# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 11:58:26 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: 4-bromo-2-{[(2R)-2-(2-chlorobenzyl)pyrrolidin-1-yl]carbonyl}aniline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccc(Br)cc1C(=O)N2CCC[C@@H]2Cc3ccccc3Cl
#
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
 SX4  SX4  4-bromo-2-{[(2R)-2-(2-chlorobenzyl)pyrrolidin-1-yl]carbonyl}aniline  ligand  41  23  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_SX4
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
 SX4  CL1   CL  CL    0  -0.128   4.2769   1.8855   0.4698
 SX4  C18   C   CR6   0  -0.128   4.8043   0.2290   0.5146
 SX4  C17   C   CR16  0  -0.196   6.1676  -0.0197   0.4525
 SX4  C16   C   CR16  0  -0.281   6.6255  -1.3275   0.4980
 SX4  C15   C   CR16  0  -0.230   5.7182  -2.3711   0.6099
 SX4  C14   C   CR16  0  -0.325   4.3599  -2.0991   0.6712
 SX4  C13   C   CR6   0   0.221   3.8653  -0.7961   0.6222
 SX4  C12   C   CH2   0  -0.532   2.3854  -0.5414   0.6663
 SX4  C11   C   CH1   0  -0.021   1.8077  -0.2505  -0.7228
 SX4  C10   C   CH2   0  -0.483   1.9932  -1.4065  -1.7102
 SX4  C9    C   CH2   0  -0.456   0.7455  -1.3546  -2.5810
 SX4  C8    C   CH2   0  -0.281  -0.3376  -1.0000  -1.5747
 SX4  N2    N   NT    0  -0.478   0.3505  -0.0698  -0.6784
 SX4  C7    C   C     0   0.533  -0.1840   1.0416  -0.1446
 SX4  O1    O   O     0  -0.494   0.5066   1.9541   0.3022
 SX4  C6    C   CR6   0  -0.121  -1.6744   1.1185  -0.0866
 SX4  C1    C   CR6   0   0.300  -2.3462   2.2854  -0.4999
 SX4  N1    N   NH2   0  -0.860  -1.6889   3.3451  -1.0623
 SX4  C5    C   CR16  0  -0.235  -2.3882   0.0520   0.4521
 SX4  C4    C   CR6   0  -0.137  -3.7641   0.1129   0.5684
 SX4  BR1   BR  BR    0  -0.063  -4.7135  -1.3391   1.3182
 SX4  C3    C   CR16  0  -0.224  -4.4486   1.2412   0.1348
 SX4  C2    C   CR16  0  -0.324  -3.7450   2.3056  -0.3919
 SX4  H17   H   HCR6  0   0.278   6.8661   0.8021   0.3719
 SX4  H16   H   HCR6  0   0.266   7.6885  -1.5227   0.4504
 SX4  H15   H   HCR6  0   0.261   6.0653  -3.3950   0.6523
 SX4  H14   H   HCR6  0   0.259   3.6564  -2.9177   0.7628
 SX4  H12   H   HCH2  0   0.256   1.8824  -1.4235   1.0698
 SX4  H12A  H   HCH2  0   0.268   2.1678   0.2906   1.3363
 SX4  H11   H   HCH1  0   0.253   2.2613   0.6611  -1.1209
 SX4  H10   H   HCH2  0   0.258   2.9194  -1.3158  -2.2757
 SX4  H10A  H   HCH2  0   0.236   2.0276  -2.3592  -1.1742
 SX4  H9    H   HCH2  0   0.240   0.8318  -0.5683  -3.3339
 SX4  H9A   H   HCH2  0   0.253   0.5421  -2.2944  -3.0930
 SX4  H8    H   HCH2  0   0.266  -1.2116  -0.5376  -2.0290
 SX4  H8A   H   HCH2  0   0.241  -0.6686  -1.8929  -1.0374
 SX4  HN1   H   HNH2  0   0.388  -0.7339   3.4909  -0.7796
 SX4  HN1A  H   HNH2  0   0.387  -2.2132   4.2014  -1.1353
 SX4  H5    H   HCR6  0   0.283  -1.8492  -0.8237   0.7918
 SX4  H3    H   HCR6  0   0.279  -5.5261   1.3046   0.2101
 SX4  H2    H   HCR6  0   0.272  -4.2876   3.1828  -0.7229

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
 SX4  CL1  C18   single    1.739  0.020  1.739
 SX4  C13  C18   aromatic  1.394  0.020  1.394
 SX4  C18  C17   aromatic  1.387  0.020  1.387
 SX4  C17  C16   aromatic  1.386  0.020  1.386
 SX4  C17  H17   single    0.930  0.020  1.080
 SX4  C15  C16   aromatic  1.387  0.020  1.387
 SX4  C16  H16   single    0.930  0.020  1.080
 SX4  C14  C15   aromatic  1.387  0.020  1.387
 SX4  C15  H15   single    0.930  0.020  1.080
 SX4  C13  C14   aromatic  1.395  0.020  1.395
 SX4  C14  H14   single    0.930  0.020  1.080
 SX4  C12  C13   single    1.502  0.020  1.502
 SX4  C11  C12   single    1.532  0.020  1.532
 SX4  C12  H12   single    0.970  0.020  1.090
 SX4  C12  H12A  single    0.970  0.020  1.090
 SX4  C10  C11   single    1.532  0.020  1.532
 SX4  N2   C11   single    1.469  0.020  1.469
 SX4  C11  H11   single    0.970  0.020  1.090
 SX4  C9   C10   single    1.522  0.020  1.522
 SX4  C10  H10   single    0.970  0.020  1.090
 SX4  C10  H10A  single    0.970  0.020  1.090
 SX4  C9   C8    single    1.520  0.020  1.520
 SX4  C9   H9    single    0.970  0.020  1.090
 SX4  C9   H9A   single    0.970  0.020  1.090
 SX4  C8   N2    single    1.464  0.020  1.464
 SX4  C8   H8    single    0.970  0.020  1.090
 SX4  C8   H8A   single    0.970  0.020  1.090
 SX4  C7   N2    single    1.344  0.020  1.344
 SX4  O1   C7    double    1.229  0.020  1.229
 SX4  C7   C6    single    1.494  0.020  1.494
 SX4  C5   C6    aromatic  1.392  0.020  1.392
 SX4  C6   C1    aromatic  1.408  0.020  1.408
 SX4  C1   C2    aromatic  1.403  0.020  1.403
 SX4  C1   N1    single    1.368  0.020  1.368
 SX4  N1   HN1   single    0.890  0.020  1.040
 SX4  N1   HN1A  single    0.890  0.020  1.040
 SX4  C5   C4    aromatic  1.382  0.020  1.382
 SX4  C5   H5    single    0.930  0.020  1.080
 SX4  BR1  C4    single    1.890  0.020  1.890
 SX4  C4   C3    aromatic  1.389  0.020  1.389
 SX4  C3   C2    aromatic  1.380  0.020  1.380
 SX4  C3   H3    single    0.930  0.020  1.080
 SX4  C2   H2    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
 SX4  C13   C18  C17  122.24  3.000
 SX4  C17   C18  CL1  117.88  3.000
 SX4  C13   C18  CL1  119.87  3.000
 SX4  H17   C17  C16  120.39  3.000
 SX4  H17   C17  C18  120.13  3.000
 SX4  C16   C17  C18  119.49  3.000
 SX4  H16   C16  C15  120.69  3.000
 SX4  H16   C16  C17  119.56  3.000
 SX4  C15   C16  C17  119.75  3.000
 SX4  H15   C15  C14  119.88  3.000
 SX4  H15   C15  C16  120.35  3.000
 SX4  C14   C15  C16  119.77  3.000
 SX4  H14   C14  C13  118.60  3.000
 SX4  H14   C14  C15  119.45  3.000
 SX4  C13   C14  C15  121.95  3.000
 SX4  C12   C13  C14  120.45  3.000
 SX4  C12   C13  C18  122.75  3.000
 SX4  C14   C13  C18  116.79  3.000
 SX4  H12A  C12  H12  107.30  3.000
 SX4  H12A  C12  C11  109.69  3.000
 SX4  H12   C12  C11  108.32  3.000
 SX4  H12A  C12  C13  110.13  3.000
 SX4  H12   C12  C13  109.12  3.000
 SX4  C11   C12  C13  112.14  3.000
 SX4  H11   C11  N2   108.66  3.000
 SX4  H11   C11  C10  110.14  3.000
 SX4  N2    C11  C10  103.45  3.000
 SX4  H11   C11  C12  109.38  3.000
 SX4  N2    C11  C12  111.71  3.000
 SX4  C10   C11  C12  113.30  3.000
 SX4  H10A  C10  H10  107.47  3.000
 SX4  H10A  C10  C9   109.62  3.000
 SX4  H10   C10  C9   113.40  3.000
 SX4  H10A  C10  C11  110.20  3.000
 SX4  H10   C10  C11  112.02  3.000
 SX4  C9    C10  C11  104.11  3.000
 SX4  H9A   C9   H9   108.18  3.000
 SX4  H9A   C9   C8   112.29  3.000
 SX4  H9    C9   C8   110.16  3.000
 SX4  H9A   C9   C10  113.11  3.000
 SX4  H9    C9   C10  110.74  3.000
 SX4  C8    C9   C10  102.31  3.000
 SX4  H8A   C8   H8   108.00  3.000
 SX4  H8A   C8   N2   111.12  3.000
 SX4  H8    C8   N2   111.29  3.000
 SX4  H8A   C8   C9   110.52  3.000
 SX4  H8    C8   C9   113.27  3.000
 SX4  N2    C8   C9   102.63  3.000
 SX4  C7    N2   C8   125.59  3.000
 SX4  C7    N2   C11  120.55  3.000
 SX4  C8    N2   C11  111.69  3.000
 SX4  C6    C7   O1   120.57  3.000
 SX4  C6    C7   N2   117.06  3.000
 SX4  O1    C7   N2   122.36  3.000
 SX4  C5    C6   C1   120.25  3.000
 SX4  C1    C6   C7   120.48  3.000
 SX4  C5    C6   C7   119.17  3.000
 SX4  C2    C1   N1   119.97  3.000
 SX4  N1    C1   C6   122.22  3.000
 SX4  C2    C1   C6   117.70  3.000
 SX4  HN1A  N1   HN1  113.03  3.000
 SX4  HN1A  N1   C1   116.01  3.000
 SX4  HN1   N1   C1   116.91  3.000
 SX4  H5    C5   C4   120.31  3.000
 SX4  H5    C5   C6   119.06  3.000
 SX4  C4    C5   C6   120.62  3.000
 SX4  C3    C4   BR1  120.02  3.000
 SX4  C3    C4   C5   120.00  3.000
 SX4  BR1   C4   C5   119.98  3.000
 SX4  H3    C3   C2   119.28  3.000
 SX4  H3    C3   C4   121.10  3.000
 SX4  C2    C3   C4   119.62  3.000
 SX4  H2    C2   C3   119.06  3.000
 SX4  H2    C2   C1   119.17  3.000
 SX4  C3    C2   C1   121.76  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
 SX4  CONST_01  C15   C14  C13  C18    0.00   0.0  0
 SX4  CONST_02  C15   C16  C17  C18    0.00   0.0  0
 SX4  CONST_03  C14   C13  C18  C17    0.00   0.0  0
 SX4  CONST_04  C14   C15  C16  C17    0.00   0.0  0
 SX4  CONST_05  C13   C18  C17  C16    0.00   0.0  0
 SX4  CONST_06  C13   C14  C15  C16    0.00   0.0  0
 SX4  CONST_07  C3    C4   C5   C6     0.00   0.0  0
 SX4  CONST_08  C3    C2   C1   C6     0.00   0.0  0
 SX4  CONST_09  C4    C5   C6   C1     0.00   0.0  0
 SX4  CONST_10  C4    C3   C2   C1     0.00   0.0  0
 SX4  CONST_11  C2    C1   C6   C5     0.00   0.0  0
 SX4  CONST_12  C2    C3   C4   C5     0.00   0.0  0
 SX4  CONST_13  C14   C13  C18  CL1  180.00   0.0  0
 SX4  CONST_14  C16   C17  C18  CL1  180.00   0.0  0
 SX4  CONST_15  C12   C13  C18  C17  180.00   0.0  0
 SX4  CONST_16  C12   C13  C14  C15  180.00   0.0  0
 SX4  CONST_17  C4    C5   C6   C7   180.00   0.0  0
 SX4  CONST_18  C2    C1   C6   C7   180.00   0.0  0
 SX4  CONST_19  BR1   C4   C5   C6   180.00   0.0  0
 SX4  CONST_20  C5    C6   C1   N1   180.00   0.0  0
 SX4  CONST_21  C3    C2   C1   N1   180.00   0.0  0
 SX4  CONST_22  C2    C3   C4   BR1  180.00   0.0  0
 SX4  CONST_23  C6    C7   N2   C11  180.00   0.0  0
 SX4  CONST_25  H14   C14  C13  C18  180.00   0.0  0
 SX4  CONST_26  H16   C16  C17  C18  180.00   0.0  0
 SX4  CONST_27  H15   C15  C16  C17  180.00   0.0  0
 SX4  CONST_28  H17   C17  C16  C15  180.00   0.0  0
 SX4  CONST_29  H2    C2   C1   C6   180.00   0.0  0
 SX4  CONST_30  H5    C5   C6   C1   180.00   0.0  0
 SX4  CONST_31  H3    C3   C2   C1   180.00   0.0  0
 SX4  CONST_32  O1    C7   N2   C11    0.00   0.0  0
 SX4  CONST_35  HN1A  N1   C1   C6   180.00   0.0  0
 SX4  Var_01    C8    C9   C10  C11  -38.55  30.0  1
 SX4  Var_02    C9    C8   N2   C11  -22.74  30.0  1
 SX4  Var_03    N2    C8   C9   C10   37.09  30.0  1
 SX4  Var_04    C11   C12  C13  C18   78.19  30.0  2
 SX4  Var_05    C5    C6   C7   N2    50.20  30.0  2

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
 SX4  chir_01  C11  C12  C10  N2  negativ

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
 SX4  plan-1  CL1   0.020
 SX4  plan-1  C18   0.020
 SX4  plan-1  C17   0.020
 SX4  plan-1  C16   0.020
 SX4  plan-1  C15   0.020
 SX4  plan-1  C14   0.020
 SX4  plan-1  C13   0.020
 SX4  plan-1  C12   0.020
 SX4  plan-1  H17   0.020
 SX4  plan-1  H16   0.020
 SX4  plan-1  H15   0.020
 SX4  plan-1  H14   0.020
 SX4  plan-2  C7    0.020
 SX4  plan-2  C6    0.020
 SX4  plan-2  C1    0.020
 SX4  plan-2  N1    0.020
 SX4  plan-2  C5    0.020
 SX4  plan-2  C4    0.020
 SX4  plan-2  BR1   0.020
 SX4  plan-2  C3    0.020
 SX4  plan-2  C2    0.020
 SX4  plan-2  H5    0.020
 SX4  plan-2  H3    0.020
 SX4  plan-2  H2    0.020
 SX4  plan-3  C1    0.020
 SX4  plan-3  N1    0.020
 SX4  plan-3  HN1   0.020
 SX4  plan-3  HN1A  0.020
 SX4  plan-4  C11   0.020
 SX4  plan-4  C8    0.020
 SX4  plan-4  N2    0.020
 SX4  plan-4  C7    0.020
 SX4  plan-4  O1    0.020
 SX4  plan-4  C6    0.020

