# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 04:02:10 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: (1r,2R,5S)-2,5-dihydroxycyclopent-3-en-1-yl 2-hydroxy-7-methoxy-5-methylnaphthalene-1-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(C)c2ccc(O)c(C(=O)O[C@H]3[C@H](O)C=C[C@@H]3O)c2c1
#
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
 NCZ  NCZ  '(1r,2R,5S)-2,5-dihydroxycyclopent-3-en-1-yl 2-hydroxy-7-methoxy-5-methylnaphthalene-1-carboxylate'  ligand  42  24  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NCZ
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
 NCZ  C1    C  CR16  0  -0.505   1.2370   0.7772   0.2534
 NCZ  C6    C  CR66  0   0.218   1.4017  -0.6216   0.1967
 NCZ  C5    C  CR66  0   0.012   2.6698  -1.1501  -0.1754
 NCZ  C7    C  CR16  0  -0.304   2.8403  -2.5524  -0.2029
 NCZ  C8    C  CR16  0  -0.390   1.8298  -3.4047   0.1313
 NCZ  C9    C  CR6   0   0.359   0.5729  -2.8897   0.5129
 NCZ  C10   C  CR6   0  -0.221   0.3543  -1.5291   0.5326
 NCZ  C11   C  C     0   0.520  -0.9923  -1.0421   0.9344
 NCZ  O3    O  O     0  -0.424  -1.5041  -1.2565   2.0018
 NCZ  O4    O  O2    0  -0.462  -1.5581  -0.3434  -0.0459
 NCZ  C12   C  CR15  0  -0.014  -2.7757   0.3563   0.1821
 NCZ  C13   C  CR15  0   0.012  -2.6700   1.7972  -0.3116
 NCZ  C14   C  CR15  0  -0.261  -4.1105   2.1021  -0.6266
 NCZ  C15   C  CR15  0  -0.265  -4.8177   0.9868  -0.7717
 NCZ  C16   C  CR15  0   0.004  -3.9654  -0.2398  -0.5671
 NCZ  O6    O  OH1   0  -0.663  -4.5559  -1.2613   0.1954
 NCZ  O5    O  OH1   0  -0.665  -2.0803   2.5998   0.6812
 NCZ  O2    O  OH1   0  -0.614  -0.4433  -3.7067   0.8275
 NCZ  C4    C  CR6   0   0.119   3.7337  -0.2656  -0.4998
 NCZ  C3    C  CR16  0  -0.463   3.5327   1.0902  -0.4420
 NCZ  C2    C  CR6   0   0.436   2.2803   1.6172  -0.0597
 NCZ  O1    O  O2    0  -0.471   2.0334   2.9368   0.0237
 NCZ  C17   C  CH3   0  -0.439   3.0686   3.8543  -0.2728
 NCZ  C18   C  CH3   0  -0.755   5.0772  -0.7997  -0.9009
 NCZ  H1    H  HCR6  0   0.251   0.2982   1.2250   0.5514
 NCZ  H7    H  HCR6  0   0.268   3.7942  -2.9699  -0.4953
 NCZ  H8    H  HCR6  0   0.280   1.9857  -4.4765   0.1013
 NCZ  H12   H  HCR5  0   0.268  -3.0180   0.3746   1.2485
 NCZ  H13   H  HCR5  0   0.241  -2.0750   1.8278  -1.2349
 NCZ  H14   H  HCR5  0   0.265  -4.4781   3.1111  -0.7650
 NCZ  H15   H  HCR5  0   0.265  -5.8626   0.9293  -1.0501
 NCZ  H16   H  HCR5  0   0.238  -3.6324  -0.6258  -1.5414
 NCZ  H6    H  HOH1  0   0.458  -5.1430  -1.7669  -0.3747
 NCZ  H5    H  HOH1  0   0.459  -1.7227   3.3903   0.2668
 NCZ  H2    H  HOH1  0   0.484  -0.1755  -4.6289   0.7423
 NCZ  H3    H  HCR6  0   0.276   4.3566   1.7477  -0.6860
 NCZ  H171  H  HCH3  0   0.230   3.9248   3.7367   0.3960
 NCZ  H172  H  HCH3  0   0.230   3.4121   3.7668  -1.3064
 NCZ  H173  H  HCH3  0   0.262   2.6478   4.8464  -0.1293
 NCZ  H181  H  HCH3  0   0.251   5.5138  -1.4237  -0.1192
 NCZ  H182  H  HCH3  0   0.252   5.0150  -1.4121  -1.8023
 NCZ  H183  H  HCH3  0   0.259   5.7729   0.0128  -1.1019

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
 NCZ  C1   C6    aromatic  1.410  0.020  1.410
 NCZ  C1   C2    aromatic  1.376  0.020  1.376
 NCZ  C1   H1    single    0.930  0.020  1.080
 NCZ  C6   C5    aromatic  1.423  0.020  1.423
 NCZ  C6   C10   aromatic  1.426  0.020  1.426
 NCZ  C5   C7    aromatic  1.413  0.020  1.413
 NCZ  C5   C4    aromatic  1.421  0.020  1.421
 NCZ  C7   C8    aromatic  1.364  0.020  1.364
 NCZ  C7   H7    single    0.930  0.020  1.080
 NCZ  C8   C9    aromatic  1.411  0.020  1.411
 NCZ  C8   H8    single    0.930  0.020  1.080
 NCZ  C9   C10   aromatic  1.378  0.020  1.378
 NCZ  C9   O2    single    1.341  0.020  1.341
 NCZ  C10  C11   single    1.487  0.020  1.487
 NCZ  C11  O3    double    1.203  0.020  1.203
 NCZ  C11  O4    single    1.330  0.020  1.330
 NCZ  O4   C12   single    1.423  0.020  1.423
 NCZ  C12  C13   single    1.527  0.020  1.527
 NCZ  C12  C16   single    1.527  0.020  1.527
 NCZ  C12  H12   single    0.970  0.020  1.090
 NCZ  C13  C14   single    1.506  0.020  1.506
 NCZ  C13  O5    single    1.406  0.020  1.406
 NCZ  C13  H13   single    0.970  0.020  1.090
 NCZ  C14  C15   double    1.329  0.020  1.329
 NCZ  C14  H14   single    0.930  0.020  1.080
 NCZ  C15  C16   single    1.508  0.020  1.508
 NCZ  C15  H15   single    0.930  0.020  1.080
 NCZ  C16  O6    single    1.405  0.020  1.405
 NCZ  C16  H16   single    0.970  0.020  1.090
 NCZ  O6   H6    single    0.850  0.020  0.980
 NCZ  O5   H5    single    0.850  0.020  0.980
 NCZ  O2   H2    single    0.850  0.020  0.980
 NCZ  C4   C3    aromatic  1.372  0.020  1.372
 NCZ  C4   C18   single    1.500  0.020  1.500
 NCZ  C3   C2    aromatic  1.411  0.020  1.411
 NCZ  C3   H3    single    0.930  0.020  1.080
 NCZ  C2   O1    single    1.345  0.020  1.345
 NCZ  O1   C17   single    1.415  0.020  1.415
 NCZ  C17  H171  single    0.970  0.020  1.090
 NCZ  C17  H172  single    0.970  0.020  1.090
 NCZ  C17  H173  single    0.970  0.020  1.090
 NCZ  C18  H181  single    0.970  0.020  1.090
 NCZ  C18  H182  single    0.970  0.020  1.090
 NCZ  C18  H183  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
 NCZ  H1    C1   C2    117.91  3.000
 NCZ  H1    C1   C6    121.54  3.000
 NCZ  C2    C1   C6    120.54  3.000
 NCZ  C10   C6   C5    118.67  3.000
 NCZ  C10   C6   C1    122.42  3.000
 NCZ  C5    C6   C1    118.89  3.000
 NCZ  C4    C5   C7    121.53  3.000
 NCZ  C4    C5   C6    119.71  3.000
 NCZ  C7    C5   C6    118.76  3.000
 NCZ  H7    C7   C8    118.59  3.000
 NCZ  H7    C7   C5    119.66  3.000
 NCZ  C8    C7   C5    121.74  3.000
 NCZ  H8    C8   C9    119.78  3.000
 NCZ  H8    C8   C7    120.32  3.000
 NCZ  C9    C8   C7    119.89  3.000
 NCZ  O2    C9   C10   118.54  3.000
 NCZ  O2    C9   C8    121.07  3.000
 NCZ  C10   C9   C8    120.37  3.000
 NCZ  C11   C10  C9    118.08  3.000
 NCZ  C11   C10  C6    121.35  3.000
 NCZ  C9    C10  C6    120.56  3.000
 NCZ  O4    C11  O3    124.51  3.000
 NCZ  O4    C11  C10   110.98  3.000
 NCZ  O3    C11  C10   124.51  3.000
 NCZ  C12   O4   C11   120.28  3.000
 NCZ  H12   C12  C16   108.19  3.000
 NCZ  H12   C12  C13   108.35  3.000
 NCZ  C16   C12  C13   105.29  3.000
 NCZ  H12   C12  O4    110.73  3.000
 NCZ  C16   C12  O4    113.34  3.000
 NCZ  C13   C12  O4    110.68  3.000
 NCZ  H13   C13  O5    110.51  3.000
 NCZ  H13   C13  C14   109.67  3.000
 NCZ  O5    C13  C14   115.68  3.000
 NCZ  H13   C13  C12   109.60  3.000
 NCZ  O5    C13  C12   109.84  3.000
 NCZ  C14   C13  C12   101.10  3.000
 NCZ  H14   C14  C15   125.99  3.000
 NCZ  H14   C14  C13   122.70  3.000
 NCZ  C15   C14  C13   111.23  3.000
 NCZ  H15   C15  C16   122.49  3.000
 NCZ  H15   C15  C14   125.89  3.000
 NCZ  C16   C15  C14   111.55  3.000
 NCZ  H16   C16  O6    110.67  3.000
 NCZ  H16   C16  C15   109.67  3.000
 NCZ  O6    C16  C15   115.32  3.000
 NCZ  H16   C16  C12   109.62  3.000
 NCZ  O6    C16  C12   110.19  3.000
 NCZ  C15   C16  C12   100.92  3.000
 NCZ  H6    O6   C16   108.49  3.000
 NCZ  H5    O5   C13   108.71  3.000
 NCZ  H2    O2   C9    110.58  3.000
 NCZ  C18   C4   C3    119.63  3.000
 NCZ  C18   C4   C5    120.65  3.000
 NCZ  C3    C4   C5    119.72  3.000
 NCZ  H3    C3   C2    120.66  3.000
 NCZ  H3    C3   C4    118.65  3.000
 NCZ  C2    C3   C4    120.69  3.000
 NCZ  O1    C2   C3    123.09  3.000
 NCZ  O1    C2   C1    116.47  3.000
 NCZ  C3    C2   C1    120.44  3.000
 NCZ  C17   O1   C2    119.27  3.000
 NCZ  H173  C17  H172  108.64  3.000
 NCZ  H173  C17  H171  108.70  3.000
 NCZ  H172  C17  H171  108.91  3.000
 NCZ  H173  C17  O1    106.32  3.000
 NCZ  H172  C17  O1    112.11  3.000
 NCZ  H171  C17  O1    112.04  3.000
 NCZ  H183  C18  H182  107.62  3.000
 NCZ  H183  C18  H181  107.66  3.000
 NCZ  H182  C18  H181  107.07  3.000
 NCZ  H183  C18  C4    110.86  3.000
 NCZ  H182  C18  C4    111.68  3.000
 NCZ  H181  C18  C4    111.74  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
 NCZ  CONST_01  C7    C5   C6   C1    180.00   0.0  0
 NCZ  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 NCZ  CONST_03  C9    C10  C6   C1    180.00   0.0  0
 NCZ  CONST_04  C4    C3   C2   C1      0.00   0.0  0
 NCZ  CONST_05  C3    C2   C1   C6      0.00   0.0  0
 NCZ  CONST_06  C8    C7   C5   C6      0.00   0.0  0
 NCZ  CONST_07  C3    C4   C5   C6      0.00   0.0  0
 NCZ  CONST_08  C8    C9   C10  C6      0.00   0.0  0
 NCZ  CONST_09  C2    C1   C6   C5      0.00   0.0  0
 NCZ  CONST_10  C9    C10  C6   C5      0.00   0.0  0
 NCZ  CONST_11  C9    C8   C7   C5      0.00   0.0  0
 NCZ  CONST_12  C2    C3   C4   C5      0.00   0.0  0
 NCZ  CONST_13  C10   C6   C5   C7      0.00   0.0  0
 NCZ  CONST_14  C3    C4   C5   C7    180.00   0.0  0
 NCZ  CONST_15  C10   C9   C8   C7      0.00   0.0  0
 NCZ  CONST_16  C4    C5   C7   C8    180.00   0.0  0
 NCZ  CONST_17  C2    C1   C6   C10   180.00   0.0  0
 NCZ  CONST_18  C4    C5   C6   C10   180.00   0.0  0
 NCZ  CONST_19  C11   C10  C6   C1      0.00   0.0  0
 NCZ  CONST_20  O1    C2   C1   C6    180.00   0.0  0
 NCZ  CONST_21  C18   C4   C5   C6    180.00   0.0  0
 NCZ  CONST_22  O2    C9   C10  C6    180.00   0.0  0
 NCZ  CONST_23  C11   C10  C6   C5    180.00   0.0  0
 NCZ  CONST_24  C18   C4   C5   C7      0.00   0.0  0
 NCZ  CONST_25  O2    C9   C8   C7    180.00   0.0  0
 NCZ  CONST_26  C11   C10  C9   C8    180.00   0.0  0
 NCZ  CONST_27  O1    C2   C3   C4    180.00   0.0  0
 NCZ  CONST_28  C18   C4   C3   C2    180.00   0.0  0
 NCZ  CONST_29  H3    C3   C2   C1    180.00   0.0  0
 NCZ  CONST_30  H7    C7   C5   C6    180.00   0.0  0
 NCZ  CONST_31  H1    C1   C6   C5    180.00   0.0  0
 NCZ  CONST_32  H8    C8   C7   C5    180.00   0.0  0
 NCZ  Var_01    C16   C15  C14  C13     0.41  30.0  1
 NCZ  Var_02    O3    C11  C10  C6   -118.90  30.0  2
 NCZ  Var_03    H181  C18  C4   C5    -59.24  30.0  2
 NCZ  Var_04    H171  C17  O1   C2    -60.76  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
 NCZ  chir_01  C12  O4  C13  C16  negativ
 NCZ  chir_02  C13  O5  C14  C12  positiv
 NCZ  chir_03  C16  O6  C12  C15  positiv

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
 NCZ  plan-1  C1   0.020
 NCZ  plan-1  C6   0.020
 NCZ  plan-1  C5   0.020
 NCZ  plan-1  C7   0.020
 NCZ  plan-1  C8   0.020
 NCZ  plan-1  C9   0.020
 NCZ  plan-1  C10  0.020
 NCZ  plan-1  C11  0.020
 NCZ  plan-1  O2   0.020
 NCZ  plan-1  C4   0.020
 NCZ  plan-1  C3   0.020
 NCZ  plan-1  C2   0.020
 NCZ  plan-1  O1   0.020
 NCZ  plan-1  C18  0.020
 NCZ  plan-1  H1   0.020
 NCZ  plan-1  H7   0.020
 NCZ  plan-1  H8   0.020
 NCZ  plan-1  H3   0.020
 NCZ  plan-2  C10  0.020
 NCZ  plan-2  C11  0.020
 NCZ  plan-2  O3   0.020
 NCZ  plan-2  O4   0.020

