  N   180.00   0.0  0
 S4V  CONST_18  C2   C3   C4  N   180.00   0.0  0
 S4V  CONST_19  H8   C    C5  C4  180.00   0.0  0
 S4V  CONST_20  H10  C2   C3  C4  180.00   0.0  0
 S4V  CONST_21  H9   C1   C   C5  180.00   0.0  0
 S4V  CONST_22  H4   C8   C7  C6  180.00   0.0  0
 S4V  CONST_23  H5   C10  N2  C6  180.00   0.0  0
 S4V  CONST_24  H11  C9   C8  C7  180.00   0.0  0
 S4V  CONST_25  H2   C5   C   C1  180.00   0.0  0
 S4V  CONST_26  H3   C7   C8  C9  180.00   0.0  0
 S4V  Var_01    C6   N1   C3  C4   79.27  30.0  2
 S4V  Var_02    C3   N1   C6  C7   -9.72  30.0  1

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
 S4V  plan-1  N1   0.020
 S4V  plan-1  C6   0.020
 S4V  plan-1  C7   0.020
 S4V  plan-1  C8   0.020
 S4V  plan-1  C10  0.020
 S4V  plan-1  C9   0.020
 S4V  plan-1  N2   0.020
 S4V  plan-1  H3   0.020
 S4V  plan-1  H4   0.020
 S4V  plan-1  H5   0.020
 S4V  plan-1  H11  0.020
 S4V  plan-2  N1   0.020
 S4V  plan-2  C4   0.020
 S4V  plan-2  C5   0.020
 S4V  plan-2  N    0.020
 S4V  plan-2  C    0.020
 S4V  plan-2  C1   0.020
 S4V  plan-2  C2   0.020
 S4V  plan-2  C3   0.020
 S4V  plan-2  H2   0.020
 S4V  plan-2  H8   0.020
 S4V  plan-2  H9   0.020
 S4V  plan-2  H10  0.020
 S4V  plan-3  C4   0.020
 S4V  plan-3  N    0.020
 S4V  plan-3  H6   0.020
 S4V  plan-3  H7   0.020

