# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 08:10:26 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 3,4,5-trimethoxy-~{N}-[(~{E})-naphthalen-1-ylmethylideneamino]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(cc(OC)c1OC)C(=O)N\N=C\c2cccc3ccccc23
#
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
 CVT  CVT  3,4,5-trimethoxy-~{N}-[(~{E})-naphthalen-1-ylmethylideneamino]benzamide  ligand  47  27  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CVT
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
 CVT  C4   C  CR66  0   0.097   6.0135  -0.0681   0.1056
 CVT  C14  C  CR16  0  -0.444  -2.9493  -1.4096   0.0078
 CVT  C5   C  CR16  0  -0.312   6.5941   1.1299   0.5848
 CVT  C6   C  CR16  0  -0.247   5.8073   2.1698   0.9891
 CVT  C7   C  CR16  0  -0.347   4.0748  -1.4270  -0.4476
 CVT  C8   C  CR16  0  -0.242   4.9064  -2.4461  -0.8341
 CVT  C9   C  CR16  0  -0.258   6.3041  -2.3072  -0.7647
 CVT  C10  C  CR16  0  -0.307   6.8424  -1.1384  -0.3030
 CVT  C12  C  C     0   0.539  -0.5988  -0.7564  -0.3045
 CVT  C13  C  CR6   0  -0.016  -2.0431  -0.3891  -0.2536
 CVT  N1   N  N     0  -0.202   1.5788   0.0313   0.0203
 CVT  N2   N  NH1   0  -0.523   0.2530   0.2351   0.0737
 CVT  C3   C  CR66  0   0.103   4.5976  -0.2019   0.0348
 CVT  C1   C  CR16  0  -0.338   4.4106   2.0490   0.9242
 CVT  C15  C  CR6   0   0.353  -4.3086  -1.1197   0.0684
 CVT  C16  C  CR6   0   0.185  -4.7550   0.1849  -0.1657
 CVT  C17  C  CR6   0   0.355  -3.8362   1.2002  -0.4457
 CVT  C18  C  CR16  0  -0.464  -2.4743   0.9121  -0.4910
 CVT  C19  C  CH3   0  -0.442  -3.4917   3.4856  -0.9684
 CVT  C2   C  CR6   0   0.068   3.7921   0.9065   0.4596
 CVT  C20  C  CH3   0  -0.411  -6.5724   0.8566   1.1360
 CVT  C21  C  CH3   0  -0.441  -4.8831  -3.3556   0.5983
 CVT  O1   O  O     0  -0.450  -0.2179  -1.8606  -0.6423
 CVT  O2   O  O2    0  -0.461  -5.2670  -2.0193   0.3353
 CVT  O3   O  O2    0  -0.478  -6.0810   0.4610  -0.1406
 CVT  O4   O  O2    0  -0.460  -4.3641   2.4129  -0.6683
 CVT  H10  H  HCR6  0   0.286  -2.5819  -2.4121   0.1765
 CVT  H2   H  HCR6  0   0.262   7.6737   1.2077   0.6278
 CVT  H3   H  HCR6  0   0.264   6.2483   3.0853   1.3591
 CVT  H8   H  H     0   0.249   1.9102   1.8865   0.8508
 CVT  H4   H  HCR6  0   0.279   3.0067  -1.5626  -0.5138
 CVT  H5   H  HCR6  0   0.260   4.4795  -3.3712  -1.1993
 CVT  H6   H  HCR6  0   0.260   6.9457  -3.1216  -1.0746
 CVT  H7   H  HCR6  0   0.258   7.9169  -1.0151  -0.2412
 CVT  H9   H  HNH1  0   0.414  -0.1068   1.0922   0.4791
 CVT  H1   H  HCR6  0   0.264   3.8019   2.8842   1.2492
 CVT  H11  H  HCR6  0   0.287  -1.7637   1.6874  -0.7424
 CVT  H12  H  HCH3  0   0.231  -2.7881   3.6794  -0.1550
 CVT  H13  H  HCH3  0   0.232  -2.9304   3.3081  -1.8892
 CVT  H14  H  HCH3  0   0.265  -4.1191   4.3626  -1.1040
 CVT  H15  H  HCH3  0   0.240  -7.6326   1.0711   1.0176
 CVT  H16  H  HCH3  0   0.225  -6.4549   0.0620   1.8759
 CVT  H17  H  HCH3  0   0.225  -6.0708   1.7558   1.4998
 CVT  H18  H  HCH3  0   0.232  -4.3749  -3.8094  -0.2559
 CVT  H20  H  HCH3  0   0.232  -4.2348  -3.4275   1.4751
 CVT  H19  H  HCH3  0   0.264  -5.7998  -3.9054   0.7948
 CVT  C11  C  C1    0  -0.089   2.3332   0.9599   0.4524

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
 CVT  C19  O4   single    1.415  0.020  1.415
 CVT  O4   C17  single    1.341  0.020  1.341
 CVT  C20  O3   single    1.424  0.020  1.424
 CVT  O3   C16  single    1.355  0.020  1.355
 CVT  C17  C16  aromatic  1.398  0.020  1.398
 CVT  C17  C18  aromatic  1.393  0.020  1.393
 CVT  C16  C15  aromatic  1.399  0.020  1.399
 CVT  C18  C13  aromatic  1.391  0.020  1.391
 CVT  C15  O2   single    1.341  0.020  1.341
 CVT  C15  C14  aromatic  1.391  0.020  1.391
 CVT  O2   C21  single    1.415  0.020  1.415
 CVT  C13  C14  aromatic  1.390  0.020  1.390
 CVT  C13  C12  single    1.491  0.020  1.491
 CVT  O1   C12  double    1.216  0.020  1.216
 CVT  C12  N2   single    1.361  0.020  1.361
 CVT  N2   N1   single    1.343  0.020  1.343
 CVT  N1   C11  double    1.272  0.020  1.272
 CVT  C1   C6   aromatic  1.403  0.020  1.403
 CVT  C1   C2   aromatic  1.380  0.020  1.380
 CVT  C11  C2   single    1.460  0.020  1.460
 CVT  C6   C5   aromatic  1.365  0.020  1.365
 CVT  C2   C3   aromatic  1.435  0.020  1.435
 CVT  C5   C4   aromatic  1.415  0.020  1.415
 CVT  C3   C4   aromatic  1.424  0.020  1.424
 CVT  C3   C7   aromatic  1.417  0.020  1.417
 CVT  C4   C10  aromatic  1.414  0.020  1.414
 CVT  C7   C8   aromatic  1.371  0.020  1.371
 CVT  C10  C9   aromatic  1.367  0.020  1.367
 CVT  C8   C9   aromatic  1.406  0.020  1.406
 CVT  C14  H10  single    0.930  0.020  1.080
 CVT  C5   H2   single    0.930  0.020  1.080
 CVT  C6   H3   single    0.930  0.020  1.080
 CVT  C11  H8   single    0.930  0.020  1.080
 CVT  C7   H4   single    0.930  0.020  1.080
 CVT  C8   H5   single    0.930  0.020  1.080
 CVT  C9   H6   single    0.930  0.020  1.080
 CVT  C10  H7   single    0.930  0.020  1.080
 CVT  N2   H9   single    0.860  0.020  1.020
 CVT  C1   H1   single    0.930  0.020  1.080
 CVT  C18  H11  single    0.930  0.020  1.080
 CVT  C19  H12  single    0.970  0.020  1.090
 CVT  C19  H13  single    0.970  0.020  1.090
 CVT  C19  H14  single    0.970  0.020  1.090
 CVT  C20  H15  single    0.970  0.020  1.090
 CVT  C20  H16  single    0.970  0.020  1.090
 CVT  C20  H17  single    0.970  0.020  1.090
 CVT  C21  H18  single    0.970  0.020  1.090
 CVT  C21  H20  single    0.970  0.020  1.090
 CVT  C21  H19  single    0.970  0.020  1.090

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
 CVT  C3   C4   C10  119.83  3.000
 CVT  C10  C4   C5   119.88  3.000
 CVT  C3   C4   C5   120.29  3.000
 CVT  H10  C14  C15  121.23  3.000
 CVT  H10  C14  C13  119.27  3.000
 CVT  C15  C14  C13  119.49  3.000
 CVT  H2   C5   C6   120.53  3.000
 CVT  H2   C5   C4   118.90  3.000
 CVT  C6   C5   C4   120.58  3.000
 CVT  H3   C6   C1   119.64  3.000
 CVT  H3   C6   C5   120.73  3.000
 CVT  C1   C6   C5   119.62  3.000
 CVT  H4   C7   C3   119.67  3.000
 CVT  H4   C7   C8   119.33  3.000
 CVT  C3   C7   C8   121.00  3.000
 CVT  H5   C8   C9   119.55  3.000
 CVT  H5   C8   C7   119.42  3.000
 CVT  C9   C8   C7   121.03  3.000
 CVT  H6   C9   C10  120.44  3.000
 CVT  H6   C9   C8   120.06  3.000
 CVT  C10  C9   C8   119.50  3.000
 CVT  H7   C10  C9   120.47  3.000
 CVT  H7   C10  C4   118.60  3.000
 CVT  C9   C10  C4   120.92  3.000
 CVT  O1   C12  N2   122.88  3.000
 CVT  N2   C12  C13  114.67  3.000
 CVT  O1   C12  C13  122.45  3.000
 CVT  C18  C13  C12  121.65  3.000
 CVT  C12  C13  C14  117.21  3.000
 CVT  C18  C13  C14  121.13  3.000
 CVT  N2   N1   C11  117.47  3.000
 CVT  H9   N2   N1   119.64  3.000
 CVT  H9   N2   C12  120.33  3.000
 CVT  N1   N2   C12  119.77  3.000
 CVT  C2   C3   C7   124.18  3.000
 CVT  C7   C3   C4   117.72  3.000
 CVT  C2   C3   C4   118.10  3.000
 CVT  H1   C1   C2   119.18  3.000
 CVT  H1   C1   C6   118.61  3.000
 CVT  C2   C1   C6   122.21  3.000
 CVT  O2   C15  C16  115.52  3.000
 CVT  O2   C15  C14  124.55  3.000
 CVT  C16  C15  C14  119.93  3.000
 CVT  O3   C16  C17  119.94  3.000
 CVT  C17  C16  C15  120.09  3.000
 CVT  O3   C16  C15  119.96  3.000
 CVT  O4   C17  C18  124.50  3.000
 CVT  C18  C17  C16  119.94  3.000
 CVT  O4   C17  C16  115.56  3.000
 CVT  H11  C18  C17  120.12  3.000
 CVT  H11  C18  C13  120.44  3.000
 CVT  C17  C18  C13  119.40  3.000
 CVT  H14  C19  H13  108.81  3.000
 CVT  H14  C19  H12  108.75  3.000
 CVT  H13  C19  H12  108.98  3.000
 CVT  H14  C19  O4   106.40  3.000
 CVT  H13  C19  O4   111.85  3.000
 CVT  H12  C19  O4   111.93  3.000
 CVT  C1   C2   C3   119.20  3.000
 CVT  C3   C2   C11  126.01  3.000
 CVT  C1   C2   C11  114.80  3.000
 CVT  H17  C20  H16  108.90  3.000
 CVT  H17  C20  H15  108.75  3.000
 CVT  H16  C20  H15  108.78  3.000
 CVT  H17  C20  O3   111.65  3.000
 CVT  H16  C20  O3   111.60  3.000
 CVT  H15  C20  O3   107.07  3.000
 CVT  H19  C21  H20  108.79  3.000
 CVT  H19  C21  H18  108.87  3.000
 CVT  H20  C21  H18  108.91  3.000
 CVT  H19  C21  O2   106.41  3.000
 CVT  H20  C21  O2   111.86  3.000
 CVT  H18  C21  O2   111.90  3.000
 CVT  C21  O2   C15  118.46  3.000
 CVT  C20  O3   C16  114.27  3.000
 CVT  C19  O4   C17  118.56  3.000
 CVT  H8   C11  C2   114.56  3.000
 CVT  H8   C11  N1   120.86  3.000
 CVT  C2   C11  N1   124.58  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
 CVT  CONST_01  C1   C6   C5   C4      0.00   0.0  0
 CVT  CONST_02  C1   C2   C3   C4      0.00   0.0  0
 CVT  CONST_03  C8   C7   C3   C4      0.00   0.0  0
 CVT  CONST_04  C8   C9   C10  C4      0.00   0.0  0
 CVT  CONST_05  C17  C16  C15  C14     0.00   0.0  0
 CVT  CONST_06  C17  C18  C13  C14     0.00   0.0  0
 CVT  CONST_07  C2   C1   C6   C5      0.00   0.0  0
 CVT  CONST_08  C2   C3   C4   C5      0.00   0.0  0
 CVT  CONST_09  C7   C3   C4   C5    180.00   0.0  0
 CVT  CONST_10  C9   C10  C4   C5    180.00   0.0  0
 CVT  CONST_11  C3   C2   C1   C6      0.00   0.0  0
 CVT  CONST_12  C3   C4   C5   C6      0.00   0.0  0
 CVT  CONST_13  C10  C4   C5   C6    180.00   0.0  0
 CVT  CONST_14  C1   C2   C3   C7    180.00   0.0  0
 CVT  CONST_15  C10  C4   C3   C7      0.00   0.0  0
 CVT  CONST_16  C10  C9   C8   C7      0.00   0.0  0
 CVT  CONST_17  C2   C3   C7   C8    180.00   0.0  0
 CVT  CONST_18  C3   C4   C10  C9      0.00   0.0  0
 CVT  CONST_19  C3   C7   C8   C9      0.00   0.0  0
 CVT  CONST_20  C2   C3   C4   C10   180.00   0.0  0
 CVT  CONST_21  C16  C17  C18  C13     0.00   0.0  0
 CVT  CONST_22  C16  C15  C14  C13     0.00   0.0  0
 CVT  CONST_23  C18  C17  C16  C15     0.00   0.0  0
 CVT  CONST_24  C18  C13  C14  C15     0.00   0.0  0
 CVT  CONST_25  C11  C2   C3   C4    180.00   0.0  0
 CVT  CONST_26  O3   C16  C15  C14   180.00   0.0  0
 CVT  CONST_27  C11  C2   C1   C6    180.00   0.0  0
 CVT  CONST_28  C7   C3   C2   C11     0.00   0.0  0
 CVT  CONST_29  C17  C18  C13  C12   180.00   0.0  0
 CVT  CONST_30  C15  C14  C13  C12   180.00   0.0  0
 CVT  CONST_31  O4   C17  C18  C13   180.00   0.0  0
 CVT  CONST_32  O2   C15  C14  C13   180.00   0.0  0
 CVT  CONST_33  O4   C17  C16  C15   180.00   0.0  0
 CVT  CONST_34  O2   C15  C16  C17   180.00   0.0  0
 CVT  CONST_35  O3   C16  C17  C18   180.00   0.0  0
 CVT  CONST_36  H3   C6   C5   C4    180.00   0.0  0
 CVT  CONST_37  H4   C7   C3   C4    180.00   0.0  0
 CVT  CONST_38  H6   C9   C10  C4    180.00   0.0  0
 CVT  CONST_39  H11  C18  C13  C14   180.00   0.0  0
 CVT  CONST_40  H1   C1   C6   C5    180.00   0.0  0
 CVT  CONST_41  H7   C10  C4   C5      0.00   0.0  0
 CVT  CONST_42  H2   C5   C4   C10     0.00   0.0  0
 CVT  CONST_43  H5   C8   C9   C10   180.00   0.0  0
 CVT  CONST_44  H10  C14  C15  C16   180.00   0.0  0
 CVT  CONST_45  N1   N2   C12  C13   180.00   0.0  0
 CVT  CONST_46  H9   N2   C12  C13     0.00   0.0  0
 CVT  CONST_47  O1   C12  N2   N1      0.00   0.0  0
 CVT  Var_01    O1   C12  C13  C14    29.12  30.0  2
 CVT  Var_02    C1   C2   C11  N1    177.48  30.0  2
 CVT  Var_03    C2   C11  N1   N2   -179.58   0.0  2
 CVT  Var_04    H18  C21  O2   C15   -61.67  30.0  3
 CVT  Var_05    H15  C20  O3   C16   178.64  30.0  3
 CVT  Var_06    H12  C19  O4   C17   -60.98  30.0  3
 CVT  Var_07    C12  N2   N1   C11  -176.25  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
 CVT  plan-1  C14  0.020
 CVT  plan-1  C12  0.020
 CVT  plan-1  C13  0.020
 CVT  plan-1  C15  0.020
 CVT  plan-1  C16  0.020
 CVT  plan-1  C17  0.020
 CVT  plan-1  C18  0.020
 CVT  plan-1  O2   0.020
 CVT  plan-1  O3   0.020
 CVT  plan-1  O4   0.020
 CVT  plan-1  H10  0.020
 CVT  plan-1  H11  0.020
 CVT  plan-2  C4   0.020
 CVT  plan-2  C5   0.020
 CVT  plan-2  C6   0.020
 CVT  plan-2  C7   0.020
 CVT  plan-2  C8   0.020
 CVT  plan-2  C9   0.020
 CVT  plan-2  C10  0.020
 CVT  plan-2  C3   0.020
 CVT  plan-2  C1   0.020
 CVT  plan-2  C2   0.020
 CVT  plan-2  H2   0.020
 CVT  plan-2  H3   0.020
 CVT  plan-2  H4   0.020
 CVT  plan-2  H5   0.020
 CVT  plan-2  H6   0.020
 CVT  plan-2  H7   0.020
 CVT  plan-2  H1   0.020
 CVT  plan-2  C11  0.020
 CVT  plan-3  C12  0.020
 CVT  plan-3  C13  0.020
 CVT  plan-3  N1   0.020
 CVT  plan-3  N2   0.020
 CVT  plan-3  O1   0.020
 CVT  plan-3  H9   0.020
 CVT  plan-4  N1   0.020
 CVT  plan-4  N2   0.020
 CVT  plan-4  C2   0.020
 CVT  plan-4  H8   0.020
 CVT  plan-4  C11  0.020

