# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 09:30:46 2021
#   Inital geometry file: a 64 line input string
#   Ligand name: N-(3-chloro-2-methylphenyl)glycinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1c(Cl)cccc1NC(=O)CN
#
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
 VXD  VXD  N-(3-chloro-2-methylphenyl)glycinamide  ligand  24  13  .  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_VXD
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
 VXD  N1   N   NH1   0  -0.676  -18.8584  34.8716  -67.0076
 VXD  C4   C   CR16  0  -0.216  -22.2403  36.6982  -68.6524
 VXD  C5   C   CR16  0  -0.274  -22.2868  35.3816  -68.2182
 VXD  C6   C   CR16  0  -0.268  -21.1498  34.7964  -67.6896
 VXD  C7   C   CR6   0   0.256  -19.9654  35.5194  -67.5789
 VXD  C8   C   C     0   0.472  -17.8183  34.3157  -67.6748
 VXD  C1   C   CH3   0  -0.689  -18.6505  37.6738  -67.8145
 VXD  C2   C   CR6   0   0.136  -19.8957  36.8581  -67.9782
 VXD  C3   C   CR6   0  -0.092  -21.0549  37.4059  -68.5305
 VXD  C9   C   CH2   0  -0.383  -17.8267  34.4884  -69.1814
 VXD  N2   N   NH2   0  -0.783  -16.8457  33.6331  -69.8062
 VXD  O1   O   O     0  -0.531  -16.9205  33.7383  -67.0847
 VXD  CL1  CL  CL    0  -0.117  -21.0331  39.0512  -69.0838
 VXD  H7   H   HNH1  0   0.416  -18.8732  34.7170  -66.0077
 VXD  H4   H   HCR6  0   0.288  -23.1151  37.1684  -69.0802
 VXD  H5   H   HCR6  0   0.275  -23.2039  34.8136  -68.2985
 VXD  H6   H   HCR6  0   0.280  -21.1678  33.7658  -67.3598
 VXD  H3   H   HCH3  0   0.270  -18.8640  38.6164  -67.3109
 VXD  H2   H   HCH3  0   0.224  -17.9023  37.1408  -67.2333
 VXD  H1   H   HCH3  0   0.264  -18.2135  37.9218  -68.7840
 VXD  H9   H   HCH2  0   0.237  -18.8175  34.2353  -69.5667
 VXD  H8   H   HCH2  0   0.215  -17.6948  35.5603  -69.3927
 VXD  H11  H   HNH2  0   0.358  -16.8754  33.7732  -70.8063
 VXD  H12  H   HNH2  0   0.339  -15.9154  33.8904  -69.5065

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
 VXD  C1   C2   single    1.498  0.020  1.498
 VXD  C2   C3   aromatic  1.396  0.020  1.396
 VXD  C3   C4   aromatic  1.386  0.020  1.386
 VXD  C4   C5   aromatic  1.387  0.020  1.387
 VXD  C5   C6   aromatic  1.384  0.020  1.384
 VXD  C6   C7   aromatic  1.392  0.020  1.392
 VXD  C7   N1   single    1.404  0.020  1.404
 VXD  N1   C8   single    1.355  0.020  1.355
 VXD  C8   O1   double    1.220  0.020  1.220
 VXD  C8   C9   single    1.516  0.020  1.516
 VXD  C9   N2   single    1.444  0.020  1.444
 VXD  C2   C7   aromatic  1.399  0.020  1.399
 VXD  N1   H7   single    0.860  0.020  1.020
 VXD  C4   H4   single    0.930  0.020  1.080
 VXD  C5   H5   single    0.930  0.020  1.080
 VXD  C6   H6   single    0.930  0.020  1.080
 VXD  C1   H3   single    0.970  0.020  1.090
 VXD  C1   H2   single    0.970  0.020  1.090
 VXD  C1   H1   single    0.970  0.020  1.090
 VXD  C9   H9   single    0.970  0.020  1.090
 VXD  C9   H8   single    0.970  0.020  1.090
 VXD  N2   H11  single    0.890  0.020  1.040
 VXD  N2   H12  single    0.890  0.020  1.040
 VXD  CL1  C3   single    1.736  0.020  1.736

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
 VXD  H7   N1  C8   115.79  3.000
 VXD  H7   N1  C7   117.45  3.000
 VXD  C8   N1  C7   126.45  3.000
 VXD  H4   C4  C3   120.31  3.000
 VXD  H4   C4  C5   120.62  3.000
 VXD  C3   C4  C5   119.07  3.000
 VXD  H5   C5  C6   120.19  3.000
 VXD  H5   C5  C4   120.24  3.000
 VXD  C6   C5  C4   119.56  3.000
 VXD  H6   C6  C7   118.99  3.000
 VXD  H6   C6  C5   120.36  3.000
 VXD  C7   C6  C5   120.65  3.000
 VXD  C2   C7  C6   121.12  3.000
 VXD  C2   C7  N1   121.23  3.000
 VXD  C6   C7  N1   117.61  3.000
 VXD  O1   C8  C9   122.59  3.000
 VXD  C9   C8  N1   115.99  3.000
 VXD  O1   C8  N1   121.40  3.000
 VXD  H1   C1  H2   108.09  3.000
 VXD  H1   C1  H3   106.99  3.000
 VXD  H2   C1  H3   108.17  3.000
 VXD  H1   C1  C2   111.06  3.000
 VXD  H2   C1  C2   111.33  3.000
 VXD  H3   C1  C2   111.02  3.000
 VXD  C3   C2  C1   121.33  3.000
 VXD  C3   C2  C7   116.56  3.000
 VXD  C1   C2  C7   122.11  3.000
 VXD  CL1  C3  C2   119.18  3.000
 VXD  CL1  C3  C4   117.82  3.000
 VXD  C2   C3  C4   123.00  3.000
 VXD  H8   C9  H9   105.46  3.000
 VXD  H8   C9  N2   114.36  3.000
 VXD  H9   C9  N2   109.04  3.000
 VXD  H8   C9  C8   107.52  3.000
 VXD  H9   C9  C8   109.21  3.000
 VXD  N2   C9  C8   111.03  3.000
 VXD  H12  N2  H11  106.58  3.000
 VXD  H12  N2  C9   110.26  3.000
 VXD  H11  N2  C9   109.05  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
 VXD  CONST_01  C7   C2  C3  C4     0.00   0.0  0
 VXD  CONST_02  C7   C6  C5  C4     0.00   0.0  0
 VXD  CONST_03  C2   C3  C4  C5     0.00   0.0  0
 VXD  CONST_04  C2   C7  C6  C5     0.00   0.0  0
 VXD  CONST_05  C3   C4  C5  C6     0.00   0.0  0
 VXD  CONST_06  C3   C2  C7  C6     0.00   0.0  0
 VXD  CONST_07  C5   C6  C7  N1   180.00   0.0  0
 VXD  CONST_08  C3   C2  C7  N1   180.00   0.0  0
 VXD  CONST_09  C1   C2  C3  C4   180.00   0.0  0
 VXD  CONST_10  CL1  C3  C4  C5   180.00   0.0  0
 VXD  CONST_11  C1   C2  C7  C6   180.00   0.0  0
 VXD  CONST_12  CL1  C3  C2  C7   180.00   0.0  0
 VXD  CONST_13  H6   C6  C5  C4   180.00   0.0  0
 VXD  CONST_14  H4   C4  C5  C6   180.00   0.0  0
 VXD  CONST_15  H5   C5  C6  C7   180.00   0.0  0
 VXD  CONST_19  O1   C8  N1  C7   180.00   0.0  0
 VXD  CONST_20  C9   C8  N1  C7     0.00   0.0  0
 VXD  Var_01    H3   C1  C2  C7  -128.81  30.0  2
 VXD  Var_02    N2   C9  C8  N1  -167.94  30.0  3
 VXD  Var_03    H11  N2  C9  C8  -179.88  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
 VXD  plan-1  N1   0.020
 VXD  plan-1  C4   0.020
 VXD  plan-1  C5   0.020
 VXD  plan-1  C6   0.020
 VXD  plan-1  C7   0.020
 VXD  plan-1  C1   0.020
 VXD  plan-1  C2   0.020
 VXD  plan-1  C3   0.020
 VXD  plan-1  CL1  0.020
 VXD  plan-1  H4   0.020
 VXD  plan-1  H5   0.020
 VXD  plan-1  H6   0.020
 VXD  plan-2  N1   0.020
 VXD  plan-2  C7   0.020
 VXD  plan-2  C8   0.020
 VXD  plan-2  C9   0.020
 VXD  plan-2  O1   0.020
 VXD  plan-2  H7   0.020

