# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 21:02:00 2022
#   Inital geometry file: a 95 line input string
#   Ligand name: 4-methanoyl-~{N}-[(3-methoxyphenyl)methyl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(CNC(=O)c2ccc(C=O)cc2)c1
#
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
 V3Q  V3Q  4-methanoyl-~{N}-[(3-methoxyphenyl)methyl]benzamide  ligand  35  20  .  2022-03-29  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_V3Q
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
 V3Q  C01  C  CH3   0  -0.436  29.1600  14.0243  -0.0288
 V3Q  C03  C  CR6   0   0.399  29.3832  16.0479  -1.2492
 V3Q  C04  C  CR16  0  -0.352  30.0056  16.7376  -2.2897
 V3Q  C05  C  CR16  0  -0.224  29.6853  18.0642  -2.5245
 V3Q  C06  C  CR16  0  -0.324  28.7496  18.7221  -1.7374
 V3Q  C07  C  CR6   0   0.130  28.1262  18.0390  -0.6999
 V3Q  C08  C  CH2   0  -0.366  27.1028  18.7298   0.1669
 V3Q  C10  C  C     0   0.537  25.6438  20.5143  -0.7116
 V3Q  C11  C  CR6   0  -0.031  24.4312  20.8009  -1.5469
 V3Q  C12  C  CR16  0  -0.255  24.3642  22.0347  -2.1971
 V3Q  C13  C  CR16  0  -0.251  23.2680  22.3576  -2.9720
 V3Q  C14  C  CR6   0  -0.013  22.2084  21.4576  -3.0880
 V3Q  C15  C  CR16  0  -0.261  22.2615  20.2386  -2.4213
 V3Q  C16  C  CR16  0  -0.273  23.3682  19.9086  -1.6550
 V3Q  C17  C  C1    0   0.119  21.0224  21.7700  -3.9050
 V3Q  C19  C  CR16  0  -0.443  28.4412  16.7047  -0.4582
 V3Q  N09  N  NH1   0  -0.635  25.9799  19.2181  -0.6022
 V3Q  O02  O  O2    0  -0.468  29.7431  14.7605  -1.0843
 V3Q  O18  O  O     0  -0.474  26.2631  21.4268  -0.1855
 V3Q  H1   H  HCH3  0   0.259  29.5985  13.0301  -0.0669
 V3Q  H2   H  HCH3  0   0.227  29.3769  14.4665   0.9474
 V3Q  H3   H  HCH3  0   0.227  28.0761  13.9333  -0.1406
 V3Q  H4   H  HCR6  0   0.259  30.7357  16.2299  -2.9078
 V3Q  H5   H  HCR6  0   0.255  30.1749  18.5918  -3.3330
 V3Q  H6   H  HCR6  0   0.249  28.5111  19.7609  -1.9295
 V3Q  H7   H  HCH2  0   0.269  26.7408  18.0424   0.9344
 V3Q  H8   H  HCH2  0   0.271  27.5512  19.5774   0.6834
 V3Q  H9   H  HCR6  0   0.268  25.1812  22.7368  -2.1002
 V3Q  H10  H  HCR6  0   0.270  23.2306  23.3098  -3.4851
 V3Q  H11  H  HCR6  0   0.277  21.4318  19.5455  -2.4967
 V3Q  H12  H  HCR6  0   0.271  23.3765  18.9630  -1.1280
 V3Q  H13  H  H     0   0.201  20.2476  20.9831  -3.9072
 V3Q  H16  H  HCR6  0   0.276  27.9368  16.1923   0.3515
 V3Q  H17  H  HNH1  0   0.409  25.4744  18.5341  -1.1422
 V3Q  O1   O  O     0  -0.368  20.8759  22.7904  -4.5335

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
 V3Q  C17  C14  single    1.474  0.020  1.474
 V3Q  C14  C13  aromatic  1.395  0.020  1.395
 V3Q  C14  C15  aromatic  1.390  0.020  1.390
 V3Q  C13  C12  aromatic  1.381  0.020  1.381
 V3Q  C05  C04  aromatic  1.385  0.020  1.385
 V3Q  C05  C06  aromatic  1.388  0.020  1.388
 V3Q  C04  C03  aromatic  1.395  0.020  1.395
 V3Q  C15  C16  aromatic  1.386  0.020  1.386
 V3Q  C12  C11  aromatic  1.396  0.020  1.396
 V3Q  C06  C07  aromatic  1.390  0.020  1.390
 V3Q  C16  C11  aromatic  1.392  0.020  1.392
 V3Q  C11  C10  single    1.500  0.020  1.500
 V3Q  C03  O02  single    1.347  0.020  1.347
 V3Q  C03  C19  aromatic  1.394  0.020  1.394
 V3Q  O02  C01  single    1.413  0.020  1.413
 V3Q  C07  C19  aromatic  1.392  0.020  1.392
 V3Q  C07  C08  single    1.509  0.020  1.509
 V3Q  C10  N09  single    1.344  0.020  1.344
 V3Q  C10  O18  double    1.222  0.020  1.222
 V3Q  N09  C08  single    1.446  0.020  1.446
 V3Q  C01  H1   single    0.970  0.020  1.090
 V3Q  C01  H2   single    0.970  0.020  1.090
 V3Q  C01  H3   single    0.970  0.020  1.090
 V3Q  C04  H4   single    0.930  0.020  1.080
 V3Q  C05  H5   single    0.930  0.020  1.080
 V3Q  C06  H6   single    0.930  0.020  1.080
 V3Q  C08  H7   single    0.970  0.020  1.090
 V3Q  C08  H8   single    0.970  0.020  1.090
 V3Q  C12  H9   single    0.930  0.020  1.080
 V3Q  C13  H10  single    0.930  0.020  1.080
 V3Q  C15  H11  single    0.930  0.020  1.080
 V3Q  C16  H12  single    0.930  0.020  1.080
 V3Q  C17  H13  single    0.930  0.020  1.080
 V3Q  C19  H16  single    0.930  0.020  1.080
 V3Q  N09  H17  single    0.860  0.020  1.020
 V3Q  C17  O1   double    1.207  0.020  1.207

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
 V3Q  H3   C01  H2   108.75  3.000
 V3Q  H3   C01  H1   108.67  3.000
 V3Q  H2   C01  H1   108.73  3.000
 V3Q  H3   C01  O02  112.09  3.000
 V3Q  H2   C01  O02  111.99  3.000
 V3Q  H1   C01  O02  106.49  3.000
 V3Q  O02  C03  C19  124.15  3.000
 V3Q  C19  C03  C04  119.45  3.000
 V3Q  O02  C03  C04  116.40  3.000
 V3Q  H4   C04  C05  120.55  3.000
 V3Q  H4   C04  C03  119.66  3.000
 V3Q  C05  C04  C03  119.79  3.000
 V3Q  H5   C05  C06  119.82  3.000
 V3Q  H5   C05  C04  119.27  3.000
 V3Q  C06  C05  C04  120.91  3.000
 V3Q  H6   C06  C07  120.34  3.000
 V3Q  H6   C06  C05  120.15  3.000
 V3Q  C07  C06  C05  119.51  3.000
 V3Q  C19  C07  C08  119.51  3.000
 V3Q  C08  C07  C06  120.54  3.000
 V3Q  C19  C07  C06  119.95  3.000
 V3Q  H8   C08  H7   107.04  3.000
 V3Q  H8   C08  N09  108.00  3.000
 V3Q  H7   C08  N09  109.20  3.000
 V3Q  H8   C08  C07  110.46  3.000
 V3Q  H7   C08  C07  109.91  3.000
 V3Q  N09  C08  C07  112.08  3.000
 V3Q  O18  C10  N09  123.95  3.000
 V3Q  O18  C10  C11  120.46  3.000
 V3Q  N09  C10  C11  115.59  3.000
 V3Q  C16  C11  C12  119.58  3.000
 V3Q  C16  C11  C10  122.55  3.000
 V3Q  C12  C11  C10  117.83  3.000
 V3Q  H9   C12  C13  119.88  3.000
 V3Q  H9   C12  C11  119.71  3.000
 V3Q  C13  C12  C11  120.40  3.000
 V3Q  H10  C13  C14  120.13  3.000
 V3Q  H10  C13  C12  119.95  3.000
 V3Q  C14  C13  C12  119.93  3.000
 V3Q  C17  C14  C15  118.84  3.000
 V3Q  C15  C14  C13  119.78  3.000
 V3Q  C17  C14  C13  121.37  3.000
 V3Q  H11  C15  C16  119.83  3.000
 V3Q  H11  C15  C14  119.88  3.000
 V3Q  C16  C15  C14  120.29  3.000
 V3Q  H12  C16  C15  118.90  3.000
 V3Q  H12  C16  C11  121.08  3.000
 V3Q  C15  C16  C11  120.00  3.000
 V3Q  O1   C17  H13  121.07  3.000
 V3Q  O1   C17  C14  124.43  3.000
 V3Q  H13  C17  C14  114.50  3.000
 V3Q  H16  C19  C07  118.56  3.000
 V3Q  H16  C19  C03  121.06  3.000
 V3Q  C07  C19  C03  120.38  3.000
 V3Q  H17  N09  C10  119.06  3.000
 V3Q  H17  N09  C08  116.45  3.000
 V3Q  C10  N09  C08  124.30  3.000
 V3Q  C03  O02  C01  118.63  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
 V3Q  CONST_01  C06  C05  C04  C03     0.00   0.0  0
 V3Q  CONST_02  C06  C07  C19  C03     0.00   0.0  0
 V3Q  CONST_03  C07  C06  C05  C04     0.00   0.0  0
 V3Q  CONST_04  C07  C19  C03  C04     0.00   0.0  0
 V3Q  CONST_05  C19  C03  C04  C05     0.00   0.0  0
 V3Q  CONST_06  C19  C07  C06  C05     0.00   0.0  0
 V3Q  CONST_07  C14  C13  C12  C11     0.00   0.0  0
 V3Q  CONST_08  C14  C15  C16  C11     0.00   0.0  0
 V3Q  CONST_09  C15  C14  C13  C12     0.00   0.0  0
 V3Q  CONST_10  C15  C16  C11  C12     0.00   0.0  0
 V3Q  CONST_11  C16  C15  C14  C13     0.00   0.0  0
 V3Q  CONST_12  C16  C11  C12  C13     0.00   0.0  0
 V3Q  CONST_13  C08  C07  C19  C03   180.00   0.0  0
 V3Q  CONST_14  O02  C03  C04  C05   180.00   0.0  0
 V3Q  CONST_15  C08  C07  C06  C05   180.00   0.0  0
 V3Q  CONST_16  O02  C03  C19  C07   180.00   0.0  0
 V3Q  CONST_17  C13  C12  C11  C10   180.00   0.0  0
 V3Q  CONST_18  C15  C16  C11  C10   180.00   0.0  0
 V3Q  CONST_19  C17  C14  C13  C12   180.00   0.0  0
 V3Q  CONST_20  C17  C14  C15  C16   180.00   0.0  0
 V3Q  CONST_21  H5   C05  C04  C03   180.00   0.0  0
 V3Q  CONST_22  H6   C06  C05  C04   180.00   0.0  0
 V3Q  CONST_23  H16  C19  C03  C04   180.00   0.0  0
 V3Q  CONST_24  H4   C04  C05  C06   180.00   0.0  0
 V3Q  CONST_25  H10  C13  C12  C11   180.00   0.0  0
 V3Q  CONST_26  H11  C15  C16  C11   180.00   0.0  0
 V3Q  CONST_27  H12  C16  C11  C12   180.00   0.0  0
 V3Q  CONST_28  H9   C12  C13  C14   180.00   0.0  0
 V3Q  CONST_29  C11  C10  N09  C08   180.00   0.0  0
 V3Q  CONST_30  H17  N09  C10  C11     0.00   0.0  0
 V3Q  CONST_31  O18  C10  N09  C08     0.00   0.0  0
 V3Q  Var_01    C04  C03  O02  C01   178.85  30.0  2
 V3Q  Var_02    N09  C08  C07  C06    59.45  30.0  2
 V3Q  Var_03    N09  C10  C11  C12  -151.48  30.0  2
 V3Q  Var_04    O1   C17  C14  C13     0.75  30.0  2
 V3Q  Var_05    C10  N09  C08  C07  -117.45  30.0  1
 V3Q  Var_06    H1   C01  O02  C03  -178.99  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
 V3Q  plan-1  C03  0.020
 V3Q  plan-1  C04  0.020
 V3Q  plan-1  C05  0.020
 V3Q  plan-1  C06  0.020
 V3Q  plan-1  C07  0.020
 V3Q  plan-1  C08  0.020
 V3Q  plan-1  C19  0.020
 V3Q  plan-1  O02  0.020
 V3Q  plan-1  H4   0.020
 V3Q  plan-1  H5   0.020
 V3Q  plan-1  H6   0.020
 V3Q  plan-1  H16  0.020
 V3Q  plan-2  C10  0.020
 V3Q  plan-2  C11  0.020
 V3Q  plan-2  C12  0.020
 V3Q  plan-2  C13  0.020
 V3Q  plan-2  C14  0.020
 V3Q  plan-2  C15  0.020
 V3Q  plan-2  C16  0.020
 V3Q  plan-2  C17  0.020
 V3Q  plan-2  H9   0.020
 V3Q  plan-2  H10  0.020
 V3Q  plan-2  H11  0.020
 V3Q  plan-2  H12  0.020
 V3Q  plan-3  C08  0.020
 V3Q  plan-3  C10  0.020
 V3Q  plan-3  C11  0.020
 V3Q  plan-3  N09  0.020
 V3Q  plan-3  O18  0.020
 V3Q  plan-3  H17  0.020
 V3Q  plan-4  C14  0.020
 V3Q  plan-4  C17  0.020
 V3Q  plan-4  H13  0.020
 V3Q  plan-4  O1   0.020

