# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 10:04:36 2022
#   Inital geometry file: a 117 line input string
#   Ligand name: (2R,4S)-4-{[(3R,5R)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-2-[(2S)-1,1,3-trihydroxypropan-2-yl]-3,4-dihydro-2H-pyrrole-5-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)C(=O)[C@H]1C[C@H](CN1)S[C@H]2C[C@@H](N=C2C(O)=O)[C@@H](CO)C(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
 FDX  FDX  "(2R,4S)-2-(1,3-dihydroxypropan-2-yl)-4-{[(3R,5R)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-3,4-dihydro-2H-pyrrole-5-carboxylic acid"  ligand  49  25  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_FDX
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
 FDX  C2   C  CR15   0  -0.470  25.1996  40.2397  15.8145
 FDX  C3   C  CR5    0   0.173  23.7177  40.4577  15.6787
 FDX  C1   C  CH2    0  -0.452  25.5302  39.4357  14.5559
 FDX  C1A  C  CH1    0  -0.417  24.7764  37.8281  17.3024
 FDX  C2A  C  CH2    0  -0.281  25.3410  36.8954  18.3769
 FDX  C31  C  C      0   0.378  22.9613  41.4178  16.5878
 FDX  C4A  C  CH2    0  -0.428  23.2766  37.7938  17.6057
 FDX  C5   C  CR15   0  -0.134  24.1496  38.9927  14.0327
 FDX  C5A  C  CH1    0  -0.285  23.0533  36.4104  18.2508
 FDX  C6   C  CH1    0  -0.315  23.9895  39.1266  12.5110
 FDX  C61  C  CH2    0  -0.149  24.7456  37.9790  11.8474
 FDX  C6A  C  C      0   0.594  22.3333  36.4883  19.5999
 FDX  C7   C  CH1    0   0.289  22.5034  39.2090  12.1393
 FDX  C8A  C  CH3    0  -0.515  21.3061  35.3715  21.4595
 FDX  C9A  C  CH3    0  -0.514  22.1848  34.0122  19.6117
 FDX  N3A  N  NH1    0  -0.581  24.3803  35.8101  18.4739
 FDX  N4   N  N      0  -0.394  23.1635  39.7878  14.7565
 FDX  N7A  N  NT     0  -0.448  21.8780  35.3303  20.1266
 FDX  O31  O  OC    -1  -0.583  23.5990  42.4448  16.8814
 FDX  O32  O  O      0  -0.579  21.8108  41.0948  16.9212
 FDX  O62  O  OH1    0  -0.665  25.1577  38.3412  10.5496
 FDX  O6A  O  O      0  -0.491  22.1854  37.5499  20.1919
 FDX  O7   O  OH1    0  -0.657  22.3662  39.0740  10.7668
 FDX  S21  S  S2     0   0.006  25.5920  39.4442  17.4086
 FDX  H1   H  HCR5   0   0.301  25.7433  41.1830  15.8696
 FDX  H2   H  HCH2   0   0.259  26.2076  38.6036  14.7431
 FDX  H3   H  HCH2   0   0.262  26.0191  40.0892  13.8298
 FDX  H4   H  HCH1   0   0.282  24.9900  37.3951  16.3217
 FDX  H5   H  HCH2   0   0.256  26.3336  36.5147  18.1385
 FDX  H6   H  HCH2   0   0.231  25.4068  37.4213  19.3353
 FDX  H7   H  HCH2   0   0.250  23.0203  38.5938  18.2978
 FDX  H8   H  HCH2   0   0.254  22.6656  37.9196  16.7148
 FDX  H9   H  HCR5   0   0.247  23.9631  37.9431  14.2970
 FDX  H10  H  HCH1   0   0.280  22.4785  35.7758  17.5746
 FDX  H11  H  HCH1   0   0.236  24.4587  40.0700  12.2060
 FDX  H12  H  HCH2   0   0.195  24.1126  37.0809  11.8449
 FDX  H13  H  HCH2   0   0.205  25.6189  37.7298  12.4663
 FDX  H14  H  HCH1   0   0.188  22.1283  40.1887  12.4690
 FDX  H16  H  HCH3   0   0.239  20.7823  34.4370  21.6475
 FDX  H17  H  HCH3   0   0.233  22.0702  35.4929  22.2315
 FDX  H18  H  HCH3   0   0.246  20.5910  36.1854  21.5565
 FDX  H19  H  HCH3   0   0.244  21.3417  33.3491  19.8018
 FDX  H20  H  HCH3   0   0.253  22.3501  34.0200  18.5396
 FDX  H21  H  HCH3   0   0.234  23.0701  33.5849  20.0882
 FDX  H22  H  HNH1   0   0.359  24.5664  35.1389  17.7400
 FDX  H25  H  HOH1   0   0.446  25.6333  37.5956  10.1730
 FDX  H26  H  HOH1   0   0.450  21.4612  39.3019  10.5278
 FDX  O1   O  OH1    0  -0.679  21.7483  38.1972  12.7625
 FDX  H15  H  HOH1   0   0.449  21.6163  38.4799  13.6768

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
 FDX  O62  C61  single  1.409  0.020  1.409
 FDX  C61  C6   single  1.526  0.020  1.526
 FDX  C7   O7   single  1.386  0.020  1.386
 FDX  C7   C6   single  1.534  0.020  1.534
 FDX  C6   C5   single  1.536  0.020  1.536
 FDX  C5   C1   single  1.541  0.020  1.541
 FDX  C5   N4   single  1.459  0.020  1.459
 FDX  C1   C2   single  1.530  0.020  1.530
 FDX  N4   C3   double  1.267  0.020  1.267
 FDX  C3   C2   single  1.504  0.020  1.504
 FDX  C3   C31  single  1.523  0.020  1.523
 FDX  O32  C31  deloc   1.241  0.020  1.241
 FDX  C2   S21  single  1.824  0.020  1.824
 FDX  C31  O31  deloc   1.244  0.020  1.244
 FDX  S21  C1A  single  1.813  0.020  1.813
 FDX  C1A  C4A  single  1.530  0.020  1.530
 FDX  C1A  C2A  single  1.531  0.020  1.531
 FDX  C4A  C5A  single  1.543  0.020  1.543
 FDX  C2A  N3A  single  1.453  0.020  1.453
 FDX  C5A  N3A  single  1.473  0.020  1.473
 FDX  C5A  C6A  single  1.531  0.020  1.531
 FDX  C6A  O6A  double  1.225  0.020  1.225
 FDX  C6A  N7A  single  1.351  0.020  1.351
 FDX  N7A  C9A  single  1.448  0.020  1.448
 FDX  N7A  C8A  single  1.451  0.020  1.451
 FDX  C2   H1   single  0.970  0.020  1.090
 FDX  C1   H2   single  0.970  0.020  1.090
 FDX  C1   H3   single  0.970  0.020  1.090
 FDX  C1A  H4   single  0.970  0.020  1.090
 FDX  C2A  H5   single  0.970  0.020  1.090
 FDX  C2A  H6   single  0.970  0.020  1.090
 FDX  C4A  H7   single  0.970  0.020  1.090
 FDX  C4A  H8   single  0.970  0.020  1.090
 FDX  C5   H9   single  0.970  0.020  1.090
 FDX  C5A  H10  single  0.970  0.020  1.090
 FDX  C6   H11  single  0.970  0.020  1.090
 FDX  C61  H12  single  0.970  0.020  1.090
 FDX  C61  H13  single  0.970  0.020  1.090
 FDX  C7   H14  single  0.970  0.020  1.090
 FDX  C8A  H16  single  0.970  0.020  1.090
 FDX  C8A  H17  single  0.970  0.020  1.090
 FDX  C8A  H18  single  0.970  0.020  1.090
 FDX  C9A  H19  single  0.970  0.020  1.090
 FDX  C9A  H20  single  0.970  0.020  1.090
 FDX  C9A  H21  single  0.970  0.020  1.090
 FDX  N3A  H22  single  0.890  0.020  1.040
 FDX  O62  H25  single  0.850  0.020  0.980
 FDX  O7   H26  single  0.850  0.020  0.980
 FDX  C7   O1   single  1.408  0.020  1.408
 FDX  O1   H15  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
 FDX  H1   C2   S21  103.05  3.000
 FDX  H1   C2   C1   112.87  3.000
 FDX  S21  C2   C1   116.32  3.000
 FDX  H1   C2   C3   111.75  3.000
 FDX  S21  C2   C3   110.73  3.000
 FDX  C1   C2   C3   102.41  3.000
 FDX  N4   C3   C31  123.38  3.000
 FDX  C31  C3   C2   121.79  3.000
 FDX  N4   C3   C2   114.83  3.000
 FDX  H3   C1   H2   107.03  3.000
 FDX  H3   C1   C5   110.32  3.000
 FDX  H2   C1   C5   113.32  3.000
 FDX  H3   C1   C2   109.22  3.000
 FDX  H2   C1   C2   113.24  3.000
 FDX  C5   C1   C2   103.69  3.000
 FDX  H4   C1A  S21  108.52  3.000
 FDX  H4   C1A  C4A  111.13  3.000
 FDX  S21  C1A  C4A  116.69  3.000
 FDX  H4   C1A  C2A  108.44  3.000
 FDX  C4A  C1A  C2A  102.04  3.000
 FDX  S21  C1A  C2A  109.64  3.000
 FDX  H6   C2A  H5   107.73  3.000
 FDX  H6   C2A  N3A  109.88  3.000
 FDX  H5   C2A  N3A  110.86  3.000
 FDX  H6   C2A  C1A  110.11  3.000
 FDX  H5   C2A  C1A  113.29  3.000
 FDX  N3A  C2A  C1A  104.96  3.000
 FDX  O32  C31  O31  128.82  3.000
 FDX  O31  C31  C3   113.99  3.000
 FDX  O32  C31  C3   117.18  3.000
 FDX  H8   C4A  H7   107.67  3.000
 FDX  H8   C4A  C5A  111.40  3.000
 FDX  H7   C4A  C5A  111.05  3.000
 FDX  H8   C4A  C1A  112.68  3.000
 FDX  H7   C4A  C1A  109.90  3.000
 FDX  C5A  C4A  C1A  104.17  3.000
 FDX  H9   C5   N4   106.66  3.000
 FDX  H9   C5   C6   107.70  3.000
 FDX  N4   C5   C6   111.94  3.000
 FDX  H9   C5   C1   110.18  3.000
 FDX  N4   C5   C1   106.28  3.000
 FDX  C6   C5   C1   113.86  3.000
 FDX  H10  C5A  N3A  109.35  3.000
 FDX  H10  C5A  C6A  109.14  3.000
 FDX  N3A  C5A  C6A  108.10  3.000
 FDX  H10  C5A  C4A  109.80  3.000
 FDX  C6A  C5A  C4A  113.01  3.000
 FDX  N3A  C5A  C4A  107.36  3.000
 FDX  H11  C6   C7   107.50  3.000
 FDX  H11  C6   C61  108.30  3.000
 FDX  C7   C6   C61  114.52  3.000
 FDX  H11  C6   C5   107.81  3.000
 FDX  C7   C6   C5   110.23  3.000
 FDX  C61  C6   C5   108.28  3.000
 FDX  H13  C61  H12  105.88  3.000
 FDX  H13  C61  O62  110.15  3.000
 FDX  H12  C61  O62  112.12  3.000
 FDX  H13  C61  C6   108.62  3.000
 FDX  H12  C61  C6   109.28  3.000
 FDX  O62  C61  C6   110.62  3.000
 FDX  O6A  C6A  N7A  120.92  3.000
 FDX  N7A  C6A  C5A  117.28  3.000
 FDX  O6A  C6A  C5A  121.79  3.000
 FDX  O1   C7   H14  108.94  3.000
 FDX  O1   C7   O7   108.38  3.000
 FDX  H14  C7   O7   110.49  3.000
 FDX  O1   C7   C6   111.94  3.000
 FDX  H14  C7   C6   107.80  3.000
 FDX  O7   C7   C6   109.31  3.000
 FDX  H18  C8A  H17  108.27  3.000
 FDX  H18  C8A  H16  108.12  3.000
 FDX  H17  C8A  H16  108.06  3.000
 FDX  H18  C8A  N7A  111.24  3.000
 FDX  H17  C8A  N7A  112.11  3.000
 FDX  H16  C8A  N7A  108.91  3.000
 FDX  H21  C9A  H20  108.08  3.000
 FDX  H21  C9A  H19  108.25  3.000
 FDX  H20  C9A  H19  107.14  3.000
 FDX  H21  C9A  N7A  111.88  3.000
 FDX  H20  C9A  N7A  112.16  3.000
 FDX  H19  C9A  N7A  109.15  3.000
 FDX  H22  N3A  C5A  109.03  3.000
 FDX  H22  N3A  C2A  109.00  3.000
 FDX  C5A  N3A  C2A  106.32  3.000
 FDX  C5   N4   C3   110.70  3.000
 FDX  C9A  N7A  C8A  115.85  3.000
 FDX  C8A  N7A  C6A  117.81  3.000
 FDX  C9A  N7A  C6A  124.76  3.000
 FDX  H25  O62  C61  107.83  3.000
 FDX  H26  O7   C7   108.40  3.000
 FDX  C1A  S21  C2   103.93  3.000
 FDX  H15  O1   C7   106.37  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
 FDX  CONST_01  C9A  N7A  C6A  C5A     0.00   0.0  0
 FDX  CONST_02  C8A  N7A  C6A  C5A   180.00   0.0  0
 FDX  CONST_03  O6A  C6A  N7A  C8A     0.00   0.0  0
 FDX  CONST_04  O6A  C6A  N7A  C9A   180.00   0.0  0
 FDX  Var_01    C5   N4   C3   C2     -1.63  30.0  1
 FDX  Var_02    C5A  N3A  C2A  C1A   -35.02  30.0  1
 FDX  Var_03    C5   N4   C3   C31   178.20  30.0  1
 FDX  Var_04    H22  N3A  C2A  C1A    82.38  30.0  1
 FDX  Var_05    H5   C2A  N3A  C5A  -157.69  30.0  1
 FDX  Var_06    H6   C2A  N3A  C5A    83.34  30.0  1
 FDX  Var_07    O32  C31  C3   C2   -143.92  30.0  2
 FDX  Var_08    O31  C31  C3   C2     36.91  30.0  2
 FDX  Var_09    O32  C31  C3   N4     36.26  30.0  2
 FDX  Var_10    O31  C31  C3   N4   -142.90  30.0  2
 FDX  Var_11    H19  C9A  N7A  C6A  -148.74  30.0  3
 FDX  Var_12    H20  C9A  N7A  C6A   -30.17  30.0  3
 FDX  Var_13    H21  C9A  N7A  C6A    91.48  30.0  3
 FDX  Var_14    H16  C8A  N7A  C6A   166.84  30.0  3
 FDX  Var_15    H17  C8A  N7A  C6A   -73.62  30.0  3
 FDX  Var_16    H18  C8A  N7A  C6A    47.77  30.0  3
 FDX  Var_17    H19  C9A  N7A  C8A    45.95  30.0  3
 FDX  Var_18    H20  C9A  N7A  C8A   164.53  30.0  3
 FDX  Var_19    H21  C9A  N7A  C8A   -73.83  30.0  3
 FDX  Var_20    H16  C8A  N7A  C9A   -26.78  30.0  3
 FDX  Var_21    H17  C8A  N7A  C9A    92.75  30.0  3
 FDX  Var_22    H18  C8A  N7A  C9A  -145.85  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
 FDX  chir_01  C2   C1   C3   S21  negativ
 FDX  chir_02  C1A  S21  C4A  C2A  positiv
 FDX  chir_03  C5   N4   C1   C6   positiv
 FDX  chir_04  C5A  N3A  C4A  C6A  positiv
 FDX  chir_05  C6   C61  C7   C5   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
 FDX  plan-1  C5A  0.020
 FDX  plan-1  C6A  0.020
 FDX  plan-1  C8A  0.020
 FDX  plan-1  C9A  0.020
 FDX  plan-1  N7A  0.020
 FDX  plan-1  O6A  0.020
 FDX  plan-2  C3   0.020
 FDX  plan-2  C31  0.020
 FDX  plan-2  O31  0.020
 FDX  plan-2  O32  0.020

