# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 08:35:32 2021
#   Inital geometry file: a 69 line input string
#   Ligand name: N-(3-methylbenzene-1-carbonyl)glycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(c1)C(=O)NCC(O)=O
#
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
 VZY  VZY  N-(3-methylbenzene-1-carbonyl)glycine  ligand  25  14  .  2022-03-29  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_VZY
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
 VZY  C4   C  CR16  0  -0.291   1.1486  10.5255   -8.4827
 VZY  C5   C  CR6   0  -0.008   0.4780  10.6291   -7.2678
 VZY  C6   C  CR16  0  -0.352  -0.6906   9.8962   -7.0664
 VZY  C7   C  C     0   0.539   1.0610  11.5149   -6.2162
 VZY  C8   C  CH2   0  -0.422   0.6600  12.8520   -4.2424
 VZY  O1   O  OH1   0  -0.592   1.9852  12.9067   -2.3169
 VZY  C9   C  C     0   0.537   1.4346  12.0791   -3.1948
 VZY  O2   O  O     0  -0.432   1.5238  10.8817   -3.1458
 VZY  N    N  NH1   0  -0.642   0.2037  12.0189   -5.3113
 VZY  O    O  O     0  -0.486   2.2532  11.7878   -6.1968
 VZY  C3   C  CR16  0  -0.228   0.6347   9.7191   -9.4862
 VZY  C2   C  CR16  0  -0.292  -0.5325   8.9992   -9.2770
 VZY  C1   C  CR6   0   0.115  -1.2080   9.0717   -8.0602
 VZY  C    C  CH3   0  -0.719  -2.4502   8.2634   -7.8227
 VZY  H1   H  HCR6  0   0.258   2.0607  11.0826   -8.6484
 VZY  H2   H  HCR6  0   0.251  -1.2086   9.9370   -6.1146
 VZY  H3   H  HCH2  0   0.288   1.2752  13.6762   -4.6106
 VZY  H4   H  HCH2  0   0.314  -0.2090  13.3028   -3.7608
 VZY  H5   H  HOH1  0   0.484   2.4540  12.4076   -1.6316
 VZY  H6   H  HNH1  0   0.417  -0.7808  11.8247   -5.3735
 VZY  H7   H  HCR6  0   0.260   1.1457   9.6532  -10.4379
 VZY  H8   H  HCR6  0   0.256  -0.9234   8.3701  -10.0680
 VZY  H9   H  HCH3  0   0.251  -2.2051   7.2165   -7.6344
 VZY  H10  H  HCH3  0   0.245  -3.0072   8.6305   -6.9619
 VZY  H11  H  HCH3  0   0.247  -3.1104   8.2889   -8.6894

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
 VZY  C3  C2   aromatic  1.387  0.020  1.387
 VZY  C3  C4   aromatic  1.386  0.020  1.386
 VZY  C2  C1   aromatic  1.394  0.020  1.394
 VZY  C4  C5   aromatic  1.391  0.020  1.391
 VZY  C1  C    single    1.501  0.020  1.501
 VZY  C1  C6   aromatic  1.391  0.020  1.391
 VZY  C5  C6   aromatic  1.394  0.020  1.394
 VZY  C5  C7   single    1.493  0.020  1.493
 VZY  O   C7   double    1.223  0.020  1.223
 VZY  C7  N    single    1.345  0.020  1.345
 VZY  N   C8   single    1.430  0.020  1.430
 VZY  C8  C9   single    1.515  0.020  1.515
 VZY  C9  O2   double    1.202  0.020  1.202
 VZY  C9  O1   single    1.326  0.020  1.326
 VZY  C4  H1   single    0.930  0.020  1.080
 VZY  C6  H2   single    0.930  0.020  1.080
 VZY  C8  H3   single    0.970  0.020  1.090
 VZY  C8  H4   single    0.970  0.020  1.090
 VZY  O1  H5   single    0.850  0.020  0.980
 VZY  N   H6   single    0.860  0.020  1.020
 VZY  C3  H7   single    0.930  0.020  1.080
 VZY  C2  H8   single    0.930  0.020  1.080
 VZY  C   H9   single    0.970  0.020  1.090
 VZY  C   H10  single    0.970  0.020  1.090
 VZY  C   H11  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
 VZY  H1   C4  C3   120.09  3.000
 VZY  H1   C4  C5   120.12  3.000
 VZY  C3   C4  C5   119.78  3.000
 VZY  C7   C5  C6   122.50  3.000
 VZY  C7   C5  C4   118.09  3.000
 VZY  C6   C5  C4   119.41  3.000
 VZY  H2   C6  C1   118.14  3.000
 VZY  H2   C6  C5   120.50  3.000
 VZY  C1   C6  C5   121.34  3.000
 VZY  O    C7  N    121.81  3.000
 VZY  N    C7  C5   116.57  3.000
 VZY  O    C7  C5   121.60  3.000
 VZY  H4   C8  H3   106.60  3.000
 VZY  H4   C8  N    108.45  3.000
 VZY  H3   C8  N    111.55  3.000
 VZY  H4   C8  C9   108.23  3.000
 VZY  H3   C8  C9   109.27  3.000
 VZY  N    C8  C9   112.51  3.000
 VZY  H5   O1  C9   110.35  3.000
 VZY  O2   C9  O1   124.33  3.000
 VZY  O1   C9  C8   110.59  3.000
 VZY  O2   C9  C8   125.07  3.000
 VZY  H6   N   C8   118.12  3.000
 VZY  H6   N   C7   120.68  3.000
 VZY  C8   N   C7   121.20  3.000
 VZY  H7   C3  C2   119.89  3.000
 VZY  H7   C3  C4   119.80  3.000
 VZY  C2   C3  C4   120.31  3.000
 VZY  H8   C2  C1   119.52  3.000
 VZY  H8   C2  C3   119.65  3.000
 VZY  C1   C2  C3   120.83  3.000
 VZY  C    C1  C2   120.75  3.000
 VZY  C    C1  C6   120.93  3.000
 VZY  C2   C1  C6   118.31  3.000
 VZY  H11  C   H10  108.11  3.000
 VZY  H11  C   H9   107.20  3.000
 VZY  H10  C   H9   107.57  3.000
 VZY  H11  C   C1   111.28  3.000
 VZY  H10  C   C1   111.52  3.000
 VZY  H9   C   C1   110.98  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
 VZY  CONST_01  C1  C2  C3  C4     0.00   0.0  0
 VZY  CONST_02  C1  C6  C5  C4     0.00   0.0  0
 VZY  CONST_03  C2  C3  C4  C5     0.00   0.0  0
 VZY  CONST_04  C2  C1  C6  C5     0.00   0.0  0
 VZY  CONST_05  C3  C2  C1  C6     0.00   0.0  0
 VZY  CONST_06  C3  C4  C5  C6     0.00   0.0  0
 VZY  CONST_07  C   C1  C6  C5   180.00   0.0  0
 VZY  CONST_08  C3  C4  C5  C7   180.00   0.0  0
 VZY  CONST_09  C1  C6  C5  C7   180.00   0.0  0
 VZY  CONST_10  C   C1  C2  C3   180.00   0.0  0
 VZY  CONST_11  H8  C2  C3  C4   180.00   0.0  0
 VZY  CONST_12  H2  C6  C5  C4   180.00   0.0  0
 VZY  CONST_13  H7  C3  C4  C5   180.00   0.0  0
 VZY  CONST_14  H1  C4  C5  C6   180.00   0.0  0
 VZY  CONST_15  C8  N   C7  C5   180.00   0.0  0
 VZY  CONST_16  H6  N   C7  C5     0.00   0.0  0
 VZY  CONST_17  O   C7  N   C8     0.00   0.0  0
 VZY  CONST_18  H5  O1  C9  C8   180.00   0.0  0
 VZY  Var_01    O   C7  C5  C4   -24.10  30.0  2
 VZY  Var_02    H9  C   C1  C6  -102.82  30.0  2
 VZY  Var_03    C9  C8  N   C7   -71.54  30.0  3
 VZY  Var_04    N   C8  C9  O1   171.93  30.0  1

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
 VZY  plan-1  C4  0.020
 VZY  plan-1  C5  0.020
 VZY  plan-1  C6  0.020
 VZY  plan-1  C7  0.020
 VZY  plan-1  C3  0.020
 VZY  plan-1  C2  0.020
 VZY  plan-1  C1  0.020
 VZY  plan-1  C   0.020
 VZY  plan-1  H1  0.020
 VZY  plan-1  H2  0.020
 VZY  plan-1  H7  0.020
 VZY  plan-1  H8  0.020
 VZY  plan-2  C5  0.020
 VZY  plan-2  C7  0.020
 VZY  plan-2  C8  0.020
 VZY  plan-2  N   0.020
 VZY  plan-2  O   0.020
 VZY  plan-2  H6  0.020
 VZY  plan-3  C8  0.020
 VZY  plan-3  O1  0.020
 VZY  plan-3  C9  0.020
 VZY  plan-3  O2  0.020
 VZY  plan-3  H5  0.020

