# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 22:47:03 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: 2-[(2S,3R,4R,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)-1-pentyl-pyrrolidin-2-yl]-N-methyl-ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCN1[C@H](CO)[C@@H](O)[C@H](O)[C@@H]1CC(=O)NC
#
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
 XRJ  XRJ  2-[(2S,3R,4R,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)-1-pentyl-pyrrolidin-2-yl]-N-methyl-ethanamide  ligand  45  19  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_XRJ
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
 XRJ  O13   O  O     0  -0.509  -0.0844   3.0998   1.6186
 XRJ  C12   C  C     0   0.566   0.1835   2.7993   0.4616
 XRJ  N14   N  NH1   0  -0.623   1.4168   2.9337  -0.0448
 XRJ  C15   C  CH3   0  -0.514   2.5281   3.4240   0.7344
 XRJ  C11   C  CH2   0  -0.628  -0.8671   2.2643  -0.4898
 XRJ  C3    C  CH1   0  -0.105  -1.5527   1.0415   0.0968
 XRJ  C4    C  CH1   0   0.033  -2.6538   0.4056  -0.7603
 XRJ  O21   O  OH1   0  -0.672  -2.2238   0.3526  -2.1017
 XRJ  C5    C  CH1   0   0.017  -2.8013  -0.9958  -0.1186
 XRJ  O20   O  OH1   0  -0.673  -4.0232  -1.2163   0.5450
 XRJ  C6    C  CH1   0  -0.142  -1.6671  -1.0414   0.9312
 XRJ  C18   C  CH2   0  -0.190  -1.1961  -2.4286   1.3151
 XRJ  O19   O  OH1   0  -0.663  -0.8520  -3.1985   0.1869
 XRJ  N2    N  NT    0  -0.429  -0.6746  -0.0555   0.5121
 XRJ  C1    C  CH2   0  -0.266   0.3360  -0.4843  -0.4530
 XRJ  C7    C  CH2   0  -0.418   1.5960  -1.0233   0.2110
 XRJ  C8    C  CH2   0  -0.414   2.7266  -1.2219  -0.7904
 XRJ  C9    C  CH2   0  -0.417   3.9702  -1.8534  -0.1770
 XRJ  C10   C  CH3   0  -0.662   5.1146  -1.9931  -1.1711
 XRJ  H14   H  HNH1  0   0.402   1.5860   2.6725  -1.0007
 XRJ  H111  H  HCH2  0   0.282  -1.6273   3.0416  -0.6113
 XRJ  H112  H  HCH2  0   0.262  -0.4614   2.0823  -1.4846
 XRJ  H151  H  HCH3  0   0.237   2.3466   4.4332   1.1055
 XRJ  H152  H  HCH3  0   0.237   2.7377   2.7788   1.5884
 XRJ  H153  H  HCH3  0   0.249   3.4097   3.4473   0.1003
 XRJ  H3    H  HCH1  0   0.249  -2.0510   1.3783   1.0142
 XRJ  H4    H  HCH1  0   0.217  -3.5924   0.9705  -0.6717
 XRJ  H21   H  HOH1  0   0.451  -2.9011  -0.0924  -2.6207
 XRJ  H5    H  HCH1  0   0.219  -2.6360  -1.7548  -0.8935
 XRJ  H20   H  HOH1  0   0.451  -4.7106  -1.3489  -0.1144
 XRJ  H6    H  HCH1  0   0.242  -2.1061  -0.6408   1.8564
 XRJ  H181  H  HCH2  0   0.212  -0.3583  -2.3314   2.0161
 XRJ  H182  H  HCH2  0   0.215  -2.0173  -2.8989   1.8711
 XRJ  H19   H  HOH1  0   0.456  -0.4862  -4.0321   0.4957
 XRJ  H11C  H  HCH2  0   0.211  -0.0398  -1.2078  -1.1834
 XRJ  H12C  H  HCH2  0   0.214   0.6376   0.3853  -1.0363
 XRJ  H71C  H  HCH2  0   0.203   1.9131  -0.3177   0.9856
 XRJ  H72C  H  HCH2  0   0.218   1.3925  -1.9708   0.7145
 XRJ  H81C  H  HCH2  0   0.206   2.3791  -1.8468  -1.6211
 XRJ  H82C  H  HCH2  0   0.204   2.9933  -0.2549  -1.2324
 XRJ  H91C  H  HCH2  0   0.209   4.2974  -1.2527   0.6775
 XRJ  H92C  H  HCH2  0   0.210   3.7122  -2.8372   0.2268
 XRJ  H101  H  HCH3  0   0.215   4.8175  -2.5962  -2.0314
 XRJ  H102  H  HCH3  0   0.216   5.4312  -1.0186  -1.5475
 XRJ  H103  H  HCH3  0   0.226   5.9847  -2.4709  -0.7196

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
 XRJ  O13  C12   double  1.225  0.020  1.225
 XRJ  C12  N14   single  1.340  0.020  1.340
 XRJ  C12  C11   single  1.515  0.020  1.515
 XRJ  N14  C15   single  1.443  0.020  1.443
 XRJ  C11  C3    single  1.520  0.020  1.520
 XRJ  C3   C4    single  1.533  0.020  1.533
 XRJ  C3   N2    single  1.465  0.020  1.465
 XRJ  C4   O21   single  1.410  0.020  1.410
 XRJ  C4   C5    single  1.548  0.020  1.548
 XRJ  C5   O20   single  1.408  0.020  1.408
 XRJ  C5   C6    single  1.546  0.020  1.546
 XRJ  C6   C18   single  1.514  0.020  1.514
 XRJ  C6   N2    single  1.460  0.020  1.460
 XRJ  C18  O19   single  1.409  0.020  1.409
 XRJ  N2   C1    single  1.462  0.020  1.462
 XRJ  C1   C7    single  1.523  0.020  1.523
 XRJ  C7   C8    single  1.523  0.020  1.523
 XRJ  C8   C9    single  1.524  0.020  1.524
 XRJ  C9   C10   single  1.522  0.020  1.522
 XRJ  N14  H14   single  0.860  0.020  1.020
 XRJ  C11  H111  single  0.970  0.020  1.090
 XRJ  C11  H112  single  0.970  0.020  1.090
 XRJ  C15  H151  single  0.970  0.020  1.090
 XRJ  C15  H152  single  0.970  0.020  1.090
 XRJ  C15  H153  single  0.970  0.020  1.090
 XRJ  C3   H3    single  0.970  0.020  1.090
 XRJ  C4   H4    single  0.970  0.020  1.090
 XRJ  O21  H21   single  0.850  0.020  0.980
 XRJ  C5   H5    single  0.970  0.020  1.090
 XRJ  O20  H20   single  0.850  0.020  0.980
 XRJ  C6   H6    single  0.970  0.020  1.090
 XRJ  C18  H181  single  0.970  0.020  1.090
 XRJ  C18  H182  single  0.970  0.020  1.090
 XRJ  O19  H19   single  0.850  0.020  0.980
 XRJ  C1   H11C  single  0.970  0.020  1.090
 XRJ  C1   H12C  single  0.970  0.020  1.090
 XRJ  C7   H71C  single  0.970  0.020  1.090
 XRJ  C7   H72C  single  0.970  0.020  1.090
 XRJ  C8   H81C  single  0.970  0.020  1.090
 XRJ  C8   H82C  single  0.970  0.020  1.090
 XRJ  C9   H91C  single  0.970  0.020  1.090
 XRJ  C9   H92C  single  0.970  0.020  1.090
 XRJ  C10  H101  single  0.970  0.020  1.090
 XRJ  C10  H102  single  0.970  0.020  1.090
 XRJ  C10  H103  single  0.970  0.020  1.090

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
 XRJ  C11   C12  N14   115.87  3.000
 XRJ  C11   C12  O13   121.88  3.000
 XRJ  N14   C12  O13   122.25  3.000
 XRJ  H14   N14  C15   118.17  3.000
 XRJ  H14   N14  C12   119.22  3.000
 XRJ  C15   N14  C12   122.60  3.000
 XRJ  H153  C15  H152  108.29  3.000
 XRJ  H153  C15  H151  108.29  3.000
 XRJ  H152  C15  H151  108.24  3.000
 XRJ  H153  C15  N14   108.48  3.000
 XRJ  H152  C15  N14   111.71  3.000
 XRJ  H151  C15  N14   111.72  3.000
 XRJ  H112  C11  H111  106.03  3.000
 XRJ  H112  C11  C3    112.70  3.000
 XRJ  H111  C11  C3    107.52  3.000
 XRJ  H112  C11  C12   111.98  3.000
 XRJ  H111  C11  C12   107.50  3.000
 XRJ  C3    C11  C12   110.77  3.000
 XRJ  H3    C3   N2    105.36  3.000
 XRJ  H3    C3   C4    105.58  3.000
 XRJ  N2    C3   C4    106.16  3.000
 XRJ  H3    C3   C11   106.30  3.000
 XRJ  N2    C3   C11   116.20  3.000
 XRJ  C4    C3   C11   116.23  3.000
 XRJ  H4    C4   C5    110.51  3.000
 XRJ  H4    C4   O21   110.89  3.000
 XRJ  C5    C4   O21   112.91  3.000
 XRJ  H4    C4   C3    110.80  3.000
 XRJ  C5    C4   C3    102.25  3.000
 XRJ  O21   C4   C3    109.17  3.000
 XRJ  H21   O21  C4    108.41  3.000
 XRJ  H5    C5   C6    110.40  3.000
 XRJ  H5    C5   O20   110.82  3.000
 XRJ  C6    C5   O20   108.18  3.000
 XRJ  H5    C5   C4    108.61  3.000
 XRJ  C6    C5   C4    103.78  3.000
 XRJ  O20   C5   C4    114.82  3.000
 XRJ  H20   O20  C5    108.58  3.000
 XRJ  H6    C6   N2    105.48  3.000
 XRJ  H6    C6   C18   104.16  3.000
 XRJ  N2    C6   C18   118.67  3.000
 XRJ  H6    C6   C5    105.53  3.000
 XRJ  N2    C6   C5    106.49  3.000
 XRJ  C18   C6   C5    115.30  3.000
 XRJ  H182  C18  H181  106.61  3.000
 XRJ  H182  C18  O19   110.75  3.000
 XRJ  H181  C18  O19   111.95  3.000
 XRJ  H182  C18  C6    106.74  3.000
 XRJ  H181  C18  C6    108.57  3.000
 XRJ  O19   C18  C6    111.94  3.000
 XRJ  H19   O19  C18   108.03  3.000
 XRJ  C1    N2   C6    117.47  3.000
 XRJ  C1    N2   C3    116.54  3.000
 XRJ  C6    N2   C3    100.34  3.000
 XRJ  H12C  C1   H11C  105.39  3.000
 XRJ  H12C  C1   C7    106.67  3.000
 XRJ  H11C  C1   C7    109.95  3.000
 XRJ  H12C  C1   N2    108.10  3.000
 XRJ  H11C  C1   N2    113.40  3.000
 XRJ  C7    C1   N2    112.83  3.000
 XRJ  H72C  C7   H71C  106.68  3.000
 XRJ  H72C  C7   C8    109.17  3.000
 XRJ  H71C  C7   C8    109.52  3.000
 XRJ  H72C  C7   C1    110.73  3.000
 XRJ  H71C  C7   C1    108.67  3.000
 XRJ  C8    C7   C1    111.93  3.000
 XRJ  H82C  C8   H81C  105.93  3.000
 XRJ  H82C  C8   C9    109.23  3.000
 XRJ  H81C  C8   C9    109.13  3.000
 XRJ  H82C  C8   C7    109.31  3.000
 XRJ  H81C  C8   C7    109.71  3.000
 XRJ  C9    C8   C7    113.27  3.000
 XRJ  H92C  C9   H91C  106.01  3.000
 XRJ  H92C  C9   C10   109.62  3.000
 XRJ  H91C  C9   C10   109.60  3.000
 XRJ  H92C  C9   C8    109.19  3.000
 XRJ  H91C  C9   C8    109.32  3.000
 XRJ  C10   C9   C8    112.87  3.000
 XRJ  H103  C10  H102  107.61  3.000
 XRJ  H103  C10  H101  107.54  3.000
 XRJ  H102  C10  H101  107.48  3.000
 XRJ  H103  C10  C9    111.69  3.000
 XRJ  H102  C10  C9    111.18  3.000
 XRJ  H101  C10  C9    111.14  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
 XRJ  CONST_01  C15   N14  C12  O13     0.00   0.0  0
 XRJ  CONST_02  C11   C12  N14  C15   180.00   0.0  0
 XRJ  CONST_03  H14   N14  C12  O13   180.00   0.0  0
 XRJ  Var_01    C7    C1   N2   C3    149.58  30.0  3
 XRJ  Var_02    C3    C11  C12  O13   -55.21  30.0  3
 XRJ  Var_03    C8    C7   C1   N2   -169.45  30.0  3
 XRJ  Var_04    C9    C8   C7   C1   -175.90  30.0  3
 XRJ  Var_05    C10   C9   C8   C7   -177.55  30.0  3
 XRJ  Var_06    H151  C15  N14  C12   -60.26  30.0  3
 XRJ  Var_07    H101  C10  C9   C8    -58.37  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
 XRJ  chir_01  C3  C11  C4  N2   negativ
 XRJ  chir_02  C4  O21  C5  C3   negativ
 XRJ  chir_03  C5  O20  C4  C6   negativ
 XRJ  chir_04  C6  N2   C5  C18  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
 XRJ  plan-1  O13  0.020
 XRJ  plan-1  C12  0.020
 XRJ  plan-1  N14  0.020
 XRJ  plan-1  C15  0.020
 XRJ  plan-1  C11  0.020
 XRJ  plan-1  H14  0.020

