# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 09:09:52 2022
#   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  24  14  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.295   0.7703  10.9201   -8.8321
 VZY  C5   C  CR6    0  -0.008   0.5588  10.7376   -7.4683
 VZY  C6   C  CR16   0  -0.350  -0.3563   9.7759   -7.0438
 VZY  C7   C  C      0   0.518   1.3553  11.5689   -6.5081
 VZY  C8   C  CH2    0  -0.411   1.4135  12.5291   -4.2498
 VZY  O1   O  OC    -1  -0.599   0.9438  13.1858   -2.0334
 VZY  C9   C  C      0   0.398   0.4824  12.5851   -3.0171
 VZY  O2   O  O      0  -0.593  -0.6288  12.0310   -3.1281
 VZY  N    N  NH1    0  -0.642   0.7912  11.7937   -5.3195
 VZY  O    O  O      0  -0.500   2.4553  12.0129   -6.8240
 VZY  C3   C  CR16   0  -0.227   0.0544  10.1662   -9.7487
 VZY  C2   C  CR16   0  -0.297  -0.8567   9.2139   -9.3136
 VZY  C1   C  CR6    0   0.116  -1.0680   8.9990   -7.9535
 VZY  C    C  CH3    0  -0.719  -2.0165   7.9352   -7.4818
 VZY  H1   H  HCR6   0   0.252   1.4831  11.6578   -9.1753
 VZY  H2   H  HCR6   0   0.247  -0.5101   9.5964   -5.9855
 VZY  H3   H  HCH2   0   0.237   2.3621  12.0670   -3.9605
 VZY  H4   H  HCH2   0   0.237   1.6507  13.5510   -4.5629
 VZY  H6   H  HNH1   0   0.391  -0.1445  11.4777   -5.1054
 VZY  H7   H  HCR6   0   0.255   0.2057  10.3217  -10.8091
 VZY  H8   H  HCR6   0   0.251  -1.4081   8.6272  -10.0391
 VZY  H9   H  HCH3   0   0.249  -1.5191   6.9644   -7.4325
 VZY  H10  H  HCH3   0   0.245  -2.4021   8.1525   -6.4863
 VZY  H11  H  HCH3   0   0.245  -2.8636   7.8293   -8.1586

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  1.388  0.020  1.388
 VZY  C3  C4   aromatic  1.386  0.020  1.386
 VZY  C2  C1   aromatic  1.393  0.020  1.393
 VZY  C4  C5   aromatic  1.392  0.020  1.392
 VZY  C1  C    single    1.501  0.020  1.501
 VZY  C1  C6   aromatic  1.392  0.020  1.392
 VZY  C5  C6   aromatic  1.394  0.020  1.394
 VZY  C5  C7   single    1.499  0.020  1.499
 VZY  O   C7   double    1.228  0.020  1.228
 VZY  C7  N    single    1.335  0.020  1.335
 VZY  N   C8   single    1.440  0.020  1.440
 VZY  C8  C9   single    1.546  0.020  1.546
 VZY  C9  O2   deloc     1.247  0.020  1.247
 VZY  C9  O1   deloc     1.241  0.020  1.241
 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  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   120.10  3.000
 VZY  H1   C4  C5   120.02  3.000
 VZY  C3   C4  C5   119.87  3.000
 VZY  C7   C5  C6   122.44  3.000
 VZY  C7   C5  C4   118.30  3.000
 VZY  C6   C5  C4   119.25  3.000
 VZY  H2   C6  C1   118.22  3.000
 VZY  H2   C6  C5   120.31  3.000
 VZY  C1   C6  C5   121.45  3.000
 VZY  O    C7  N    123.15  3.000
 VZY  N    C7  C5   116.05  3.000
 VZY  O    C7  C5   120.79  3.000
 VZY  H4   C8  H3   106.38  3.000
 VZY  H4   C8  N    110.98  3.000
 VZY  H3   C8  N    110.82  3.000
 VZY  H4   C8  C9   108.95  3.000
 VZY  H3   C8  C9   109.06  3.000
 VZY  N    C8  C9   110.53  3.000
 VZY  O2   C9  O1   128.09  3.000
 VZY  O1   C9  C8   115.19  3.000
 VZY  O2   C9  C8   116.72  3.000
 VZY  H6   N   C8   113.74  3.000
 VZY  H6   N   C7   121.82  3.000
 VZY  C8   N   C7   124.41  3.000
 VZY  H7   C3  C2   119.83  3.000
 VZY  H7   C3  C4   119.84  3.000
 VZY  C2   C3  C4   120.33  3.000
 VZY  H8   C2  C1   119.53  3.000
 VZY  H8   C2  C3   119.71  3.000
 VZY  C1   C2  C3   120.76  3.000
 VZY  C    C1  C2   120.79  3.000
 VZY  C    C1  C6   120.87  3.000
 VZY  C2   C1  C6   118.32  3.000
 VZY  H11  C   H10  108.17  3.000
 VZY  H11  C   H9   107.21  3.000
 VZY  H10  C   H9   107.30  3.000
 VZY  H11  C   C1   111.40  3.000
 VZY  H10  C   C1   111.68  3.000
 VZY  H9   C   C1   110.88  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  Var_01    O   C7  C5  C4   -26.27  30.0  2
 VZY  Var_02    H9  C   C1  C6   -93.64  30.0  2
 VZY  Var_03    C9  C8  N   C7  -179.53  30.0  3
 VZY  Var_04    N   C8  C9  O1   179.03  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
 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

