# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 19:37:28 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 3-(3-methylsulfonylphenyl)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=O)(=O)c1cccc(c1)c2cccc(c2)C(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
 VM7  VM7  '3-(3-methylsulfonylphenyl)benzoic acid'  ligand  30  19  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VM7
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
 VM7  C    C  C      0   0.293   4.8733  -0.3426   0.8233
 VM7  O    O  O      0  -0.542   4.7163  -1.4708   1.3254
 VM7  C1   C  CR6    0   0.151   3.6276   0.3428   0.2731
 VM7  C10  C  CR16   0  -0.173  -0.0721  -1.8437  -0.5815
 VM7  C11  C  CR16   0  -0.296   1.3264   1.5782  -0.7304
 VM7  C12  C  CR16   0  -0.233   2.5193   2.2796  -0.6539
 VM7  C13  C  CR16   0  -0.329   3.6520   1.6816  -0.1197
 VM7  C2   C  CR16   0  -0.375   2.4281  -0.3538   0.1764
 VM7  C3   C  CR6    0   0.101   1.2653   0.2522  -0.3006
 VM7  C4   C  CR6    0   0.064  -0.0167  -0.4812  -0.2850
 VM7  C5   C  CR16   0  -0.328  -1.2021   0.1741   0.0491
 VM7  C6   C  CR6    0  -0.166  -2.3974  -0.5259   0.0507
 VM7  C7   C  CH3    0  -0.802  -4.5299   0.8185  -1.1556
 VM7  C8   C  CR16   0  -0.287  -2.4570  -1.8765  -0.2657
 VM7  C9   C  CR16   0  -0.262  -1.2757  -2.5324  -0.5730
 VM7  O1   O  OS     0  -0.669  -4.8383  -0.6354   1.0192
 VM7  O2   O  OS     0  -0.554  -3.5829   1.5331   1.1976
 VM7  O3   O  OC    -1  -0.769   5.9460   0.2857   0.7137
 VM7  S    S  S      0   1.208  -3.9053   0.3279   0.4366
 VM7  H7   H  HCR6   0   0.238   0.8319  -2.3687  -0.8610
 VM7  H8   H  HCR6   0   0.270   0.4536   2.0612  -1.1504
 VM7  H9   H  HCR6   0   0.275   2.5657   3.2957  -1.0198
 VM7  H10  H  HCR6   0   0.243   4.5611   2.2577  -0.0083
 VM7  H    H  HCR6   0   0.258   2.3968  -1.3846   0.5092
 VM7  H1   H  HCR6   0   0.266  -1.1823   1.2279   0.2956
 VM7  H3   H  HCH3   0   0.307  -3.8686   1.5723  -1.5767
 VM7  H4   H  HCH3   0   0.270  -4.5732  -0.0478  -1.8115
 VM7  H2   H  HCH3   0   0.326  -5.5278   1.2289  -1.0058
 VM7  H5   H  HCR6   0   0.257  -3.3957  -2.4135  -0.2758
 VM7  H6   H  HCR6   0   0.258  -1.2963  -3.5875  -0.8090

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
 VM7  C7   S    single    1.779  0.020  1.779
 VM7  O2   S    double    1.461  0.020  1.461
 VM7  S    C6   single    1.775  0.020  1.775
 VM7  S    O1   double    1.462  0.020  1.462
 VM7  C8   C6   aromatic  1.388  0.020  1.388
 VM7  C8   C9   aromatic  1.386  0.020  1.386
 VM7  C6   C5   aromatic  1.385  0.020  1.385
 VM7  C9   C10  aromatic  1.387  0.020  1.387
 VM7  C5   C4   aromatic  1.395  0.020  1.395
 VM7  C10  C4   aromatic  1.395  0.020  1.395
 VM7  O    C    deloc     1.245  0.020  1.245
 VM7  C4   C3   single    1.477  0.020  1.477
 VM7  C2   C3   aromatic  1.395  0.020  1.395
 VM7  C2   C1   aromatic  1.390  0.020  1.390
 VM7  C3   C11  aromatic  1.395  0.020  1.395
 VM7  C    C1   single    1.525  0.020  1.525
 VM7  C    O3   deloc     1.248  0.020  1.248
 VM7  C1   C13  aromatic  1.396  0.020  1.396
 VM7  C11  C12  aromatic  1.386  0.020  1.386
 VM7  C13  C12  aromatic  1.388  0.020  1.388
 VM7  C10  H7   single    0.930  0.020  1.080
 VM7  C11  H8   single    0.930  0.020  1.080
 VM7  C12  H9   single    0.930  0.020  1.080
 VM7  C13  H10  single    0.930  0.020  1.080
 VM7  C2   H    single    0.930  0.020  1.080
 VM7  C5   H1   single    0.930  0.020  1.080
 VM7  C7   H3   single    0.970  0.020  1.090
 VM7  C7   H4   single    0.970  0.020  1.090
 VM7  C7   H2   single    0.970  0.020  1.090
 VM7  C8   H5   single    0.930  0.020  1.080
 VM7  C9   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
 VM7  O3   C    C1   116.38  3.000
 VM7  O3   C    O    126.88  3.000
 VM7  C1   C    O    116.74  3.000
 VM7  C2   C1   C13  118.44  3.000
 VM7  C13  C1   C    121.24  3.000
 VM7  C2   C1   C    120.32  3.000
 VM7  H7   C10  C9   119.06  3.000
 VM7  H7   C10  C4   119.69  3.000
 VM7  C9   C10  C4   121.20  3.000
 VM7  H8   C11  C3   120.55  3.000
 VM7  H8   C11  C12  119.32  3.000
 VM7  C3   C11  C12  120.11  3.000
 VM7  H9   C12  C13  120.02  3.000
 VM7  H9   C12  C11  119.60  3.000
 VM7  C13  C12  C11  120.38  3.000
 VM7  H10  C13  C12  119.73  3.000
 VM7  H10  C13  C1   119.77  3.000
 VM7  C12  C13  C1   120.49  3.000
 VM7  H    C2   C3   119.61  3.000
 VM7  H    C2   C1   118.69  3.000
 VM7  C3   C2   C1   121.68  3.000
 VM7  C4   C3   C2   120.27  3.000
 VM7  C2   C3   C11  118.79  3.000
 VM7  C4   C3   C11  120.87  3.000
 VM7  C5   C4   C3   120.46  3.000
 VM7  C3   C4   C10  121.13  3.000
 VM7  C5   C4   C10  118.41  3.000
 VM7  H1   C5   C6   120.50  3.000
 VM7  H1   C5   C4   119.75  3.000
 VM7  C6   C5   C4   119.75  3.000
 VM7  S    C6   C8   118.75  3.000
 VM7  C8   C6   C5   121.89  3.000
 VM7  S    C6   C5   119.35  3.000
 VM7  H2   C7   H4   110.28  3.000
 VM7  H2   C7   H3   110.43  3.000
 VM7  H4   C7   H3   110.05  3.000
 VM7  H2   C7   S    107.60  3.000
 VM7  H4   C7   S    109.51  3.000
 VM7  H3   C7   S    108.91  3.000
 VM7  H5   C8   C9   120.18  3.000
 VM7  H5   C8   C6   121.49  3.000
 VM7  C9   C8   C6   118.32  3.000
 VM7  H6   C9   C8   119.61  3.000
 VM7  H6   C9   C10  119.98  3.000
 VM7  C8   C9   C10  120.41  3.000
 VM7  O2   S    O1   118.47  3.000
 VM7  O1   S    C7   108.31  3.000
 VM7  O2   S    C7   108.42  3.000
 VM7  O1   S    C6   108.16  3.000
 VM7  O2   S    C6   108.81  3.000
 VM7  C7   S    C6   103.67  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
 VM7  CONST_01  C4   C3   C2   C1   180.00   0.0  0
 VM7  CONST_02  C11  C3   C2   C1     0.00   0.0  0
 VM7  CONST_03  C11  C12  C13  C1     0.00   0.0  0
 VM7  CONST_04  C6   C8   C9   C10    0.00   0.0  0
 VM7  CONST_05  C6   C5   C4   C10    0.00   0.0  0
 VM7  CONST_09  C4   C3   C11  C12  180.00   0.0  0
 VM7  CONST_10  C2   C3   C11  C12    0.00   0.0  0
 VM7  CONST_11  C2   C1   C13  C12    0.00   0.0  0
 VM7  CONST_12  C3   C2   C1   C13    0.00   0.0  0
 VM7  CONST_13  C3   C11  C12  C13    0.00   0.0  0
 VM7  CONST_15  C6   C5   C4   C3   180.00   0.0  0
 VM7  CONST_16  C9   C10  C4   C3   180.00   0.0  0
 VM7  CONST_17  C8   C6   C5   C4     0.00   0.0  0
 VM7  CONST_18  C8   C9   C10  C4     0.00   0.0  0
 VM7  CONST_19  C9   C8   C6   C5     0.00   0.0  0
 VM7  CONST_20  C9   C10  C4   C5     0.00   0.0  0
 VM7  CONST_21  C3   C2   C1   C    180.00   0.0  0
 VM7  CONST_22  C12  C13  C1   C    180.00   0.0  0
 VM7  CONST_23  S    C6   C5   C4   180.00   0.0  0
 VM7  CONST_24  S    C6   C8   C9   180.00   0.0  0
 VM7  CONST_25  H9   C12  C13  C1   180.00   0.0  0
 VM7  CONST_26  H5   C8   C9   C10  180.00   0.0  0
 VM7  CONST_27  H1   C5   C4   C10  180.00   0.0  0
 VM7  CONST_28  H    C2   C3   C11  180.00   0.0  0
 VM7  CONST_29  H10  C13  C12  C11  180.00   0.0  0
 VM7  CONST_30  H8   C11  C12  C13  180.00   0.0  0
 VM7  CONST_31  H7   C10  C4   C3     0.00   0.0  0
 VM7  CONST_32  H6   C9   C10  C4   180.00   0.0  0
 VM7  Var_01    C2   C1   C    O     -8.77  30.0  2
 VM7  Var_02    C7   S    C6   C5    93.17  30.0  2
 VM7  Var_03    H3   C7   S    C6   -68.04  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
 VM7  plan-1  C    0.020
 VM7  plan-1  C1   0.020
 VM7  plan-1  C11  0.020
 VM7  plan-1  C12  0.020
 VM7  plan-1  C13  0.020
 VM7  plan-1  C2   0.020
 VM7  plan-1  C3   0.020
 VM7  plan-1  C4   0.020
 VM7  plan-1  H8   0.020
 VM7  plan-1  H9   0.020
 VM7  plan-1  H10  0.020
 VM7  plan-1  H    0.020
 VM7  plan-2  C10  0.020
 VM7  plan-2  C3   0.020
 VM7  plan-2  C4   0.020
 VM7  plan-2  C5   0.020
 VM7  plan-2  C6   0.020
 VM7  plan-2  C8   0.020
 VM7  plan-2  C9   0.020
 VM7  plan-2  S    0.020
 VM7  plan-2  H7   0.020
 VM7  plan-2  H1   0.020
 VM7  plan-2  H5   0.020
 VM7  plan-2  H6   0.020
 VM7  plan-3  C    0.020
 VM7  plan-3  O    0.020
 VM7  plan-3  C1   0.020
 VM7  plan-3  O3   0.020

