# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 15:22:23 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: 2-[(2R,3S,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
 YWN  YWN  2-[(2R,3S,4R,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)-1-pentyl-pyrrolidin-2-yl]-N-methyl-ethanamide  ligand  45  19  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YWN
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
 YWN  C1    C  CH2   0  -0.276   0.7860  -0.3311  -0.2853
 YWN  N2    N  NT    0  -0.463  -0.5965  -0.3432   0.1212
 YWN  C3    C  CH1   0  -0.043  -1.4809   0.7312  -0.2971
 YWN  C4    C  CH1   0   0.009  -2.8244   0.2699   0.2485
 YWN  C5    C  CH1   0  -0.031  -2.7849  -1.2178  -0.0885
 YWN  C6    C  CH1   0  -0.058  -1.3139  -1.6131   0.1105
 YWN  C7    C  CH2   0  -0.431   1.7025  -0.9971   0.7356
 YWN  C8    C  CH2   0  -0.410   3.1413  -1.0815   0.2435
 YWN  C9    C  CH2   0  -0.418   4.1026  -1.6556   1.2767
 YWN  C10   C  CH3   0  -0.661   5.5325  -1.7581   0.7639
 YWN  C11   C  CH2   0  -0.578  -1.0725   2.1066   0.2266
 YWN  C12   C  C     0   0.526  -0.0751   2.8307  -0.6529
 YWN  O13   O  O     0  -0.499  -0.2159   2.9116  -1.8675
 YWN  N14   N  NH1   0  -0.623   0.9456   3.4173  -0.0114
 YWN  C15   C  CH3   0  -0.513   1.9743   4.1584  -0.7017
 YWN  C18   C  CH2   0  -0.204  -0.8703  -2.6369  -0.9244
 YWN  O19   O  OH1   0  -0.665  -1.0103  -2.1054  -2.2224
 YWN  O20   O  OH1   0  -0.668  -3.6200  -2.0106   0.7222
 YWN  O21   O  OH1   0  -0.677  -2.8892   0.4753   1.6382
 YWN  H11C  H  HCH2  0   0.202   0.9446  -0.7806  -1.2769
 YWN  H12C  H  HCH2  0   0.234   1.1128   0.7053  -0.3824
 YWN  H71C  H  HCH2  0   0.213   1.6576  -0.4289   1.6699
 YWN  H72C  H  HCH2  0   0.216   1.3432  -2.0041   0.9716
 YWN  H3    H  HCH1  0   0.213  -1.5801   0.8032  -1.3928
 YWN  H6    H  HCH1  0   0.224  -1.2117  -2.1130   1.0844
 YWN  H4    H  HCH1  0   0.216  -3.6510   0.7832  -0.2619
 YWN  H111  H  HCH2  0   0.279  -1.9623   2.7445   0.2441
 YWN  H112  H  HCH2  0   0.255  -0.7229   2.0258   1.2568
 YWN  H5    H  HCH1  0   0.233  -3.0517  -1.3271  -1.1454
 YWN  H21   H  HOH1  0   0.442  -3.4242  -0.2386   2.0054
 YWN  H20   H  HOH1  0   0.460  -4.5140  -1.9731   0.3678
 YWN  H181  H  HCH2  0   0.213   0.1646  -2.9465  -0.7298
 YWN  H182  H  HCH2  0   0.213  -1.4924  -3.5320  -0.7823
 YWN  H81C  H  HCH2  0   0.209   3.1743  -1.6963  -0.6629
 YWN  H82C  H  HCH2  0   0.206   3.4856  -0.0841  -0.0545
 YWN  H91C  H  HCH2  0   0.210   4.0822  -1.0317   2.1756
 YWN  H92C  H  HCH2  0   0.211   3.7528  -2.6454   1.5864
 YWN  H101  H  HCH3  0   0.216   5.5937  -2.4087  -0.1106
 YWN  H102  H  HCH3  0   0.216   5.9190  -0.7794   0.4730
 YWN  H103  H  HCH3  0   0.225   6.2015  -2.1634   1.5242
 YWN  H14   H  HNH1  0   0.402   1.0397   3.2849   0.9811
 YWN  H151  H  HCH3  0   0.236   2.5053   3.5356  -1.4228
 YWN  H152  H  HCH3  0   0.238   1.5642   5.0195  -1.2302
 YWN  H153  H  HCH3  0   0.249   2.6898   4.5179   0.0321
 YWN  H19   H  HOH1  0   0.456  -0.6889  -2.7586  -2.8501

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
 YWN  C1   N2    single  1.441  0.020  1.441
 YWN  C1   C7    single  1.525  0.020  1.525
 YWN  N2   C3    single  1.453  0.020  1.453
 YWN  N2   C6    single  1.459  0.020  1.459
 YWN  C3   C4    single  1.522  0.020  1.522
 YWN  C3   C11   single  1.527  0.020  1.527
 YWN  C4   C5    single  1.526  0.020  1.526
 YWN  C4   O21   single  1.406  0.020  1.406
 YWN  C5   C6    single  1.536  0.020  1.536
 YWN  C5   O20   single  1.408  0.020  1.408
 YWN  C6   C18   single  1.522  0.020  1.522
 YWN  C7   C8    single  1.523  0.020  1.523
 YWN  C8   C9    single  1.524  0.020  1.524
 YWN  C9   C10   single  1.522  0.020  1.522
 YWN  C11  C12   single  1.514  0.020  1.514
 YWN  C12  O13   double  1.225  0.020  1.225
 YWN  C12  N14   single  1.341  0.020  1.341
 YWN  N14  C15   single  1.444  0.020  1.444
 YWN  C18  O19   single  1.410  0.020  1.410
 YWN  C1   H11C  single  0.970  0.020  1.090
 YWN  C1   H12C  single  0.970  0.020  1.090
 YWN  C7   H71C  single  0.970  0.020  1.090
 YWN  C7   H72C  single  0.970  0.020  1.090
 YWN  C3   H3    single  0.970  0.020  1.090
 YWN  C6   H6    single  0.970  0.020  1.090
 YWN  C4   H4    single  0.970  0.020  1.090
 YWN  C11  H111  single  0.970  0.020  1.090
 YWN  C11  H112  single  0.970  0.020  1.090
 YWN  C5   H5    single  0.970  0.020  1.090
 YWN  O21  H21   single  0.850  0.020  0.980
 YWN  O20  H20   single  0.850  0.020  0.980
 YWN  C18  H181  single  0.970  0.020  1.090
 YWN  C18  H182  single  0.970  0.020  1.090
 YWN  C8   H81C  single  0.970  0.020  1.090
 YWN  C8   H82C  single  0.970  0.020  1.090
 YWN  C9   H91C  single  0.970  0.020  1.090
 YWN  C9   H92C  single  0.970  0.020  1.090
 YWN  C10  H101  single  0.970  0.020  1.090
 YWN  C10  H102  single  0.970  0.020  1.090
 YWN  C10  H103  single  0.970  0.020  1.090
 YWN  N14  H14   single  0.860  0.020  1.020
 YWN  C15  H151  single  0.970  0.020  1.090
 YWN  C15  H152  single  0.970  0.020  1.090
 YWN  C15  H153  single  0.970  0.020  1.090
 YWN  O19  H19   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
 YWN  H12C  C1   H11C  105.35  3.000
 YWN  H12C  C1   C7    107.12  3.000
 YWN  H11C  C1   C7    109.77  3.000
 YWN  H12C  C1   N2    108.69  3.000
 YWN  H11C  C1   N2    112.89  3.000
 YWN  C7    C1   N2    112.58  3.000
 YWN  C6    N2   C3    110.01  3.000
 YWN  C6    N2   C1    118.50  3.000
 YWN  C3    N2   C1    119.77  3.000
 YWN  H3    C3   C11   107.82  3.000
 YWN  H3    C3   C4    107.25  3.000
 YWN  C11   C3   C4    112.71  3.000
 YWN  H3    C3   N2    112.90  3.000
 YWN  C11   C3   N2    113.86  3.000
 YWN  C4    C3   N2    102.12  3.000
 YWN  H4    C4   O21   110.87  3.000
 YWN  H4    C4   C5    111.86  3.000
 YWN  O21   C4   C5    111.21  3.000
 YWN  H4    C4   C3    110.86  3.000
 YWN  O21   C4   C3    110.53  3.000
 YWN  C5    C4   C3    101.16  3.000
 YWN  H5    C5   O20   110.78  3.000
 YWN  H5    C5   C6    109.42  3.000
 YWN  O20   C5   C6    110.39  3.000
 YWN  H5    C5   C4    107.70  3.000
 YWN  O20   C5   C4    113.98  3.000
 YWN  C6    C5   C4    104.31  3.000
 YWN  H6    C6   C18   105.63  3.000
 YWN  H6    C6   C5    108.71  3.000
 YWN  C18   C6   C5    111.36  3.000
 YWN  H6    C6   N2    110.10  3.000
 YWN  C18   C6   N2    116.57  3.000
 YWN  C5    C6   N2    104.36  3.000
 YWN  H72C  C7   H71C  106.26  3.000
 YWN  H72C  C7   C8    109.19  3.000
 YWN  H71C  C7   C8    110.09  3.000
 YWN  H72C  C7   C1    110.41  3.000
 YWN  H71C  C7   C1    108.67  3.000
 YWN  C8    C7   C1    112.06  3.000
 YWN  H82C  C8   H81C  106.03  3.000
 YWN  H82C  C8   C9    109.20  3.000
 YWN  H81C  C8   C9    109.30  3.000
 YWN  H82C  C8   C7    109.52  3.000
 YWN  H81C  C8   C7    109.08  3.000
 YWN  C9    C8   C7    113.44  3.000
 YWN  H92C  C9   H91C  106.10  3.000
 YWN  H92C  C9   C10   109.55  3.000
 YWN  H91C  C9   C10   109.42  3.000
 YWN  H92C  C9   C8    109.32  3.000
 YWN  H91C  C9   C8    109.29  3.000
 YWN  C10   C9   C8    112.92  3.000
 YWN  H103  C10  H102  107.56  3.000
 YWN  H103  C10  H101  107.60  3.000
 YWN  H102  C10  H101  107.51  3.000
 YWN  H103  C10  C9    111.49  3.000
 YWN  H102  C10  C9    111.22  3.000
 YWN  H101  C10  C9    111.26  3.000
 YWN  H112  C11  H111  106.77  3.000
 YWN  H112  C11  C12   111.89  3.000
 YWN  H111  C11  C12   105.43  3.000
 YWN  H112  C11  C3    110.04  3.000
 YWN  H111  C11  C3    108.23  3.000
 YWN  C12   C11  C3    114.06  3.000
 YWN  N14   C12  O13   122.19  3.000
 YWN  N14   C12  C11   115.65  3.000
 YWN  O13   C12  C11   122.12  3.000
 YWN  H14   N14  C15   118.22  3.000
 YWN  H14   N14  C12   119.07  3.000
 YWN  C15   N14  C12   122.57  3.000
 YWN  H153  C15  H152  108.29  3.000
 YWN  H153  C15  H151  108.36  3.000
 YWN  H152  C15  H151  108.28  3.000
 YWN  H153  C15  N14   108.43  3.000
 YWN  H152  C15  N14   111.66  3.000
 YWN  H151  C15  N14   111.71  3.000
 YWN  H182  C18  H181  106.31  3.000
 YWN  H182  C18  O19   111.71  3.000
 YWN  H181  C18  O19   111.30  3.000
 YWN  H182  C18  C6    107.15  3.000
 YWN  H181  C18  C6    110.12  3.000
 YWN  O19   C18  C6    110.10  3.000
 YWN  H19   O19  C18   108.17  3.000
 YWN  H20   O20  C5    108.48  3.000
 YWN  H21   O21  C4    107.07  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
 YWN  CONST_01  C15   N14  C12  C11  180.00   0.0  0
 YWN  CONST_02  C15   N14  C12  O13    0.00   0.0  0
 YWN  CONST_03  H14   N14  C12  C11    0.00   0.0  0
 YWN  Var_01    C7    C1   N2   C3   149.52  30.0  1
 YWN  Var_02    C8    C7   C1   N2   175.24  30.0  3
 YWN  Var_03    O13   C12  C11  C3    46.97  30.0  3
 YWN  Var_04    C9    C8   C7   C1   176.08  30.0  3
 YWN  Var_05    C10   C9   C8   C7   178.96  30.0  3
 YWN  Var_06    H101  C10  C9   C8   -60.36  30.0  3
 YWN  Var_07    H151  C15  N14  C12  -59.74  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
 YWN  chir_01  C3  N2   C4  C11  negativ
 YWN  chir_02  C4  O21  C3  C5   negativ
 YWN  chir_03  C5  O20  C4  C6   negativ
 YWN  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
 YWN  plan-1  C11  0.020
 YWN  plan-1  C12  0.020
 YWN  plan-1  O13  0.020
 YWN  plan-1  N14  0.020
 YWN  plan-1  C15  0.020
 YWN  plan-1  H14  0.020

