# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 02:54:20 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: (4R,5R)-5-amino-1-[2-(1,3-benzodioxol-5-yl)ethyl]-4-(2,4,5-trifluorophenyl)piperidin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1CN(CCc2ccc3OCOc3c2)C(=O)C[C@@H]1c4cc(F)c(F)cc4F
#
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
 GGO  GGO  (4R,5R)-5-amino-1-[2-(1,3-benzodioxol-5-yl)ethyl]-4-(2,4,5-trifluorophenyl)piperidin-2-one  ligand  47  28  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GGO
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
 GGO  C5    C  CH2   0  -0.297   1.8829   1.7144  -3.4441
 GGO  C6    C  CH2   0  -0.525   3.3357   1.3910  -3.8063
 GGO  C7    C  CR6   0   0.111   3.6161   1.7075  -5.2490
 GGO  C8    C  CR16  0  -0.327   3.4909   0.7271  -6.2246
 GGO  C10   C  CR56  0   0.283   4.0363   2.2853  -7.9144
 GGO  C15   C  CR16  0  -0.391   3.9595   3.0197  -5.6180
 GGO  C20   C  CR6   0  -0.010   1.3517   0.8059   2.1968
 GGO  C21   C  CR16  0  -0.452   0.0157   0.7674   2.5972
 GGO  C22   C  CR6   0   0.410  -0.3258   0.6073   3.9210
 GGO  C24   C  CR6   0   0.402   0.6578   0.4789   4.8867
 GGO  C26   C  CR16  0  -0.556   1.9875   0.5138   4.5323
 GGO  N     N  NH2   0  -0.787   1.8293   3.5240   1.0597
 GGO  C     C  CH1   0  -0.101   1.3365   2.4188   0.2654
 GGO  C3    C  CH2   0  -0.250   1.8526   2.6030  -1.1525
 GGO  N4    N  NT    0  -0.469   1.5885   1.4816  -2.0402
 GGO  C9    C  CR16  0  -0.330   3.7007   0.9969  -7.5833
 GGO  O     O  O     0  -0.489   4.2944   2.8097  -9.1378
 GGO  C12   C  CH2   0   0.075   4.6063   4.1826  -8.9387
 GGO  O13   O  O     0  -0.489   4.5028   4.4421  -7.5439
 GGO  C14   C  CR56  0   0.313   4.1627   3.2724  -6.9510
 GGO  C16   C  C     0   0.550   1.2973   0.2274  -1.6377
 GGO  O17   O  O     0  -0.509   1.1832  -0.6995  -2.4313
 GGO  C18   C  CH2   0  -0.542   1.0605  -0.0079  -0.1630
 GGO  C19   C  CH1   0  -0.388   1.7218   1.0153   0.7517
 GGO  F     F  F     0  -0.305  -1.6099   0.5731   4.2909
 GGO  F25   F  F     0  -0.299   0.3075   0.3221   6.1639
 GGO  C27   C  CR6   0   0.509   2.3046   0.6803   3.1956
 GGO  F28   F  F     0  -0.303   3.6056   0.7187   2.8730
 GGO  H51   H  HCH2  0   0.253   1.6723   2.7641  -3.6575
 GGO  H52   H  HCH2  0   0.261   1.2072   1.1224  -4.0601
 GGO  H61   H  HCH2  0   0.250   4.0081   1.9616  -3.1607
 GGO  H62   H  HCH2  0   0.256   3.5255   0.3344  -3.6113
 GGO  H8    H  HCR6  0   0.250   3.2275  -0.2813  -5.9303
 GGO  H15   H  HCR6  0   0.265   4.0639   3.8008  -4.8750
 GGO  H21   H  HCR6  0   0.298  -0.7806   0.8642   1.8698
 GGO  H26   H  HCR6  0   0.315   2.7624   0.4158   5.2813
 GGO  HN1   H  HNH2  0   0.344   2.8317   3.4437   1.1887
 GGO  HN2   H  HNH2  0   0.356   1.4191   3.5004   1.9845
 GGO  H     H  HCH1  0   0.246   0.2427   2.4870   0.2506
 GGO  H31   H  HCH2  0   0.262   1.3926   3.4951  -1.5815
 GGO  H32   H  HCH2  0   0.236   2.9327   2.7918  -1.1127
 GGO  H9    H  HCR6  0   0.271   3.6051   0.2223  -8.3320
 GGO  H121  H  HCH2  0   0.237   5.6256   4.3836  -9.2779
 GGO  H122  H  HCH2  0   0.238   3.8956   4.8075  -9.4844
 GGO  H181  H  HCH2  0   0.274  -0.0248  -0.0119  -0.0178
 GGO  H182  H  HCH2  0   0.283   1.4038  -1.0168   0.0681
 GGO  H19   H  HCH1  0   0.271   2.8063   0.9161   0.6474

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
 GGO  C5   C6    single    1.532  0.020  1.532
 GGO  C5   N4    single    1.453  0.020  1.453
 GGO  C5   H51   single    0.970  0.020  1.090
 GGO  C5   H52   single    0.970  0.020  1.090
 GGO  C6   C7    single    1.503  0.020  1.503
 GGO  C6   H61   single    0.970  0.020  1.090
 GGO  C6   H62   single    0.970  0.020  1.090
 GGO  C7   C15   aromatic  1.406  0.020  1.406
 GGO  C7   C8    aromatic  1.389  0.020  1.389
 GGO  C8   C9    aromatic  1.401  0.020  1.401
 GGO  C8   H8    single    0.930  0.020  1.080
 GGO  C10  C14   aromatic  1.385  0.020  1.385
 GGO  C10  O     single    1.356  0.020  1.356
 GGO  C10  C9    aromatic  1.372  0.020  1.372
 GGO  C15  C14   aromatic  1.372  0.020  1.372
 GGO  C15  H15   single    0.930  0.020  1.080
 GGO  C20  C27   aromatic  1.386  0.020  1.386
 GGO  C20  C19   single    1.506  0.020  1.506
 GGO  C20  C21   aromatic  1.395  0.020  1.395
 GGO  C21  C22   aromatic  1.376  0.020  1.376
 GGO  C21  H21   single    0.930  0.020  1.080
 GGO  C22  C24   aromatic  1.384  0.020  1.384
 GGO  C22  F     single    1.337  0.020  1.337
 GGO  C24  C26   aromatic  1.377  0.020  1.377
 GGO  C24  F25   single    1.334  0.020  1.334
 GGO  C26  C27   aromatic  1.384  0.020  1.384
 GGO  C26  H26   single    0.930  0.020  1.080
 GGO  N    C     single    1.447  0.020  1.447
 GGO  N    HN1   single    0.890  0.020  1.040
 GGO  N    HN2   single    0.890  0.020  1.040
 GGO  C    C19   single    1.535  0.020  1.535
 GGO  C    C3    single    1.520  0.020  1.520
 GGO  C    H     single    0.970  0.020  1.090
 GGO  C3   N4    single    1.454  0.020  1.454
 GGO  C3   H31   single    0.970  0.020  1.090
 GGO  C3   H32   single    0.970  0.020  1.090
 GGO  N4   C16   single    1.349  0.020  1.349
 GGO  C9   H9    single    0.930  0.020  1.080
 GGO  O    C12   single    1.422  0.020  1.422
 GGO  C12  O13   single    1.422  0.020  1.422
 GGO  C12  H121  single    0.970  0.020  1.090
 GGO  C12  H122  single    0.970  0.020  1.090
 GGO  O13  C14   single    1.355  0.020  1.355
 GGO  C16  O17   double    1.226  0.020  1.226
 GGO  C16  C18   single    1.512  0.020  1.512
 GGO  C18  C19   single    1.523  0.020  1.523
 GGO  C18  H181  single    0.970  0.020  1.090
 GGO  C18  H182  single    0.970  0.020  1.090
 GGO  C19  H19   single    0.970  0.020  1.090
 GGO  C27  F28   single    1.341  0.020  1.341

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
 GGO  H52   C5   H51   107.00  3.000
 GGO  H52   C5   N4    109.48  3.000
 GGO  H51   C5   N4    107.69  3.000
 GGO  H52   C5   C6    109.87  3.000
 GGO  H51   C5   C6    109.87  3.000
 GGO  N4    C5   C6    112.75  3.000
 GGO  H62   C6   H61   107.04  3.000
 GGO  H62   C6   C7    110.06  3.000
 GGO  H61   C6   C7    110.01  3.000
 GGO  H62   C6   C5    109.10  3.000
 GGO  H61   C6   C5    109.49  3.000
 GGO  C7    C6   C5    111.06  3.000
 GGO  C15   C7   C8    119.77  3.000
 GGO  C8    C7   C6    120.58  3.000
 GGO  C15   C7   C6    119.60  3.000
 GGO  H8    C8   C9    118.64  3.000
 GGO  H8    C8   C7    119.23  3.000
 GGO  C9    C8   C7    122.13  3.000
 GGO  C14   C10  O     109.54  3.000
 GGO  O     C10  C9    128.87  3.000
 GGO  C14   C10  C9    121.58  3.000
 GGO  H15   C15  C14   121.29  3.000
 GGO  H15   C15  C7    121.11  3.000
 GGO  C14   C15  C7    117.59  3.000
 GGO  C27   C20  C19   122.34  3.000
 GGO  C19   C20  C21   120.96  3.000
 GGO  C27   C20  C21   116.68  3.000
 GGO  H21   C21  C22   118.29  3.000
 GGO  H21   C21  C20   120.59  3.000
 GGO  C22   C21  C20   121.12  3.000
 GGO  F     C22  C24   119.15  3.000
 GGO  F     C22  C21   120.50  3.000
 GGO  C24   C22  C21   120.36  3.000
 GGO  F25   C24  C26   120.21  3.000
 GGO  F25   C24  C22   119.50  3.000
 GGO  C26   C24  C22   120.29  3.000
 GGO  H26   C26  C27   121.03  3.000
 GGO  H26   C26  C24   120.74  3.000
 GGO  C27   C26  C24   118.23  3.000
 GGO  HN2   N    HN1   106.42  3.000
 GGO  HN2   N    C     110.23  3.000
 GGO  HN1   N    C     110.24  3.000
 GGO  H     C    C19   108.17  3.000
 GGO  H     C    C3    108.58  3.000
 GGO  C19   C    C3    108.73  3.000
 GGO  H     C    N     107.44  3.000
 GGO  C3    C    N     107.69  3.000
 GGO  C19   C    N     116.04  3.000
 GGO  H32   C3   H31   106.76  3.000
 GGO  H32   C3   N4    109.49  3.000
 GGO  H31   C3   N4    108.29  3.000
 GGO  H32   C3   C     108.73  3.000
 GGO  H31   C3   C     108.81  3.000
 GGO  N4    C3   C     114.47  3.000
 GGO  C16   N4   C3    125.03  3.000
 GGO  C16   N4   C5    118.75  3.000
 GGO  C3    N4   C5    115.42  3.000
 GGO  H9    C9   C10   121.81  3.000
 GGO  H9    C9   C8    121.34  3.000
 GGO  C10   C9   C8    116.84  3.000
 GGO  C12   O    C10   106.79  3.000
 GGO  H122  C12  H121  110.27  3.000
 GGO  H122  C12  O13   109.76  3.000
 GGO  H121  C12  O13   109.80  3.000
 GGO  H122  C12  O     109.86  3.000
 GGO  H121  C12  O     109.80  3.000
 GGO  O13   C12  O     107.30  3.000
 GGO  C14   O13  C12   106.85  3.000
 GGO  O13   C14  C15   128.42  3.000
 GGO  O13   C14  C10   109.50  3.000
 GGO  C15   C14  C10   122.08  3.000
 GGO  C18   C16  O17   119.95  3.000
 GGO  C18   C16  N4    118.00  3.000
 GGO  O17   C16  N4    122.01  3.000
 GGO  H182  C18  H181  106.29  3.000
 GGO  H182  C18  C19   110.94  3.000
 GGO  H181  C18  C19   110.68  3.000
 GGO  H182  C18  C16   107.55  3.000
 GGO  H181  C18  C16   106.57  3.000
 GGO  C19   C18  C16   114.40  3.000
 GGO  H19   C19  C18   108.19  3.000
 GGO  H19   C19  C     107.55  3.000
 GGO  C18   C19  C     108.36  3.000
 GGO  H19   C19  C20   108.81  3.000
 GGO  C18   C19  C20   112.09  3.000
 GGO  C     C19  C20   111.68  3.000
 GGO  F28   C27  C26   117.26  3.000
 GGO  F28   C27  C20   119.41  3.000
 GGO  C26   C27  C20   123.33  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
 GGO  CONST_01  C10  C14  C15  C7      0.00   0.0  0
 GGO  CONST_02  C10  C9   C8   C7      0.00   0.0  0
 GGO  CONST_03  C14  C15  C7   C8      0.00   0.0  0
 GGO  CONST_04  C14  C10  C9   C8      0.00   0.0  0
 GGO  CONST_05  C9   C8   C7   C15     0.00   0.0  0
 GGO  CONST_06  C9   C10  C14  C15     0.00   0.0  0
 GGO  CONST_07  C24  C26  C27  C20     0.00   0.0  0
 GGO  CONST_08  C24  C22  C21  C20     0.00   0.0  0
 GGO  CONST_09  C26  C27  C20  C21     0.00   0.0  0
 GGO  CONST_10  C26  C24  C22  C21     0.00   0.0  0
 GGO  CONST_11  C27  C20  C21  C22     0.00   0.0  0
 GGO  CONST_12  C27  C26  C24  C22     0.00   0.0  0
 GGO  CONST_13  C19  C20  C21  C22   180.00   0.0  0
 GGO  CONST_14  C19  C20  C27  C26   180.00   0.0  0
 GGO  CONST_15  C18  C16  N4   C3      0.00   0.0  0
 GGO  CONST_16  C14  C15  C7   C6    180.00   0.0  0
 GGO  CONST_17  C9   C8   C7   C6    180.00   0.0  0
 GGO  CONST_18  F    C22  C21  C20   180.00   0.0  0
 GGO  CONST_19  F28  C27  C20  C21   180.00   0.0  0
 GGO  CONST_20  F25  C24  C22  C21   180.00   0.0  0
 GGO  CONST_21  F28  C27  C26  C24   180.00   0.0  0
 GGO  CONST_22  F    C22  C24  C26   180.00   0.0  0
 GGO  CONST_23  F28  C27  C20  C19     0.00   0.0  0
 GGO  CONST_24  C27  C26  C24  F25   180.00   0.0  0
 GGO  CONST_25  C18  C16  N4   C5    180.00   0.0  0
 GGO  CONST_26  O17  C16  N4   C3    180.00   0.0  0
 GGO  CONST_27  H9   C9   C8   C7    180.00   0.0  0
 GGO  CONST_28  H15  C15  C7   C8    180.00   0.0  0
 GGO  CONST_29  H8   C8   C9   C10   180.00   0.0  0
 GGO  CONST_30  H26  C26  C27  C20   180.00   0.0  0
 GGO  CONST_31  H21  C21  C22  C24   180.00   0.0  0
 GGO  CONST_32  O17  C16  N4   C5      0.00   0.0  0
 GGO  Var_01    O13  C12  O    C10    -0.71  30.0  1
 GGO  Var_02    C16  N4   C3   C     -19.63  30.0  1
 GGO  Var_03    C19  C18  C16  N4    -24.28  30.0  1
 GGO  Var_04    C14  C10  O    C12     0.42  30.0  1
 GGO  Var_05    C15  C7   C6   C5     84.28  30.0  2
 GGO  Var_06    C3   N4   C5   C6     87.86  30.0  3
 GGO  Var_07    N4   C5   C6   C7   -177.27  30.0  1

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
 GGO  chir_01  C    N    C19  C3   positiv
 GGO  chir_02  C19  C20  C    C18  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
 GGO  plan-1  C20  0.020
 GGO  plan-1  C21  0.020
 GGO  plan-1  C22  0.020
 GGO  plan-1  C24  0.020
 GGO  plan-1  C26  0.020
 GGO  plan-1  C19  0.020
 GGO  plan-1  F    0.020
 GGO  plan-1  F25  0.020
 GGO  plan-1  C27  0.020
 GGO  plan-1  F28  0.020
 GGO  plan-1  H21  0.020
 GGO  plan-1  H26  0.020
 GGO  plan-2  C6   0.020
 GGO  plan-2  C7   0.020
 GGO  plan-2  C8   0.020
 GGO  plan-2  C10  0.020
 GGO  plan-2  C15  0.020
 GGO  plan-2  C9   0.020
 GGO  plan-2  O    0.020
 GGO  plan-2  O13  0.020
 GGO  plan-2  C14  0.020
 GGO  plan-2  H8   0.020
 GGO  plan-2  H15  0.020
 GGO  plan-2  H9   0.020
 GGO  plan-3  C5   0.020
 GGO  plan-3  C3   0.020
 GGO  plan-3  N4   0.020
 GGO  plan-3  C16  0.020
 GGO  plan-3  O17  0.020
 GGO  plan-3  C18  0.020

