# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 20:19:30 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: 2-[(2S,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
 XQO  XQO  2-[(2S,3S,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_XQO
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
 XQO  O13   O  O     0  -0.508   0.1892   3.0879  -1.4578
 XQO  C12   C  C     0   0.562  -0.1736   2.7421  -0.3401
 XQO  N14   N  NH1   0  -0.622  -1.4502   2.8333   0.0578
 XQO  C15   C  CH3   0  -0.517  -2.5043   3.2900  -0.8162
 XQO  C11   C  CH2   0  -0.619   0.7997   2.1801   0.6746
 XQO  C3    C  CH1   0  -0.126   1.4958   0.9469   0.1235
 XQO  C4    C  CH1   0   0.047   2.4505   0.2383   1.0958
 XQO  O21   O  OH1   0  -0.673   3.6391   0.9263   1.3702
 XQO  C5    C  CH1   0  -0.002   2.6488  -1.1534   0.4236
 XQO  O20   O  OH1   0  -0.670   3.9365  -1.3107  -0.1297
 XQO  C6    C  CH1   0  -0.144   1.6130  -1.1377  -0.7201
 XQO  C18   C  CH2   0  -0.184   1.1146  -2.4887  -1.1887
 XQO  O19   O  OH1   0  -0.663   0.6285  -3.2786  -0.1284
 XQO  N2    N  NT    0  -0.428   0.6235  -0.1204  -0.3644
 XQO  C1    C  CH2   0  -0.292  -0.4464  -0.5436   0.5436
 XQO  C7    C  CH2   0  -0.420  -1.7512  -0.7950  -0.1979
 XQO  C8    C  CH2   0  -0.415  -2.8889  -1.1820   0.7371
 XQO  C9    C  CH2   0  -0.417  -4.2205  -1.3596   0.0180
 XQO  C10   C  CH3   0  -0.662  -5.3542  -1.7506   0.9559
 XQO  H14   H  HNH1  0   0.400  -1.7011   2.5184   0.9789
 XQO  H111  H  HCH2  0   0.285   1.5675   2.9348   0.8628
 XQO  H112  H  HCH2  0   0.253   0.3224   1.9850   1.6368
 XQO  H151  H  HCH3  0   0.241  -2.3027   4.2905  -1.1987
 XQO  H152  H  HCH3  0   0.235  -2.6417   2.6198  -1.6661
 XQO  H153  H  HCH3  0   0.250  -3.4315   3.3205  -0.2511
 XQO  H3    H  HCH1  0   0.242   2.0821   1.2796  -0.7437
 XQO  H4    H  HCH1  0   0.229   1.9395   0.1088   2.0565
 XQO  H21   H  HOH1  0   0.438   4.2269   0.8090   0.6144
 XQO  H5    H  HCH1  0   0.228   2.4414  -1.9529   1.1410
 XQO  H20   H  HOH1  0   0.457   4.5290  -1.6355   0.5549
 XQO  H6    H  HCH1  0   0.246   2.1424  -0.7337  -1.5942
 XQO  H181  H  HCH2  0   0.212   0.3509  -2.3255  -1.9585
 XQO  H182  H  HCH2  0   0.212   1.9614  -2.9815  -1.6834
 XQO  H19   H  HOH1  0   0.457   0.2438  -4.0758  -0.5030
 XQO  H11C  H  HCH2  0   0.232  -0.1790  -1.4294   1.1255
 XQO  H12C  H  HCH2  0   0.220  -0.6266   0.2379   1.2835
 XQO  H71C  H  HCH2  0   0.209  -2.0190   0.1142  -0.7453
 XQO  H72C  H  HCH2  0   0.217  -1.6146  -1.5785  -0.9490
 XQO  H81C  H  HCH2  0   0.208  -2.6318  -2.1095   1.2604
 XQO  H82C  H  HCH2  0   0.204  -3.0003  -0.4167   1.5141
 XQO  H91C  H  HCH2  0   0.208  -4.4776  -0.4282  -0.4962
 XQO  H92C  H  HCH2  0   0.211  -4.1119  -2.1174  -0.7639
 XQO  H101  H  HCH3  0   0.216  -5.1487  -2.7021   1.4497
 XQO  H102  H  HCH3  0   0.215  -5.4961  -1.0003   1.7364
 XQO  H103  H  HCH3  0   0.226  -6.2996  -1.8533   0.4218

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
 XQO  O13  C12   double  1.225  0.020  1.225
 XQO  C12  N14   single  1.340  0.020  1.340
 XQO  C12  C11   single  1.514  0.020  1.514
 XQO  N14  C15   single  1.443  0.020  1.443
 XQO  C11  C3    single  1.520  0.020  1.520
 XQO  C3   C4    single  1.536  0.020  1.536
 XQO  C3   N2    single  1.462  0.020  1.462
 XQO  C4   O21   single  1.400  0.020  1.400
 XQO  C4   C5    single  1.558  0.020  1.558
 XQO  C5   O20   single  1.410  0.020  1.410
 XQO  C5   C6    single  1.543  0.020  1.543
 XQO  C6   C18   single  1.514  0.020  1.514
 XQO  C6   N2    single  1.463  0.020  1.463
 XQO  C18  O19   single  1.409  0.020  1.409
 XQO  N2   C1    single  1.466  0.020  1.466
 XQO  C1   C7    single  1.522  0.020  1.522
 XQO  C7   C8    single  1.523  0.020  1.523
 XQO  C8   C9    single  1.524  0.020  1.524
 XQO  C9   C10   single  1.522  0.020  1.522
 XQO  N14  H14   single  0.860  0.020  1.020
 XQO  C11  H111  single  0.970  0.020  1.090
 XQO  C11  H112  single  0.970  0.020  1.090
 XQO  C15  H151  single  0.970  0.020  1.090
 XQO  C15  H152  single  0.970  0.020  1.090
 XQO  C15  H153  single  0.970  0.020  1.090
 XQO  C3   H3    single  0.970  0.020  1.090
 XQO  C4   H4    single  0.970  0.020  1.090
 XQO  O21  H21   single  0.850  0.020  0.980
 XQO  C5   H5    single  0.970  0.020  1.090
 XQO  O20  H20   single  0.850  0.020  0.980
 XQO  C6   H6    single  0.970  0.020  1.090
 XQO  C18  H181  single  0.970  0.020  1.090
 XQO  C18  H182  single  0.970  0.020  1.090
 XQO  O19  H19   single  0.850  0.020  0.980
 XQO  C1   H11C  single  0.970  0.020  1.090
 XQO  C1   H12C  single  0.970  0.020  1.090
 XQO  C7   H71C  single  0.970  0.020  1.090
 XQO  C7   H72C  single  0.970  0.020  1.090
 XQO  C8   H81C  single  0.970  0.020  1.090
 XQO  C8   H82C  single  0.970  0.020  1.090
 XQO  C9   H91C  single  0.970  0.020  1.090
 XQO  C9   H92C  single  0.970  0.020  1.090
 XQO  C10  H101  single  0.970  0.020  1.090
 XQO  C10  H102  single  0.970  0.020  1.090
 XQO  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
 XQO  C11   C12  N14   116.01  3.000
 XQO  C11   C12  O13   121.73  3.000
 XQO  N14   C12  O13   122.26  3.000
 XQO  H14   N14  C15   118.14  3.000
 XQO  H14   N14  C12   119.23  3.000
 XQO  C15   N14  C12   122.50  3.000
 XQO  H153  C15  H152  108.36  3.000
 XQO  H153  C15  H151  108.34  3.000
 XQO  H152  C15  H151  108.29  3.000
 XQO  H153  C15  N14   108.50  3.000
 XQO  H152  C15  N14   111.67  3.000
 XQO  H151  C15  N14   111.58  3.000
 XQO  H112  C11  H111  106.18  3.000
 XQO  H112  C11  C3    112.02  3.000
 XQO  H111  C11  C3    107.52  3.000
 XQO  H112  C11  C12   112.09  3.000
 XQO  H111  C11  C12   108.10  3.000
 XQO  C3    C11  C12   110.65  3.000
 XQO  H3    C3   N2    106.03  3.000
 XQO  H3    C3   C4    107.92  3.000
 XQO  N2    C3   C4    104.20  3.000
 XQO  H3    C3   C11   106.56  3.000
 XQO  N2    C3   C11   116.11  3.000
 XQO  C4    C3   C11   115.44  3.000
 XQO  H4    C4   C5    109.39  3.000
 XQO  H4    C4   O21   106.38  3.000
 XQO  C5    C4   O21   114.54  3.000
 XQO  H4    C4   C3    108.64  3.000
 XQO  C5    C4   C3    102.59  3.000
 XQO  O21   C4   C3    115.15  3.000
 XQO  H21   O21  C4    107.69  3.000
 XQO  H5    C5   C6    111.48  3.000
 XQO  H5    C5   O20   110.42  3.000
 XQO  C6    C5   O20   108.86  3.000
 XQO  H5    C5   C4    110.23  3.000
 XQO  C6    C5   C4    103.02  3.000
 XQO  O20   C5   C4    112.64  3.000
 XQO  H20   O20  C5    108.72  3.000
 XQO  H6    C6   N2    105.28  3.000
 XQO  H6    C6   C18   103.91  3.000
 XQO  N2    C6   C18   118.23  3.000
 XQO  H6    C6   C5    105.66  3.000
 XQO  N2    C6   C5    106.31  3.000
 XQO  C18   C6   C5    116.18  3.000
 XQO  H182  C18  H181  106.72  3.000
 XQO  H182  C18  O19   110.72  3.000
 XQO  H181  C18  O19   111.81  3.000
 XQO  H182  C18  C6    106.63  3.000
 XQO  H181  C18  C6    108.28  3.000
 XQO  O19   C18  C6    112.39  3.000
 XQO  H19   O19  C18   108.05  3.000
 XQO  C1    N2   C6    116.33  3.000
 XQO  C1    N2   C3    116.07  3.000
 XQO  C6    N2   C3    100.67  3.000
 XQO  H12C  C1   H11C  105.06  3.000
 XQO  H12C  C1   C7    107.89  3.000
 XQO  H11C  C1   C7    109.59  3.000
 XQO  H12C  C1   N2    109.50  3.000
 XQO  H11C  C1   N2    112.65  3.000
 XQO  C7    C1   N2    111.82  3.000
 XQO  H72C  C7   H71C  106.39  3.000
 XQO  H72C  C7   C8    109.44  3.000
 XQO  H71C  C7   C8    109.60  3.000
 XQO  H72C  C7   C1    110.23  3.000
 XQO  H71C  C7   C1    108.43  3.000
 XQO  C8    C7   C1    112.55  3.000
 XQO  H82C  C8   H81C  106.04  3.000
 XQO  H82C  C8   C9    109.09  3.000
 XQO  H81C  C8   C9    109.38  3.000
 XQO  H82C  C8   C7    109.50  3.000
 XQO  H81C  C8   C7    109.46  3.000
 XQO  C9    C8   C7    113.13  3.000
 XQO  H92C  C9   H91C  106.07  3.000
 XQO  H92C  C9   C10   109.65  3.000
 XQO  H91C  C9   C10   109.46  3.000
 XQO  H92C  C9   C8    109.34  3.000
 XQO  H91C  C9   C8    109.14  3.000
 XQO  C10   C9   C8    112.95  3.000
 XQO  H103  C10  H102  107.59  3.000
 XQO  H103  C10  H101  107.61  3.000
 XQO  H102  C10  H101  107.47  3.000
 XQO  H103  C10  C9    111.59  3.000
 XQO  H102  C10  C9    111.14  3.000
 XQO  H101  C10  C9    111.24  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
 XQO  CONST_01  C15   N14  C12  O13     0.00   0.0  0
 XQO  CONST_02  C11   C12  N14  C15   180.00   0.0  0
 XQO  CONST_03  H14   N14  C12  O13   180.00   0.0  0
 XQO  Var_01    C7    C1   N2   C3    139.21  30.0  3
 XQO  Var_02    C3    C11  C12  O13   -57.90  30.0  3
 XQO  Var_03    C8    C7   C1   N2   -177.72  30.0  3
 XQO  Var_04    C9    C8   C7   C1    176.72  30.0  3
 XQO  Var_05    C10   C9   C8   C7    179.83  30.0  3
 XQO  Var_06    H151  C15  N14  C12   -58.00  30.0  3
 XQO  Var_07    H101  C10  C9   C8    -60.87  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
 XQO  chir_01  C3  C11  C4  N2   negativ
 XQO  chir_02  C4  O21  C5  C3   positiv
 XQO  chir_03  C5  O20  C4  C6   negativ
 XQO  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
 XQO  plan-1  O13  0.020
 XQO  plan-1  C12  0.020
 XQO  plan-1  N14  0.020
 XQO  plan-1  C15  0.020
 XQO  plan-1  C11  0.020
 XQO  plan-1  H14  0.020

