# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 15:29:12 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: 3-(4-hydroxyphenyl)-4-oxo-4H-chromen-7-yl beta-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](Oc2ccc3C(=O)C(=COc3c2)c4ccc(O)cc4)[C@H](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
 DZN  DZN  '3-(4-hydroxyphenyl)-4-oxo-4H-chromen-7-yl beta-D-glucopyranoside'  ligand  50  30  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DZN
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
 DZN  O6    O  OH1   0  -0.666   3.6516   0.3968  -3.8403
 DZN  C6    C  CH2   0  -0.155   2.9229   0.6122  -5.0248
 DZN  C5    C  CH1   0  -0.025   1.5627  -0.0309  -4.8707
 DZN  O5    O  O2    0  -0.493   0.8897   0.6355  -3.8169
 DZN  C4    C  CH1   0   0.040   0.7133   0.0623  -6.1380
 DZN  O4    O  OH1   0  -0.670   1.3735  -0.6399  -7.1597
 DZN  C3    C  CH1   0  -0.011  -0.6694  -0.5241  -5.8649
 DZN  O3    O  OH1   0  -0.670  -1.4460  -0.3254  -7.0202
 DZN  C2    C  CH1   0  -0.023  -1.3025   0.1209  -4.6371
 DZN  O2    O  OH1   0  -0.664  -2.4984  -0.5599  -4.3625
 DZN  C1    C  CH1   0   0.261  -0.3160   0.0249  -3.4765
 DZN  O1    O  O2    0  -0.494  -0.8618   0.7228  -2.3975
 DZN  C18   C  CR6   0   0.386  -0.4385   0.4588  -1.1435
 DZN  C19   C  CR16  0  -0.341   0.7858  -0.1607  -0.8462
 DZN  C20   C  CR16  0  -0.282   1.1178  -0.3959   0.4680
 DZN  C21   C  CR66  0  -0.134   0.2748  -0.0171   1.5175
 DZN  C22   C  CR66  0   0.392  -0.9227   0.6139   1.1872
 DZN  C23   C  CR16  0  -0.436  -1.2931   0.8521  -0.1276
 DZN  O24   O  O     0  -0.428  -1.7870   1.0136   2.1435
 DZN  C25   C  CR16  0   0.040  -1.4932   0.7981   3.4275
 DZN  C26   C  CR6   0  -0.227  -0.3794   0.1900   3.8796
 DZN  C27   C  CR6   0   0.431   0.6205  -0.2708   2.9175
 DZN  O35   O  OC    0  -0.423   1.6557  -0.8311   3.2460
 DZN  C28   C  CR6   0   0.068  -0.1993  -0.0281   5.3257
 DZN  C29   C  CR16  0  -0.289  -1.2117  -0.6067   6.0870
 DZN  C30   C  CR16  0  -0.371  -1.0766  -0.7823   7.4560
 DZN  C31   C  CR6   0   0.346   0.0937  -0.3848   8.0947
 DZN  O34   O  OH1   0  -0.630   0.2879  -0.5310   9.4192
 DZN  C32   C  CR16  0  -0.326   1.1205   0.1881   7.3445
 DZN  C33   C  CR16  0  -0.274   0.9720   0.3588   5.9803
 DZN  H6    H  HOH1  0   0.457   4.5418   0.7344  -3.9735
 DZN  H6C1  H  HCH2  0   0.199   2.7919   1.6822  -5.2388
 DZN  H6C2  H  HCH2  0   0.216   3.4186   0.1687  -5.8943
 DZN  H5    H  HCH1  0   0.231   1.6997  -1.0946  -4.6155
 DZN  H4    H  HCH1  0   0.217   0.5966   1.1264  -6.3980
 DZN  HA    H  HOH1  0   0.456   0.8380  -0.5843  -7.9582
 DZN  H3    H  HCH1  0   0.221  -0.5436  -1.5994  -5.6593
 DZN  HB    H  HOH1  0   0.458  -2.2460  -0.8554  -6.9499
 DZN  H2    H  HCH1  0   0.234  -1.4789   1.1863  -4.8459
 DZN  HC    H  HOH1  0   0.460  -3.0294  -0.0298  -3.7602
 DZN  H1    H  HCH1  0   0.222  -0.1553  -1.0325  -3.2046
 DZN  H19   H  HCR6  0   0.296   1.4854  -0.4300  -1.6249
 DZN  H20   H  HCR6  0   0.276   2.0586  -0.8758   0.7013
 DZN  H23   H  HCR6  0   0.294  -2.2366   1.3316  -0.3557
 DZN  H25   H  HCR6  0   0.307  -2.2671   1.1826   4.0792
 DZN  H29   H  HCR6  0   0.258  -2.1226  -0.9413   5.6057
 DZN  H30   H  HCR6  0   0.273  -1.8824  -1.2384   8.0195
 DZN  H34   H  HOH1  0   0.475  -0.4945  -0.9117   9.8340
 DZN  H32   H  HCR6  0   0.265   2.0317   0.5058   7.8358
 DZN  H33   H  HCR6  0   0.252   1.7768   0.8216   5.4253

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
 DZN  O6   C6    single    1.407  0.020  1.407
 DZN  O6   H6    single    0.850  0.020  0.980
 DZN  C6   C5    single    1.512  0.020  1.512
 DZN  C6   H6C1  single    0.970  0.020  1.090
 DZN  C6   H6C2  single    0.970  0.020  1.090
 DZN  C5   O5    single    1.417  0.020  1.417
 DZN  C5   C4    single    1.528  0.020  1.528
 DZN  C5   H5    single    0.970  0.020  1.090
 DZN  O5   C1    single    1.394  0.020  1.394
 DZN  C4   O4    single    1.405  0.020  1.405
 DZN  C4   C3    single    1.527  0.020  1.527
 DZN  C4   H4    single    0.970  0.020  1.090
 DZN  O4   HA    single    0.850  0.020  0.980
 DZN  C3   O3    single    1.406  0.020  1.406
 DZN  C3   C2    single    1.525  0.020  1.525
 DZN  C3   H3    single    0.970  0.020  1.090
 DZN  O3   HB    single    0.850  0.020  0.980
 DZN  C2   O2    single    1.403  0.020  1.403
 DZN  C2   C1    single    1.526  0.020  1.526
 DZN  C2   H2    single    0.970  0.020  1.090
 DZN  O2   HC    single    0.850  0.020  0.980
 DZN  C1   O1    single    1.396  0.020  1.396
 DZN  C1   H1    single    0.970  0.020  1.090
 DZN  O1   C18   single    1.349  0.020  1.349
 DZN  C18  C19   aromatic  1.404  0.020  1.404
 DZN  C18  C23   aromatic  1.385  0.020  1.385
 DZN  C19  C20   aromatic  1.376  0.020  1.376
 DZN  C19  H19   single    0.930  0.020  1.080
 DZN  C20  C21   aromatic  1.398  0.020  1.398
 DZN  C20  H20   single    0.930  0.020  1.080
 DZN  C21  C22   aromatic  1.393  0.020  1.393
 DZN  C21  C27   aromatic  1.464  0.020  1.464
 DZN  C22  C23   aromatic  1.387  0.020  1.387
 DZN  C22  O24   aromatic  1.350  0.020  1.350
 DZN  C23  H23   single    0.930  0.020  1.080
 DZN  O24  C25   aromatic  1.335  0.020  1.335
 DZN  C25  C26   aromatic  1.347  0.020  1.347
 DZN  C25  H25   single    0.930  0.020  1.080
 DZN  C26  C27   aromatic  1.462  0.020  1.462
 DZN  C26  C28   single    1.473  0.020  1.473
 DZN  C27  O35   double    1.222  0.020  1.222
 DZN  C28  C29   aromatic  1.393  0.020  1.393
 DZN  C28  C33   aromatic  1.397  0.020  1.397
 DZN  C29  C30   aromatic  1.387  0.020  1.387
 DZN  C29  H29   single    0.930  0.020  1.080
 DZN  C30  C31   aromatic  1.391  0.020  1.391
 DZN  C30  H30   single    0.930  0.020  1.080
 DZN  C31  O34   single    1.347  0.020  1.347
 DZN  C31  C32   aromatic  1.395  0.020  1.395
 DZN  O34  H34   single    0.850  0.020  0.980
 DZN  C32  C33   aromatic  1.383  0.020  1.383
 DZN  C32  H32   single    0.930  0.020  1.080
 DZN  C33  H33   single    0.930  0.020  1.080

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
 DZN  H6    O6   C6    108.01  3.000
 DZN  H6C2  C6   H6C1  107.08  3.000
 DZN  H6C2  C6   C5    108.42  3.000
 DZN  H6C1  C6   C5    109.07  3.000
 DZN  H6C2  C6   O6    111.84  3.000
 DZN  H6C1  C6   O6    112.00  3.000
 DZN  C5    C6   O6    108.35  3.000
 DZN  H5    C5   C4    108.65  3.000
 DZN  H5    C5   O5    109.92  3.000
 DZN  C4    C5   O5    108.91  3.000
 DZN  H5    C5   C6    108.78  3.000
 DZN  C4    C5   C6    112.91  3.000
 DZN  O5    C5   C6    107.64  3.000
 DZN  C1    O5   C5    112.74  3.000
 DZN  H4    C4   C3    108.50  3.000
 DZN  H4    C4   O4    111.16  3.000
 DZN  C3    C4   O4    111.34  3.000
 DZN  H4    C4   C5    108.27  3.000
 DZN  C3    C4   C5    109.37  3.000
 DZN  O4    C4   C5    108.15  3.000
 DZN  HA    O4   C4    108.24  3.000
 DZN  H3    C3   C2    108.06  3.000
 DZN  H3    C3   O3    110.74  3.000
 DZN  C2    C3   O3    111.87  3.000
 DZN  H3    C3   C4    107.75  3.000
 DZN  C2    C3   C4    110.96  3.000
 DZN  O3    C3   C4    107.40  3.000
 DZN  HB    O3   C3    108.74  3.000
 DZN  H2    C2   C1    108.00  3.000
 DZN  H2    C2   O2    111.74  3.000
 DZN  C1    C2   O2    111.81  3.000
 DZN  H2    C2   C3    108.88  3.000
 DZN  C1    C2   C3    108.51  3.000
 DZN  O2    C2   C3    107.83  3.000
 DZN  HC    O2   C2    109.00  3.000
 DZN  H1    C1   O1    110.21  3.000
 DZN  H1    C1   C2    109.98  3.000
 DZN  O1    C1   C2    107.68  3.000
 DZN  H1    C1   O5    110.73  3.000
 DZN  O1    C1   O5    107.94  3.000
 DZN  C2    C1   O5    110.23  3.000
 DZN  C18   O1   C1    119.85  3.000
 DZN  C23   C18  C19   120.54  3.000
 DZN  C23   C18  O1    115.64  3.000
 DZN  C19   C18  O1    123.82  3.000
 DZN  H19   C19  C20   119.30  3.000
 DZN  H19   C19  C18   121.45  3.000
 DZN  C20   C19  C18   119.22  3.000
 DZN  H20   C20  C21   118.86  3.000
 DZN  H20   C20  C19   119.46  3.000
 DZN  C21   C20  C19   121.68  3.000
 DZN  C27   C21  C22   120.54  3.000
 DZN  C27   C21  C20   121.89  3.000
 DZN  C22   C21  C20   117.57  3.000
 DZN  O24   C22  C23   116.74  3.000
 DZN  O24   C22  C21   121.10  3.000
 DZN  C23   C22  C21   122.15  3.000
 DZN  H23   C23  C22   120.58  3.000
 DZN  H23   C23  C18   120.60  3.000
 DZN  C22   C23  C18   118.82  3.000
 DZN  C25   O24  C22   119.53  3.000
 DZN  H25   C25  C26   123.33  3.000
 DZN  H25   C25  O24   111.38  3.000
 DZN  C26   C25  O24   125.29  3.000
 DZN  C28   C26  C27   121.03  3.000
 DZN  C28   C26  C25   119.82  3.000
 DZN  C27   C26  C25   119.14  3.000
 DZN  O35   C27  C26   123.16  3.000
 DZN  O35   C27  C21   122.44  3.000
 DZN  C26   C27  C21   114.40  3.000
 DZN  C33   C28  C29   117.95  3.000
 DZN  C33   C28  C26   121.43  3.000
 DZN  C29   C28  C26   120.61  3.000
 DZN  H29   C29  C30   118.78  3.000
 DZN  H29   C29  C28   119.78  3.000
 DZN  C30   C29  C28   121.43  3.000
 DZN  H30   C30  C31   120.46  3.000
 DZN  H30   C30  C29   119.61  3.000
 DZN  C31   C30  C29   119.93  3.000
 DZN  C32   C31  O34   117.87  3.000
 DZN  C32   C31  C30   119.32  3.000
 DZN  O34   C31  C30   122.80  3.000
 DZN  H34   O34  C31   110.44  3.000
 DZN  H32   C32  C33   120.11  3.000
 DZN  H32   C32  C31   119.74  3.000
 DZN  C33   C32  C31   120.15  3.000
 DZN  H33   C33  C32   118.63  3.000
 DZN  H33   C33  C28   120.14  3.000
 DZN  C32   C33  C28   121.22  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
 DZN  CONST_01  C21  C20  C19  C18    0.00   0.0  0
 DZN  CONST_02  C21  C22  C23  C18    0.00   0.0  0
 DZN  CONST_03  O24  C22  C23  C18  180.00   0.0  0
 DZN  CONST_04  C22  C23  C18  C19    0.00   0.0  0
 DZN  CONST_05  C22  C21  C20  C19    0.00   0.0  0
 DZN  CONST_06  C27  C21  C20  C19  180.00   0.0  0
 DZN  CONST_07  C23  C18  C19  C20    0.00   0.0  0
 DZN  CONST_08  C23  C22  C21  C20    0.00   0.0  0
 DZN  CONST_09  O24  C22  C21  C20  180.00   0.0  0
 DZN  CONST_10  C26  C27  C21  C20  180.00   0.0  0
 DZN  CONST_11  C25  O24  C22  C21    0.00   0.0  0
 DZN  CONST_12  C25  C26  C27  C21    0.00   0.0  0
 DZN  CONST_13  C28  C26  C27  C21  180.00   0.0  0
 DZN  CONST_14  C26  C27  C21  C22    0.00   0.0  0
 DZN  CONST_15  C26  C25  O24  C22    0.00   0.0  0
 DZN  CONST_16  C27  C21  C22  C23  180.00   0.0  0
 DZN  CONST_17  C25  O24  C22  C23  180.00   0.0  0
 DZN  CONST_18  C27  C21  C22  O24    0.00   0.0  0
 DZN  CONST_19  C27  C26  C25  O24    0.00   0.0  0
 DZN  CONST_20  C28  C26  C25  O24  180.00   0.0  0
 DZN  CONST_23  C30  C29  C28  C26  180.00   0.0  0
 DZN  CONST_24  C32  C33  C28  C26  180.00   0.0  0
 DZN  CONST_27  C31  C30  C29  C28    0.00   0.0  0
 DZN  CONST_28  C31  C32  C33  C28    0.00   0.0  0
 DZN  CONST_29  C32  C33  C28  C29    0.00   0.0  0
 DZN  CONST_30  C32  C31  C30  C29    0.00   0.0  0
 DZN  CONST_31  C33  C28  C29  C30    0.00   0.0  0
 DZN  CONST_32  C33  C32  C31  C30    0.00   0.0  0
 DZN  CONST_33  C20  C19  C18  O1   180.00   0.0  0
 DZN  CONST_34  C22  C23  C18  O1   180.00   0.0  0
 DZN  CONST_35  O35  C27  C21  C20    0.00   0.0  0
 DZN  CONST_36  O35  C27  C21  C22  180.00   0.0  0
 DZN  CONST_37  O35  C27  C26  C25  180.00   0.0  0
 DZN  CONST_38  C28  C26  C27  O35    0.00   0.0  0
 DZN  CONST_39  O34  C31  C30  C29  180.00   0.0  0
 DZN  CONST_40  C33  C32  C31  O34  180.00   0.0  0
 DZN  CONST_41  H20  C20  C19  C18  180.00   0.0  0
 DZN  CONST_42  H23  C23  C18  C19  180.00   0.0  0
 DZN  CONST_43  H19  C19  C20  C21  180.00   0.0  0
 DZN  CONST_44  H25  C25  O24  C22  180.00   0.0  0
 DZN  CONST_45  H29  C29  C28  C26    0.00   0.0  0
 DZN  CONST_46  H33  C33  C28  C26    0.00   0.0  0
 DZN  CONST_47  H30  C30  C29  C28  180.00   0.0  0
 DZN  CONST_48  H32  C32  C33  C28  180.00   0.0  0
 DZN  Var_01    C19  C18  O1   C1    20.52  30.0  2

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
 DZN  chir_01  C5  C6  O5  C4  negativ
 DZN  chir_02  C4  O4  C5  C3  positiv
 DZN  chir_03  C3  O3  C2  C4  positiv
 DZN  chir_04  C2  O2  C3  C1  positiv
 DZN  chir_05  C1  O1  O5  C2  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
 DZN  plan-1  C26  0.020
 DZN  plan-1  C28  0.020
 DZN  plan-1  C29  0.020
 DZN  plan-1  C30  0.020
 DZN  plan-1  C31  0.020
 DZN  plan-1  O34  0.020
 DZN  plan-1  C32  0.020
 DZN  plan-1  C33  0.020
 DZN  plan-1  H29  0.020
 DZN  plan-1  H30  0.020
 DZN  plan-1  H32  0.020
 DZN  plan-1  H33  0.020
 DZN  plan-2  O1   0.020
 DZN  plan-2  C18  0.020
 DZN  plan-2  C19  0.020
 DZN  plan-2  C20  0.020
 DZN  plan-2  C21  0.020
 DZN  plan-2  C22  0.020
 DZN  plan-2  C23  0.020
 DZN  plan-2  O24  0.020
 DZN  plan-2  C27  0.020
 DZN  plan-2  H19  0.020
 DZN  plan-2  H20  0.020
 DZN  plan-2  H23  0.020
 DZN  plan-3  C21  0.020
 DZN  plan-3  C26  0.020
 DZN  plan-3  C27  0.020
 DZN  plan-3  O35  0.020

