# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 21 06:35:54 2020
#   Inital geometry file: a 147 line input string
#   Ligand name: (4-carboxy-1,3-benzodioxol-5-yl)-N-{2-[(4-methoxybenzyl)carbamoyl]benzyl}methanaminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(CNC(=O)c2ccccc2C[NH2+]Cc3ccc4OCOc4c3C(O)=O)cc1
#
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
 OM1  OM1  (4-carboxy-1,3-benzodioxol-5-yl)-N-{2-[(4-methoxybenzyl)carbamoyl]benzyl}methanaminium  ligand  58  33  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_OM1
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
 OM1  C15   C  CR16  0  -0.245   1.5486  -3.9730  -2.0279
 OM1  C16   C  CR16  0  -0.232   0.4977  -4.6769  -1.4637
 OM1  C14   C  CR16  0  -0.265   1.8298  -2.6871  -1.5898
 OM1  C17   C  CR16  0  -0.293  -0.2713  -4.0887  -0.4690
 OM1  C23   C  CR16  0  -0.314  -2.9177   1.8628   1.0874
 OM1  C6    C  CR16  0  -0.266   5.1151   1.2063  -1.1344
 OM1  C10   C  CR16  0  -0.276   5.4723   0.9787   1.2144
 OM1  C24   C  CR16  0  -0.321  -3.5815   3.0004   0.6141
 OM1  C7    C  CR16  0  -0.328   6.4774   1.2898  -1.3421
 OM1  C9    C  CR16  0  -0.372   6.8478   1.0622   1.0262
 OM1  C13   C  CR6   0  -0.049   1.0608  -2.0905  -0.5956
 OM1  C30   C  CR6   0  -0.190  -4.7208   0.3973   0.3828
 OM1  C5    C  CR6   0   0.028   4.5880   1.0525   0.1490
 OM1  C18   C  CR6   0   0.107  -0.0103  -2.7973  -0.0289
 OM1  C22   C  CR6   0   0.096  -3.4467   0.5883   0.9828
 OM1  C25   C  CR56  0   0.317  -4.8097   2.8009   0.0485
 OM1  C29   C  CR56  0   0.338  -5.3750   1.5337  -0.0511
 OM1  C8    C  CR6   0   0.375   7.3590   1.2194  -0.2587
 OM1  C2    C  C     0   0.541   1.3592  -0.6847  -0.1847
 OM1  C27   C  CH2   0   0.069  -6.7402   2.9914  -1.0338
 OM1  C12   C  CH3   0  -0.438   9.6029   1.2647   0.5104
 OM1  C4    C  CH2   0  -0.328   3.1055   0.9434   0.3583
 OM1  C19   C  CH2   0  -0.424  -0.8692  -2.2239   1.0623
 OM1  C21   C  CH2   0  -0.414  -2.6267  -0.5289   1.5648
 OM1  N3    N  NH1   0  -0.615   2.6446  -0.3850  -0.0184
 OM1  N20   N  NT2   1  -0.677  -1.7970  -1.1924   0.5227
 OM1  O33   O  OH1   0  -0.611  -4.5556  -1.9212   0.0736
 OM1  O1    O  O     0  -0.517   0.4621   0.1494  -0.0283
 OM1  O32   O  O     0  -0.413  -6.5986  -1.0341   0.1503
 OM1  O26   O  O     0  -0.474  -5.6559   3.7127  -0.4668
 OM1  O28   O  O     0  -0.460  -6.5791   1.6330  -0.6355
 OM1  O11   O  O2    0  -0.469   8.6687   1.3141  -0.5501
 OM1  H15   H  HCR6  0   0.274   2.1506  -4.4195  -2.8078
 OM1  H16   H  HCR6  0   0.274   0.2732  -5.6822  -1.7936
 OM1  H14   H  HCR6  0   0.273   2.6438  -2.1376  -2.0451
 OM1  H17   H  HCR6  0   0.273  -1.0829  -4.6486  -0.0215
 OM1  H23   H  HCR6  0   0.274  -1.9542   1.9945   1.5627
 OM1  H24   H  HCR6  0   0.291  -3.1434   3.9843   0.7060
 OM1  H6    H  HCR6  0   0.257   4.4475   1.2675  -1.9860
 OM1  H7    H  HCR6  0   0.264   6.8717   1.4161  -2.3428
 OM1  H10   H  HCR6  0   0.258   5.0925   0.8552   2.2217
 OM1  H9    H  HCR6  0   0.281   7.4965   1.0043   1.8892
 OM1  H41C  H  HCH2  0   0.264   2.8523   1.1452   1.4021
 OM1  H42C  H  HCH2  0   0.267   2.5781   1.6806  -0.2484
 OM1  H191  H  HCH2  0   0.322  -1.4703  -3.0002   1.5317
 OM1  H192  H  HCH2  0   0.316  -0.2793  -1.7431   1.8422
 OM1  H211  H  HCH2  0   0.320  -1.9317  -0.1219   2.2967
 OM1  H212  H  HCH2  0   0.315  -3.2155  -1.2927   2.0660
 OM1  H3    H  HNH1  0   0.418   3.3246  -1.1291  -0.0345
 OM1  H33   H  HOH1  0   0.500  -5.0364  -2.7592  -0.0165
 OM1  H271  H  HCH2  0   0.255  -7.6846   3.3756  -0.6490
 OM1  H272  H  HCH2  0   0.248  -6.7076   3.0616  -2.1242
 OM1  H121  H  HCH3  0   0.230   9.4466   2.0718   1.2306
 OM1  H122  H  HCH3  0   0.229   9.5698   0.3089   1.0400
 OM1  H123  H  HCH3  0   0.261  10.5862   1.3804   0.0616
 OM1  H20   H  HNT2  0   0.477  -1.1863  -0.4891   0.0631
 OM1  H220  H  HNT2  0   0.458  -2.4020  -1.6029  -0.1903
 OM1  C31   C  C     0   0.523  -5.4032  -0.9052   0.2025

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
 OM1  C15  C16   aromatic  1.385  0.020  1.385
 OM1  C15  C14   aromatic  1.387  0.020  1.387
 OM1  C16  C17   aromatic  1.388  0.020  1.388
 OM1  C14  C13   aromatic  1.391  0.020  1.391
 OM1  C17  C18   aromatic  1.389  0.020  1.389
 OM1  C23  C24   aromatic  1.400  0.020  1.400
 OM1  C23  C22   aromatic  1.384  0.020  1.384
 OM1  C6   C7    aromatic  1.381  0.020  1.381
 OM1  C6   C5    aromatic  1.396  0.020  1.396
 OM1  C10  C9    aromatic  1.391  0.020  1.391
 OM1  C10  C5    aromatic  1.387  0.020  1.387
 OM1  C24  C25   aromatic  1.367  0.020  1.367
 OM1  C7   C8    aromatic  1.398  0.020  1.398
 OM1  C9   C8    aromatic  1.392  0.020  1.392
 OM1  C13  C18   aromatic  1.403  0.020  1.403
 OM1  C13  C2    single    1.495  0.020  1.495
 OM1  C30  C22   aromatic  1.421  0.020  1.421
 OM1  C30  C29   aromatic  1.381  0.020  1.381
 OM1  C30  C31   single    1.482  0.020  1.482
 OM1  C5   C4    single    1.501  0.020  1.501
 OM1  C18  C19   single    1.502  0.020  1.502
 OM1  C22  C21   single    1.503  0.020  1.503
 OM1  C25  C29   aromatic  1.391  0.020  1.391
 OM1  C25  O26   single    1.346  0.020  1.346
 OM1  C29  O28   single    1.342  0.020  1.342
 OM1  C8   O11   single    1.345  0.020  1.345
 OM1  C2   N3    single    1.330  0.020  1.330
 OM1  C2   O1    double    1.235  0.020  1.235
 OM1  C31  O33   single    1.329  0.020  1.329
 OM1  C31  O32   double    1.203  0.020  1.203
 OM1  C27  O26   single    1.420  0.020  1.420
 OM1  C27  O28   single    1.425  0.020  1.425
 OM1  C12  O11   single    1.414  0.020  1.414
 OM1  C4   N3    single    1.456  0.020  1.456
 OM1  C19  N20   single    1.489  0.020  1.489
 OM1  C21  N20   single    1.488  0.020  1.488
 OM1  C15  H15   single    0.930  0.020  1.080
 OM1  C16  H16   single    0.930  0.020  1.080
 OM1  C14  H14   single    0.930  0.020  1.080
 OM1  C17  H17   single    0.930  0.020  1.080
 OM1  C23  H23   single    0.930  0.020  1.080
 OM1  C24  H24   single    0.930  0.020  1.080
 OM1  C6   H6    single    0.930  0.020  1.080
 OM1  C7   H7    single    0.930  0.020  1.080
 OM1  C10  H10   single    0.930  0.020  1.080
 OM1  C9   H9    single    0.930  0.020  1.080
 OM1  C4   H41C  single    0.970  0.020  1.090
 OM1  C4   H42C  single    0.970  0.020  1.090
 OM1  C19  H191  single    0.970  0.020  1.090
 OM1  C19  H192  single    0.970  0.020  1.090
 OM1  C21  H211  single    0.970  0.020  1.090
 OM1  C21  H212  single    0.970  0.020  1.090
 OM1  N3   H3    single    0.860  0.020  1.020
 OM1  O33  H33   single    0.850  0.020  0.980
 OM1  C27  H271  single    0.970  0.020  1.090
 OM1  C27  H272  single    0.970  0.020  1.090
 OM1  C12  H121  single    0.970  0.020  1.090
 OM1  C12  H122  single    0.970  0.020  1.090
 OM1  C12  H123  single    0.970  0.020  1.090
 OM1  N20  H20   single    0.890  0.020  1.040
 OM1  N20  H220  single    0.890  0.020  1.040

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
 OM1  H15   C15  C14   119.84  3.000
 OM1  H15   C15  C16   120.41  3.000
 OM1  C14   C15  C16   119.75  3.000
 OM1  H16   C16  C17   119.83  3.000
 OM1  H16   C16  C15   120.37  3.000
 OM1  C17   C16  C15   119.80  3.000
 OM1  H14   C14  C13   119.90  3.000
 OM1  H14   C14  C15   119.34  3.000
 OM1  C13   C14  C15   120.74  3.000
 OM1  H17   C17  C18   119.38  3.000
 OM1  H17   C17  C16   119.49  3.000
 OM1  C18   C17  C16   121.12  3.000
 OM1  H23   C23  C22   119.05  3.000
 OM1  H23   C23  C24   118.15  3.000
 OM1  C22   C23  C24   122.80  3.000
 OM1  H6    C6   C5    119.74  3.000
 OM1  H6    C6   C7    119.09  3.000
 OM1  C5    C6   C7    121.17  3.000
 OM1  H10   C10  C5    119.80  3.000
 OM1  H10   C10  C9    118.63  3.000
 OM1  C5    C10  C9    121.57  3.000
 OM1  H24   C24  C25   122.16  3.000
 OM1  H24   C24  C23   121.26  3.000
 OM1  C25   C24  C23   116.58  3.000
 OM1  H7    C7   C8    119.48  3.000
 OM1  H7    C7   C6    120.35  3.000
 OM1  C8    C7   C6    120.17  3.000
 OM1  H9    C9   C8    121.51  3.000
 OM1  H9    C9   C10   118.82  3.000
 OM1  C8    C9   C10   119.67  3.000
 OM1  C2    C13  C18   121.02  3.000
 OM1  C2    C13  C14   119.30  3.000
 OM1  C18   C13  C14   119.64  3.000
 OM1  C31   C30  C29   117.84  3.000
 OM1  C31   C30  C22   125.63  3.000
 OM1  C29   C30  C22   116.53  3.000
 OM1  C4    C5   C10   121.25  3.000
 OM1  C4    C5   C6    120.60  3.000
 OM1  C10   C5   C6    118.14  3.000
 OM1  C19   C18  C13   122.52  3.000
 OM1  C19   C18  C17   118.52  3.000
 OM1  C13   C18  C17   118.94  3.000
 OM1  C21   C22  C30   123.55  3.000
 OM1  C21   C22  C23   116.53  3.000
 OM1  C30   C22  C23   119.89  3.000
 OM1  O26   C25  C29   109.51  3.000
 OM1  O26   C25  C24   128.63  3.000
 OM1  C29   C25  C24   121.85  3.000
 OM1  O28   C29  C25   109.17  3.000
 OM1  O28   C29  C30   128.51  3.000
 OM1  C25   C29  C30   122.31  3.000
 OM1  O11   C8   C9    124.44  3.000
 OM1  O11   C8   C7    116.26  3.000
 OM1  C9    C8   C7    119.30  3.000
 OM1  O1    C2   N3    122.27  3.000
 OM1  O1    C2   C13   121.67  3.000
 OM1  N3    C2   C13   116.05  3.000
 OM1  H272  C27  H271  110.83  3.000
 OM1  H272  C27  O28   109.67  3.000
 OM1  H271  C27  O28   109.60  3.000
 OM1  H272  C27  O26   110.05  3.000
 OM1  H271  C27  O26   109.98  3.000
 OM1  O28   C27  O26   106.63  3.000
 OM1  H123  C12  H122  108.70  3.000
 OM1  H123  C12  H121  108.83  3.000
 OM1  H122  C12  H121  108.78  3.000
 OM1  H123  C12  O11   106.52  3.000
 OM1  H122  C12  O11   111.95  3.000
 OM1  H121  C12  O11   111.96  3.000
 OM1  H42C  C4   H41C  107.12  3.000
 OM1  H42C  C4   N3    108.65  3.000
 OM1  H41C  C4   N3    110.02  3.000
 OM1  H42C  C4   C5    110.54  3.000
 OM1  H41C  C4   C5    110.40  3.000
 OM1  N3    C4   C5    110.06  3.000
 OM1  H192  C19  H191  107.77  3.000
 OM1  H192  C19  N20   106.92  3.000
 OM1  H191  C19  N20   107.84  3.000
 OM1  H192  C19  C18   112.26  3.000
 OM1  H191  C19  C18   110.90  3.000
 OM1  N20   C19  C18   110.94  3.000
 OM1  H212  C21  H211  107.38  3.000
 OM1  H212  C21  N20   108.16  3.000
 OM1  H211  C21  N20   106.36  3.000
 OM1  H212  C21  C22   113.91  3.000
 OM1  H211  C21  C22   109.32  3.000
 OM1  N20   C21  C22   111.37  3.000
 OM1  H3    N3   C4    117.65  3.000
 OM1  H3    N3   C2    118.91  3.000
 OM1  C4    N3   C2    122.95  3.000
 OM1  H220  N20  H20   108.16  3.000
 OM1  H220  N20  C21   109.75  3.000
 OM1  H20   N20  C21   109.62  3.000
 OM1  H220  N20  C19   110.11  3.000
 OM1  H20   N20  C19   105.25  3.000
 OM1  C21   N20  C19   113.74  3.000
 OM1  H33   O33  C31   110.68  3.000
 OM1  C27   O26  C25   106.78  3.000
 OM1  C27   O28  C29   107.08  3.000
 OM1  C12   O11  C8    118.58  3.000
 OM1  O32   C31  O33   123.18  3.000
 OM1  O32   C31  C30   123.85  3.000
 OM1  O33   C31  C30   112.96  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
 OM1  CONST_01  C18   C17  C16  C15     0.00   0.0  0
 OM1  CONST_02  C18   C13  C14  C15     0.00   0.0  0
 OM1  CONST_03  C13   C14  C15  C16     0.00   0.0  0
 OM1  CONST_04  C13   C18  C17  C16     0.00   0.0  0
 OM1  CONST_05  C17   C16  C15  C14     0.00   0.0  0
 OM1  CONST_06  C17   C18  C13  C14     0.00   0.0  0
 OM1  CONST_07  C29   C25  C24  C23     0.00   0.0  0
 OM1  CONST_08  C29   C30  C22  C23     0.00   0.0  0
 OM1  CONST_09  C9    C8   C7   C6      0.00   0.0  0
 OM1  CONST_10  C9    C10  C5   C6      0.00   0.0  0
 OM1  CONST_11  C7    C8   C9   C10     0.00   0.0  0
 OM1  CONST_12  C7    C6   C5   C10     0.00   0.0  0
 OM1  CONST_13  C30   C22  C23  C24     0.00   0.0  0
 OM1  CONST_14  C30   C29  C25  C24     0.00   0.0  0
 OM1  CONST_15  C8    C7   C6   C5      0.00   0.0  0
 OM1  CONST_16  C8    C9   C10  C5      0.00   0.0  0
 OM1  CONST_17  C25   C24  C23  C22     0.00   0.0  0
 OM1  CONST_18  C25   C29  C30  C22     0.00   0.0  0
 OM1  CONST_19  C2    C13  C14  C15   180.00   0.0  0
 OM1  CONST_20  C19   C18  C17  C16   180.00   0.0  0
 OM1  CONST_21  C19   C18  C13  C14   180.00   0.0  0
 OM1  CONST_22  C2    C13  C18  C17   180.00   0.0  0
 OM1  CONST_23  C31   C30  C22  C23   180.00   0.0  0
 OM1  CONST_24  O11   C8   C7   C6    180.00   0.0  0
 OM1  CONST_25  O11   C8   C9   C10   180.00   0.0  0
 OM1  CONST_26  C21   C22  C23  C24   180.00   0.0  0
 OM1  CONST_27  C4    C5   C6   C7    180.00   0.0  0
 OM1  CONST_28  C4    C5   C10  C9    180.00   0.0  0
 OM1  CONST_29  C31   C30  C29  C25   180.00   0.0  0
 OM1  CONST_30  C21   C22  C30  C29   180.00   0.0  0
 OM1  CONST_31  O28   C29  C30  C31     0.00   0.0  0
 OM1  CONST_32  H17   C17  C16  C15   180.00   0.0  0
 OM1  CONST_33  H14   C14  C15  C16   180.00   0.0  0
 OM1  CONST_34  H16   C16  C15  C14   180.00   0.0  0
 OM1  CONST_35  H15   C15  C16  C17   180.00   0.0  0
 OM1  CONST_36  H10   C10  C5   C6    180.00   0.0  0
 OM1  CONST_37  H6    C6   C5   C10   180.00   0.0  0
 OM1  CONST_38  H9    C9   C8   C7    180.00   0.0  0
 OM1  CONST_39  H7    C7   C8   C9    180.00   0.0  0
 OM1  CONST_40  H23   C23  C22  C30   180.00   0.0  0
 OM1  CONST_41  H24   C24  C23  C22   180.00   0.0  0
 OM1  CONST_42  C4    N3   C2   C13   180.00   0.0  0
 OM1  CONST_43  H3    N3   C2   C13     0.00   0.0  0
 OM1  CONST_44  H33   O33  C31  C30   180.00   0.0  0
 OM1  CONST_45  O1    C2   N3   C4      0.00   0.0  0
 OM1  Var_01    O28   C27  O26  C25     8.89  30.0  1
 OM1  Var_02    O26   C27  O28  C29    -8.75  30.0  1
 OM1  Var_03    N3    C2   C13  C14   -44.06  30.0  2
 OM1  Var_04    N20   C19  C18  C17  -107.12  30.0  2
 OM1  Var_05    N20   C21  C22  C23   -96.04  30.0  2
 OM1  Var_06    N3    C4   C5   C6     76.23  30.0  2
 OM1  Var_07    O33   C31  C30  C22   -28.91  30.0  2
 OM1  Var_08    C2    N3   C4   C5   -166.55  30.0  3
 OM1  Var_09    C21   N20  C19  C18  -176.82  30.0  3
 OM1  Var_10    C19   N20  C21  C22   174.63  30.0  3
 OM1  Var_11    H121  C12  O11  C8    -59.87  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
 OM1  plan-1  C15  0.020
 OM1  plan-1  C16  0.020
 OM1  plan-1  C14  0.020
 OM1  plan-1  C17  0.020
 OM1  plan-1  C13  0.020
 OM1  plan-1  C18  0.020
 OM1  plan-1  C2   0.020
 OM1  plan-1  C19  0.020
 OM1  plan-1  H15  0.020
 OM1  plan-1  H16  0.020
 OM1  plan-1  H14  0.020
 OM1  plan-1  H17  0.020
 OM1  plan-2  C6   0.020
 OM1  plan-2  C10  0.020
 OM1  plan-2  C7   0.020
 OM1  plan-2  C9   0.020
 OM1  plan-2  C5   0.020
 OM1  plan-2  C8   0.020
 OM1  plan-2  C4   0.020
 OM1  plan-2  O11  0.020
 OM1  plan-2  H6   0.020
 OM1  plan-2  H7   0.020
 OM1  plan-2  H10  0.020
 OM1  plan-2  H9   0.020
 OM1  plan-3  C23  0.020
 OM1  plan-3  C24  0.020
 OM1  plan-3  C30  0.020
 OM1  plan-3  C22  0.020
 OM1  plan-3  C25  0.020
 OM1  plan-3  C29  0.020
 OM1  plan-3  C21  0.020
 OM1  plan-3  O26  0.020
 OM1  plan-3  O28  0.020
 OM1  plan-3  H23  0.020
 OM1  plan-3  H24  0.020
 OM1  plan-3  C31  0.020
 OM1  plan-4  C13  0.020
 OM1  plan-4  C2   0.020
 OM1  plan-4  C4   0.020
 OM1  plan-4  N3   0.020
 OM1  plan-4  O1   0.020
 OM1  plan-4  H3   0.020
 OM1  plan-5  C30  0.020
 OM1  plan-5  O33  0.020
 OM1  plan-5  O32  0.020
 OM1  plan-5  H33  0.020
 OM1  plan-5  C31  0.020

