# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 08:33:58 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: (1S,2R)-1-[(5-chloro-2,4-dihydroxyphenyl)carbonyl]-2-{4-[(3,3-difluoropyrrolidin-1-yl)methyl]phenyl}pyrrolidinium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cc(O)c(cc1Cl)C(=O)[NH+]2CCC[C@@H]2c3ccc(CN4CCC(F)(F)C4)cc3
#
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
 BD0  BD0  (1S,2R)-1-[(5-chloro-2,4-dihydroxyphenyl)carbonyl]-2-{4-[(3,3-difluoropyrrolidin-1-yl)methyl]phenyl}pyrrolidinium  ligand  54  30  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BD0
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
 BD0  C4    C   CR6   0   0.409   1.9165   0.8804   1.4956
 BD0  C6    C   CR6   0  -0.176   2.0605  -0.0222   0.4067
 BD0  C7    C   CR16  0  -0.224   1.5319   0.3582  -0.8431
 BD0  C8    C   CR6   0  -0.144   0.8887   1.5481  -1.0142
 BD0  C10   C   C     0   0.614   2.6953  -1.2860   0.6569
 BD0  N12   N   NT1   1  -0.658   2.7333  -2.2871  -0.4401
 BD0  C13   C   CH2   0  -0.299   4.0472  -3.0244  -0.6140
 BD0  C15   C   CH2   0  -0.444   2.1580  -4.4517  -1.1781
 BD0  C17   C   CR6   0   0.143   0.2927  -2.7810  -0.4536
 BD0  C20   C   CR6   0   0.082  -2.1546  -1.4545  -0.7712
 BD0  C21   C   CH2   0  -0.321  -3.4602  -0.7264  -0.9478
 BD0  C24   C   CH2   0  -0.586  -3.2360   2.4862   0.8462
 BD0  C28   C   CH2   0  -0.387  -4.9154   0.9771  -0.0294
 BD0  C2    C   CR6   0   0.457   0.7404   2.4365   0.0720
 BD0  C3    C   CR16  0  -0.475   1.2582   2.0906   1.3072
 BD0  O5    O   OH1   0  -0.593   2.3713   0.6350   2.7116
 BD0  CL9   CL  CL    0  -0.072   0.2395   1.9874  -2.5464
 BD0  O11   O   O     0  -0.394   3.1616  -1.6459   1.7128
 BD0  C14   C   CH2   0  -0.491   3.6578  -4.4769  -0.9030
 BD0  C16   C   CH1   0  -0.253   1.6520  -3.3698  -0.2461
 BD0  C18   C   CR16  0  -0.279  -0.4844  -2.4524   0.6538
 BD0  C19   C   CR16  0  -0.259  -1.6971  -1.8030   0.4967
 BD0  N22   N   NR5   0  -0.441  -3.6302   0.3167   0.0339
 BD0  C23   C   CH2   0  -0.276  -2.6503   1.3899  -0.0475
 BD0  C25   C   CR5   0   0.754  -4.7178   2.1327   0.9326
 BD0  F26   F   F     0  -0.348  -5.5373   3.1831   0.6436
 BD0  F27   F   F     0  -0.353  -5.0554   1.7580   2.2046
 BD0  C29   C   CR16  0  -0.282  -1.3825  -1.7954  -1.8761
 BD0  C30   C   CR16  0  -0.315  -0.1753  -2.4597  -1.7235
 BD0  H7    H   HCR6  0   0.282   1.6168  -0.2734  -1.7157
 BD0  H13   H   HCH2  0   0.313   4.5669  -2.5400  -1.4353
 BD0  H13A  H   HCH2  0   0.313   4.6360  -2.9193   0.2910
 BD0  H15   H   HCH2  0   0.269   1.9506  -4.2047  -2.2210
 BD0  H15A  H   HCH2  0   0.297   1.6717  -5.3989  -0.9530
 BD0  H21   H   HCH2  0   0.221  -3.5208  -0.3342  -1.9766
 BD0  H21A  H   HCH2  0   0.266  -4.2859  -1.4363  -0.8385
 BD0  H24A  H   HCH2  0   0.270  -3.0914   3.4783   0.4216
 BD0  H28   H   HCH2  0   0.225  -5.1364   1.3811  -1.0316
 BD0  H28A  H   HCH2  0   0.269  -5.7343   0.3147   0.2575
 BD0  HO1   H   HOH1  0   0.497   0.0579   4.1162   0.6412
 BD0  H3    H   HCR6  0   0.312   1.1553   2.7649   2.1488
 BD0  HO5   H   HOH1  0   0.493   2.8166  -0.2324   2.7401
 BD0  H14   H   HCH2  0   0.285   4.2244  -4.8717  -1.7432
 BD0  H14A  H   HCH2  0   0.274   3.8712  -5.0963  -0.0329
 BD0  H16   H   HCH1  0   0.340   1.7676  -3.7019   0.7875
 BD0  H18   H   HCR6  0   0.270  -0.1338  -2.6994   1.6490
 BD0  H19   H   HCR6  0   0.258  -2.2846  -1.5431   1.3680
 BD0  H23   H   HCH2  0   0.213  -2.5337   1.7536  -1.0800
 BD0  H23A  H   HCH2  0   0.243  -1.6744   1.0478   0.2944
 BD0  H29   H   HCR6  0   0.260  -1.7196  -1.5304  -2.8705
 BD0  H30   H   HCR6  0   0.269   0.4037  -2.6989  -2.6077
 BD0  H241  H   HNT1  0   0.480   2.5361  -1.8363  -1.3327
 BD0  O1    O   OH1   0  -0.580   0.0910   3.5659  -0.1523
 BD0  H24   H   HCH2  0   0.271  -2.7904   2.4823   1.8406

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
 BD0  C4   C6    aromatic  1.422  0.020  1.422
 BD0  C4   C3    aromatic  1.390  0.020  1.390
 BD0  C4   O5    single    1.321  0.020  1.321
 BD0  C6   C7    aromatic  1.409  0.020  1.409
 BD0  C6   C10   single    1.436  0.020  1.436
 BD0  C7   C8    aromatic  1.363  0.020  1.363
 BD0  C7   H7    single    0.930  0.020  1.080
 BD0  C8   C2    aromatic  1.411  0.020  1.411
 BD0  C8   CL9   single    1.721  0.020  1.721
 BD0  C10  N12   single    1.486  0.020  1.486
 BD0  C10  O11   double    1.209  0.020  1.209
 BD0  N12  C13   single    1.517  0.020  1.517
 BD0  N12  C16   single    1.542  0.020  1.542
 BD0  C13  C14   single    1.531  0.020  1.531
 BD0  C13  H13   single    0.970  0.020  1.090
 BD0  C13  H13A  single    0.970  0.020  1.090
 BD0  C15  C14   single    1.525  0.020  1.525
 BD0  C15  C16   single    1.515  0.020  1.515
 BD0  C15  H15   single    0.970  0.020  1.090
 BD0  C15  H15A  single    0.970  0.020  1.090
 BD0  C17  C16   single    1.496  0.020  1.496
 BD0  C17  C18   aromatic  1.392  0.020  1.392
 BD0  C17  C30   aromatic  1.391  0.020  1.391
 BD0  C20  C21   single    1.505  0.020  1.505
 BD0  C20  C19   aromatic  1.392  0.020  1.392
 BD0  C20  C29   aromatic  1.390  0.020  1.390
 BD0  C21  N22   single    1.442  0.020  1.442
 BD0  C21  H21   single    0.970  0.020  1.090
 BD0  C21  H21A  single    0.970  0.020  1.090
 BD0  C24  C23   single    1.531  0.020  1.531
 BD0  C24  C25   single    1.526  0.020  1.526
 BD0  C24  H24   single    0.970  0.020  1.090
 BD0  C24  H24A  single    0.970  0.020  1.090
 BD0  C28  N22   single    1.446  0.020  1.446
 BD0  C28  C25   single    1.517  0.020  1.517
 BD0  C28  H28   single    0.970  0.020  1.090
 BD0  C28  H28A  single    0.970  0.020  1.090
 BD0  O1   C2    single    1.322  0.020  1.322
 BD0  O1   HO1   single    0.850  0.020  0.980
 BD0  C2   C3    aromatic  1.383  0.020  1.383
 BD0  C3   H3    single    0.930  0.020  1.080
 BD0  O5   HO5   single    0.850  0.020  0.980
 BD0  C14  H14   single    0.970  0.020  1.090
 BD0  C14  H14A  single    0.970  0.020  1.090
 BD0  C16  H16   single    0.970  0.020  1.090
 BD0  C18  C19   aromatic  1.385  0.020  1.385
 BD0  C18  H18   single    0.930  0.020  1.080
 BD0  C19  H19   single    0.930  0.020  1.080
 BD0  N22  C23   single    1.456  0.020  1.456
 BD0  C23  H23   single    0.970  0.020  1.090
 BD0  C23  H23A  single    0.970  0.020  1.090
 BD0  C25  F26   single    1.363  0.020  1.363
 BD0  C25  F27   single    1.368  0.020  1.368
 BD0  C29  C30   aromatic  1.386  0.020  1.386
 BD0  C29  H29   single    0.930  0.020  1.080
 BD0  C30  H30   single    0.930  0.020  1.080
 BD0  N12  H241  single    0.890  0.020  1.040

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
 BD0  O5    C4   C3   116.70  3.000
 BD0  O5    C4   C6   123.51  3.000
 BD0  C3    C4   C6   119.79  3.000
 BD0  C10   C6   C7   123.91  3.000
 BD0  C10   C6   C4   118.04  3.000
 BD0  C7    C6   C4   118.02  3.000
 BD0  H7    C7   C8   116.48  3.000
 BD0  H7    C7   C6   121.93  3.000
 BD0  C8    C7   C6   121.59  3.000
 BD0  CL9   C8   C2   119.01  3.000
 BD0  CL9   C8   C7   120.83  3.000
 BD0  C2    C8   C7   120.16  3.000
 BD0  O11   C10  N12  115.75  3.000
 BD0  O11   C10  C6   125.77  3.000
 BD0  N12   C10  C6   118.40  3.000
 BD0  H241  N12  C16  106.56  3.000
 BD0  H241  N12  C13  106.40  3.000
 BD0  C16   N12  C13  106.29  3.000
 BD0  H241  N12  C10  110.10  3.000
 BD0  C16   N12  C10  111.24  3.000
 BD0  C13   N12  C10  115.75  3.000
 BD0  H13A  C13  H13  109.15  3.000
 BD0  H13A  C13  C14  112.79  3.000
 BD0  H13   C13  C14  113.71  3.000
 BD0  H13A  C13  N12  109.12  3.000
 BD0  H13   C13  N12  106.52  3.000
 BD0  C14   C13  N12  105.22  3.000
 BD0  H15A  C15  H15  108.04  3.000
 BD0  H15A  C15  C16  110.18  3.000
 BD0  H15   C15  C16  111.27  3.000
 BD0  H15A  C15  C14  112.82  3.000
 BD0  H15   C15  C14  111.28  3.000
 BD0  C16   C15  C14  103.25  3.000
 BD0  C30   C17  C18  118.94  3.000
 BD0  C30   C17  C16  121.55  3.000
 BD0  C18   C17  C16  119.33  3.000
 BD0  C29   C20  C19  118.68  3.000
 BD0  C29   C20  C21  120.47  3.000
 BD0  C19   C20  C21  120.86  3.000
 BD0  H21A  C21  H21  106.40  3.000
 BD0  H21A  C21  N22  108.19  3.000
 BD0  H21   C21  N22  111.80  3.000
 BD0  H21A  C21  C20  109.20  3.000
 BD0  H21   C21  C20  109.21  3.000
 BD0  N22   C21  C20  111.85  3.000
 BD0  H24A  C24  H24  107.75  3.000
 BD0  H24A  C24  C25  111.24  3.000
 BD0  H24   C24  C25  110.16  3.000
 BD0  H24A  C24  C23  111.96  3.000
 BD0  H24   C24  C23  111.94  3.000
 BD0  C25   C24  C23  103.81  3.000
 BD0  H28A  C28  H28  108.10  3.000
 BD0  H28A  C28  C25  113.16  3.000
 BD0  H28   C28  C25  108.87  3.000
 BD0  H28A  C28  N22  112.21  3.000
 BD0  H28   C28  N22  112.65  3.000
 BD0  C25   C28  N22  101.80  3.000
 BD0  C3    C2   O1   123.30  3.000
 BD0  C3    C2   C8   119.38  3.000
 BD0  O1    C2   C8   117.32  3.000
 BD0  H3    C3   C2   120.16  3.000
 BD0  H3    C3   C4   118.78  3.000
 BD0  C2    C3   C4   121.05  3.000
 BD0  HO5   O5   C4   110.44  3.000
 BD0  H14A  C14  H14  107.98  3.000
 BD0  H14A  C14  C15  110.25  3.000
 BD0  H14   C14  C15  112.27  3.000
 BD0  H14A  C14  C13  109.80  3.000
 BD0  H14   C14  C13  110.96  3.000
 BD0  C15   C14  C13  105.57  3.000
 BD0  H16   C16  C17  110.32  3.000
 BD0  H16   C16  C15  109.26  3.000
 BD0  C17   C16  C15  119.95  3.000
 BD0  H16   C16  N12  104.98  3.000
 BD0  C17   C16  N12  110.08  3.000
 BD0  C15   C16  N12  100.94  3.000
 BD0  H18   C18  C19  119.64  3.000
 BD0  H18   C18  C17  119.74  3.000
 BD0  C19   C18  C17  120.62  3.000
 BD0  H19   C19  C18  119.77  3.000
 BD0  H19   C19  C20  119.65  3.000
 BD0  C18   C19  C20  120.57  3.000
 BD0  C23   N22  C28  105.01  3.000
 BD0  C23   N22  C21  114.57  3.000
 BD0  C28   N22  C21  113.90  3.000
 BD0  H23A  C23  H23  107.66  3.000
 BD0  H23A  C23  N22  110.73  3.000
 BD0  H23   C23  N22  111.55  3.000
 BD0  H23A  C23  C24  112.61  3.000
 BD0  H23   C23  C24  110.58  3.000
 BD0  N22   C23  C24  103.76  3.000
 BD0  F27   C25  F26  105.05  3.000
 BD0  F27   C25  C28  110.42  3.000
 BD0  F26   C25  C28  111.99  3.000
 BD0  F27   C25  C24  110.83  3.000
 BD0  F26   C25  C24  113.16  3.000
 BD0  C28   C25  C24  105.49  3.000
 BD0  H29   C29  C30  119.30  3.000
 BD0  H29   C29  C20  119.80  3.000
 BD0  C30   C29  C20  120.90  3.000
 BD0  H30   C30  C29  118.77  3.000
 BD0  H30   C30  C17  120.94  3.000
 BD0  C29   C30  C17  120.27  3.000
 BD0  HO1   O1   C2   111.35  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
 BD0  CONST_01  C8   C7   C6   C4     0.00   0.0  0
 BD0  CONST_02  C8   C2   C3   C4     0.00   0.0  0
 BD0  CONST_03  C2   C3   C4   C6     0.00   0.0  0
 BD0  CONST_04  C2   C8   C7   C6     0.00   0.0  0
 BD0  CONST_05  C3   C4   C6   C7     0.00   0.0  0
 BD0  CONST_06  C3   C2   C8   C7     0.00   0.0  0
 BD0  CONST_07  C20  C19  C18  C17    0.00   0.0  0
 BD0  CONST_08  C20  C29  C30  C17    0.00   0.0  0
 BD0  CONST_09  C29  C30  C17  C18    0.00   0.0  0
 BD0  CONST_10  C29  C20  C19  C18    0.00   0.0  0
 BD0  CONST_11  C30  C29  C20  C19    0.00   0.0  0
 BD0  CONST_12  C30  C17  C18  C19    0.00   0.0  0
 BD0  CONST_13  C19  C18  C17  C16  180.00   0.0  0
 BD0  CONST_14  C29  C30  C17  C16  180.00   0.0  0
 BD0  CONST_15  O1   C2   C3   C4   180.00   0.0  0
 BD0  CONST_16  CL9  C8   C7   C6   180.00   0.0  0
 BD0  CONST_17  O5   C4   C6   C7   180.00   0.0  0
 BD0  CONST_18  O1   C2   C8   C7   180.00   0.0  0
 BD0  CONST_19  C10  C6   C7   C8   180.00   0.0  0
 BD0  CONST_20  C3   C4   C6   C10  180.00   0.0  0
 BD0  CONST_21  C18  C19  C20  C21  180.00   0.0  0
 BD0  CONST_22  C30  C29  C20  C21  180.00   0.0  0
 BD0  CONST_23  O5   C4   C3   C2   180.00   0.0  0
 BD0  CONST_24  CL9  C8   C2   C3   180.00   0.0  0
 BD0  CONST_25  H7   C7   C6   C4   180.00   0.0  0
 BD0  CONST_26  H3   C3   C4   C6   180.00   0.0  0
 BD0  CONST_27  H19  C19  C18  C17  180.00   0.0  0
 BD0  CONST_28  H29  C29  C30  C17  180.00   0.0  0
 BD0  CONST_29  H18  C18  C19  C20  180.00   0.0  0
 BD0  CONST_30  H30  C30  C29  C20  180.00   0.0  0
 BD0  Var_01    C15  C14  C13  N12   11.82  30.0  1
 BD0  Var_02    C16  C15  C14  C13  -34.78  30.0  1
 BD0  Var_03    C28  N22  C23  C24   41.47  30.0  1
 BD0  Var_04    N22  C28  C25  C24   30.92  30.0  1
 BD0  Var_05    C23  C24  C25  C28   -6.43  30.0  1
 BD0  Var_06    C25  C24  C23  N22  -20.32  30.0  1
 BD0  Var_07    C25  C28  N22  C23  -45.13  30.0  1
 BD0  Var_08    N12  C10  C6   C4   174.20  30.0  2
 BD0  Var_09    N22  C21  C20  C19   42.12  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
 BD0  chir_01  N12  C10  C13  C16  negativ
 BD0  chir_02  C16  N12  C15  C17  positiv

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
 BD0  plan-1  C4    0.020
 BD0  plan-1  C6    0.020
 BD0  plan-1  C7    0.020
 BD0  plan-1  C8    0.020
 BD0  plan-1  C10   0.020
 BD0  plan-1  C2    0.020
 BD0  plan-1  C3    0.020
 BD0  plan-1  O5    0.020
 BD0  plan-1  CL9   0.020
 BD0  plan-1  H7    0.020
 BD0  plan-1  H3    0.020
 BD0  plan-1  O1    0.020
 BD0  plan-2  C17   0.020
 BD0  plan-2  C20   0.020
 BD0  plan-2  C21   0.020
 BD0  plan-2  C16   0.020
 BD0  plan-2  C18   0.020
 BD0  plan-2  C19   0.020
 BD0  plan-2  C29   0.020
 BD0  plan-2  C30   0.020
 BD0  plan-2  H18   0.020
 BD0  plan-2  H19   0.020
 BD0  plan-2  H29   0.020
 BD0  plan-2  H30   0.020
 BD0  plan-3  C6    0.020
 BD0  plan-3  C10   0.020
 BD0  plan-3  N12   0.020
 BD0  plan-3  C13   0.020
 BD0  plan-3  O11   0.020
 BD0  plan-3  C16   0.020
 BD0  plan-3  H241  0.020

