# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 21:44:14 2022
#   Inital geometry file: a 86 line input string
#   Ligand name: 3,5,7-trihydroxy-2-(3,4,5-trihydroxyphenyl)chromenium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cc(O)c2cc(O)c([o+]c2c1)c3cc(O)c(O)c(O)c3
#
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
 DLM  DLM  3,5,7-trihydroxy-2-(3,4,5-trihydroxyphenyl)chromenium  ligand  33  22  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_DLM
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
 DLM  O12  O  O     1  -0.411   0.6656   0.5064   0.2534
 DLM  C11  C  CR6   0   0.305  -0.0942  -0.4673  -0.2084
 DLM  C14  C  CR6   0   0.041  -1.5174  -0.1803  -0.1387
 DLM  C15  C  CR16  0  -0.398  -1.9764   0.6728   0.8694
 DLM  C1   C  CR16  0  -0.474   4.7455   0.4475   0.4259
 DLM  C2   C  CR6   0   0.377   4.1030  -0.6410  -0.1090
 DLM  C3   C  CR66  0  -0.076   2.6755  -0.6547  -0.1671
 DLM  C18  C  CR6   0   0.363  -3.7432  -0.3778  -1.0199
 DLM  C19  C  CR16  0  -0.407  -2.3959  -0.7024  -1.0897
 DLM  C17  C  CR6   0   0.112  -4.2132   0.4445   0.0042
 DLM  O24  O  OH1   0  -0.652  -5.5334   0.7854   0.0510
 DLM  C16  C  CR6   0   0.355  -3.3266   0.9752   0.9435
 DLM  C10  C  CR6   0   0.314   0.5143  -1.6373  -0.6614
 DLM  O27  O  OH1   0  -0.607  -0.2653  -2.6403  -1.0682
 DLM  C9   C  CR16  0  -0.237   1.8996  -1.7075  -0.6396
 DLM  C4   C  CR66  0   0.420   2.0004   0.4862   0.3199
 DLM  C5   C  CR16  0  -0.444   2.6303   1.5846   0.8571
 DLM  C6   C  CR6   0   0.417   4.0187   1.5512   0.9092
 DLM  O29  O  OH1   0  -0.594   4.6313   2.6056   1.4273
 DLM  O30  O  OH1   0  -0.591   4.8519  -1.6488  -0.5439
 DLM  H1   H  HCR6  0   0.280  -1.3094   1.0860   1.6137
 DLM  H2   H  HCR6  0   0.311   5.8282   0.4524   0.4693
 DLM  H3   H  HOH1  0   0.476  -4.6937   1.9779   1.8114
 DLM  H4   H  HOH1  0   0.475  -5.4594  -0.5096  -1.8370
 DLM  H5   H  HCR6  0   0.283  -2.0556  -1.3253  -1.9030
 DLM  H6   H  HOH1  0   0.492  -6.0313   0.1491   0.5825
 DLM  H7   H  HOH1  0   0.498   0.2589  -3.3983  -1.3541
 DLM  H8   H  HCR6  0   0.317   2.3575  -2.6261  -0.9890
 DLM  H9   H  HCR6  0   0.310   2.0701   2.4347   1.2211
 DLM  H10  H  HOH1  0   0.493   5.5909   2.4994   1.4196
 DLM  H11  H  HOH1  0   0.496   4.3565  -2.3322  -1.0085
 DLM  O21  O  OH1   0  -0.622  -3.7544   1.7817   1.9241
 DLM  O22  O  OH1   0  -0.622  -4.5696  -0.8670  -1.9546

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
 DLM  O22  C18  single    1.340  0.020  1.340
 DLM  O24  C17  single    1.364  0.020  1.364
 DLM  C18  C17  aromatic  1.395  0.020  1.395
 DLM  C18  C19  aromatic  1.388  0.020  1.388
 DLM  C17  C16  aromatic  1.396  0.020  1.396
 DLM  C19  C14  aromatic  1.396  0.020  1.396
 DLM  C16  O21  single    1.340  0.020  1.340
 DLM  C16  C15  aromatic  1.386  0.020  1.386
 DLM  C14  C15  aromatic  1.398  0.020  1.398
 DLM  C14  C11  single    1.454  0.020  1.454
 DLM  O12  C11  aromatic  1.319  0.020  1.319
 DLM  O12  C4   aromatic  1.337  0.020  1.337
 DLM  C5   C4   aromatic  1.375  0.020  1.375
 DLM  C5   C6   aromatic  1.390  0.020  1.390
 DLM  C11  C10  aromatic  1.394  0.020  1.394
 DLM  O29  C6   single    1.325  0.020  1.325
 DLM  C4   C3   aromatic  1.412  0.020  1.412
 DLM  C6   C1   aromatic  1.407  0.020  1.407
 DLM  C10  O27  single    1.334  0.020  1.334
 DLM  C10  C9   aromatic  1.387  0.020  1.387
 DLM  C3   C9   aromatic  1.391  0.020  1.391
 DLM  C3   C2   aromatic  1.429  0.020  1.429
 DLM  C1   C2   aromatic  1.373  0.020  1.373
 DLM  C2   O30  single    1.329  0.020  1.329
 DLM  C15  H1   single    0.930  0.020  1.080
 DLM  C1   H2   single    0.930  0.020  1.080
 DLM  O21  H3   single    0.850  0.020  0.980
 DLM  O22  H4   single    0.850  0.020  0.980
 DLM  C19  H5   single    0.930  0.020  1.080
 DLM  O24  H6   single    0.850  0.020  0.980
 DLM  O27  H7   single    0.850  0.020  0.980
 DLM  C9   H8   single    0.930  0.020  1.080
 DLM  C5   H9   single    0.930  0.020  1.080
 DLM  O29  H10  single    0.850  0.020  0.980
 DLM  O30  H11  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
 DLM  C4   O12  C11  125.57  3.000
 DLM  C10  C11  C14  127.48  3.000
 DLM  C10  C11  O12  118.81  3.000
 DLM  C14  C11  O12  113.68  3.000
 DLM  C19  C14  C15  120.85  3.000
 DLM  C15  C14  C11  118.46  3.000
 DLM  C19  C14  C11  120.64  3.000
 DLM  H1   C15  C16  118.74  3.000
 DLM  H1   C15  C14  121.79  3.000
 DLM  C16  C15  C14  119.45  3.000
 DLM  H2   C1   C6   119.92  3.000
 DLM  H2   C1   C2   119.14  3.000
 DLM  C6   C1   C2   120.94  3.000
 DLM  O30  C2   C3   122.85  3.000
 DLM  O30  C2   C1   117.73  3.000
 DLM  C3   C2   C1   119.41  3.000
 DLM  C4   C3   C9   117.52  3.000
 DLM  C9   C3   C2   125.35  3.000
 DLM  C4   C3   C2   117.12  3.000
 DLM  C17  C18  C19  120.13  3.000
 DLM  C19  C18  O22  118.57  3.000
 DLM  C17  C18  O22  121.30  3.000
 DLM  H5   C19  C18  118.62  3.000
 DLM  H5   C19  C14  122.05  3.000
 DLM  C18  C19  C14  119.29  3.000
 DLM  C16  C17  O24  119.76  3.000
 DLM  C16  C17  C18  120.27  3.000
 DLM  O24  C17  C18  119.90  3.000
 DLM  H6   O24  C17  110.65  3.000
 DLM  C17  C16  O21  121.23  3.000
 DLM  O21  C16  C15  118.79  3.000
 DLM  C17  C16  C15  119.98  3.000
 DLM  C9   C10  O27  123.39  3.000
 DLM  C9   C10  C11  118.24  3.000
 DLM  O27  C10  C11  118.35  3.000
 DLM  H7   O27  C10  111.31  3.000
 DLM  H8   C9   C10  117.36  3.000
 DLM  H8   C9   C3   121.02  3.000
 DLM  C10  C9   C3   121.61  3.000
 DLM  C5   C4   C3   124.11  3.000
 DLM  C3   C4   O12  118.19  3.000
 DLM  C5   C4   O12  117.69  3.000
 DLM  H9   C5   C6   121.59  3.000
 DLM  H9   C5   C4   121.47  3.000
 DLM  C6   C5   C4   116.94  3.000
 DLM  O29  C6   C5   117.22  3.000
 DLM  O29  C6   C1   121.31  3.000
 DLM  C5   C6   C1   121.47  3.000
 DLM  H10  O29  C6   111.65  3.000
 DLM  H11  O30  C2   113.95  3.000
 DLM  H3   O21  C16  110.32  3.000
 DLM  H4   O22  C18  110.37  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
 DLM  CONST_03  C9   C10  C11  O12    0.00  0.0  0
 DLM  CONST_04  C6   C5   C4   O12  180.00  0.0  0
 DLM  CONST_05  C9   C3   C4   O12    0.00  0.0  0
 DLM  CONST_06  C2   C3   C4   O12  180.00  0.0  0
 DLM  CONST_07  C18  C19  C14  C11  180.00  0.0  0
 DLM  CONST_08  C16  C15  C14  C11  180.00  0.0  0
 DLM  CONST_09  C5   C4   O12  C11  180.00  0.0  0
 DLM  CONST_10  C3   C4   O12  C11    0.00  0.0  0
 DLM  CONST_11  C3   C9   C10  C11    0.00  0.0  0
 DLM  CONST_12  C17  C18  C19  C14    0.00  0.0  0
 DLM  CONST_13  C17  C16  C15  C14    0.00  0.0  0
 DLM  CONST_14  C4   O12  C11  C14  180.00  0.0  0
 DLM  CONST_15  C9   C10  C11  C14  180.00  0.0  0
 DLM  CONST_16  C18  C17  C16  C15    0.00  0.0  0
 DLM  CONST_17  C18  C19  C14  C15    0.00  0.0  0
 DLM  CONST_19  C4   C5   C6   C1     0.00  0.0  0
 DLM  CONST_20  C4   C3   C2   C1     0.00  0.0  0
 DLM  CONST_21  C9   C3   C2   C1   180.00  0.0  0
 DLM  CONST_22  C5   C4   C3   C2     0.00  0.0  0
 DLM  CONST_23  C10  C9   C3   C2   180.00  0.0  0
 DLM  CONST_24  C5   C6   C1   C2     0.00  0.0  0
 DLM  CONST_25  C6   C5   C4   C3     0.00  0.0  0
 DLM  CONST_26  C6   C1   C2   C3     0.00  0.0  0
 DLM  CONST_27  C16  C17  C18  C19    0.00  0.0  0
 DLM  CONST_28  C16  C15  C14  C19    0.00  0.0  0
 DLM  CONST_30  C4   O12  C11  C10    0.00  0.0  0
 DLM  CONST_31  C4   C3   C9   C10    0.00  0.0  0
 DLM  CONST_32  C5   C4   C3   C9   180.00  0.0  0
 DLM  CONST_33  O27  C10  C11  O12  180.00  0.0  0
 DLM  CONST_34  O22  C18  C19  C14  180.00  0.0  0
 DLM  CONST_35  O21  C16  C15  C14  180.00  0.0  0
 DLM  CONST_36  O27  C10  C11  C14    0.00  0.0  0
 DLM  CONST_37  O24  C17  C16  C15  180.00  0.0  0
 DLM  CONST_38  O29  C6   C1   C2   180.00  0.0  0
 DLM  CONST_39  C18  C17  C16  O21  180.00  0.0  0
 DLM  CONST_40  C16  C17  C18  O22  180.00  0.0  0
 DLM  CONST_41  O27  C10  C9   C3   180.00  0.0  0
 DLM  CONST_42  O24  C17  C18  C19  180.00  0.0  0
 DLM  CONST_43  O30  C2   C3   C9     0.00  0.0  0
 DLM  CONST_44  O29  C6   C5   C4   180.00  0.0  0
 DLM  CONST_45  O30  C2   C3   C4   180.00  0.0  0
 DLM  CONST_46  O30  C2   C1   C6   180.00  0.0  0
 DLM  CONST_47  H9   C5   C4   O12    0.00  0.0  0
 DLM  CONST_48  H5   C19  C14  C11    0.00  0.0  0
 DLM  CONST_49  H1   C15  C14  C11    0.00  0.0  0
 DLM  CONST_50  H8   C9   C10  C11  180.00  0.0  0
 DLM  CONST_51  H2   C1   C2   C3   180.00  0.0  0

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
 DLM  plan-1  C11  0.020
 DLM  plan-1  C14  0.020
 DLM  plan-1  C15  0.020
 DLM  plan-1  C18  0.020
 DLM  plan-1  C19  0.020
 DLM  plan-1  C17  0.020
 DLM  plan-1  O24  0.020
 DLM  plan-1  C16  0.020
 DLM  plan-1  H1   0.020
 DLM  plan-1  H5   0.020
 DLM  plan-1  O21  0.020
 DLM  plan-1  O22  0.020
 DLM  plan-2  O12  0.020
 DLM  plan-2  C11  0.020
 DLM  plan-2  C14  0.020
 DLM  plan-2  C1   0.020
 DLM  plan-2  C2   0.020
 DLM  plan-2  C3   0.020
 DLM  plan-2  C10  0.020
 DLM  plan-2  O27  0.020
 DLM  plan-2  C9   0.020
 DLM  plan-2  C4   0.020
 DLM  plan-2  C5   0.020
 DLM  plan-2  C6   0.020
 DLM  plan-2  O29  0.020
 DLM  plan-2  O30  0.020
 DLM  plan-2  H2   0.020
 DLM  plan-2  H8   0.020
 DLM  plan-2  H9   0.020

