# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 23:45:13 2021
#   Inital geometry file: a 110 line input string
#   Ligand name: N-[(3S,4R,5S,6R)-4,5-dihydroxy-6-({[(2S,3S,4S,5R)-2,3,4-trihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]methoxy}methyl)tetrahydro-2H-pyran-3-yl]acetamide (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@H]1CO[C@H](COC[C@]2(O)O[C@H](CO)[C@@H](O)[C@@H]2O)[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
 NZY  NZY  'N-[(3S,4R,5S,6R)-4,5-dihydroxy-6-({[(2S,3S,4S,5R)-2,3,4-trihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]methoxy}methyl)tetrahydro-2H-pyran-3-yl]acetamide (non-preferred name)'  ligand  50  25  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NZY
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
 NZY  C13   C  CH2   0  -0.206  40.9382  -72.2126  -62.8369
 NZY  C23   C  CT    0   0.470  40.7231  -73.7174  -63.0471
 NZY  C33   C  CH1   0  -0.046  39.5422  -74.3209  -62.2775
 NZY  C43   C  CH1   0  -0.021  38.3630  -74.0809  -63.2136
 NZY  C53   C  CH1   0   0.012  39.0207  -74.2753  -64.5771
 NZY  C63   C  CH2   0  -0.169  38.4489  -73.4252  -65.6973
 NZY  O23   O  OH1   0  -0.673  41.9121  -74.3997  -62.8166
 NZY  O33   O  OH1   0  -0.657  39.4276  -73.7598  -61.0020
 NZY  O43   O  OH1   0  -0.665  37.2956  -74.9752  -63.0375
 NZY  O53   O  O2    0  -0.516  40.3842  -73.9103  -64.4023
 NZY  O63   O  OH1   0  -0.669  37.1070  -73.7992  -65.8902
 NZY  C114  C  CH2   0  -0.172  43.0193  -70.2213  -58.0617
 NZY  C214  C  CH1   0  -0.146  43.6789  -71.5044  -57.5604
 NZY  C314  C  CH1   0   0.025  44.6368  -72.0363  -58.6295
 NZY  C414  C  CH1   0   0.033  43.8785  -72.1928  -59.9419
 NZY  C513  C  CH1   0  -0.010  43.2401  -70.8520  -60.3134
 NZY  C614  C  CH2   0  -0.170  42.4747  -70.8935  -61.6188
 NZY  C811  C  CH3   0  -0.810  43.2776  -73.1390  -55.1579
 NZY  O313  O  OH1   0  -0.668  45.1687  -73.2915  -58.2801
 NZY  O413  O  OH1   0  -0.675  44.7187  -72.5831  -60.9991
 NZY  O513  O  O2    0  -0.486  42.3628  -70.4444  -59.2851
 NZY  O613  O  O2    0  -0.490  41.6172  -72.0077  -61.6262
 NZY  O711  O  O     0  -0.496  44.9479  -71.7260  -54.1936
 NZY  H1    H  HCH2  0   0.232  41.5354  -71.8516  -63.6854
 NZY  H2    H  HCH2  0   0.222  39.9863  -71.6676  -62.8606
 NZY  H3    H  HCH1  0   0.232  39.7093  -75.4084  -62.2237
 NZY  H4    H  HCH1  0   0.224  38.0241  -73.0404  -63.1050
 NZY  H5    H  HCH1  0   0.229  38.9574  -75.3359  -64.8574
 NZY  H6    H  HCH2  0   0.192  38.5448  -72.3656  -65.4220
 NZY  H7    H  HCH2  0   0.214  39.0488  -73.5787  -66.6040
 NZY  H8    H  HOH1  0   0.451  42.4748  -73.8543  -62.2518
 NZY  H9    H  HOH1  0   0.455  38.7450  -74.2380  -60.5212
 NZY  H10   H  HOH1  0   0.458  36.6818  -74.6000  -62.4007
 NZY  H11   H  HOH1  0   0.459  36.7570  -73.2874  -66.6244
 NZY  H12   H  HCH2  0   0.210  43.7776  -69.4305  -58.1665
 NZY  H13   H  HCH2  0   0.256  42.2722  -69.8751  -57.3464
 NZY  H14   H  HCH1  0   0.275  42.8970  -72.2481  -57.4015
 NZY  H15   H  HCH1  0   0.218  45.4402  -71.2977  -58.7769
 NZY  H16   H  HCH1  0   0.219  43.0767  -72.9286  -59.7819
 NZY  H17   H  HCH1  0   0.229  44.0396  -70.1033  -60.4406
 NZY  H18   H  HCH2  0   0.222  43.1861  -70.9435  -62.4513
 NZY  H19   H  HCH2  0   0.230  41.9145  -69.9558  -61.7321
 NZY  H20   H  HCH3  0   0.270  43.3020  -73.6249  -54.1862
 NZY  H21   H  HCH3  0   0.268  42.2604  -72.7919  -55.3449
 NZY  H22   H  HCH3  0   0.263  43.5154  -73.8780  -55.9236
 NZY  H24   H  HOH1  0   0.459  45.8899  -73.1604  -57.6575
 NZY  H25   H  HOH1  0   0.455  45.1404  -73.4135  -60.7542
 NZY  N211  N  NH1   0  -0.622  44.3583  -71.2732  -56.3088
 NZY  C711  C  C     0   0.494  44.2639  -71.9972  -55.1704
 NZY  H23   H  HNH1  0   0.390  45.0482  -70.5337  -56.2953

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
 NZY  O23   C23   single  1.390  0.020  1.390
 NZY  O53   C53   single  1.422  0.020  1.422
 NZY  O53   C23   single  1.410  0.020  1.410
 NZY  C53   C63   single  1.518  0.020  1.518
 NZY  C53   C43   single  1.526  0.020  1.526
 NZY  C63   O63   single  1.406  0.020  1.406
 NZY  C23   C13   single  1.535  0.020  1.535
 NZY  C23   C33   single  1.533  0.020  1.533
 NZY  C13   O613  single  1.403  0.020  1.403
 NZY  C33   C43   single  1.525  0.020  1.525
 NZY  C33   O33   single  1.398  0.020  1.398
 NZY  C43   O43   single  1.404  0.020  1.404
 NZY  O613  C614  single  1.406  0.020  1.406
 NZY  C614  C513  single  1.514  0.020  1.514
 NZY  O413  C414  single  1.406  0.020  1.406
 NZY  C513  C414  single  1.531  0.020  1.531
 NZY  C513  O513  single  1.412  0.020  1.412
 NZY  C414  C314  single  1.524  0.020  1.524
 NZY  O513  C114  single  1.406  0.020  1.406
 NZY  C314  O313  single  1.407  0.020  1.407
 NZY  C314  C214  single  1.531  0.020  1.531
 NZY  C114  C214  single  1.527  0.020  1.527
 NZY  C214  N211  single  1.443  0.020  1.443
 NZY  N211  C711  single  1.352  0.020  1.352
 NZY  C811  C711  single  1.509  0.020  1.509
 NZY  C711  O711  double  1.223  0.020  1.223
 NZY  C13   H1    single  0.970  0.020  1.090
 NZY  C13   H2    single  0.970  0.020  1.090
 NZY  C33   H3    single  0.970  0.020  1.090
 NZY  C43   H4    single  0.970  0.020  1.090
 NZY  C53   H5    single  0.970  0.020  1.090
 NZY  C63   H6    single  0.970  0.020  1.090
 NZY  C63   H7    single  0.970  0.020  1.090
 NZY  O23   H8    single  0.850  0.020  0.980
 NZY  O33   H9    single  0.850  0.020  0.980
 NZY  O43   H10   single  0.850  0.020  0.980
 NZY  O63   H11   single  0.850  0.020  0.980
 NZY  C114  H12   single  0.970  0.020  1.090
 NZY  C114  H13   single  0.970  0.020  1.090
 NZY  C214  H14   single  0.970  0.020  1.090
 NZY  C314  H15   single  0.970  0.020  1.090
 NZY  C414  H16   single  0.970  0.020  1.090
 NZY  C513  H17   single  0.970  0.020  1.090
 NZY  C614  H18   single  0.970  0.020  1.090
 NZY  C614  H19   single  0.970  0.020  1.090
 NZY  C811  H20   single  0.970  0.020  1.090
 NZY  C811  H21   single  0.970  0.020  1.090
 NZY  C811  H22   single  0.970  0.020  1.090
 NZY  N211  H23   single  0.860  0.020  1.020
 NZY  O313  H24   single  0.850  0.020  0.980
 NZY  O413  H25   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
 NZY  H2    C13   H1    106.96  3.000
 NZY  H2    C13   O613  111.47  3.000
 NZY  H1    C13   O613  110.82  3.000
 NZY  H2    C13   C23   111.26  3.000
 NZY  H1    C13   C23   107.01  3.000
 NZY  O613  C13   C23   109.23  3.000
 NZY  O53   C23   O23   107.32  3.000
 NZY  O53   C23   C33   104.09  3.000
 NZY  O23   C23   C33   112.48  3.000
 NZY  C33   C23   C13   115.16  3.000
 NZY  O53   C23   C13   107.43  3.000
 NZY  O23   C23   C13   109.80  3.000
 NZY  H3    C33   O33   111.35  3.000
 NZY  H3    C33   C43   107.63  3.000
 NZY  O33   C33   C43   115.69  3.000
 NZY  H3    C33   C23   107.23  3.000
 NZY  O33   C33   C23   111.29  3.000
 NZY  C43   C33   C23   103.04  3.000
 NZY  H4    C43   O43   110.86  3.000
 NZY  H4    C43   C53   109.97  3.000
 NZY  O43   C43   C53   111.02  3.000
 NZY  H4    C43   C33   109.07  3.000
 NZY  O43   C43   C33   114.26  3.000
 NZY  C53   C43   C33   101.25  3.000
 NZY  H5    C53   O53   109.53  3.000
 NZY  H5    C53   C63   109.30  3.000
 NZY  O53   C53   C63   107.94  3.000
 NZY  H5    C53   C43   109.02  3.000
 NZY  C63   C53   C43   115.19  3.000
 NZY  O53   C53   C43   105.70  3.000
 NZY  H7    C63   H6    107.09  3.000
 NZY  H7    C63   O63   111.78  3.000
 NZY  H6    C63   O63   111.97  3.000
 NZY  H7    C63   C53   108.98  3.000
 NZY  H6    C63   C53   108.79  3.000
 NZY  O63   C63   C53   108.16  3.000
 NZY  H8    O23   C23   108.55  3.000
 NZY  H9    O33   C33   108.33  3.000
 NZY  H10   O43   C43   108.67  3.000
 NZY  C53   O53   C23   112.56  3.000
 NZY  H11   O63   C63   108.10  3.000
 NZY  H13   C114  H12   107.83  3.000
 NZY  H13   C114  O513  107.53  3.000
 NZY  H12   C114  O513  110.66  3.000
 NZY  H13   C114  C214  110.32  3.000
 NZY  H12   C114  C214  109.71  3.000
 NZY  O513  C114  C214  110.72  3.000
 NZY  H14   C214  N211  108.69  3.000
 NZY  H14   C214  C314  108.26  3.000
 NZY  N211  C214  C314  111.52  3.000
 NZY  H14   C214  C114  108.12  3.000
 NZY  N211  C214  C114  110.70  3.000
 NZY  C314  C214  C114  109.45  3.000
 NZY  H15   C314  O313  110.83  3.000
 NZY  H15   C314  C414  108.46  3.000
 NZY  O313  C314  C414  108.08  3.000
 NZY  H15   C314  C214  108.48  3.000
 NZY  O313  C314  C214  111.90  3.000
 NZY  C414  C314  C214  109.01  3.000
 NZY  H16   C414  O413  111.06  3.000
 NZY  H16   C414  C513  108.49  3.000
 NZY  O413  C414  C513  108.06  3.000
 NZY  H16   C414  C314  107.83  3.000
 NZY  C513  C414  C314  109.06  3.000
 NZY  O413  C414  C314  112.26  3.000
 NZY  H17   C513  O513  109.79  3.000
 NZY  H17   C513  C614  106.61  3.000
 NZY  O513  C513  C614  108.77  3.000
 NZY  H17   C513  C414  108.68  3.000
 NZY  O513  C513  C414  109.59  3.000
 NZY  C614  C513  C414  113.34  3.000
 NZY  H19   C614  H18   106.96  3.000
 NZY  H19   C614  O613  111.41  3.000
 NZY  H18   C614  O613  110.84  3.000
 NZY  H19   C614  C513  108.87  3.000
 NZY  H18   C614  C513  109.14  3.000
 NZY  O613  C614  C513  109.55  3.000
 NZY  H22   C811  H21   107.37  3.000
 NZY  H22   C811  H20   108.66  3.000
 NZY  H21   C811  H20   108.44  3.000
 NZY  H22   C811  C711  111.38  3.000
 NZY  H21   C811  C711  111.55  3.000
 NZY  H20   C811  C711  109.34  3.000
 NZY  H24   O313  C314  108.82  3.000
 NZY  H25   O413  C414  108.06  3.000
 NZY  C513  O513  C114  112.92  3.000
 NZY  C614  O613  C13   114.55  3.000
 NZY  H23   N211  C711  115.33  3.000
 NZY  H23   N211  C214  116.74  3.000
 NZY  C711  N211  C214  127.70  3.000
 NZY  O711  C711  N211  120.97  3.000
 NZY  O711  C711  C811  121.80  3.000
 NZY  N211  C711  C811  117.24  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
 NZY  CONST_01  C811  C711  N211  C214     0.00   0.0  0
 NZY  CONST_02  O711  C711  N211  C214   180.00   0.0  0
 NZY  CONST_03  H23   N211  C711  C811   180.00   0.0  0
 NZY  Var_01    H12   C114  O513  C513    60.27  30.0  1
 NZY  Var_02    C513  C614  O613  C13   -174.84  30.0  3
 NZY  Var_03    H1    C13   O613  C614    30.12  30.0  1
 NZY  Var_04    H20   C811  C711  N211  -179.61  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
 NZY  chir_01  C23   O53   C13   C33   negativ
 NZY  chir_02  C33   O33   C23   C43   positiv
 NZY  chir_03  C43   O43   C33   C53   negativ
 NZY  chir_04  C53   O53   C43   C63   negativ
 NZY  chir_05  C214  C314  C114  N211  positiv
 NZY  chir_06  C314  O313  C214  C414  positiv
 NZY  chir_07  C414  O413  C314  C513  negativ
 NZY  chir_08  C513  O513  C414  C614  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
 NZY  plan-1  C214  0.020
 NZY  plan-1  C811  0.020
 NZY  plan-1  O711  0.020
 NZY  plan-1  N211  0.020
 NZY  plan-1  C711  0.020
 NZY  plan-1  H23   0.020

