# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:59:17 2022
#   Inital geometry file: a 115 line input string
#   Ligand name: 2-{[(2E)-3-(naphthalen-2-yl)but-2-enoyl]amino}benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C\C(=C/C(=O)Nc1ccccc1C(O)=O)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
 55C  55C  '2-{[(2E)-3-(naphthalen-2-yl)but-2-enoyl]amino}benzoic acid'  ligand  41  25  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_55C
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
 55C  C5   C  CR66   0   0.100  -4.7906   1.1170  -0.0003
 55C  C3   C  CR16   0  -0.257  -7.1336   1.2230   0.5805
 55C  C2   C  CR16   0  -0.257  -7.1496  -0.1743   0.7784
 55C  C4   C  CR16   0  -0.307  -5.9804   1.8538   0.1987
 55C  N1   N  NH1    0  -0.793   2.2864  -0.3717   0.0027
 55C  O21  O  O      0  -0.483   1.4951  -2.4420  -0.5592
 55C  C13  C  C      0   0.555   1.3048  -1.2651  -0.2759
 55C  C15  C  CR6    0   0.349   3.6652  -0.5314   0.0345
 55C  C17  C  CR16   0  -0.326   4.3102  -1.7403  -0.2535
 55C  C16  C  CR16   0  -0.250   5.6919  -1.8265  -0.2019
 55C  C20  C  CR16   0  -0.264   6.4598  -0.7213   0.1343
 55C  C19  C  CR16   0  -0.283   5.8224   0.4758   0.4172
 55C  C18  C  CR6    0  -0.228   4.4374   0.6046   0.3759
 55C  C21  C  C      0   0.466   3.8363   1.9697   0.7016
 55C  O22  O  O      0  -0.605   2.5798   2.0782   0.6737
 55C  O23  O  OC    -1  -0.560   4.6222   2.8857   0.9735
 55C  C12  C  C1     0  -0.456  -0.0331  -0.6418  -0.1924
 55C  C14  C  CH3    0  -0.738  -1.3523  -2.6079  -1.0649
 55C  C10  C  CR6    0   0.082  -2.4423  -0.4155  -0.3760
 55C  C9   C  CR16   0  -0.306  -2.4453   0.9906  -0.5775
 55C  C8   C  CR16   0  -0.299  -3.5791   1.7292  -0.3986
 55C  C6   C  CR66   0   0.151  -4.8057  -0.2873   0.1955
 55C  C7   C  CR16   0  -0.378  -3.6196  -1.0261  -0.0098
 55C  C1   C  CR16   0  -0.313  -6.0129  -0.9122   0.5903
 55C  H1   H  HCR6   0   0.260  -8.0394   1.7949   0.7337
 55C  H2   H  HCR6   0   0.260  -8.0679  -0.6601   1.0809
 55C  H3   H  HCR6   0   0.257  -5.9666   2.9264   0.0473
 55C  H4   H  HNH1   0   0.435   2.0446   0.6075   0.2473
 55C  H5   H  HCR6   0   0.274   3.7351  -2.6118  -0.5182
 55C  H6   H  HCR6   0   0.254   6.1670  -2.7724  -0.4303
 55C  H7   H  HCR6   0   0.248   7.5389  -0.7903   0.1750
 55C  H8   H  HCR6   0   0.249   6.4092   1.3458   0.6791
 55C  H10  H  H      0   0.253  -0.0509   0.3674   0.2038
 55C  H11  H  HCH3   0   0.255  -1.2868  -3.3394  -0.2575
 55C  H12  H  HCH3   0   0.240  -2.3139  -2.7393  -1.5557
 55C  H13  H  HCH3   0   0.265  -0.5708  -2.8539  -1.7778
 55C  H14  H  HCR6   0   0.257  -1.5409   1.4829  -0.9106
 55C  H15  H  HCR6   0   0.258  -3.5612   2.7981  -0.5734
 55C  H16  H  HCR6   0   0.261  -3.6558  -2.0972   0.1490
 55C  H17  H  HCR6   0   0.256  -6.0252  -1.9851   0.7401
 55C  C11  C  C      0   0.120  -1.2026  -1.2071  -0.5407

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
 55C  C20  C16  aromatic  1.387  0.020  1.387
 55C  C20  C19  aromatic  1.385  0.020  1.385
 55C  C16  C17  aromatic  1.385  0.020  1.385
 55C  C19  C18  aromatic  1.392  0.020  1.392
 55C  C17  C15  aromatic  1.400  0.020  1.400
 55C  C18  C15  aromatic  1.415  0.020  1.415
 55C  C18  C21  single    1.527  0.020  1.527
 55C  C15  N1   single    1.388  0.020  1.388
 55C  O22  C21  deloc     1.261  0.020  1.261
 55C  C21  O23  deloc     1.237  0.020  1.237
 55C  O21  C13  double    1.225  0.020  1.225
 55C  N1   C13  single    1.356  0.020  1.356
 55C  C13  C12  single    1.478  0.020  1.478
 55C  C12  C11  double    1.345  0.020  1.345
 55C  C14  C11  single    1.503  0.020  1.503
 55C  C11  C10  single    1.480  0.020  1.480
 55C  C10  C9   aromatic  1.420  0.020  1.420
 55C  C10  C7   aromatic  1.376  0.020  1.376
 55C  C9   C8   aromatic  1.365  0.020  1.365
 55C  C7   C6   aromatic  1.412  0.020  1.412
 55C  C8   C5   aromatic  1.415  0.020  1.415
 55C  C6   C5   aromatic  1.418  0.020  1.418
 55C  C6   C1   aromatic  1.415  0.020  1.415
 55C  C5   C4   aromatic  1.414  0.020  1.414
 55C  C1   C2   aromatic  1.368  0.020  1.368
 55C  C4   C3   aromatic  1.369  0.020  1.369
 55C  C2   C3   aromatic  1.411  0.020  1.411
 55C  C3   H1   single    0.930  0.020  1.080
 55C  C2   H2   single    0.930  0.020  1.080
 55C  C4   H3   single    0.930  0.020  1.080
 55C  N1   H4   single    0.860  0.020  1.020
 55C  C17  H5   single    0.930  0.020  1.080
 55C  C16  H6   single    0.930  0.020  1.080
 55C  C20  H7   single    0.930  0.020  1.080
 55C  C19  H8   single    0.930  0.020  1.080
 55C  C12  H10  single    0.930  0.020  1.080
 55C  C14  H11  single    0.970  0.020  1.090
 55C  C14  H12  single    0.970  0.020  1.090
 55C  C14  H13  single    0.970  0.020  1.090
 55C  C9   H14  single    0.930  0.020  1.080
 55C  C8   H15  single    0.930  0.020  1.080
 55C  C7   H16  single    0.930  0.020  1.080
 55C  C1   H17  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
 55C  C6   C5   C8   118.47  3.000
 55C  C6   C5   C4   119.19  3.000
 55C  C8   C5   C4   122.34  3.000
 55C  H1   C3   C4   120.08  3.000
 55C  H1   C3   C2   119.60  3.000
 55C  C4   C3   C2   120.33  3.000
 55C  H2   C2   C1   120.09  3.000
 55C  H2   C2   C3   119.56  3.000
 55C  C1   C2   C3   120.35  3.000
 55C  H3   C4   C3   120.39  3.000
 55C  H3   C4   C5   119.06  3.000
 55C  C3   C4   C5   120.55  3.000
 55C  H4   N1   C15  109.54  3.000
 55C  H4   N1   C13  120.09  3.000
 55C  C15  N1   C13  130.37  3.000
 55C  C12  C13  O21  123.95  3.000
 55C  C12  C13  N1   111.45  3.000
 55C  O21  C13  N1   124.60  3.000
 55C  C18  C15  C17  119.42  3.000
 55C  C18  C15  N1   117.07  3.000
 55C  C17  C15  N1   123.51  3.000
 55C  H5   C17  C16  119.43  3.000
 55C  H5   C17  C15  120.20  3.000
 55C  C16  C17  C15  120.37  3.000
 55C  H6   C16  C20  120.28  3.000
 55C  H6   C16  C17  118.96  3.000
 55C  C20  C16  C17  120.77  3.000
 55C  H7   C20  C19  120.41  3.000
 55C  H7   C20  C16  120.69  3.000
 55C  C19  C20  C16  118.90  3.000
 55C  H8   C19  C18  118.22  3.000
 55C  H8   C19  C20  119.66  3.000
 55C  C18  C19  C20  122.13  3.000
 55C  C21  C18  C19  117.92  3.000
 55C  C21  C18  C15  123.66  3.000
 55C  C19  C18  C15  118.41  3.000
 55C  O23  C21  O22  125.02  3.000
 55C  O23  C21  C18  117.31  3.000
 55C  O22  C21  C18  117.67  3.000
 55C  H10  C12  C11  118.14  3.000
 55C  H10  C12  C13  115.33  3.000
 55C  C11  C12  C13  126.53  3.000
 55C  H13  C14  H12  108.22  3.000
 55C  H13  C14  H11  106.90  3.000
 55C  H12  C14  H11  107.81  3.000
 55C  H13  C14  C11  111.61  3.000
 55C  H12  C14  C11  110.98  3.000
 55C  H11  C14  C11  111.14  3.000
 55C  C7   C10  C9   118.38  3.000
 55C  C7   C10  C11  120.60  3.000
 55C  C9   C10  C11  121.02  3.000
 55C  H14  C9   C8   119.23  3.000
 55C  H14  C9   C10  119.49  3.000
 55C  C8   C9   C10  121.25  3.000
 55C  H15  C8   C9   119.94  3.000
 55C  H15  C8   C5   119.12  3.000
 55C  C9   C8   C5   120.94  3.000
 55C  C1   C6   C7   121.72  3.000
 55C  C1   C6   C5   119.00  3.000
 55C  C7   C6   C5   119.27  3.000
 55C  H16  C7   C6   117.89  3.000
 55C  H16  C7   C10  120.42  3.000
 55C  C6   C7   C10  121.68  3.000
 55C  H17  C1   C6   119.04  3.000
 55C  H17  C1   C2   120.38  3.000
 55C  C6   C1   C2   120.58  3.000
 55C  C10  C11  C14  116.99  3.000
 55C  C10  C11  C12  118.35  3.000
 55C  C14  C11  C12  124.65  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
 55C  CONST_01  C10  C9   C8   C5      0.00   0.0  0
 55C  CONST_02  C10  C7   C6   C5      0.00   0.0  0
 55C  CONST_03  C2   C1   C6   C5      0.00   0.0  0
 55C  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 55C  CONST_05  C8   C5   C4   C3    180.00   0.0  0
 55C  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 55C  CONST_07  C6   C1   C2   C3      0.00   0.0  0
 55C  CONST_08  C7   C6   C1   C2    180.00   0.0  0
 55C  CONST_09  C9   C8   C5   C4    180.00   0.0  0
 55C  CONST_10  C7   C6   C5   C4    180.00   0.0  0
 55C  CONST_11  C1   C6   C5   C4      0.00   0.0  0
 55C  CONST_12  C1   C2   C3   C4      0.00   0.0  0
 55C  CONST_13  C20  C16  C17  C15     0.00   0.0  0
 55C  CONST_14  C20  C19  C18  C15     0.00   0.0  0
 55C  CONST_15  C19  C20  C16  C17     0.00   0.0  0
 55C  CONST_16  C19  C18  C15  C17     0.00   0.0  0
 55C  CONST_17  C18  C19  C20  C16     0.00   0.0  0
 55C  CONST_18  C18  C15  C17  C16     0.00   0.0  0
 55C  CONST_19  C1   C6   C7   C10   180.00   0.0  0
 55C  CONST_20  C6   C7   C10  C9      0.00   0.0  0
 55C  CONST_21  C6   C5   C8   C9      0.00   0.0  0
 55C  CONST_22  C7   C10  C9   C8      0.00   0.0  0
 55C  CONST_23  C7   C6   C5   C8      0.00   0.0  0
 55C  CONST_24  C1   C6   C5   C8    180.00   0.0  0
 55C  CONST_25  C16  C17  C15  N1    180.00   0.0  0
 55C  CONST_26  C19  C18  C15  N1    180.00   0.0  0
 55C  CONST_27  C21  C18  C15  C17   180.00   0.0  0
 55C  CONST_28  C21  C18  C19  C20   180.00   0.0  0
 55C  CONST_29  C8   C9   C10  C11   180.00   0.0  0
 55C  CONST_30  C6   C7   C10  C11   180.00   0.0  0
 55C  CONST_31  H14  C9   C8   C5    180.00   0.0  0
 55C  CONST_32  H16  C7   C6   C5    180.00   0.0  0
 55C  CONST_33  H17  C1   C6   C5    180.00   0.0  0
 55C  CONST_34  H1   C3   C4   C5    180.00   0.0  0
 55C  CONST_35  H3   C4   C3   C2    180.00   0.0  0
 55C  CONST_36  H15  C8   C5   C4      0.00   0.0  0
 55C  CONST_37  H2   C2   C3   C4    180.00   0.0  0
 55C  CONST_38  H6   C16  C17  C15   180.00   0.0  0
 55C  CONST_39  H8   C19  C18  C15   180.00   0.0  0
 55C  CONST_40  H7   C20  C16  C17   180.00   0.0  0
 55C  CONST_41  H5   C17  C16  C20   180.00   0.0  0
 55C  CONST_42  C17  C15  N1   C13     0.00   0.0  0
 55C  CONST_43  C18  C15  N1   C13   180.00   0.0  0
 55C  CONST_44  H4   N1   C15  C17   180.00   0.0  0
 55C  CONST_45  C15  N1   C13  O21     0.00   0.0  0
 55C  CONST_46  C12  C13  N1   C15   180.00   0.0  0
 55C  Var_01    O22  C21  C18  C15     0.65  30.0  2
 55C  Var_02    C9   C10  C11  C12    34.41  30.0  2
 55C  Var_03    C10  C11  C12  C13   179.76   0.0  2
 55C  Var_04    H11  C14  C11  C10  -101.29  30.0  3
 55C  Var_05    C11  C12  C13  N1    172.69  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
 55C  plan-1  N1   0.020
 55C  plan-1  C15  0.020
 55C  plan-1  C17  0.020
 55C  plan-1  C16  0.020
 55C  plan-1  C20  0.020
 55C  plan-1  C19  0.020
 55C  plan-1  C18  0.020
 55C  plan-1  C21  0.020
 55C  plan-1  H5   0.020
 55C  plan-1  H6   0.020
 55C  plan-1  H7   0.020
 55C  plan-1  H8   0.020
 55C  plan-2  C5   0.020
 55C  plan-2  C3   0.020
 55C  plan-2  C2   0.020
 55C  plan-2  C4   0.020
 55C  plan-2  C10  0.020
 55C  plan-2  C9   0.020
 55C  plan-2  C8   0.020
 55C  plan-2  C6   0.020
 55C  plan-2  C7   0.020
 55C  plan-2  C1   0.020
 55C  plan-2  H1   0.020
 55C  plan-2  H2   0.020
 55C  plan-2  H3   0.020
 55C  plan-2  H14  0.020
 55C  plan-2  H15  0.020
 55C  plan-2  H16  0.020
 55C  plan-2  H17  0.020
 55C  plan-2  C11  0.020
 55C  plan-3  N1   0.020
 55C  plan-3  O21  0.020
 55C  plan-3  C13  0.020
 55C  plan-3  C15  0.020
 55C  plan-3  C12  0.020
 55C  plan-3  H4   0.020
 55C  plan-4  C18  0.020
 55C  plan-4  C21  0.020
 55C  plan-4  O22  0.020
 55C  plan-4  O23  0.020
 55C  plan-5  C13  0.020
 55C  plan-5  C12  0.020
 55C  plan-5  C14  0.020
 55C  plan-5  C10  0.020
 55C  plan-5  H10  0.020
 55C  plan-5  C11  0.020

