# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 23:24:03 2020
#   Inital geometry file: a 43 line input string
#   Ligand name: methylbenzene
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccccc1
#
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
 MBN  MBN  'methylbenzene            '  ligand  15  7  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_MBN
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
 MBN  C    C  CH3   0  -0.720   0.0030   0.0235   2.4505
 MBN  C1   C  CR6   0   0.097   0.0089  -0.0109   0.9493
 MBN  C2   C  CR16  0  -0.299   1.2084  -0.0037   0.2389
 MBN  C3   C  CR16  0  -0.241   1.2169  -0.0059  -1.1495
 MBN  C4   C  CR16  0  -0.275   0.0203  -0.0176  -1.8549
 MBN  C5   C  CR16  0  -0.241  -1.1816  -0.0288  -1.1597
 MBN  C6   C  CR16  0  -0.300  -1.1843  -0.0264   0.2292
 MBN  H1   H  HCH3  0   0.242   0.8744  -0.4820   2.8661
 MBN  H2A  H  HCH3  0   0.247   0.0210   1.0520   2.8175
 MBN  H3A  H  HCH3  0   0.242  -0.8894  -0.4501   2.8589
 MBN  H2   H  HCR6  0   0.245   2.1478   0.0005   0.7800
 MBN  H3   H  HCR6  0   0.252   2.1598  -0.0019  -1.6819
 MBN  H4   H  HCR6  0   0.252   0.0252  -0.0220  -2.9372
 MBN  H5   H  HCR6  0   0.252  -2.1203  -0.0431  -1.6990
 MBN  H6   H  HCR6  0   0.245  -2.1281  -0.0405   0.7623

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
 MBN  C   C1   single    1.502  0.020  1.502
 MBN  C   H1   single    0.970  0.020  1.090
 MBN  C   H2A  single    0.970  0.020  1.090
 MBN  C   H3A  single    0.970  0.020  1.090
 MBN  C1  C2   aromatic  1.394  0.020  1.394
 MBN  C1  C6   aromatic  1.394  0.020  1.394
 MBN  C2  C3   aromatic  1.388  0.020  1.388
 MBN  C2  H2   single    0.930  0.020  1.080
 MBN  C3  C4   aromatic  1.389  0.020  1.389
 MBN  C3  H3   single    0.930  0.020  1.080
 MBN  C4  C5   aromatic  1.388  0.020  1.388
 MBN  C4  H4   single    0.930  0.020  1.080
 MBN  C5  C6   aromatic  1.389  0.020  1.389
 MBN  C5  H5   single    0.930  0.020  1.080
 MBN  C6  H6   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
 MBN  H3A  C   H2A  107.27  3.000
 MBN  H3A  C   H1   108.07  3.000
 MBN  H2A  C   H1   107.19  3.000
 MBN  H3A  C   C1   111.59  3.000
 MBN  H2A  C   C1   110.94  3.000
 MBN  H1   C   C1   111.57  3.000
 MBN  C6   C1  C2   118.26  3.000
 MBN  C6   C1  C    120.89  3.000
 MBN  C2   C1  C    120.84  3.000
 MBN  H2   C2  C3   119.59  3.000
 MBN  H2   C2  C1   119.42  3.000
 MBN  C3   C2  C1   120.99  3.000
 MBN  H3   C3  C4   120.03  3.000
 MBN  H3   C3  C2   119.80  3.000
 MBN  C4   C3  C2   120.17  3.000
 MBN  H4   C4  C5   120.30  3.000
 MBN  H4   C4  C3   120.26  3.000
 MBN  C5   C4  C3   119.44  3.000
 MBN  H5   C5  C6   119.76  3.000
 MBN  H5   C5  C4   120.08  3.000
 MBN  C6   C5  C4   120.16  3.000
 MBN  H6   C6  C5   119.57  3.000
 MBN  H6   C6  C1   119.43  3.000
 MBN  C5   C6  C1   121.00  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
 MBN  CONST_01  C4  C3  C2  C1    0.00   0.0  0
 MBN  CONST_02  C4  C5  C6  C1    0.00   0.0  0
 MBN  CONST_03  C5  C6  C1  C2    0.00   0.0  0
 MBN  CONST_04  C5  C4  C3  C2    0.00   0.0  0
 MBN  CONST_05  C6  C1  C2  C3    0.00   0.0  0
 MBN  CONST_06  C6  C5  C4  C3    0.00   0.0  0
 MBN  CONST_07  C3  C2  C1  C   180.00   0.0  0
 MBN  CONST_08  C5  C6  C1  C   180.00   0.0  0
 MBN  CONST_09  H3  C3  C2  C1  180.00   0.0  0
 MBN  CONST_10  H5  C5  C6  C1  180.00   0.0  0
 MBN  CONST_11  H6  C6  C1  C2  180.00   0.0  0
 MBN  CONST_12  H4  C4  C3  C2  180.00   0.0  0
 MBN  CONST_13  H2  C2  C3  C4  180.00   0.0  0
 MBN  Var_01    H1  C   C1  C2  -31.66  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
 MBN  plan-1  C   0.020
 MBN  plan-1  C1  0.020
 MBN  plan-1  C2  0.020
 MBN  plan-1  C3  0.020
 MBN  plan-1  C4  0.020
 MBN  plan-1  C5  0.020
 MBN  plan-1  C6  0.020
 MBN  plan-1  H2  0.020
 MBN  plan-1  H3  0.020
 MBN  plan-1  H4  0.020
 MBN  plan-1  H5  0.020
 MBN  plan-1  H6  0.020

