# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 01:24:39 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: (1S,2R,3S,4R,5R)-2,3,4-trihydroxy-N-octyl-6-oxa-8-azabicyclo[3.2.1]octane-8-carbothioamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCNC(=S)N1[C@H]2CO[C@@H]1[C@H](O)[C@@H](O)[C@@H]2O
#
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
 NCW  NCW  (1S,2R,3S,4R,5R)-2,3,4-trihydroxy-N-octyl-6-oxa-8-azabicyclo[3.2.1]octane-8-carbothioamide  ligand  50  22  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_NCW
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
 NCW  S1    S  S1    0  -0.423    1.2612  -2.7374   0.5135
 NCW  C7    C  C     0   0.420    1.1788  -1.2562  -0.2851
 NCW  N1    N  NR5   0  -0.461    2.2932  -0.6366  -0.7271
 NCW  C5    C  CR15  0  -0.223    3.6557  -1.0168  -0.4105
 NCW  C4    C  CH1   0   0.069    4.0273  -0.3246   0.9021
 NCW  O4    O  OH1   0  -0.666    5.3263  -0.7216   1.2563
 NCW  C3    C  CH1   0  -0.037    3.9202   1.1969   0.7515
 NCW  O3    O  OH1   0  -0.678    3.9850   1.7655   2.0440
 NCW  C2    C  CH1   0   0.052    2.6392   1.6207   0.0183
 NCW  O2    O  OH1   0  -0.667    2.6973   2.9548  -0.4172
 NCW  C6    C  CH2   0  -0.162    4.3702  -0.4412  -1.6274
 NCW  O1    O  O     0  -0.495    3.5749   0.6808  -2.0176
 NCW  C1    C  CR15  0   0.100    2.4322   0.7255  -1.2053
 NCW  N2    N  NH1   0  -0.636    0.0162  -0.6402  -0.5164
 NCW  C8    C  CH2   0  -0.225   -1.2855  -1.1898  -0.1915
 NCW  C9    C  CH2   0  -0.470   -2.3510  -0.1079  -0.2624
 NCW  C10   C  CH2   0  -0.417   -3.7380  -0.6702   0.0198
 NCW  C11   C  CH2   0  -0.412   -4.8320   0.3892  -0.0171
 NCW  C12   C  CH2   0  -0.412   -6.2237  -0.1892   0.2072
 NCW  C13   C  CH2   0  -0.406   -7.3272   0.8606   0.1800
 NCW  C14   C  CH2   0  -0.419   -8.7195   0.2734   0.3791
 NCW  C15   C  CH3   0  -0.662   -9.8170   1.3282   0.3538
 NCW  H2    H  HNH1  0   0.408    0.0038   0.1855  -1.0962
 NCW  H5    H  HCR5  0   0.296    3.7587  -2.0969  -0.3290
 NCW  H1    H  HCR5  0   0.283    1.5854   1.0636  -1.8084
 NCW  H4    H  HCH1  0   0.224    3.2962  -0.6570   1.6547
 NCW  H6C1  H  HCH2  0   0.247    5.3922  -0.1242  -1.4113
 NCW  H6C2  H  HCH2  0   0.250    4.3996  -1.1693  -2.4413
 NCW  HA    H  HOH1  0   0.453    5.5784  -0.2495   2.0573
 NCW  H3    H  HCH1  0   0.238    4.7737   1.5385   0.1513
 NCW  HB    H  HOH1  0   0.461    4.4879   2.5835   2.0047
 NCW  HC    H  HCH1  0   0.224    1.7794   1.4631   0.6859
 NCW  HD    H  HOH1  0   0.457    2.5906   3.5334   0.3438
 NCW  H8C1  H  HCH2  0   0.233   -1.5319  -2.0095  -0.8738
 NCW  H8C2  H  HCH2  0   0.242   -1.2450  -1.6151   0.8112
 NCW  H9C1  H  HCH2  0   0.232   -2.1161   0.6815   0.4575
 NCW  H9C2  H  HCH2  0   0.228   -2.3449   0.3569  -1.2543
 NCW  H101  H  HCH2  0   0.216   -3.9657  -1.4515  -0.7127
 NCW  H102  H  HCH2  0   0.216   -3.7410  -1.1606   0.9991
 NCW  H111  H  HCH2  0   0.210   -4.6276   1.1516   0.7421
 NCW  H112  H  HCH2  0   0.209   -4.8062   0.9068  -0.9825
 NCW  H121  H  HCH2  0   0.207   -6.4250  -0.9467  -0.5581
 NCW  H122  H  HCH2  0   0.207   -6.2472  -0.7164   1.1676
 NCW  H131  H  HCH2  0   0.206   -7.1366   1.6103   0.9558
 NCW  H132  H  HCH2  0   0.206   -7.2951   1.3987  -0.7743
 NCW  H141  H  HCH2  0   0.210   -8.9093  -0.4733  -0.3982
 NCW  H142  H  HCH2  0   0.210   -8.7509  -0.2670   1.3305
 NCW  H151  H  HCH3  0   0.216   -9.6771   2.0615   1.1498
 NCW  H152  H  HCH3  0   0.215   -9.8212   1.8691  -0.5945
 NCW  H153  H  HCH3  0   0.225  -10.8047   0.8844   0.4834

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
 NCW  S1   C7    double  1.685  0.020  1.685
 NCW  C7   N1    single  1.350  0.020  1.350
 NCW  C7   N2    single  1.336  0.020  1.336
 NCW  N1   C5    single  1.450  0.020  1.450
 NCW  N1   C1    single  1.450  0.020  1.450
 NCW  C5   C4    single  1.530  0.020  1.530
 NCW  C5   C6    single  1.524  0.020  1.524
 NCW  C4   O4    single  1.404  0.020  1.404
 NCW  C4   C3    single  1.533  0.020  1.533
 NCW  C3   O3    single  1.414  0.020  1.414
 NCW  C3   C2    single  1.536  0.020  1.536
 NCW  C2   O2    single  1.405  0.020  1.405
 NCW  C2   C1    single  1.530  0.020  1.530
 NCW  C6   O1    single  1.430  0.020  1.430
 NCW  O1   C1    single  1.403  0.020  1.403
 NCW  N2   C8    single  1.450  0.020  1.450
 NCW  C8   C9    single  1.520  0.020  1.520
 NCW  C9   C10   single  1.523  0.020  1.523
 NCW  C10  C11   single  1.523  0.020  1.523
 NCW  C11  C12   single  1.524  0.020  1.524
 NCW  C12  C13   single  1.523  0.020  1.523
 NCW  C13  C14   single  1.524  0.020  1.524
 NCW  C14  C15   single  1.522  0.020  1.522
 NCW  N2   H2    single  0.860  0.020  1.020
 NCW  C5   H5    single  0.970  0.020  1.090
 NCW  C1   H1    single  0.970  0.020  1.090
 NCW  C4   H4    single  0.970  0.020  1.090
 NCW  C6   H6C1  single  0.970  0.020  1.090
 NCW  C6   H6C2  single  0.970  0.020  1.090
 NCW  O4   HA    single  0.850  0.020  0.980
 NCW  C3   H3    single  0.970  0.020  1.090
 NCW  O3   HB    single  0.850  0.020  0.980
 NCW  C2   HC    single  0.970  0.020  1.090
 NCW  O2   HD    single  0.850  0.020  0.980
 NCW  C8   H8C1  single  0.970  0.020  1.090
 NCW  C8   H8C2  single  0.970  0.020  1.090
 NCW  C9   H9C1  single  0.970  0.020  1.090
 NCW  C9   H9C2  single  0.970  0.020  1.090
 NCW  C10  H101  single  0.970  0.020  1.090
 NCW  C10  H102  single  0.970  0.020  1.090
 NCW  C11  H111  single  0.970  0.020  1.090
 NCW  C11  H112  single  0.970  0.020  1.090
 NCW  C12  H121  single  0.970  0.020  1.090
 NCW  C12  H122  single  0.970  0.020  1.090
 NCW  C13  H131  single  0.970  0.020  1.090
 NCW  C13  H132  single  0.970  0.020  1.090
 NCW  C14  H141  single  0.970  0.020  1.090
 NCW  C14  H142  single  0.970  0.020  1.090
 NCW  C15  H151  single  0.970  0.020  1.090
 NCW  C15  H152  single  0.970  0.020  1.090
 NCW  C15  H153  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
 NCW  N2    C7   N1    116.76  3.000
 NCW  N2    C7   S1    122.01  3.000
 NCW  N1    C7   S1    121.23  3.000
 NCW  C1    N1   C5    103.20  3.000
 NCW  C1    N1   C7    128.19  3.000
 NCW  C5    N1   C7    125.75  3.000
 NCW  H5    C5   C6    112.98  3.000
 NCW  H5    C5   C4    111.22  3.000
 NCW  C6    C5   C4    113.60  3.000
 NCW  H5    C5   N1    111.45  3.000
 NCW  C6    C5   N1     99.63  3.000
 NCW  C4    C5   N1    107.27  3.000
 NCW  H4    C4   C3    108.70  3.000
 NCW  H4    C4   O4    110.90  3.000
 NCW  C3    C4   O4    111.73  3.000
 NCW  H4    C4   C5    106.78  3.000
 NCW  C3    C4   C5    110.36  3.000
 NCW  O4    C4   C5    108.26  3.000
 NCW  HA    O4   C4    108.26  3.000
 NCW  H3    C3   C2    107.55  3.000
 NCW  H3    C3   O3    109.82  3.000
 NCW  C2    C3   O3    111.33  3.000
 NCW  H3    C3   C4    107.96  3.000
 NCW  C2    C3   C4    112.28  3.000
 NCW  O3    C3   C4    107.84  3.000
 NCW  HB    O3   C3    109.21  3.000
 NCW  HC    C2   C1    107.20  3.000
 NCW  HC    C2   O2    110.90  3.000
 NCW  C1    C2   O2    108.26  3.000
 NCW  HC    C2   C3    108.83  3.000
 NCW  C1    C2   C3    109.46  3.000
 NCW  O2    C2   C3    112.06  3.000
 NCW  HD    O2   C2    108.75  3.000
 NCW  H6C2  C6   H6C1  108.41  3.000
 NCW  H6C2  C6   O1    109.56  3.000
 NCW  H6C1  C6   O1    110.30  3.000
 NCW  H6C2  C6   C5    110.84  3.000
 NCW  H6C1  C6   C5    112.99  3.000
 NCW  O1    C6   C5    104.69  3.000
 NCW  C1    O1   C6    108.67  3.000
 NCW  H1    C1   O1    108.75  3.000
 NCW  H1    C1   C2    111.41  3.000
 NCW  O1    C1   C2    111.81  3.000
 NCW  H1    C1   N1    113.46  3.000
 NCW  O1    C1   N1    103.83  3.000
 NCW  C2    C1   N1    107.38  3.000
 NCW  H2    N2   C8    115.33  3.000
 NCW  H2    N2   C7    119.18  3.000
 NCW  C8    N2   C7    124.60  3.000
 NCW  H8C2  C8   H8C1  106.83  3.000
 NCW  H8C2  C8   C9    110.28  3.000
 NCW  H8C1  C8   C9    110.25  3.000
 NCW  H8C2  C8   N2    108.70  3.000
 NCW  H8C1  C8   N2    110.27  3.000
 NCW  C9    C8   N2    110.43  3.000
 NCW  H9C2  C9   H9C1  106.77  3.000
 NCW  H9C2  C9   C10   109.24  3.000
 NCW  H9C1  C9   C10   109.88  3.000
 NCW  H9C2  C9   C8    109.90  3.000
 NCW  H9C1  C9   C8    109.42  3.000
 NCW  C10   C9   C8    111.53  3.000
 NCW  H102  C10  H101  106.15  3.000
 NCW  H102  C10  C11   109.34  3.000
 NCW  H101  C10  C11   109.31  3.000
 NCW  H102  C10  C9    109.48  3.000
 NCW  H101  C10  C9    109.20  3.000
 NCW  C11   C10  C9    113.13  3.000
 NCW  H112  C11  H111  106.11  3.000
 NCW  H112  C11  C12   109.30  3.000
 NCW  H111  C11  C12   109.43  3.000
 NCW  H112  C11  C10   109.45  3.000
 NCW  H111  C11  C10   109.47  3.000
 NCW  C12   C11  C10   112.86  3.000
 NCW  H122  C12  H121  106.00  3.000
 NCW  H122  C12  C13   109.37  3.000
 NCW  H121  C12  C13   109.33  3.000
 NCW  H122  C12  C11   109.34  3.000
 NCW  H121  C12  C11   109.11  3.000
 NCW  C13   C12  C11   113.42  3.000
 NCW  H132  C13  H131  106.00  3.000
 NCW  H132  C13  C14   109.25  3.000
 NCW  H131  C13  C14   109.27  3.000
 NCW  H132  C13  C12   109.43  3.000
 NCW  H131  C13  C12   109.45  3.000
 NCW  C14   C13  C12   113.20  3.000
 NCW  H142  C14  H141  105.99  3.000
 NCW  H142  C14  C15   109.63  3.000
 NCW  H141  C14  C15   109.63  3.000
 NCW  H142  C14  C13   109.27  3.000
 NCW  H141  C14  C13   109.17  3.000
 NCW  C15   C14  C13   112.92  3.000
 NCW  H153  C15  H152  107.55  3.000
 NCW  H153  C15  H151  107.63  3.000
 NCW  H152  C15  H151  107.53  3.000
 NCW  H153  C15  C14   111.65  3.000
 NCW  H152  C15  C14   111.13  3.000
 NCW  H151  C15  C14   111.16  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
 NCW  CONST_01  C5    N1   C7   S1      0.00   0.0  0
 NCW  CONST_02  C1    N1   C7   S1    180.00   0.0  0
 NCW  CONST_03  N2    C7   N1   C5    180.00   0.0  0
 NCW  CONST_04  N2    C7   N1   C1      0.00   0.0  0
 NCW  CONST_05  C8    N2   C7   N1    180.00   0.0  0
 NCW  CONST_06  H2    N2   C7   N1      0.00   0.0  0
 NCW  CONST_07  C8    N2   C7   S1      0.00   0.0  0
 NCW  Var_01    H6C1  C6   O1   C1   -126.44  30.0  3
 NCW  Var_02    C9    C8   N2   C7    165.87  30.0  3
 NCW  Var_03    C10   C9   C8   N2    177.70  30.0  3
 NCW  Var_04    C11   C10  C9   C8    178.96  30.0  3
 NCW  Var_05    C12   C11  C10  C9    177.56  30.0  3
 NCW  Var_06    C13   C12  C11  C10   179.70  30.0  3
 NCW  Var_07    C14   C13  C12  C11   178.93  30.0  3
 NCW  Var_08    C15   C14  C13  C12   179.88  30.0  3
 NCW  Var_09    H151  C15  C14  C13   -60.63  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
 NCW  chir_01  C5  N1  C4  C6  positiv
 NCW  chir_02  C4  O4  C5  C3  positiv
 NCW  chir_03  C3  O3  C4  C2  negativ
 NCW  chir_04  C2  O2  C3  C1  positiv
 NCW  chir_05  C1  O1  N1  C2  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
 NCW  plan-1  S1  0.020
 NCW  plan-1  C7  0.020
 NCW  plan-1  N1  0.020
 NCW  plan-1  C5  0.020
 NCW  plan-1  C1  0.020
 NCW  plan-1  N2  0.020
 NCW  plan-1  C8  0.020
 NCW  plan-1  H2  0.020

