# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 15 19:35:32 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: (3S,4aR,6S,8aR)-6-{[(2S)-2-carboxy-4,4-difluoropyrrolidin-1-yl]methyl}decahydroisoquinoline-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H]1C[C@H]2C[C@H](CC[C@H]2CN1)CN3CC(F)(F)C[C@H]3C(O)=O
#
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
 LY5  LY5  '(3S,4aR,6S,8aR)-6-{[(2S)-2-carboxy-4,4-difluoropyrrolidin-1-yl]methyl}decahydroisoquinoline-3-carboxylic acid'  ligand  48  24  .  2021-08-13  2021-08-13  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_LY5
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
 LY5  F2    F  F     0  -0.352  -5.0908   1.0685  -0.1276
 LY5  C15   C  CT    0   0.723  -4.3084   0.2698  -0.9208
 LY5  F1    F  F     0  -0.336  -4.9205   0.2519  -2.1339
 LY5  C14   C  CH2   0  -0.579  -4.1779  -1.0957  -0.2916
 LY5  C12   C  CH1   0  -0.189  -3.0812  -0.8259   0.7433
 LY5  C13   C  C     0   0.543  -2.3717  -2.1029   1.1443
 LY5  O4    O  O     0  -0.418  -1.2387  -2.3911   0.8659
 LY5  O3    O  OH1   0  -0.597  -3.1839  -2.8860   1.8463
 LY5  C16   C  CH2   0  -0.366  -2.8922   0.8127  -0.9736
 LY5  N2    N  NT    0  -0.441  -2.1901   0.1073   0.0906
 LY5  C11   C  CH2   0  -0.258  -1.4157   0.9434   0.9816
 LY5  C7    C  CH1   0  -0.263  -0.1957   1.5611   0.3105
 LY5  C6    C  CH2   0  -0.392   0.7959   0.4994  -0.1584
 LY5  C8    C  CH2   0  -0.423   0.4867   2.5477   1.2549
 LY5  C9    C  CH2   0  -0.430   1.7215   3.1702   0.6119
 LY5  C4    C  CH1   0  -0.223   2.7143   2.1379   0.0808
 LY5  C5    C  CH1   0  -0.250   2.0170   1.1234  -0.8351
 LY5  C3    C  CH2   0  -0.287   3.4648   1.4128   1.1907
 LY5  N1    N  NH1   0  -0.605   4.4296   0.4863   0.6196
 LY5  C1    C  CH1   0  -0.188   3.7956  -0.5550  -0.1580
 LY5  C2    C  CH2   0  -0.426   3.0223   0.0793  -1.3222
 LY5  C10   C  C     0   0.534   4.8450  -1.5073  -0.6863
 LY5  O1    O  O     0  -0.437   6.0350  -1.3766  -0.5486
 LY5  O2    O  OH1   0  -0.596   4.2955  -2.5311  -1.3303
 LY5  H141  H  HCH2  0   0.293  -5.1076  -1.4629   0.1390
 LY5  H142  H  HCH2  0   0.283  -3.8351  -1.8043  -1.0489
 LY5  H12   H  HCH1  0   0.269  -3.5440  -0.4077   1.6517
 LY5  HO3   H  HOH1  0   0.484  -2.7346  -3.7129   2.0773
 LY5  H161  H  HCH2  0   0.253  -2.4542   0.6087  -1.9551
 LY5  H162  H  HCH2  0   0.252  -2.8870   1.8982  -0.8320
 LY5  H111  H  HCH2  0   0.209  -2.0386   1.7456   1.4134
 LY5  H112  H  HCH2  0   0.231  -1.0741   0.3311   1.8211
 LY5  H7    H  HCH1  0   0.217  -0.5301   2.1263  -0.5708
 LY5  H61   H  HCH2  0   0.206   1.0944  -0.1012   0.7075
 LY5  H62   H  HCH2  0   0.233   0.3004  -0.1896  -0.8459
 LY5  H81   H  HCH2  0   0.228  -0.2128   3.3388   1.5397
 LY5  H82   H  HCH2  0   0.211   0.7581   2.0319   2.1829
 LY5  H91   H  HCH2  0   0.221   1.4002   3.7988  -0.2251
 LY5  H92   H  HCH2  0   0.225   2.2221   3.8371   1.3205
 LY5  H4    H  HCH1  0   0.225   3.4684   2.6668  -0.5144
 LY5  H5    H  HCH1  0   0.228   1.6561   1.6631  -1.7197
 LY5  H31   H  HCH2  0   0.234   4.0099   2.1398   1.7972
 LY5  H32   H  HCH2  0   0.197   2.7556   0.9102   1.8667
 LY5  HN1   H  HNH1  0   0.351   4.9779   0.0750   1.3640
 LY5  H1    H  HCH1  0   0.246   3.0931  -1.1647   0.4368
 LY5  H21   H  HCH2  0   0.242   2.5097  -0.6923  -1.8996
 LY5  H22   H  HCH2  0   0.236   3.7415   0.5615  -1.9919
 LY5  HO2   H  HOH1  0   0.482   4.9878  -3.1191  -1.6668

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
 LY5  F1   C15   single  1.359  0.020  1.359
 LY5  C15  F2    single  1.371  0.020  1.371
 LY5  C15  C16   single  1.518  0.020  1.518
 LY5  C15  C14   single  1.509  0.020  1.509
 LY5  C16  N2    single  1.457  0.020  1.457
 LY5  C14  C12   single  1.532  0.020  1.532
 LY5  N2   C12   single  1.446  0.020  1.446
 LY5  N2   C11   single  1.447  0.020  1.447
 LY5  C5   C2    single  1.529  0.020  1.529
 LY5  C5   C6    single  1.529  0.020  1.529
 LY5  C5   C4    single  1.534  0.020  1.534
 LY5  C2   C1    single  1.535  0.020  1.535
 LY5  C7   C6    single  1.526  0.020  1.526
 LY5  C7   C11   single  1.523  0.020  1.523
 LY5  C7   C8    single  1.527  0.020  1.527
 LY5  C12  C13   single  1.515  0.020  1.515
 LY5  C9   C4    single  1.528  0.020  1.528
 LY5  C9   C8    single  1.525  0.020  1.525
 LY5  C4   C3    single  1.523  0.020  1.523
 LY5  O1   C10   double  1.205  0.020  1.205
 LY5  O4   C13   double  1.202  0.020  1.202
 LY5  C13  O3    single  1.329  0.020  1.329
 LY5  C1   C10   single  1.512  0.020  1.512
 LY5  C1   N1    single  1.446  0.020  1.446
 LY5  C10  O2    single  1.329  0.020  1.329
 LY5  C3   N1    single  1.454  0.020  1.454
 LY5  C14  H141  single  0.970  0.020  1.090
 LY5  C14  H142  single  0.970  0.020  1.090
 LY5  C12  H12   single  0.970  0.020  1.090
 LY5  O3   HO3   single  0.850  0.020  0.980
 LY5  C16  H161  single  0.970  0.020  1.090
 LY5  C16  H162  single  0.970  0.020  1.090
 LY5  C11  H111  single  0.970  0.020  1.090
 LY5  C11  H112  single  0.970  0.020  1.090
 LY5  C7   H7    single  0.970  0.020  1.090
 LY5  C6   H61   single  0.970  0.020  1.090
 LY5  C6   H62   single  0.970  0.020  1.090
 LY5  C8   H81   single  0.970  0.020  1.090
 LY5  C8   H82   single  0.970  0.020  1.090
 LY5  C9   H91   single  0.970  0.020  1.090
 LY5  C9   H92   single  0.970  0.020  1.090
 LY5  C4   H4    single  0.970  0.020  1.090
 LY5  C5   H5    single  0.970  0.020  1.090
 LY5  C3   H31   single  0.970  0.020  1.090
 LY5  C3   H32   single  0.970  0.020  1.090
 LY5  N1   HN1   single  0.890  0.020  1.040
 LY5  C1   H1    single  0.970  0.020  1.090
 LY5  C2   H21   single  0.970  0.020  1.090
 LY5  C2   H22   single  0.970  0.020  1.090
 LY5  O2   HO2   single  0.850  0.020  0.980

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
 LY5  C16   C15  C14   104.92  3.000
 LY5  C14   C15  F1    113.53  3.000
 LY5  C16   C15  F1    113.20  3.000
 LY5  C14   C15  F2    109.59  3.000
 LY5  C16   C15  F2    110.14  3.000
 LY5  F1    C15  F2    105.49  3.000
 LY5  H142  C14  H141  108.87  3.000
 LY5  H142  C14  C12   110.98  3.000
 LY5  H141  C14  C12   113.81  3.000
 LY5  H142  C14  C15   108.97  3.000
 LY5  H141  C14  C15   113.35  3.000
 LY5  C12   C14  C15   100.62  3.000
 LY5  H12   C12  N2    112.71  3.000
 LY5  H12   C12  C13   107.36  3.000
 LY5  N2    C12  C13   112.02  3.000
 LY5  H12   C12  C14   108.85  3.000
 LY5  C13   C12  C14   111.45  3.000
 LY5  N2    C12  C14   104.47  3.000
 LY5  O3    C13  O4    123.87  3.000
 LY5  O3    C13  C12   110.51  3.000
 LY5  O4    C13  C12   125.62  3.000
 LY5  HO3   O3   C13   110.21  3.000
 LY5  H162  C16  H161  107.40  3.000
 LY5  H162  C16  N2    112.54  3.000
 LY5  H161  C16  N2    111.84  3.000
 LY5  H162  C16  C15   110.77  3.000
 LY5  H161  C16  C15   109.76  3.000
 LY5  N2    C16  C15   104.54  3.000
 LY5  C11   N2   C16   115.34  3.000
 LY5  C11   N2   C12   115.14  3.000
 LY5  C16   N2   C12   110.19  3.000
 LY5  H112  C11  H111  106.43  3.000
 LY5  H112  C11  C7    108.36  3.000
 LY5  H111  C11  C7    109.25  3.000
 LY5  H112  C11  N2    108.44  3.000
 LY5  H111  C11  N2    111.03  3.000
 LY5  C7    C11  N2    113.07  3.000
 LY5  H7    C7   C8    107.44  3.000
 LY5  H7    C7   C6    108.00  3.000
 LY5  C8    C7   C6    110.44  3.000
 LY5  H7    C7   C11   108.54  3.000
 LY5  C8    C7   C11   110.33  3.000
 LY5  C6    C7   C11   111.94  3.000
 LY5  H62   C6   H61   105.98  3.000
 LY5  H62   C6   C5    109.95  3.000
 LY5  H61   C6   C5    110.85  3.000
 LY5  H62   C6   C7    109.72  3.000
 LY5  H61   C6   C7    108.40  3.000
 LY5  C5    C6   C7    111.77  3.000
 LY5  H82   C8   H81   106.16  3.000
 LY5  H82   C8   C9    110.40  3.000
 LY5  H81   C8   C9    109.42  3.000
 LY5  H82   C8   C7    109.29  3.000
 LY5  H81   C8   C7    110.04  3.000
 LY5  C9    C8   C7    111.40  3.000
 LY5  H92   C9   H91   106.22  3.000
 LY5  H92   C9   C4    109.86  3.000
 LY5  H91   C9   C4    108.24  3.000
 LY5  H92   C9   C8    110.25  3.000
 LY5  H91   C9   C8    108.60  3.000
 LY5  C4    C9   C8    113.39  3.000
 LY5  H4    C4   C3    106.64  3.000
 LY5  H4    C4   C5    107.90  3.000
 LY5  C3    C4   C5    110.12  3.000
 LY5  H4    C4   C9    108.04  3.000
 LY5  C3    C4   C9    112.86  3.000
 LY5  C5    C4   C9    111.04  3.000
 LY5  H5    C5   C2    107.18  3.000
 LY5  H5    C5   C4    107.79  3.000
 LY5  C2    C5   C4    110.05  3.000
 LY5  H5    C5   C6    107.14  3.000
 LY5  C4    C5   C6    111.63  3.000
 LY5  C2    C5   C6    112.79  3.000
 LY5  H32   C3   H31   106.52  3.000
 LY5  H32   C3   N1    112.18  3.000
 LY5  H31   C3   N1    108.11  3.000
 LY5  H32   C3   C4    110.32  3.000
 LY5  H31   C3   C4    109.48  3.000
 LY5  N1    C3   C4    110.11  3.000
 LY5  HN1   N1   C1    109.91  3.000
 LY5  HN1   N1   C3    109.23  3.000
 LY5  C1    N1   C3    112.27  3.000
 LY5  H1    C1   C10   106.38  3.000
 LY5  H1    C1   C2    108.44  3.000
 LY5  C10   C1   C2    110.17  3.000
 LY5  H1    C1   N1    112.76  3.000
 LY5  C10   C1   N1    109.69  3.000
 LY5  C2    C1   N1    109.34  3.000
 LY5  H22   C2   H21   107.24  3.000
 LY5  H22   C2   C1    108.37  3.000
 LY5  H21   C2   C1    110.23  3.000
 LY5  H22   C2   C5    109.03  3.000
 LY5  H21   C2   C5    110.02  3.000
 LY5  C1    C2   C5    111.83  3.000
 LY5  O2    C10  O1    123.19  3.000
 LY5  O2    C10  C1    111.56  3.000
 LY5  O1    C10  C1    125.24  3.000
 LY5  HO2   O2   C10   109.91  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
 LY5  CONST_01  HO3  O3   C13  C12  180.00   0.0  0
 LY5  CONST_02  HO2  O2   C10  C1   180.00   0.0  0
 LY5  Var_01    C12  N2   C16  C15    1.16  30.0  1
 LY5  Var_02    N2   C16  C15  C14  -24.83  30.0  1
 LY5  Var_03    C16  C15  C14  C12   37.35  30.0  1
 LY5  Var_04    C4   C9   C8   C7   -53.68  30.0  1
 LY5  Var_05    C1   N1   C3   C4   -62.94  30.0  1
 LY5  Var_06    C7   C11  N2   C12  161.03  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
 LY5  chir_01  C12  C14  N2   C13  positiv
 LY5  chir_02  C7   C8   C11  C6   positiv
 LY5  chir_03  C4   C5   C9   C3   negativ
 LY5  chir_04  C5   C2   C6   C4   negativ
 LY5  chir_05  C1   N1   C2   C10  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
 LY5  plan-1  C12  0.020
 LY5  plan-1  C13  0.020
 LY5  plan-1  O4   0.020
 LY5  plan-1  O3   0.020
 LY5  plan-1  HO3  0.020
 LY5  plan-2  C1   0.020
 LY5  plan-2  C10  0.020
 LY5  plan-2  O1   0.020
 LY5  plan-2  O2   0.020
 LY5  plan-2  HO2  0.020

