# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 05:59:17 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: (1R,3R)-N-[(1R)-1-(4-bromophenyl)ethyl]-2,2-dichloro-3-methyl-1-[(S)-methylsulfinyl]cyclopropanecarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](NC(=O)[C@@]1([C@@H](C)C1(Cl)Cl)[S@](C)=O)c2ccc(Br)cc2
#
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
 MS2  MS2  (1R,3R)-N-[(1R)-1-(4-bromophenyl)ethyl]-2,2-dichloro-3-methyl-1-[(S)-methylsulfinyl]cyclopropanecarboxamide  ligand  37  21  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_MS2
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
 MS2  C     C   CH3   0  -0.669   5.4437   0.6979   0.8594
 MS2  BR1   BR  BR    0  -0.043  -5.6726   0.9103  -0.1777
 MS2  C1    C   CR6   0  -0.122  -4.0243   0.0323   0.0998
 MS2  C2A   C   CR16  0  -0.209  -3.5898  -0.2113   1.3931
 MS2  C3A   C   CR16  0  -0.311  -2.3751  -0.8557   1.5845
 MS2  C4    C   CR6   0   0.126  -1.6004  -1.2653   0.5064
 MS2  C3B   C   CR16  0  -0.293  -2.0613  -1.0092  -0.7824
 MS2  C2B   C   CR16  0  -0.211  -3.2680  -0.3600  -0.9953
 MS2  C5    C   CH1   0  -0.155  -0.2836  -1.9671   0.7345
 MS2  C6    C   CH3   0  -0.648  -0.2185  -3.3224   0.0371
 MS2  N1    N   NH1   0  -0.629   0.7953  -1.0877   0.2928
 MS2  C7    C   C     0   0.608   2.0443  -1.1782   0.7670
 MS2  O1    O   O     0  -0.451   2.4147  -2.0074   1.5754
 MS2  C8    C   CT    0  -0.344   3.0153  -0.1737   0.1898
 MS2  C9A   C   CT    0  -0.117   2.9123   1.2930   0.4660
 MS2  CL15  CL  CL    0  -0.027   1.5598   1.8709   1.4173
 MS2  CL16  CL  CL    0  -0.023   3.3420   2.4238  -0.8019
 MS2  C17   C   CH1   0  -0.181   3.9779   0.5051   1.1373
 MS2  O9B   O   O     0  -0.744   3.9798  -2.1937  -1.2209
 MS2  S9B   S   S3    0   0.789   3.7323  -0.7217  -1.3944
 MS2  C12   C   CH3   0  -0.817   2.2948  -0.5758  -2.4711
 MS2  H1    H   HCH3  0   0.239   5.6638   0.9301  -0.1796
 MS2  H2    H   HCH3  0   0.265   5.8222   1.5133   1.4742
 MS2  H3    H   HCH3  0   0.262   5.9877  -0.2068   1.1280
 MS2  H3A   H   HCR6  0   0.270  -2.0331  -1.0411   2.5951
 MS2  H3B   H   HCR6  0   0.268  -1.4876  -1.3204  -1.6476
 MS2  H2B   H   HCR6  0   0.284  -3.6057  -0.1720  -2.0054
 MS2  H5    H   HCH1  0   0.276  -0.1622  -2.1236   1.8086
 MS2  H61   H   HCH3  0   0.249   0.7354  -3.8093   0.2341
 MS2  H62   H   HCH3  0   0.244  -1.0116  -3.9712   0.4087
 MS2  H63   H   HCH3  0   0.230  -0.3377  -3.2231  -1.0421
 MS2  H99   H   HNH1  0   0.408   0.5520  -0.2928  -0.2772
 MS2  H17   H   HCH1  0   0.319   3.7675   0.2907   2.1807
 MS2  H121  H   HCH3  0   0.281   1.8987   0.4375  -2.4562
 MS2  H122  H   HCH3  0   0.314   2.6466  -0.8018  -3.4765
 MS2  H123  H   HCH3  0   0.281   1.5372  -1.3013  -2.1829
 MS2  H2A   H   HCR6  0   0.282  -4.1780   0.0928   2.2484

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
 MS2  C    C17   single    1.504  0.020  1.504
 MS2  C    H1    single    0.970  0.020  1.090
 MS2  C    H2    single    0.970  0.020  1.090
 MS2  C    H3    single    0.970  0.020  1.090
 MS2  BR1  C1    single    1.888  0.020  1.888
 MS2  C1   C2A   aromatic  1.386  0.020  1.386
 MS2  C1   C2B   aromatic  1.387  0.020  1.387
 MS2  C2A  C3A   aromatic  1.388  0.020  1.388
 MS2  C2A  H2A   single    0.930  0.020  1.080
 MS2  C3A  C4    aromatic  1.389  0.020  1.389
 MS2  C3A  H3A   single    0.930  0.020  1.080
 MS2  C4   C3B   aromatic  1.393  0.020  1.393
 MS2  C4   C5    single    1.509  0.020  1.509
 MS2  C3B  C2B   aromatic  1.387  0.020  1.387
 MS2  C3B  H3B   single    0.930  0.020  1.080
 MS2  C2B  H2B   single    0.930  0.020  1.080
 MS2  C5   C6    single    1.526  0.020  1.526
 MS2  C5   N1    single    1.460  0.020  1.460
 MS2  C5   H5    single    0.970  0.020  1.090
 MS2  C6   H61   single    0.970  0.020  1.090
 MS2  C6   H62   single    0.970  0.020  1.090
 MS2  C6   H63   single    0.970  0.020  1.090
 MS2  N1   C7    single    1.339  0.020  1.339
 MS2  N1   H99   single    0.860  0.020  1.020
 MS2  C7   O1    double    1.216  0.020  1.216
 MS2  C7   C8    single    1.512  0.020  1.512
 MS2  C8   C9A   single    1.496  0.020  1.496
 MS2  C8   C17   single    1.512  0.020  1.512
 MS2  C8   S9B   single    1.823  0.020  1.823
 MS2  C9A  CL15  single    1.752  0.020  1.752
 MS2  C9A  CL16  single    1.752  0.020  1.752
 MS2  C9A  C17   single    1.486  0.020  1.486
 MS2  C17  H17   single    0.970  0.020  1.090
 MS2  O9B  S9B   double    1.503  0.020  1.503
 MS2  S9B  C12   single    1.802  0.020  1.802
 MS2  C12  H121  single    0.970  0.020  1.090
 MS2  C12  H122  single    0.970  0.020  1.090
 MS2  C12  H123  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
 MS2  H3    C    H2    108.00  3.000
 MS2  H3    C    H1    108.18  3.000
 MS2  H2    C    H1    108.01  3.000
 MS2  H3    C    C17   109.55  3.000
 MS2  H2    C    C17   109.29  3.000
 MS2  H1    C    C17   113.65  3.000
 MS2  C2B   C1   C2A   121.06  3.000
 MS2  C2B   C1   BR1   119.43  3.000
 MS2  C2A   C1   BR1   119.51  3.000
 MS2  H2A   C2A  C3A   119.82  3.000
 MS2  H2A   C2A  C1    121.20  3.000
 MS2  C3A   C2A  C1    118.98  3.000
 MS2  H3A   C3A  C4    119.84  3.000
 MS2  H3A   C3A  C2A   118.98  3.000
 MS2  C4    C3A  C2A   121.18  3.000
 MS2  C5    C4   C3B   120.94  3.000
 MS2  C5    C4   C3A   120.42  3.000
 MS2  C3B   C4   C3A   118.65  3.000
 MS2  H3B   C3B  C2B   118.20  3.000
 MS2  H3B   C3B  C4    120.72  3.000
 MS2  C2B   C3B  C4    121.08  3.000
 MS2  H2B   C2B  C3B   119.77  3.000
 MS2  H2B   C2B  C1    121.18  3.000
 MS2  C3B   C2B  C1    119.05  3.000
 MS2  H5    C5   N1    107.55  3.000
 MS2  H5    C5   C6    108.51  3.000
 MS2  N1    C5   C6    111.42  3.000
 MS2  H5    C5   C4    108.19  3.000
 MS2  N1    C5   C4    108.59  3.000
 MS2  C6    C5   C4    112.41  3.000
 MS2  H63   C6   H62   108.19  3.000
 MS2  H63   C6   H61   108.39  3.000
 MS2  H62   C6   H61   108.04  3.000
 MS2  H63   C6   C5    111.52  3.000
 MS2  H62   C6   C5    109.99  3.000
 MS2  H61   C6   C5    110.61  3.000
 MS2  H99   N1   C7    118.60  3.000
 MS2  H99   N1   C5    117.88  3.000
 MS2  C7    N1   C5    122.77  3.000
 MS2  C8    C7   O1    120.76  3.000
 MS2  C8    C7   N1    114.78  3.000
 MS2  O1    C7   N1    124.45  3.000
 MS2  S9B   C8   C17   115.42  3.000
 MS2  S9B   C8   C9A   118.83  3.000
 MS2  C17   C8   C9A    59.20  3.000
 MS2  S9B   C8   C7    112.62  3.000
 MS2  C17   C8   C7    117.91  3.000
 MS2  C9A   C8   C7    122.46  3.000
 MS2  C17   C9A  CL16  119.56  3.000
 MS2  C17   C9A  CL15  118.91  3.000
 MS2  CL16  C9A  CL15  111.68  3.000
 MS2  C17   C9A  C8     60.92  3.000
 MS2  CL16  C9A  C8    118.83  3.000
 MS2  CL15  C9A  C8    118.48  3.000
 MS2  H17   C17  C9A   113.58  3.000
 MS2  H17   C17  C8    112.97  3.000
 MS2  C9A   C17  C8     59.88  3.000
 MS2  H17   C17  C     113.06  3.000
 MS2  C9A   C17  C     123.20  3.000
 MS2  C8    C17  C     124.21  3.000
 MS2  C12   S9B  O9B   106.25  3.000
 MS2  C12   S9B  C8    100.44  3.000
 MS2  O9B   S9B  C8    105.01  3.000
 MS2  H123  C12  H122  109.35  3.000
 MS2  H123  C12  H121  111.35  3.000
 MS2  H122  C12  H121  108.88  3.000
 MS2  H123  C12  S9B   110.07  3.000
 MS2  H122  C12  S9B   106.09  3.000
 MS2  H121  C12  S9B   110.95  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
 MS2  CONST_01  C4    C3A  C2A  C1      0.00   0.0  0
 MS2  CONST_02  C4    C3B  C2B  C1      0.00   0.0  0
 MS2  CONST_03  C3B   C2B  C1   C2A     0.00   0.0  0
 MS2  CONST_04  C3B   C4   C3A  C2A     0.00   0.0  0
 MS2  CONST_05  C2B   C1   C2A  C3A     0.00   0.0  0
 MS2  CONST_06  C2B   C3B  C4   C3A     0.00   0.0  0
 MS2  CONST_07  C3A   C2A  C1   BR1   180.00   0.0  0
 MS2  CONST_08  C3B   C2B  C1   BR1   180.00   0.0  0
 MS2  CONST_09  C5    C4   C3A  C2A   180.00   0.0  0
 MS2  CONST_10  C5    C4   C3B  C2B   180.00   0.0  0
 MS2  CONST_11  H3A   C3A  C2A  C1    180.00   0.0  0
 MS2  CONST_12  H3B   C3B  C2B  C1    180.00   0.0  0
 MS2  CONST_13  H2B   C2B  C1   C2A   180.00   0.0  0
 MS2  CONST_14  H2A   C2A  C3A  C4    180.00   0.0  0
 MS2  CONST_15  C8    C7   N1   C5    180.00   0.0  0
 MS2  CONST_16  H99   N1   C7   C8      0.00   0.0  0
 MS2  CONST_17  O1    C7   N1   C5      0.00   0.0  0
 MS2  Var_01    C9A   C8   C17  C    -111.78  30.0  1
 MS2  Var_02    C17   C9A  C8   C7    105.46  30.0  1
 MS2  Var_03    O9B   S9B  C8   C9A   167.32  30.0  3
 MS2  Var_04    H1    C    C17  C8     37.65  30.0  3
 MS2  Var_05    H121  C12  S9B  C8     57.03  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 MS2  chir_01  C5   C4   C6   N1   negativ
 MS2  chir_02  C8   C9A  C17  S9B  both
 MS2  chir_03  C17  C    C8   C9A  both

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
 MS2  plan-1  BR1  0.020
 MS2  plan-1  C1   0.020
 MS2  plan-1  C2A  0.020
 MS2  plan-1  C3A  0.020
 MS2  plan-1  C4   0.020
 MS2  plan-1  C3B  0.020
 MS2  plan-1  C2B  0.020
 MS2  plan-1  C5   0.020
 MS2  plan-1  H3A  0.020
 MS2  plan-1  H3B  0.020
 MS2  plan-1  H2B  0.020
 MS2  plan-1  H2A  0.020
 MS2  plan-2  C5   0.020
 MS2  plan-2  N1   0.020
 MS2  plan-2  C7   0.020
 MS2  plan-2  O1   0.020
 MS2  plan-2  C8   0.020
 MS2  plan-2  H99  0.020
 MS2  plan-3  C8   0.020
 MS2  plan-3  O9B  0.020
 MS2  plan-3  S9B  0.020
 MS2  plan-3  C12  0.020

