# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 14:50:27 2021
#   Inital geometry file: a 60 line input string
#   Ligand name: 2-(2-methylphenyl)acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccccc1CC(N)=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
 R9S  R9S  2-(2-methylphenyl)acetamide  ligand  22  11  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_R9S
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
 R9S  C4   C  CR16  0  -0.262  25.2209   2.8520  60.5469
 R9S  C5   C  CR16  0  -0.309  23.9169   2.4119  60.7300
 R9S  C6   C  CR6   0   0.127  23.5165   1.1477  60.3126
 R9S  C7   C  CH2   0  -0.698  22.0957   0.7078  60.5169
 R9S  C8   C  C     0   0.524  21.2783   0.7956  59.2369
 R9S  O    O  O     0  -0.481  21.4261   1.7123  58.4436
 R9S  N    N  NH2   0  -0.799  20.3785  -0.1833  59.0694
 R9S  C1   C  CR6   0   0.076  24.4446   0.3003  59.6921
 R9S  C    C  CH3   0  -0.747  24.0522  -1.0707  59.2201
 R9S  C3   C  CR16  0  -0.256  26.1420   2.0160  59.9348
 R9S  C2   C  CR16  0  -0.297  25.7496   0.7516  59.5151
 R9S  H1   H  HCR6  0   0.252  25.5122   3.8387  60.8827
 R9S  H2   H  HCR6  0   0.247  23.1964   3.0602  61.2148
 R9S  H3   H  HCH2  0   0.302  21.6085   1.3619  61.2457
 R9S  H4   H  HCH2  0   0.270  22.0504  -0.2994  60.9374
 R9S  H5   H  HNH2  0   0.401  19.7624  -0.1818  58.2727
 R9S  H6   H  HNH2  0   0.408  20.2782  -0.9334  59.7308
 R9S  H7   H  HCH3  0   0.245  23.6269  -1.6733  60.0253
 R9S  H8   H  HCH3  0   0.247  23.3043  -1.0314  58.4256
 R9S  H9   H  HCH3  0   0.255  24.9126  -1.6100  58.8262
 R9S  H10  H  HCR6  0   0.252  27.1640   2.3410  59.7864
 R9S  H11  H  HCR6  0   0.246  26.4725   0.0997  59.0387

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
 R9S  N   C8   single    1.340  0.020  1.340
 R9S  O   C8   double    1.221  0.020  1.221
 R9S  C8  C7   single    1.521  0.020  1.521
 R9S  C   C1   single    1.502  0.020  1.502
 R9S  C2  C1   aromatic  1.392  0.020  1.392
 R9S  C2  C3   aromatic  1.389  0.020  1.389
 R9S  C1  C6   aromatic  1.402  0.020  1.402
 R9S  C3  C4   aromatic  1.386  0.020  1.386
 R9S  C6  C7   single    1.501  0.020  1.501
 R9S  C6  C5   aromatic  1.390  0.020  1.390
 R9S  C4  C5   aromatic  1.388  0.020  1.388
 R9S  C4  H1   single    0.930  0.020  1.080
 R9S  C5  H2   single    0.930  0.020  1.080
 R9S  C7  H3   single    0.970  0.020  1.090
 R9S  C7  H4   single    0.970  0.020  1.090
 R9S  N   H5   single    0.860  0.020  1.020
 R9S  N   H6   single    0.860  0.020  1.020
 R9S  C   H7   single    0.970  0.020  1.090
 R9S  C   H8   single    0.970  0.020  1.090
 R9S  C   H9   single    0.970  0.020  1.090
 R9S  C3  H10  single    0.930  0.020  1.080
 R9S  C2  H11  single    0.930  0.020  1.080

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
 R9S  H1   C4  C3  120.53  3.000
 R9S  H1   C4  C5  120.05  3.000
 R9S  C3   C4  C5  119.42  3.000
 R9S  H2   C5  C6  119.13  3.000
 R9S  H2   C5  C4  119.59  3.000
 R9S  C6   C5  C4  121.27  3.000
 R9S  C1   C6  C7  120.65  3.000
 R9S  C7   C6  C5  119.88  3.000
 R9S  C1   C6  C5  119.47  3.000
 R9S  H4   C7  H3  106.05  3.000
 R9S  H4   C7  C8  110.78  3.000
 R9S  H3   C7  C8  106.67  3.000
 R9S  H4   C7  C6  111.21  3.000
 R9S  H3   C7  C6  109.69  3.000
 R9S  C8   C7  C6  112.15  3.000
 R9S  N    C8  O   123.26  3.000
 R9S  O    C8  C7  121.66  3.000
 R9S  N    C8  C7  115.07  3.000
 R9S  H6   N   H5  117.43  3.000
 R9S  H6   N   C8  122.00  3.000
 R9S  H5   N   C8  120.56  3.000
 R9S  C2   C1  C   120.06  3.000
 R9S  C2   C1  C6  118.75  3.000
 R9S  C    C1  C6  121.19  3.000
 R9S  H9   C   H8  107.20  3.000
 R9S  H9   C   H7  107.52  3.000
 R9S  H8   C   H7  106.83  3.000
 R9S  H9   C   C1  111.05  3.000
 R9S  H8   C   C1  112.01  3.000
 R9S  H7   C   C1  111.95  3.000
 R9S  H10  C3  C2  119.91  3.000
 R9S  H10  C3  C4  120.45  3.000
 R9S  C2   C3  C4  119.65  3.000
 R9S  H11  C2  C3  119.47  3.000
 R9S  H11  C2  C1  119.09  3.000
 R9S  C3   C2  C1  121.44  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
 R9S  CONST_01  C1   C2  C3  C4    0.00   0.0  0
 R9S  CONST_02  C1   C6  C5  C4    0.00   0.0  0
 R9S  CONST_03  C2   C1  C6  C5    0.00   0.0  0
 R9S  CONST_04  C2   C3  C4  C5    0.00   0.0  0
 R9S  CONST_05  C3   C2  C1  C6    0.00   0.0  0
 R9S  CONST_06  C3   C4  C5  C6    0.00   0.0  0
 R9S  CONST_07  C7   C6  C5  C4  180.00   0.0  0
 R9S  CONST_08  C    C1  C6  C5  180.00   0.0  0
 R9S  CONST_09  C2   C1  C6  C7  180.00   0.0  0
 R9S  CONST_10  C3   C2  C1  C   180.00   0.0  0
 R9S  CONST_11  H11  C2  C3  C4  180.00   0.0  0
 R9S  CONST_12  H10  C3  C4  C5  180.00   0.0  0
 R9S  CONST_13  H1   C4  C5  C6  180.00   0.0  0
 R9S  CONST_14  H2   C5  C6  C1  180.00   0.0  0
 R9S  CONST_15  H5   N   C8  C7  180.00   0.0  0
 R9S  CONST_16  H6   N   C8  C7    0.00   0.0  0
 R9S  Var_01    C8   C7  C6  C5  102.01  30.0  2
 R9S  Var_02    H7   C   C1  C6  -55.95  30.0  2
 R9S  Var_03    N    C8  C7  C6  143.31  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
 R9S  plan-1  C4   0.020
 R9S  plan-1  C5   0.020
 R9S  plan-1  C6   0.020
 R9S  plan-1  C7   0.020
 R9S  plan-1  C1   0.020
 R9S  plan-1  C    0.020
 R9S  plan-1  C3   0.020
 R9S  plan-1  C2   0.020
 R9S  plan-1  H1   0.020
 R9S  plan-1  H2   0.020
 R9S  plan-1  H10  0.020
 R9S  plan-1  H11  0.020
 R9S  plan-2  C7   0.020
 R9S  plan-2  C8   0.020
 R9S  plan-2  O    0.020
 R9S  plan-2  N    0.020
 R9S  plan-2  H5   0.020
 R9S  plan-2  H6   0.020

