# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 01:59:23 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: (3S,4S,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)piperidin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1CNC(=O)[C@@H](O)[C@H]1O
#
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
 IF7  IF7  (3S,4S,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)piperidin-2-one  ligand  22  11  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_IF7
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
 IF7  O     O  O     0  -0.505  -2.7410  -1.0725   0.1870
 IF7  C2    C  C     0   0.491  -1.5638  -0.7764   0.0076
 IF7  C3    C  CH1   0  -0.059  -1.2222   0.5257  -0.7076
 IF7  O3    O  OH1   0  -0.670  -2.2553   1.4537  -0.5359
 IF7  C4    C  CH1   0  -0.006   0.0860   1.1041  -0.1957
 IF7  O2    O  OH1   0  -0.667  -0.0127   1.4307   1.1688
 IF7  C5    C  CH1   0  -0.346   1.1710   0.0541  -0.3828
 IF7  C6    C  CH2   0  -0.132   2.5464   0.6017  -0.0397
 IF7  O1    O  OH1   0  -0.672   3.5105  -0.3810  -0.3454
 IF7  C1    C  CH2   0  -0.225   0.8568  -1.1959   0.4313
 IF7  N     N  NH1   0  -0.622  -0.5453  -1.5678   0.3513
 IF7  H3    H  HCH1  0   0.246  -1.0909   0.2710  -1.7711
 IF7  H     H  HNH1  0   0.400  -0.8002  -2.4352   0.8022
 IF7  HA    H  HOH1  0   0.449  -3.0632   0.9511  -0.3635
 IF7  H4    H  HCH1  0   0.242   0.3394   1.9897  -0.7974
 IF7  H2    H  HOH1  0   0.451  -0.7851   1.9955   1.2838
 IF7  H5    H  HCH1  0   0.263   1.1698  -0.2075  -1.4471
 IF7  H61C  H  HCH2  0   0.207   2.7150   1.5202  -0.6179
 IF7  H62C  H  HCH2  0   0.204   2.5803   0.8778   1.0208
 IF7  H11C  H  HCH2  0   0.259   1.4526  -2.0347   0.0736
 IF7  H12C  H  HCH2  0   0.237   1.1256  -1.0364   1.4800
 IF7  H1    H  HOH1  0   0.457   4.3615  -0.0813  -0.0136

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
 IF7  O   C2    double  1.227  0.020  1.227
 IF7  C2  C3    single  1.524  0.020  1.524
 IF7  C2  N     single  1.335  0.020  1.335
 IF7  C3  O3    single  1.399  0.020  1.399
 IF7  C3  C4    single  1.519  0.020  1.519
 IF7  C4  O2    single  1.407  0.020  1.407
 IF7  C4  C5    single  1.521  0.020  1.521
 IF7  C5  C6    single  1.520  0.020  1.520
 IF7  C5  C1    single  1.524  0.020  1.524
 IF7  C6  O1    single  1.410  0.020  1.410
 IF7  C1  N     single  1.453  0.020  1.453
 IF7  C3  H3    single  0.970  0.020  1.090
 IF7  N   H     single  0.860  0.020  1.020
 IF7  O3  HA    single  0.850  0.020  0.980
 IF7  C4  H4    single  0.970  0.020  1.090
 IF7  O2  H2    single  0.850  0.020  0.980
 IF7  C5  H5    single  0.970  0.020  1.090
 IF7  C6  H61C  single  0.970  0.020  1.090
 IF7  C6  H62C  single  0.970  0.020  1.090
 IF7  C1  H11C  single  0.970  0.020  1.090
 IF7  C1  H12C  single  0.970  0.020  1.090
 IF7  O1  H1    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
 IF7  N     C2  C3    117.15  3.000
 IF7  N     C2  O     123.46  3.000
 IF7  C3    C2  O     119.32  3.000
 IF7  H3    C3  C4    108.10  3.000
 IF7  H3    C3  O3    111.09  3.000
 IF7  C4    C3  O3    109.99  3.000
 IF7  H3    C3  C2    106.40  3.000
 IF7  C4    C3  C2    111.10  3.000
 IF7  O3    C3  C2    110.09  3.000
 IF7  HA    O3  C3    107.10  3.000
 IF7  H4    C4  C5    108.91  3.000
 IF7  H4    C4  O2    111.09  3.000
 IF7  C5    C4  O2    109.25  3.000
 IF7  H4    C4  C3    108.69  3.000
 IF7  C5    C4  C3    108.06  3.000
 IF7  O2    C4  C3    110.78  3.000
 IF7  H2    O2  C4    107.94  3.000
 IF7  H5    C5  C1    108.82  3.000
 IF7  H5    C5  C6    107.83  3.000
 IF7  C1    C5  C6    111.19  3.000
 IF7  H5    C5  C4    106.46  3.000
 IF7  C1    C5  C4    110.69  3.000
 IF7  C6    C5  C4    111.65  3.000
 IF7  H62C  C6  H61C  107.09  3.000
 IF7  H62C  C6  O1    111.34  3.000
 IF7  H61C  C6  O1    111.33  3.000
 IF7  H62C  C6  C5    109.70  3.000
 IF7  H61C  C6  C5    108.75  3.000
 IF7  O1    C6  C5    108.58  3.000
 IF7  H1    O1  C6    108.25  3.000
 IF7  H12C  C1  H11C  107.01  3.000
 IF7  H12C  C1  N     109.09  3.000
 IF7  H11C  C1  N     108.22  3.000
 IF7  H12C  C1  C5    109.97  3.000
 IF7  H11C  C1  C5    110.08  3.000
 IF7  N     C1  C5    112.30  3.000
 IF7  H     N   C1    116.02  3.000
 IF7  H     N   C2    115.56  3.000
 IF7  C1    N   C2    126.78  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
 IF7  CONST_02  C1  N   C2  O   180.00   0.0  0
 IF7  CONST_03  H   N   C2  C3  180.00   0.0  0
 IF7  Var_01    C5  C1  N   C2  -20.61  30.0  1

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
 IF7  chir_01  C3  C2  O3  C4  negativ
 IF7  chir_02  C4  O2  C3  C5  positiv
 IF7  chir_03  C5  C4  C6  C1  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
 IF7  plan-1  O   0.020
 IF7  plan-1  C2  0.020
 IF7  plan-1  C3  0.020
 IF7  plan-1  C1  0.020
 IF7  plan-1  N   0.020
 IF7  plan-1  H   0.020

