# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 05:50:27 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: 2-(3,4-dihydroxy-5-methoxyphenyl)-3,5,7-trihydroxychromenium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(cc(O)c1O)c2[o+]c3cc(O)cc(O)c3cc2O
#
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
 P5M  P5M  2-(3,4-dihydroxy-5-methoxyphenyl)-3,5,7-trihydroxychromenium  ligand  36  23  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_P5M
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
 P5M  O30  O  OH1   0  -0.595   4.8354  -1.7252   0.4832
 P5M  C2   C  CR6   0   0.375   4.1677  -0.6649   0.0439
 P5M  C3   C  CR66  0  -0.083   2.7509  -0.7203   0.1674
 P5M  C9   C  CR16  0  -0.224   2.0477  -1.7990   0.7010
 P5M  C10  C  CR6   0   0.309   0.6678  -1.7811   0.7882
 P5M  O27  O  OH1   0  -0.613  -0.0477  -2.8050   1.2604
 P5M  C1   C  CR16  0  -0.509   4.7593   0.4451  -0.5055
 P5M  C6   C  CR6   0   0.414   3.9741   1.5255  -0.9534
 P5M  O29  O  OH1   0  -0.599   4.5329   2.6036  -1.4892
 P5M  C5   C  CR16  0  -0.451   2.5887   1.5078  -0.8539
 P5M  C4   C  CR66  0   0.429   2.0165   0.3857  -0.2933
 P5M  O12  O  O     1  -0.422   0.6848   0.3510  -0.1770
 P5M  C11  C  CR6   0   0.318  -0.0177  -0.6494   0.3280
 P5M  C14  C  CR6   0   0.032  -1.4445  -0.4308   0.2898
 P5M  C15  C  CR16  0  -0.439  -2.3059  -1.0510   1.2015
 P5M  C16  C  CR6   0   0.323  -3.6639  -0.7889   1.1647
 P5M  O22  O  OH1   0  -0.622  -4.5473  -1.3269   2.0235
 P5M  C19  C  CR16  0  -0.426  -1.9616   0.4598  -0.6659
 P5M  C18  C  CR6   0   0.344  -3.3194   0.6989  -0.7126
 P5M  O21  O  O2    0  -0.486  -3.9415   1.5054  -1.5899
 P5M  C23  C  CH3   0  -0.439  -3.1617   2.2259  -2.5274
 P5M  C17  C  CR6   0   0.230  -4.1851   0.0804   0.2039
 P5M  O24  O  OH1   0  -0.597  -5.5014   0.2955   0.1941
 P5M  H1   H  HOH1  0   0.497   5.7869  -1.6230   0.3543
 P5M  H2   H  HCR6  0   0.328   2.5835  -2.6775   1.0416
 P5M  H3   H  HOH1  0   0.496   0.5241  -3.5418   1.5081
 P5M  H4   H  HCR6  0   0.312   5.8382   0.4944  -0.5999
 P5M  H5   H  HOH1  0   0.492   5.4950   2.5282  -1.5160
 P5M  H6   H  HCR6  0   0.306   1.9869   2.3378  -1.1977
 P5M  H7   H  HCR6  0   0.292  -1.9287  -1.7080   1.9716
 P5M  H8   H  HOH1  0   0.481  -4.0968  -1.9065   2.6480
 P5M  H9   H  HCR6  0   0.297  -1.3050   0.9335  -1.3808
 P5M  H10  H  HCH3  0   0.237  -2.4526   2.8926  -2.0314
 P5M  H11  H  HCH3  0   0.238  -2.6165   1.5566  -3.1966
 P5M  H12  H  HCH3  0   0.270  -3.8568   2.8205  -3.1130
 P5M  H13  H  HOH1  0   0.483  -5.7334   0.9226  -0.5039

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
 P5M  O22  C16  single    1.344  0.020  1.344
 P5M  O24  C17  single    1.334  0.020  1.334
 P5M  C16  C17  aromatic  1.397  0.020  1.397
 P5M  C16  C15  aromatic  1.384  0.020  1.384
 P5M  C17  C18  aromatic  1.404  0.020  1.404
 P5M  C15  C14  aromatic  1.399  0.020  1.399
 P5M  C18  O21  single    1.344  0.020  1.344
 P5M  C18  C19  aromatic  1.380  0.020  1.380
 P5M  O21  C23  single    1.416  0.020  1.416
 P5M  C14  C19  aromatic  1.405  0.020  1.405
 P5M  C14  C11  single    1.444  0.020  1.444
 P5M  O12  C11  aromatic  1.323  0.020  1.323
 P5M  O12  C4   aromatic  1.337  0.020  1.337
 P5M  C5   C4   aromatic  1.379  0.020  1.379
 P5M  C5   C6   aromatic  1.389  0.020  1.389
 P5M  C11  C10  aromatic  1.401  0.020  1.401
 P5M  O29  C6   single    1.327  0.020  1.327
 P5M  C4   C3   aromatic  1.405  0.020  1.405
 P5M  C6   C1   aromatic  1.409  0.020  1.409
 P5M  C10  O27  single    1.335  0.020  1.335
 P5M  C10  C9   aromatic  1.383  0.020  1.383
 P5M  C3   C9   aromatic  1.394  0.020  1.394
 P5M  C3   C2   aromatic  1.423  0.020  1.423
 P5M  C1   C2   aromatic  1.373  0.020  1.373
 P5M  C2   O30  single    1.328  0.020  1.328
 P5M  O30  H1   single    0.850  0.020  0.980
 P5M  C9   H2   single    0.930  0.020  1.080
 P5M  O27  H3   single    0.850  0.020  0.980
 P5M  C1   H4   single    0.930  0.020  1.080
 P5M  O29  H5   single    0.850  0.020  0.980
 P5M  C5   H6   single    0.930  0.020  1.080
 P5M  C15  H7   single    0.930  0.020  1.080
 P5M  O22  H8   single    0.850  0.020  0.980
 P5M  C19  H9   single    0.930  0.020  1.080
 P5M  C23  H10  single    0.970  0.020  1.090
 P5M  C23  H11  single    0.970  0.020  1.090
 P5M  C23  H12  single    0.970  0.020  1.090
 P5M  O24  H13  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
 P5M  H1   O30  C2   111.52  3.000
 P5M  C1   C2   C3   119.69  3.000
 P5M  C1   C2   O30  124.16  3.000
 P5M  C3   C2   O30  116.16  3.000
 P5M  C4   C3   C9   118.10  3.000
 P5M  C9   C3   C2   124.44  3.000
 P5M  C4   C3   C2   117.46  3.000
 P5M  H2   C9   C10  118.95  3.000
 P5M  H2   C9   C3   119.88  3.000
 P5M  C10  C9   C3   121.17  3.000
 P5M  C11  C10  O27  118.26  3.000
 P5M  O27  C10  C9   123.16  3.000
 P5M  C11  C10  C9   118.56  3.000
 P5M  H3   O27  C10  111.02  3.000
 P5M  H4   C1   C6   119.48  3.000
 P5M  H4   C1   C2   120.03  3.000
 P5M  C6   C1   C2   120.48  3.000
 P5M  C5   C6   O29  117.34  3.000
 P5M  O29  C6   C1   121.11  3.000
 P5M  C5   C6   C1   121.56  3.000
 P5M  H5   O29  C6   111.56  3.000
 P5M  H6   C5   C4   121.54  3.000
 P5M  H6   C5   C6   121.50  3.000
 P5M  C4   C5   C6   116.96  3.000
 P5M  O12  C4   C5   118.02  3.000
 P5M  C5   C4   C3   123.85  3.000
 P5M  O12  C4   C3   118.13  3.000
 P5M  C11  O12  C4   125.58  3.000
 P5M  C14  C11  O12  113.59  3.000
 P5M  O12  C11  C10  118.46  3.000
 P5M  C14  C11  C10  127.92  3.000
 P5M  C19  C14  C15  119.84  3.000
 P5M  C19  C14  C11  118.53  3.000
 P5M  C15  C14  C11  121.60  3.000
 P5M  H7   C15  C16  118.48  3.000
 P5M  H7   C15  C14  121.27  3.000
 P5M  C16  C15  C14  120.20  3.000
 P5M  C17  C16  O22  116.32  3.000
 P5M  C17  C16  C15  120.16  3.000
 P5M  O22  C16  C15  123.52  3.000
 P5M  H8   O22  C16  110.33  3.000
 P5M  H9   C19  C18  119.99  3.000
 P5M  H9   C19  C14  120.30  3.000
 P5M  C18  C19  C14  119.68  3.000
 P5M  C17  C18  O21  113.89  3.000
 P5M  O21  C18  C19  125.56  3.000
 P5M  C17  C18  C19  120.55  3.000
 P5M  C23  O21  C18  118.84  3.000
 P5M  H12  C23  H11  108.94  3.000
 P5M  H12  C23  H10  109.03  3.000
 P5M  H11  C23  H10  109.16  3.000
 P5M  H12  C23  O21  106.44  3.000
 P5M  H11  C23  O21  111.63  3.000
 P5M  H10  C23  O21  111.55  3.000
 P5M  O24  C17  C18  122.17  3.000
 P5M  C18  C17  C16  119.55  3.000
 P5M  O24  C17  C16  118.28  3.000
 P5M  H13  O24  C17  110.29  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
 P5M  CONST_01  O12  C4   C3   C2   180.00   0.0  0
 P5M  CONST_02  C5   C4   C3   C2     0.00   0.0  0
 P5M  CONST_03  C10  C9   C3   C2   180.00   0.0  0
 P5M  CONST_04  C5   C6   C1   C2     0.00   0.0  0
 P5M  CONST_05  C11  O12  C4   C3     0.00   0.0  0
 P5M  CONST_06  C6   C5   C4   C3     0.00   0.0  0
 P5M  CONST_07  C11  C10  C9   C3     0.00   0.0  0
 P5M  CONST_08  C6   C1   C2   C3     0.00   0.0  0
 P5M  CONST_09  C14  C11  C10  C9   180.00   0.0  0
 P5M  CONST_10  O12  C11  C10  C9     0.00   0.0  0
 P5M  CONST_11  O12  C4   C3   C9     0.00   0.0  0
 P5M  CONST_12  C5   C4   C3   C9   180.00   0.0  0
 P5M  CONST_13  C1   C2   C3   C9   180.00   0.0  0
 P5M  CONST_16  C4   O12  C11  C10    0.00   0.0  0
 P5M  CONST_17  C4   C3   C9   C10    0.00   0.0  0
 P5M  CONST_18  C4   C5   C6   C1     0.00   0.0  0
 P5M  CONST_19  C4   C3   C2   C1     0.00   0.0  0
 P5M  CONST_20  O12  C4   C5   C6   180.00   0.0  0
 P5M  CONST_21  C11  O12  C4   C5   180.00   0.0  0
 P5M  CONST_22  C14  C11  O12  C4   180.00   0.0  0
 P5M  CONST_25  C16  C15  C14  C11  180.00   0.0  0
 P5M  CONST_26  C18  C19  C14  C11  180.00   0.0  0
 P5M  CONST_27  C17  C16  C15  C14    0.00   0.0  0
 P5M  CONST_28  C17  C18  C19  C14    0.00   0.0  0
 P5M  CONST_29  C18  C17  C16  C15    0.00   0.0  0
 P5M  CONST_30  C18  C19  C14  C15    0.00   0.0  0
 P5M  CONST_31  C19  C18  C17  C16    0.00   0.0  0
 P5M  CONST_32  C19  C14  C15  C16    0.00   0.0  0
 P5M  CONST_33  C4   C3   C2   O30  180.00   0.0  0
 P5M  CONST_34  C9   C3   C2   O30    0.00   0.0  0
 P5M  CONST_35  C6   C1   C2   O30  180.00   0.0  0
 P5M  CONST_36  O29  C6   C1   C2   180.00   0.0  0
 P5M  CONST_37  O27  C10  C9   C3   180.00   0.0  0
 P5M  CONST_38  C14  C11  C10  O27    0.00   0.0  0
 P5M  CONST_39  O12  C11  C10  O27  180.00   0.0  0
 P5M  CONST_40  C4   C5   C6   O29  180.00   0.0  0
 P5M  CONST_41  O22  C16  C15  C14  180.00   0.0  0
 P5M  CONST_42  O21  C18  C19  C14  180.00   0.0  0
 P5M  CONST_43  O24  C17  C16  C15  180.00   0.0  0
 P5M  CONST_44  O21  C18  C17  C16  180.00   0.0  0
 P5M  CONST_45  C18  C17  C16  O22  180.00   0.0  0
 P5M  CONST_46  O24  C17  C18  C19  180.00   0.0  0
 P5M  CONST_47  H2   C9   C3   C2     0.00   0.0  0
 P5M  CONST_48  H6   C5   C4   C3   180.00   0.0  0
 P5M  CONST_49  H4   C1   C2   C3   180.00   0.0  0
 P5M  CONST_50  H7   C15  C14  C11    0.00   0.0  0
 P5M  CONST_51  H9   C19  C14  C11    0.00   0.0  0
 P5M  Var_01    C17  C18  O21  C23  177.44  30.0  2
 P5M  Var_02    H10  C23  O21  C18  -59.98  30.0  3

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
 P5M  plan-1  C11  0.020
 P5M  plan-1  C14  0.020
 P5M  plan-1  C15  0.020
 P5M  plan-1  C16  0.020
 P5M  plan-1  O22  0.020
 P5M  plan-1  C19  0.020
 P5M  plan-1  C18  0.020
 P5M  plan-1  O21  0.020
 P5M  plan-1  C17  0.020
 P5M  plan-1  O24  0.020
 P5M  plan-1  H7   0.020
 P5M  plan-1  H9   0.020
 P5M  plan-2  O30  0.020
 P5M  plan-2  C2   0.020
 P5M  plan-2  C3   0.020
 P5M  plan-2  C9   0.020
 P5M  plan-2  C10  0.020
 P5M  plan-2  O27  0.020
 P5M  plan-2  C1   0.020
 P5M  plan-2  C6   0.020
 P5M  plan-2  O29  0.020
 P5M  plan-2  C5   0.020
 P5M  plan-2  C4   0.020
 P5M  plan-2  O12  0.020
 P5M  plan-2  C11  0.020
 P5M  plan-2  C14  0.020
 P5M  plan-2  H2   0.020
 P5M  plan-2  H4   0.020
 P5M  plan-2  H6   0.020

