# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 21:37:35 2021
#   Inital geometry file: a 71 line input string
#   Ligand name: ~{N}4-phenylbenzene-1,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccc(Nc2ccccc2)cc1
#
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
 SOJ  SOJ  ~{N}4-phenylbenzene-1,4-diamine  ligand  26  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 GRAND
;

data_comp_SOJ
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
 SOJ  N1   N  NH2   0  -0.861  46.3316  92.1830   8.0147
 SOJ  C4   C  CR16  0  -0.319  44.6643  93.7839   7.2908
 SOJ  C5   C  CR16  0  -0.309  43.4701  94.4538   7.5022
 SOJ  C6   C  CR6   0   0.355  40.2733  94.4359   9.1106
 SOJ  C7   C  CR16  0  -0.337  39.9991  93.0632   9.1442
 SOJ  C8   C  CR16  0  -0.245  38.7124  92.6113   9.4022
 SOJ  C10  C  CR16  0  -0.245  37.9335  94.8616   9.5799
 SOJ  C    C  CR6   0   0.286  42.7005  94.2167   8.6390
 SOJ  C1   C  CR16  0  -0.295  43.1650  93.2769   9.5584
 SOJ  C11  C  CR16  0  -0.350  39.2125  95.3276   9.3324
 SOJ  C2   C  CR16  0  -0.322  44.3414  92.5819   9.3359
 SOJ  C3   C  CR6   0   0.288  45.1216  92.8251   8.1998
 SOJ  C9   C  CR16  0  -0.295  37.6673  93.4972   9.6244
 SOJ  H1   H  HNH2  0   0.376  46.4255  91.2978   8.4866
 SOJ  H2   H  HNH2  0   0.376  46.6468  92.1235   7.0596
 SOJ  H3   H  HCR6  0   0.256  45.2430  93.9994   6.3998
 SOJ  H4   H  HCR6  0   0.257  43.1329  95.1764   6.7682
 SOJ  H5   H  HCR6  0   0.263  40.7845  92.3423   8.9620
 SOJ  H6   H  HCR6  0   0.250  38.5300  91.5439   9.4215
 SOJ  H7   H  HCR6  0   0.251  37.1363  95.5758   9.7445
 SOJ  H8   H  HNH1  0   0.389  41.5477  95.9127   8.5631
 SOJ  H9   H  HCR6  0   0.264  42.6069  93.0854  10.4667
 SOJ  H10  H  HCR6  0   0.255  39.4012  96.3951   9.3078
 SOJ  H11  H  HCR6  0   0.256  44.6728  91.8541  10.0674
 SOJ  H12  H  HCR6  0   0.245  36.6680  93.1352   9.8256
 SOJ  N    N  NH1   0  -0.788  41.5269  94.9520   8.8640

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
 SOJ  C4   C5   aromatic  1.386  0.020  1.386
 SOJ  C4   C3   aromatic  1.398  0.020  1.398
 SOJ  C5   C    aromatic  1.393  0.020  1.393
 SOJ  N1   C3   single    1.382  0.020  1.382
 SOJ  C3   C2   aromatic  1.400  0.020  1.400
 SOJ  C    N    single    1.403  0.020  1.403
 SOJ  C    C1   aromatic  1.394  0.020  1.394
 SOJ  N    C6   single    1.378  0.020  1.378
 SOJ  C7   C6   aromatic  1.400  0.020  1.400
 SOJ  C7   C8   aromatic  1.388  0.020  1.388
 SOJ  C6   C11  aromatic  1.403  0.020  1.403
 SOJ  C8   C9   aromatic  1.388  0.020  1.388
 SOJ  C2   C1   aromatic  1.384  0.020  1.384
 SOJ  C11  C10  aromatic  1.384  0.020  1.384
 SOJ  C9   C10  aromatic  1.391  0.020  1.391
 SOJ  N1   H1   single    0.890  0.020  1.040
 SOJ  N1   H2   single    0.890  0.020  1.040
 SOJ  C4   H3   single    0.930  0.020  1.080
 SOJ  C5   H4   single    0.930  0.020  1.080
 SOJ  C7   H5   single    0.930  0.020  1.080
 SOJ  C8   H6   single    0.930  0.020  1.080
 SOJ  C10  H7   single    0.930  0.020  1.080
 SOJ  N    H8   single    0.860  0.020  1.020
 SOJ  C1   H9   single    0.930  0.020  1.080
 SOJ  C11  H10  single    0.930  0.020  1.080
 SOJ  C2   H11  single    0.930  0.020  1.080
 SOJ  C9   H12  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
 SOJ  H2   N1   H1   111.28  3.000
 SOJ  H2   N1   C3   115.35  3.000
 SOJ  H1   N1   C3   115.28  3.000
 SOJ  H3   C4   C3   119.74  3.000
 SOJ  H3   C4   C5   119.30  3.000
 SOJ  C3   C4   C5   120.95  3.000
 SOJ  H4   C5   C    119.62  3.000
 SOJ  H4   C5   C4   119.16  3.000
 SOJ  C    C5   C4   121.22  3.000
 SOJ  C11  C6   N    118.55  3.000
 SOJ  C11  C6   C7   118.11  3.000
 SOJ  N    C6   C7   123.34  3.000
 SOJ  H5   C7   C8   119.18  3.000
 SOJ  H5   C7   C6   120.48  3.000
 SOJ  C8   C7   C6   120.34  3.000
 SOJ  H6   C8   C9   119.95  3.000
 SOJ  H6   C8   C7   118.71  3.000
 SOJ  C9   C8   C7   121.34  3.000
 SOJ  H7   C10  C9   120.08  3.000
 SOJ  H7   C10  C11  119.05  3.000
 SOJ  C9   C10  C11  120.87  3.000
 SOJ  C1   C    N    121.74  3.000
 SOJ  C1   C    C5   117.95  3.000
 SOJ  N    C    C5   120.25  3.000
 SOJ  H9   C1   C2   118.94  3.000
 SOJ  H9   C1   C    120.03  3.000
 SOJ  C2   C1   C    121.03  3.000
 SOJ  H10  C11  C10  119.77  3.000
 SOJ  H10  C11  C6   119.37  3.000
 SOJ  C10  C11  C6   120.86  3.000
 SOJ  H11  C2   C3   119.61  3.000
 SOJ  H11  C2   C1   119.24  3.000
 SOJ  C3   C2   C1   121.13  3.000
 SOJ  C2   C3   C4   117.69  3.000
 SOJ  C2   C3   N1   121.06  3.000
 SOJ  C4   C3   N1   121.19  3.000
 SOJ  H12  C9   C10  120.73  3.000
 SOJ  H12  C9   C8   120.79  3.000
 SOJ  C10  C9   C8   118.48  3.000
 SOJ  H8   N    C    115.78  3.000
 SOJ  H8   N    C6   115.44  3.000
 SOJ  C    N    C6   126.40  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
 SOJ  CONST_01  C1   C    C5   C4     0.00   0.0  0
 SOJ  CONST_02  C1   C2   C3   C4     0.00   0.0  0
 SOJ  CONST_03  C2   C3   C4   C5     0.00   0.0  0
 SOJ  CONST_04  C2   C1   C    C5     0.00   0.0  0
 SOJ  CONST_05  C9   C8   C7   C6     0.00   0.0  0
 SOJ  CONST_06  C9   C10  C11  C6     0.00   0.0  0
 SOJ  CONST_07  C10  C11  C6   C7     0.00   0.0  0
 SOJ  CONST_08  C10  C9   C8   C7     0.00   0.0  0
 SOJ  CONST_09  C11  C6   C7   C8     0.00   0.0  0
 SOJ  CONST_10  C11  C10  C9   C8     0.00   0.0  0
 SOJ  CONST_11  C3   C4   C5   C      0.00   0.0  0
 SOJ  CONST_12  C3   C2   C1   C      0.00   0.0  0
 SOJ  CONST_13  C5   C4   C3   N1   180.00   0.0  0
 SOJ  CONST_14  C1   C2   C3   N1   180.00   0.0  0
 SOJ  CONST_15  N    C    C5   C4   180.00   0.0  0
 SOJ  CONST_16  N    C6   C7   C8   180.00   0.0  0
 SOJ  CONST_17  N    C6   C11  C10  180.00   0.0  0
 SOJ  CONST_18  C2   C1   C    N    180.00   0.0  0
 SOJ  CONST_19  H11  C2   C3   C4   180.00   0.0  0
 SOJ  CONST_20  H9   C1   C    C5   180.00   0.0  0
 SOJ  CONST_21  H6   C8   C7   C6   180.00   0.0  0
 SOJ  CONST_22  H7   C10  C11  C6   180.00   0.0  0
 SOJ  CONST_23  H10  C11  C6   C7   180.00   0.0  0
 SOJ  CONST_24  H12  C9   C8   C7   180.00   0.0  0
 SOJ  CONST_25  H3   C4   C5   C    180.00   0.0  0
 SOJ  CONST_26  H4   C5   C    C1   180.00   0.0  0
 SOJ  CONST_27  H5   C7   C6   C11  180.00   0.0  0
 SOJ  Var_01    C6   N    C    C5   126.49  30.0  2
 SOJ  Var_02    C    N    C6   C7    -1.27  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
 SOJ  plan-1  N1   0.020
 SOJ  plan-1  C4   0.020
 SOJ  plan-1  C5   0.020
 SOJ  plan-1  C    0.020
 SOJ  plan-1  C1   0.020
 SOJ  plan-1  C2   0.020
 SOJ  plan-1  C3   0.020
 SOJ  plan-1  H3   0.020
 SOJ  plan-1  H4   0.020
 SOJ  plan-1  H9   0.020
 SOJ  plan-1  H11  0.020
 SOJ  plan-1  N    0.020
 SOJ  plan-2  C6   0.020
 SOJ  plan-2  C7   0.020
 SOJ  plan-2  C8   0.020
 SOJ  plan-2  C10  0.020
 SOJ  plan-2  C11  0.020
 SOJ  plan-2  C9   0.020
 SOJ  plan-2  H5   0.020
 SOJ  plan-2  H6   0.020
 SOJ  plan-2  H7   0.020
 SOJ  plan-2  H10  0.020
 SOJ  plan-2  H12  0.020
 SOJ  plan-2  N    0.020
 SOJ  plan-3  N1   0.020
 SOJ  plan-3  C3   0.020
 SOJ  plan-3  H1   0.020
 SOJ  plan-3  H2   0.020

