# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 30 07:46:03 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: 3-naphthalen-2-ylbenzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cccc(c1)c2ccc3ccccc3c2
#
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
 TVC  TVC  '3-naphthalen-2-ylbenzoic acid'  ligand  31  19  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TVC
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
 TVC  C    C  C     0   0.536   4.3299  -0.7752   0.5987
 TVC  O    O  OH1   0  -0.593   5.5422  -0.2420   0.5653
 TVC  C1   C  CR6   0  -0.060   3.2684   0.1680   0.1637
 TVC  C10  C  CR16  0  -0.256  -5.2162   0.8113   0.5696
 TVC  C11  C  CR16  0  -0.258  -5.4961  -0.5186   0.1883
 TVC  C12  C  CR16  0  -0.308  -4.4821  -1.3576  -0.1868
 TVC  C13  C  CR66  0   0.102  -3.1423  -0.9059  -0.1985
 TVC  C14  C  CR16  0  -0.299  -2.0667  -1.7423  -0.5777
 TVC  C15  C  CR16  0  -0.306  -0.7829  -1.2766  -0.5802
 TVC  C16  C  CR16  0  -0.329   1.9524  -0.2848   0.1675
 TVC  C2   C  CR16  0  -0.274   3.5519   1.4723  -0.2363
 TVC  C3   C  CR16  0  -0.226   2.5153   2.3061  -0.6257
 TVC  C4   C  CR16  0  -0.301   1.2068   1.8497  -0.6195
 TVC  C5   C  CR6   0   0.113   0.9051   0.5460  -0.2200
 TVC  C6   C  CR6   0   0.090  -0.4888   0.0598  -0.2066
 TVC  C7   C  CR16  0  -0.387  -1.5227   0.8851   0.1657
 TVC  C8   C  CR66  0   0.147  -2.8604   0.4316   0.1800
 TVC  C9   C  CR16  0  -0.316  -3.9293   1.2753   0.5664
 TVC  O1   O  O     0  -0.437   4.1169  -1.9120   0.9469
 TVC  H11  H  HOH1  0   0.489   6.1985  -0.8959   0.8484
 TVC  H6   H  HCR6  0   0.260  -6.5191  -0.8715   0.1932
 TVC  H7   H  HCR6  0   0.257  -4.6953  -2.3782  -0.4808
 TVC  H8   H  HCR6  0   0.258  -2.2737  -2.7630  -0.8764
 TVC  H9   H  HCR6  0   0.258   0.0195  -1.9326  -0.8941
 TVC  H10  H  HCR6  0   0.265   1.7430  -1.2941   0.4975
 TVC  H    H  HCR6  0   0.270   4.5670   1.8430  -0.2524
 TVC  H1   H  HCR6  0   0.269   2.7305   3.3168  -0.9453
 TVC  H2   H  HCR6  0   0.266   0.4134   2.5100  -0.9470
 TVC  H3   H  HCR6  0   0.256  -1.3230   1.9034   0.4789
 TVC  H4   H  HCR6  0   0.256  -3.7136   2.2965   0.8573
 TVC  H5   H  HCR6  0   0.259  -6.0277   1.4642   0.8639

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
 TVC  C12  C11  aromatic  1.369  0.020  1.369
 TVC  C12  C13  aromatic  1.414  0.020  1.414
 TVC  O1   C    double    1.208  0.020  1.208
 TVC  C14  C15  aromatic  1.366  0.020  1.366
 TVC  C14  C13  aromatic  1.414  0.020  1.414
 TVC  C11  C10  aromatic  1.411  0.020  1.411
 TVC  C15  C6   aromatic  1.419  0.020  1.419
 TVC  C13  C8   aromatic  1.418  0.020  1.418
 TVC  C    C1   single    1.485  0.020  1.485
 TVC  C    O    single    1.325  0.020  1.325
 TVC  C2   C3   aromatic  1.386  0.020  1.386
 TVC  C2   C1   aromatic  1.393  0.020  1.393
 TVC  C3   C4   aromatic  1.386  0.020  1.386
 TVC  C1   C16  aromatic  1.392  0.020  1.392
 TVC  C4   C5   aromatic  1.396  0.020  1.396
 TVC  C16  C5   aromatic  1.392  0.020  1.392
 TVC  C10  C9   aromatic  1.368  0.020  1.368
 TVC  C6   C5   single    1.476  0.020  1.476
 TVC  C6   C7   aromatic  1.374  0.020  1.374
 TVC  C8   C9   aromatic  1.416  0.020  1.416
 TVC  C8   C7   aromatic  1.412  0.020  1.412
 TVC  O    H11  single    0.850  0.020  0.980
 TVC  C10  H5   single    0.930  0.020  1.080
 TVC  C11  H6   single    0.930  0.020  1.080
 TVC  C12  H7   single    0.930  0.020  1.080
 TVC  C14  H8   single    0.930  0.020  1.080
 TVC  C15  H9   single    0.930  0.020  1.080
 TVC  C16  H10  single    0.930  0.020  1.080
 TVC  C2   H    single    0.930  0.020  1.080
 TVC  C3   H1   single    0.930  0.020  1.080
 TVC  C4   H2   single    0.930  0.020  1.080
 TVC  C7   H3   single    0.930  0.020  1.080
 TVC  C9   H4   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
 TVC  O1   C    C1   123.79  3.000
 TVC  C1   C    O    113.02  3.000
 TVC  O1   C    O    123.19  3.000
 TVC  H11  O    C    109.93  3.000
 TVC  C2   C1   C16  119.85  3.000
 TVC  C16  C1   C    117.93  3.000
 TVC  C2   C1   C    122.22  3.000
 TVC  H5   C10  C9   120.09  3.000
 TVC  H5   C10  C11  119.55  3.000
 TVC  C9   C10  C11  120.36  3.000
 TVC  H6   C11  C12  120.12  3.000
 TVC  H6   C11  C10  119.57  3.000
 TVC  C12  C11  C10  120.31  3.000
 TVC  H7   C12  C13  119.03  3.000
 TVC  H7   C12  C11  120.40  3.000
 TVC  C13  C12  C11  120.57  3.000
 TVC  C8   C13  C14  118.56  3.000
 TVC  C8   C13  C12  119.17  3.000
 TVC  C14  C13  C12  122.27  3.000
 TVC  H8   C14  C15  120.03  3.000
 TVC  H8   C14  C13  119.06  3.000
 TVC  C15  C14  C13  120.91  3.000
 TVC  H9   C15  C6   119.56  3.000
 TVC  H9   C15  C14  119.37  3.000
 TVC  C6   C15  C14  121.05  3.000
 TVC  H10  C16  C5   119.73  3.000
 TVC  H10  C16  C1   119.15  3.000
 TVC  C5   C16  C1   121.10  3.000
 TVC  H    C2   C3   119.46  3.000
 TVC  H    C2   C1   121.09  3.000
 TVC  C3   C2   C1   119.44  3.000
 TVC  H1   C3   C4   119.80  3.000
 TVC  H1   C3   C2   119.75  3.000
 TVC  C4   C3   C2   120.44  3.000
 TVC  H2   C4   C5   119.83  3.000
 TVC  H2   C4   C3   119.31  3.000
 TVC  C5   C4   C3   120.85  3.000
 TVC  C6   C5   C4   120.93  3.000
 TVC  C6   C5   C16  120.75  3.000
 TVC  C4   C5   C16  118.32  3.000
 TVC  C7   C6   C5   121.00  3.000
 TVC  C7   C6   C15  118.75  3.000
 TVC  C5   C6   C15  120.24  3.000
 TVC  H3   C7   C8   118.24  3.000
 TVC  H3   C7   C6   120.25  3.000
 TVC  C8   C7   C6   121.50  3.000
 TVC  C9   C8   C7   121.77  3.000
 TVC  C7   C8   C13  119.23  3.000
 TVC  C9   C8   C13  119.00  3.000
 TVC  H4   C9   C8   118.99  3.000
 TVC  H4   C9   C10  120.42  3.000
 TVC  C8   C9   C10  120.59  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
 TVC  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 TVC  CONST_02  C4   C5   C16  C1     0.00   0.0  0
 TVC  CONST_03  C6   C5   C16  C1   180.00   0.0  0
 TVC  CONST_04  C13  C12  C11  C10    0.00   0.0  0
 TVC  CONST_05  C13  C8   C9   C10    0.00   0.0  0
 TVC  CONST_06  C7   C8   C9   C10  180.00   0.0  0
 TVC  CONST_07  C14  C13  C12  C11  180.00   0.0  0
 TVC  CONST_08  C8   C13  C12  C11    0.00   0.0  0
 TVC  CONST_09  C8   C9   C10  C11    0.00   0.0  0
 TVC  CONST_10  C9   C10  C11  C12    0.00   0.0  0
 TVC  CONST_11  C15  C14  C13  C12  180.00   0.0  0
 TVC  CONST_12  C9   C8   C13  C12    0.00   0.0  0
 TVC  CONST_13  C7   C8   C13  C12  180.00   0.0  0
 TVC  CONST_14  C6   C15  C14  C13    0.00   0.0  0
 TVC  CONST_15  C6   C7   C8   C13    0.00   0.0  0
 TVC  CONST_16  C5   C6   C15  C14  180.00   0.0  0
 TVC  CONST_17  C7   C6   C15  C14    0.00   0.0  0
 TVC  CONST_18  C9   C8   C13  C14  180.00   0.0  0
 TVC  CONST_19  C7   C8   C13  C14    0.00   0.0  0
 TVC  CONST_20  C8   C13  C14  C15    0.00   0.0  0
 TVC  CONST_23  C8   C7   C6   C15    0.00   0.0  0
 TVC  CONST_24  C3   C2   C1   C16    0.00   0.0  0
 TVC  CONST_25  C3   C4   C5   C16    0.00   0.0  0
 TVC  CONST_27  C5   C4   C3   C2     0.00   0.0  0
 TVC  CONST_28  C5   C16  C1   C2     0.00   0.0  0
 TVC  CONST_29  C6   C5   C4   C3   180.00   0.0  0
 TVC  CONST_31  C8   C7   C6   C5   180.00   0.0  0
 TVC  CONST_32  C9   C8   C7   C6   180.00   0.0  0
 TVC  CONST_33  C3   C2   C1   C    180.00   0.0  0
 TVC  CONST_34  C5   C16  C1   C    180.00   0.0  0
 TVC  CONST_35  H1   C3   C2   C1   180.00   0.0  0
 TVC  CONST_36  H7   C12  C11  C10  180.00   0.0  0
 TVC  CONST_37  H4   C9   C10  C11  180.00   0.0  0
 TVC  CONST_38  H5   C10  C11  C12  180.00   0.0  0
 TVC  CONST_39  H8   C14  C13  C12    0.00   0.0  0
 TVC  CONST_40  H6   C11  C12  C13  180.00   0.0  0
 TVC  CONST_41  H9   C15  C14  C13  180.00   0.0  0
 TVC  CONST_42  H3   C7   C8   C13  180.00   0.0  0
 TVC  CONST_43  H    C2   C1   C16  180.00   0.0  0
 TVC  CONST_44  H2   C4   C5   C16  180.00   0.0  0
 TVC  CONST_45  H10  C16  C1   C2   180.00   0.0  0
 TVC  CONST_46  H11  O    C    C1   180.00   0.0  0
 TVC  Var_01    C2   C1   C    O      0.17  30.0  2

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
 TVC  plan-1  C    0.020
 TVC  plan-1  C1   0.020
 TVC  plan-1  C16  0.020
 TVC  plan-1  C2   0.020
 TVC  plan-1  C3   0.020
 TVC  plan-1  C4   0.020
 TVC  plan-1  C5   0.020
 TVC  plan-1  C6   0.020
 TVC  plan-1  H10  0.020
 TVC  plan-1  H    0.020
 TVC  plan-1  H1   0.020
 TVC  plan-1  H2   0.020
 TVC  plan-2  C10  0.020
 TVC  plan-2  C11  0.020
 TVC  plan-2  C12  0.020
 TVC  plan-2  C13  0.020
 TVC  plan-2  C14  0.020
 TVC  plan-2  C15  0.020
 TVC  plan-2  C5   0.020
 TVC  plan-2  C6   0.020
 TVC  plan-2  C7   0.020
 TVC  plan-2  C8   0.020
 TVC  plan-2  C9   0.020
 TVC  plan-2  H6   0.020
 TVC  plan-2  H7   0.020
 TVC  plan-2  H8   0.020
 TVC  plan-2  H9   0.020
 TVC  plan-2  H3   0.020
 TVC  plan-2  H4   0.020
 TVC  plan-2  H5   0.020
 TVC  plan-3  C    0.020
 TVC  plan-3  O    0.020
 TVC  plan-3  C1   0.020
 TVC  plan-3  O1   0.020
 TVC  plan-3  H11  0.020

