# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 13:00:48 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: (2S)-4-(2,5-difluorophenyl)-N-[(3R,4S)-3-fluoro-1-methylpiperidin-4-yl]-2-(hydroxymethyl)-N-methyl-2-phenyl-2,5-dihydro-1H-pyrrole-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CC[C@@H]([C@H](F)C1)N(C)C(=O)N2CC(=C[C@@]2(CO)c3ccccc3)c4cc(F)ccc4F
#
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
 K30  K30  (2S)-4-(2,5-difluorophenyl)-N-[(3R,4S)-3-fluoro-1-methylpiperidin-4-yl]-2-(hydroxymethyl)-N-methyl-2-phenyl-2,5-dihydro-1H-pyrrole-1-carboxamide  ligand  61  33  .  2021-08-12  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_K30
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
 K30  C28   C  CH3   0  -0.517   7.5342  -1.4562  -0.1719
 K30  C22   C  CH3   0  -0.564   1.5399  -0.9257   1.6070
 K30  C18   C  CR16  0  -0.271  -0.3061   4.8050   1.8836
 K30  C17   C  CR16  0  -0.242  -0.1803   4.9816   0.5140
 K30  C19   C  CR16  0  -0.245  -0.6537   3.5543   2.3797
 K30  C16   C  CR16  0  -0.320  -0.3979   3.9198  -0.3570
 K30  C20   C  CR16  0  -0.292  -0.8724   2.4990   1.5077
 K30  C7    C  CR16  0  -0.403  -5.6632  -3.0232   0.2136
 K30  C6    C  CR16  0  -0.384  -4.6255  -3.0803   1.1316
 K30  C9    C  CR16  0  -0.454  -4.4805  -1.2888  -0.9850
 K30  C27   C  CH2   0  -0.448   4.3292   0.2087   0.8266
 K30  C26   C  CH2   0  -0.281   5.7514   0.0727   0.3020
 K30  C2    C  CR15  0  -0.245  -2.3439   0.8535  -0.5119
 K30  C24   C  CH2   0  -0.333   5.2791  -2.0738  -0.6551
 K30  C     C  CH2   0  -0.304  -0.8485  -0.9077  -0.2095
 K30  C14   C  CH2   0  -0.157  -0.8753   1.7471  -2.2700
 K30  C15   C  CR6   0   0.197  -0.7448   2.6651   0.1293
 K30  C8    C  CR6   0   0.543  -5.5694  -2.1213  -0.8282
 K30  C5    C  CR6   0   0.514  -3.5379  -2.2447   0.9775
 K30  C4    C  CR6   0  -0.124  -3.4277  -1.3380  -0.0703
 K30  C12   C  CH1   0  -0.139   3.3750  -0.5895  -0.0572
 K30  C3    C  CR5   0   0.064  -2.2754  -0.4429  -0.2332
 K30  C23   C  CH1   0   0.211   3.8395  -2.0310  -0.1847
 K30  C10   C  C     0   0.737   1.2417   0.4674  -0.4034
 K30  C1    C  CR5   0   0.008  -0.9861   1.4548  -0.7645
 K30  N25   N  NT    0  -0.413   6.1503  -1.3187   0.2192
 K30  N     N  NR5   0  -0.561  -0.1175   0.3446  -0.3533
 K30  N11   N  NT    0  -0.502   1.9669  -0.4724   0.2912
 K30  O     O  O     0  -0.511   1.7786   1.3663  -1.0389
 K30  F     F  F     0  -0.304  -2.5606  -2.2975   1.8973
 K30  F29   F  F     0  -0.379   3.7515  -2.6957   1.0425
 K30  H28   H  HCH3  0   0.193   7.7439  -1.0578  -1.1767
 K30  H28A  H  HCH3  0   0.234   8.1756  -0.9287   0.5354
 K30  H28B  H  HCH3  0   0.234   7.8247  -2.5082  -0.1645
 K30  H22   H  HCH3  0   0.263   2.3523  -0.8202   2.3228
 K30  H22A  H  HCH3  0   0.249   0.7223  -0.3080   1.9722
 K30  H22B  H  HCH3  0   0.242   1.2209  -1.9680   1.6186
 K30  H18   H  HCR6  0   0.254  -0.1347   5.6324   2.5600
 K30  H17   H  HCR6  0   0.253   0.0933   5.9501   0.1154
 K30  H19   H  HCR6  0   0.254  -0.7546   3.4002   3.4464
 K30  H16   H  HCR6  0   0.248  -0.2885   4.0918  -1.4181
 K30  H20   H  HCR6  0   0.246  -1.1435   1.5284   1.9071
 K30  H7    H  HCR6  0   0.294  -6.5245  -3.6698   0.3122
 K30  H6    H  HCR6  0   0.294  -4.6673  -3.7655   1.9675
 K30  H9    H  HCR6  0   0.287  -4.4331  -0.6094  -1.8260
 K30  H27   H  HCH2  0   0.230   4.2929  -0.1296   1.8641
 K30  H27A  H  HCH2  0   0.247   4.0373   1.2598   0.8176
 K30  H26   H  HCH2  0   0.190   5.8255   0.5761  -0.6796
 K30  H26A  H  HCH2  0   0.241   6.4395   0.5929   0.9721
 K30  H24   H  HCH2  0   0.254   5.6167  -3.1127  -0.6902
 K30  H24A  H  HCH2  0   0.203   5.3026  -1.7033  -1.6958
 K30  H     H  HCH2  0   0.258  -0.6070  -1.4324   0.7113
 K30  HA    H  HCH2  0   0.261  -0.6473  -1.6003  -1.0356
 K30  H14   H  HCH2  0   0.231   0.0715   2.2408  -2.4962
 K30  H14A  H  HCH2  0   0.216  -0.8748   0.7820  -2.7953
 K30  H12   H  HCH1  0   0.261   3.4726  -0.1921  -1.0698
 K30  H23   H  HCH1  0   0.227   3.2010  -2.5686  -0.8906
 K30  HO21  H  HOH1  0   0.460  -1.8107   2.8926  -3.5197
 K30  H2    H  HCR5  0   0.277  -3.2513   1.4354  -0.5852
 K30  O21   O  OH1   0  -0.668  -1.9808   2.5364  -2.6435
 K30  F13   F  F     0  -0.313  -6.5644  -2.0579  -1.7263

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
 K30  C28  N25   single    1.445  0.020  1.445
 K30  C28  H28   single    0.970  0.020  1.090
 K30  C28  H28A  single    0.970  0.020  1.090
 K30  C28  H28B  single    0.970  0.020  1.090
 K30  C22  H22   single    0.970  0.020  1.090
 K30  C22  H22A  single    0.970  0.020  1.090
 K30  C22  H22B  single    0.970  0.020  1.090
 K30  C18  H18   single    0.930  0.020  1.080
 K30  C17  C18   aromatic  1.387  0.020  1.387
 K30  C17  H17   single    0.930  0.020  1.080
 K30  C19  C18   aromatic  1.390  0.020  1.390
 K30  C19  H19   single    0.930  0.020  1.080
 K30  C16  C17   aromatic  1.390  0.020  1.390
 K30  C16  H16   single    0.930  0.020  1.080
 K30  C20  C19   aromatic  1.386  0.020  1.386
 K30  C20  H20   single    0.930  0.020  1.080
 K30  C7   C8    aromatic  1.381  0.020  1.381
 K30  C7   C6    aromatic  1.387  0.020  1.387
 K30  C7   H7    single    0.930  0.020  1.080
 K30  C6   C5    aromatic  1.380  0.020  1.380
 K30  C6   H6    single    0.930  0.020  1.080
 K30  C9   C4    aromatic  1.396  0.020  1.396
 K30  C9   H9    single    0.930  0.020  1.080
 K30  C27  H27   single    0.970  0.020  1.090
 K30  C27  H27A  single    0.970  0.020  1.090
 K30  C26  C27   single    1.522  0.020  1.522
 K30  C26  H26   single    0.970  0.020  1.090
 K30  C26  H26A  single    0.970  0.020  1.090
 K30  C2   C1    single    1.506  0.020  1.506
 K30  C24  C23   single    1.515  0.020  1.515
 K30  C24  N25   single    1.447  0.020  1.447
 K30  C24  H24   single    0.970  0.020  1.090
 K30  C24  H24A  single    0.970  0.020  1.090
 K30  C    N     single    1.457  0.020  1.457
 K30  C    H     single    0.970  0.020  1.090
 K30  C    HA    single    0.970  0.020  1.090
 K30  C14  C1    single    1.538  0.020  1.538
 K30  C14  H14   single    0.970  0.020  1.090
 K30  C14  H14A  single    0.970  0.020  1.090
 K30  C15  C16   aromatic  1.390  0.020  1.390
 K30  C15  C20   aromatic  1.394  0.020  1.394
 K30  C8   C9    aromatic  1.380  0.020  1.380
 K30  C5   C4    aromatic  1.390  0.020  1.390
 K30  C5   F     single    1.343  0.020  1.343
 K30  C4   C3    single    1.468  0.020  1.468
 K30  C12  C27   single    1.526  0.020  1.526
 K30  C12  N11   single    1.455  0.020  1.455
 K30  C12  H12   single    0.970  0.020  1.090
 K30  C3   C2    double    1.328  0.020  1.328
 K30  C3   C     single    1.501  0.020  1.501
 K30  C23  C12   single    1.520  0.020  1.520
 K30  C23  F29   single    1.398  0.020  1.398
 K30  C23  H23   single    0.970  0.020  1.090
 K30  C10  O     double    1.225  0.020  1.225
 K30  C1   C15   single    1.524  0.020  1.524
 K30  N25  C26   single    1.450  0.020  1.450
 K30  N    C10   single    1.366  0.020  1.366
 K30  N    C1    single    1.468  0.020  1.468
 K30  N11  C22   single    1.456  0.020  1.456
 K30  N11  C10   single    1.375  0.020  1.375
 K30  O21  C14   single    1.409  0.020  1.409
 K30  O21  HO21  single    0.850  0.020  0.980
 K30  F13  C8    single    1.342  0.020  1.342
 K30  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
 K30  H28B  C28  H28A  107.77  3.000
 K30  H28B  C28  H28   107.71  3.000
 K30  H28A  C28  H28   107.74  3.000
 K30  H28B  C28  N25   110.18  3.000
 K30  H28A  C28  N25   109.98  3.000
 K30  H28   C28  N25   113.27  3.000
 K30  H22B  C22  H22A  108.62  3.000
 K30  H22B  C22  H22   107.72  3.000
 K30  H22A  C22  H22   106.58  3.000
 K30  H22B  C22  N11   113.15  3.000
 K30  H22A  C22  N11   110.31  3.000
 K30  H22   C22  N11   110.22  3.000
 K30  H18   C18  C19   120.30  3.000
 K30  C19   C18  C17   119.34  3.000
 K30  H18   C18  C17   120.36  3.000
 K30  H17   C17  C16   119.48  3.000
 K30  C16   C17  C18   120.48  3.000
 K30  H17   C17  C18   120.04  3.000
 K30  H19   C19  C20   119.79  3.000
 K30  C20   C19  C18   120.00  3.000
 K30  H19   C19  C18   120.21  3.000
 K30  H16   C16  C15   120.84  3.000
 K30  C15   C16  C17   120.62  3.000
 K30  H16   C16  C17   118.54  3.000
 K30  H20   C20  C15   119.59  3.000
 K30  C15   C20  C19   121.12  3.000
 K30  H20   C20  C19   119.29  3.000
 K30  H7    C7   C8    120.88  3.000
 K30  H7    C7   C6    120.73  3.000
 K30  C8    C7   C6    118.39  3.000
 K30  H6    C6   C5    120.02  3.000
 K30  H6    C6   C7    120.58  3.000
 K30  C5    C6   C7    119.40  3.000
 K30  H9    C9   C4    119.90  3.000
 K30  H9    C9   C8    120.12  3.000
 K30  C4    C9   C8    119.98  3.000
 K30  H27A  C27  H27   107.31  3.000
 K30  H27A  C27  C12   109.38  3.000
 K30  H27   C27  C12   111.56  3.000
 K30  C12   C27  C26   109.75  3.000
 K30  H27A  C27  C26   109.48  3.000
 K30  H27   C27  C26   109.32  3.000
 K30  H26A  C26  H26   106.59  3.000
 K30  H26A  C26  N25   108.59  3.000
 K30  H26   C26  N25   111.58  3.000
 K30  N25   C26  C27   111.26  3.000
 K30  H26A  C26  C27   109.55  3.000
 K30  H26   C26  C27   109.14  3.000
 K30  H2    C2   C1    122.05  3.000
 K30  H2    C2   C3    125.69  3.000
 K30  C1    C2   C3    112.24  3.000
 K30  H24A  C24  H24   106.37  3.000
 K30  H24A  C24  N25   112.42  3.000
 K30  H24   C24  N25   109.24  3.000
 K30  H24A  C24  C23   107.65  3.000
 K30  H24   C24  C23   109.29  3.000
 K30  N25   C24  C23   111.70  3.000
 K30  HA    C    H     107.01  3.000
 K30  HA    C    N     112.11  3.000
 K30  H     C    N     112.76  3.000
 K30  HA    C    C3    110.99  3.000
 K30  H     C    C3    111.97  3.000
 K30  N     C    C3    102.08  3.000
 K30  H14A  C14  H14   107.33  3.000
 K30  H14A  C14  O21   111.45  3.000
 K30  H14   C14  O21   111.86  3.000
 K30  O21   C14  C1    108.03  3.000
 K30  H14A  C14  C1    107.53  3.000
 K30  H14   C14  C1    110.57  3.000
 K30  C1    C15  C20   118.09  3.000
 K30  C1    C15  C16   123.47  3.000
 K30  C20   C15  C16   118.44  3.000
 K30  F13   C8   C9    118.73  3.000
 K30  F13   C8   C7    119.03  3.000
 K30  C9    C8   C7    122.24  3.000
 K30  F     C5   C4    118.96  3.000
 K30  F     C5   C6    118.24  3.000
 K30  C4    C5   C6    122.79  3.000
 K30  C3    C4   C5    122.93  3.000
 K30  C3    C4   C9    119.86  3.000
 K30  C5    C4   C9    117.21  3.000
 K30  H12   C12  N11   106.21  3.000
 K30  H12   C12  C23   103.89  3.000
 K30  N11   C12  C23   113.08  3.000
 K30  C23   C12  C27   110.71  3.000
 K30  H12   C12  C27   106.90  3.000
 K30  N11   C12  C27   115.10  3.000
 K30  C4    C3   C     123.75  3.000
 K30  C     C3   C2    110.78  3.000
 K30  C4    C3   C2    125.31  3.000
 K30  H23   C23  F29   107.23  3.000
 K30  H23   C23  C12   110.00  3.000
 K30  F29   C23  C12   110.98  3.000
 K30  H23   C23  C24   109.91  3.000
 K30  F29   C23  C24   108.59  3.000
 K30  C12   C23  C24   110.07  3.000
 K30  O     C10  N11   122.17  3.000
 K30  N11   C10  N     116.41  3.000
 K30  O     C10  N     121.42  3.000
 K30  N     C1   C15   110.04  3.000
 K30  N     C1   C14   112.04  3.000
 K30  C15   C1   C14   114.33  3.000
 K30  N     C1   C2    100.63  3.000
 K30  C15   C1   C2    111.19  3.000
 K30  C14   C1   C2    107.76  3.000
 K30  C24   N25  C26   111.69  3.000
 K30  C26   N25  C28   111.74  3.000
 K30  C24   N25  C28   111.31  3.000
 K30  C1    N    C10   120.69  3.000
 K30  C1    N    C     112.37  3.000
 K30  C10   N    C     125.47  3.000
 K30  C10   N11  C12   116.38  3.000
 K30  C10   N11  C22   120.97  3.000
 K30  C12   N11  C22   118.37  3.000
 K30  HO21  O21  C14   108.09  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
 K30  CONST_01  C15  C16  C17  C18    0.00   0.0  0
 K30  CONST_02  C15  C20  C19  C18    0.00   0.0  0
 K30  CONST_03  C20  C19  C18  C17    0.00   0.0  0
 K30  CONST_04  C20  C15  C16  C17    0.00   0.0  0
 K30  CONST_05  C16  C17  C18  C19    0.00   0.0  0
 K30  CONST_06  C16  C15  C20  C19    0.00   0.0  0
 K30  CONST_07  C4   C9   C8   C7     0.00   0.0  0
 K30  CONST_08  C4   C5   C6   C7     0.00   0.0  0
 K30  CONST_09  C9   C8   C7   C6     0.00   0.0  0
 K30  CONST_10  C9   C4   C5   C6     0.00   0.0  0
 K30  CONST_11  C5   C6   C7   C8     0.00   0.0  0
 K30  CONST_12  C5   C4   C9   C8     0.00   0.0  0
 K30  CONST_13  C1   C15  C16  C17  180.00   0.0  0
 K30  CONST_14  C1   C15  C20  C19  180.00   0.0  0
 K30  CONST_15  C3   C4   C5   C6   180.00   0.0  0
 K30  CONST_16  C3   C4   C9   C8   180.00   0.0  0
 K30  CONST_17  F    C5   C6   C7   180.00   0.0  0
 K30  CONST_18  F13  C8   C7   C6   180.00   0.0  0
 K30  CONST_19  F    C5   C4   C9   180.00   0.0  0
 K30  CONST_20  F13  C8   C9   C4   180.00   0.0  0
 K30  CONST_21  F    C5   C4   C3     0.00   0.0  0
 K30  CONST_22  H16  C16  C17  C18  180.00   0.0  0
 K30  CONST_23  H20  C20  C19  C18  180.00   0.0  0
 K30  CONST_24  H19  C19  C18  C17  180.00   0.0  0
 K30  CONST_25  H17  C17  C18  C19  180.00   0.0  0
 K30  CONST_26  H18  C18  C17  C16  180.00   0.0  0
 K30  CONST_27  H9   C9   C8   C7   180.00   0.0  0
 K30  CONST_28  H7   C7   C8   C9   180.00   0.0  0
 K30  CONST_29  H6   C6   C7   C8   180.00   0.0  0
 K30  Var_01    C2   C3   C4   C9    45.20  30.0  2
 K30  Var_02    C24  N25  C26  C27   59.33  30.0  1
 K30  Var_03    C23  C24  N25  C26  -59.13  30.0  1
 K30  Var_04    N    C    C3   C2     6.64  30.0  1
 K30  Var_05    C1   C2   C3   C      1.92  30.0  1
 K30  Var_06    N25  C26  C27  C12  -56.39  30.0  1
 K30  Var_07    C1   N    C    C3   -13.13  30.0  1
 K30  Var_08    H28  C28  N25  C26  -62.87  30.0  3
 K30  Var_09    H22  C22  N11  C12   29.11  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
 K30  chir_01  C12  C27  N11  C23  positiv
 K30  chir_02  C23  F29  C12  C24  negativ
 K30  chir_03  C1   C2   N    C15  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
 K30  plan-1  C18  0.020
 K30  plan-1  C17  0.020
 K30  plan-1  C19  0.020
 K30  plan-1  C16  0.020
 K30  plan-1  C20  0.020
 K30  plan-1  C15  0.020
 K30  plan-1  C1   0.020
 K30  plan-1  H18  0.020
 K30  plan-1  H17  0.020
 K30  plan-1  H19  0.020
 K30  plan-1  H16  0.020
 K30  plan-1  H20  0.020
 K30  plan-2  C7   0.020
 K30  plan-2  C6   0.020
 K30  plan-2  C9   0.020
 K30  plan-2  C8   0.020
 K30  plan-2  C5   0.020
 K30  plan-2  C4   0.020
 K30  plan-2  C3   0.020
 K30  plan-2  F    0.020
 K30  plan-2  H7   0.020
 K30  plan-2  H6   0.020
 K30  plan-2  H9   0.020
 K30  plan-2  F13  0.020
 K30  plan-3  C22  0.020
 K30  plan-3  C    0.020
 K30  plan-3  C12  0.020
 K30  plan-3  C10  0.020
 K30  plan-3  C1   0.020
 K30  plan-3  N    0.020
 K30  plan-3  N11  0.020
 K30  plan-3  O    0.020

