# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 18:13:37 2020
#   Inital geometry file: a 164 line input string
#   Ligand name: (R)-(4-carboxy-1,3-benzodioxol-5-yl)methyl-[[2-(cyclohexylmethylcarbamoyl)phenyl]methyl]-methyl-azanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[NH+](Cc1ccccc1C(=O)NCC2CCCCC2)Cc3ccc4OCOc4c3C(O)=O
#
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
 OM3  OM3  (R)-(4-carboxy-1,3-benzodioxol-5-yl)methyl-[[2-(cyclohexylmethylcarbamoyl)phenyl]methyl]-methyl-azanium  ligand  63  32  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_OM3
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
 OM3  C1    C  CR16  0  -0.245   2.2324  -4.8116  -2.1071
 OM3  C2    C  CR16  0  -0.231   1.5266  -5.4921  -1.1296
 OM3  C3    C  CR16  0  -0.271   2.2569  -3.4247  -2.0978
 OM3  C4    C  CR16  0  -0.285   0.8425  -4.7796  -0.1548
 OM3  C5    C  CR16  0  -0.321  -4.0643  -0.4330   1.1692
 OM3  C6    C  CR16  0  -0.323  -4.9983   0.5259   0.7586
 OM3  C7    C  CR6   0  -0.063   1.5764  -2.7029  -1.1209
 OM3  C8    C  CR6   0  -0.194  -2.1958   1.0816   0.8154
 OM3  C9    C  CR6   0   0.093   0.8482  -3.3901  -0.1370
 OM3  C10   C  CR6   0   0.103  -2.7024  -0.1923   1.2089
 OM3  C11   C  CR56  0   0.318  -4.4980   1.7357   0.3720
 OM3  C12   C  CR56  0   0.334  -3.1319   2.0065   0.3894
 OM3  C13   C  C     0   0.540   1.5822  -1.2080  -1.1927
 OM3  C15   C  CH2   0  -0.432   4.8141   3.4328   1.2176
 OM3  C16   C  CH2   0  -0.432   5.3829   3.3861  -0.1971
 OM3  C17   C  CH2   0  -0.424   4.3679   2.0487   1.6777
 OM3  C18   C  CH2   0  -0.423   4.3944   2.7589  -1.1757
 OM3  C19   C  CH2   0  -0.451   3.3759   1.4383   0.6923
 OM3  C20   C  CH2   0   0.068  -4.2141   3.8609  -0.2029
 OM3  C21   C  CH1   0  -0.246   3.9567   1.3682  -0.7181
 OM3  C22   C  CH3   0  -0.551  -2.0049  -2.8249  -0.3157
 OM3  C23   C  CH2   0  -0.421   0.1067  -2.6995   0.9733
 OM3  C24   C  CH2   0  -0.414  -1.8310  -1.3352   1.6465
 OM3  N26   N  NC1   0  -0.615   2.7503  -0.6490  -1.4911
 OM3  N27   N  NT1   1  -0.545  -1.1086  -1.9716   0.4949
 OM3  O28   O  OC    0  -0.609  -0.0134   0.8079   1.6565
 OM3  O29   O  OC    0  -0.518   0.5488  -0.5524  -1.0098
 OM3  O30   O  OC    0  -0.416  -0.3599   2.4516   0.1993
 OM3  O31   O  O     0  -0.474  -5.1673   2.8173  -0.0692
 OM3  O32   O  O     0  -0.457  -2.9324   3.2648  -0.0317
 OM3  H1    H  HCR6  0   0.275   2.7599  -5.3529  -2.8806
 OM3  H2    H  HCR6  0   0.274   1.5018  -6.5734  -1.1235
 OM3  H3    H  HCR6  0   0.279   2.7941  -2.9047  -2.8807
 OM3  H4    H  HCR6  0   0.274   0.2945  -5.3144   0.6108
 OM3  H5    H  HCR6  0   0.281  -4.4319  -1.4035   1.4751
 OM3  H6    H  HCR6  0   0.291  -6.0574   0.3104   0.7489
 OM3  H231  H  HCH2  0   0.323  -0.2134  -3.4252   1.7197
 OM3  H232  H  HCH2  0   0.312   0.7317  -1.9627   1.4775
 OM3  H241  H  HCH2  0   0.318  -1.0879  -1.0424   2.3800
 OM3  H242  H  HCH2  0   0.317  -2.4395  -2.1166   2.0998
 OM3  H26   H  HNC1  0   0.417   3.5565  -1.2505  -1.5633
 OM3  H28   H  H     0   0.496   0.9036   1.1171   1.5962
 OM3  H152  H  HCH2  0   0.211   3.9556   4.1128   1.2392
 OM3  H161  H  HCH2  0   0.230   5.6512   4.3908  -0.5320
 OM3  H162  H  HCH2  0   0.211   6.3092   2.8012  -0.1942
 OM3  H171  H  HCH2  0   0.214   5.2404   1.3923   1.7612
 OM3  H172  H  HCH2  0   0.231   3.9220   2.1032   2.6735
 OM3  H181  H  HCH2  0   0.213   3.5121   3.4040  -1.2623
 OM3  H182  H  HCH2  0   0.231   4.8369   2.7005  -2.1741
 OM3  H191  H  HCH2  0   0.231   3.0733   0.4420   1.0308
 OM3  H192  H  HCH2  0   0.203   2.4774   2.0698   0.6594
 OM3  H21   H  HCH1  0   0.226   4.8505   0.7301  -0.6891
 OM3  H201  H  HCH2  0   0.255  -4.2821   4.3028  -1.1967
 OM3  H202  H  HCH2  0   0.248  -4.3748   4.6171   0.5702
 OM3  H221  H  HCH3  0   0.296  -2.9032  -2.2666  -0.5612
 OM3  H222  H  HCH3  0   0.294  -1.5046  -3.1082  -1.2363
 OM3  H223  H  HCH3  0   0.288  -2.2680  -3.7153   0.2502
 OM3  H227  H  HNT1  0   0.483  -0.7022  -1.2465  -0.1376
 OM3  C14   C  C     0   0.512  -0.7766   1.5178   0.8362
 OM3  C25   C  CH2   0  -0.272   2.9812   0.7634  -1.7235
 OM3  H151  H  HCH2  0   0.229   5.5542   3.8430   1.9088
 OM3  H251  H  HCH2  0   0.254   2.0253   1.2854  -1.6933
 OM3  H252  H  HCH2  0   0.260   3.3796   0.8764  -2.7352

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
 OM3  C1   C2    aromatic  1.384  0.020  1.384
 OM3  C1   C3    aromatic  1.387  0.020  1.387
 OM3  C2   C4    aromatic  1.388  0.020  1.388
 OM3  C3   C7    aromatic  1.392  0.020  1.392
 OM3  C4   C9    aromatic  1.390  0.020  1.390
 OM3  C5   C6    aromatic  1.400  0.020  1.400
 OM3  C5   C10   aromatic  1.384  0.020  1.384
 OM3  C6   C11   aromatic  1.365  0.020  1.365
 OM3  C7   C9    aromatic  1.404  0.020  1.404
 OM3  C7   C13   aromatic  1.497  0.020  1.497
 OM3  C8   C10   aromatic  1.426  0.020  1.426
 OM3  C8   C12   aromatic  1.383  0.020  1.383
 OM3  C8   C14   aromatic  1.485  0.020  1.485
 OM3  C9   C23   single    1.503  0.020  1.503
 OM3  C10  C24   aromatic  1.502  0.020  1.502
 OM3  C11  C12   aromatic  1.393  0.020  1.393
 OM3  C11  O31   aromatic  1.346  0.020  1.346
 OM3  C12  O32   aromatic  1.342  0.020  1.342
 OM3  C13  N26   single    1.329  0.020  1.329
 OM3  C13  O29   double    1.237  0.020  1.237
 OM3  C14  O28   deloc     1.326  0.020  1.326
 OM3  C14  O30   deloc     1.205  0.020  1.205
 OM3  C15  C16   single    1.526  0.020  1.526
 OM3  C15  C17   single    1.525  0.020  1.525
 OM3  C16  C18   single    1.526  0.020  1.526
 OM3  C17  C19   single    1.526  0.020  1.526
 OM3  C18  C21   single    1.528  0.020  1.528
 OM3  C19  C21   single    1.527  0.020  1.527
 OM3  C20  O31   single    1.420  0.020  1.420
 OM3  C20  O32   single    1.424  0.020  1.424
 OM3  C21  C25   single    1.526  0.020  1.526
 OM3  C22  N27   single    1.479  0.020  1.479
 OM3  C23  N27   single    1.495  0.020  1.495
 OM3  C24  N27   single    1.501  0.020  1.501
 OM3  C25  N26   single    1.450  0.020  1.450
 OM3  C1   H1    single    0.930  0.020  1.080
 OM3  C2   H2    single    0.930  0.020  1.080
 OM3  C3   H3    single    0.930  0.020  1.080
 OM3  C4   H4    single    0.930  0.020  1.080
 OM3  C5   H5    single    0.930  0.020  1.080
 OM3  C6   H6    single    0.930  0.020  1.080
 OM3  C23  H231  single    0.970  0.020  1.090
 OM3  C23  H232  single    0.970  0.020  1.090
 OM3  C24  H241  single    0.970  0.020  1.090
 OM3  C24  H242  single    0.970  0.020  1.090
 OM3  N26  H26   single    0.860  0.020  1.020
 OM3  O28  H28   single    0.850  0.020  0.980
 OM3  C15  H151  single    0.970  0.020  1.090
 OM3  C15  H152  single    0.970  0.020  1.090
 OM3  C16  H161  single    0.970  0.020  1.090
 OM3  C16  H162  single    0.970  0.020  1.090
 OM3  C17  H171  single    0.970  0.020  1.090
 OM3  C17  H172  single    0.970  0.020  1.090
 OM3  C18  H181  single    0.970  0.020  1.090
 OM3  C18  H182  single    0.970  0.020  1.090
 OM3  C19  H191  single    0.970  0.020  1.090
 OM3  C19  H192  single    0.970  0.020  1.090
 OM3  C21  H21   single    0.970  0.020  1.090
 OM3  C20  H201  single    0.970  0.020  1.090
 OM3  C20  H202  single    0.970  0.020  1.090
 OM3  C25  H251  single    0.970  0.020  1.090
 OM3  C25  H252  single    0.970  0.020  1.090
 OM3  C22  H221  single    0.970  0.020  1.090
 OM3  C22  H222  single    0.970  0.020  1.090
 OM3  C22  H223  single    0.970  0.020  1.090
 OM3  N27  H227  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
 OM3  H1    C1   C3    119.77  3.000
 OM3  H1    C1   C2    120.51  3.000
 OM3  C3    C1   C2    119.72  3.000
 OM3  H2    C2   C4    119.87  3.000
 OM3  H2    C2   C1    120.47  3.000
 OM3  C4    C2   C1    119.66  3.000
 OM3  H3    C3   C7    120.06  3.000
 OM3  H3    C3   C1    118.96  3.000
 OM3  C7    C3   C1    120.96  3.000
 OM3  H4    C4   C9    119.13  3.000
 OM3  H4    C4   C2    119.51  3.000
 OM3  C9    C4   C2    121.36  3.000
 OM3  H5    C5   C10   118.84  3.000
 OM3  H5    C5   C6    118.08  3.000
 OM3  C10   C5   C6    123.08  3.000
 OM3  H6    C6   C11   122.22  3.000
 OM3  H6    C6   C5    121.31  3.000
 OM3  C11   C6   C5    116.46  3.000
 OM3  C13   C7   C9    121.64  3.000
 OM3  C13   C7   C3    118.83  3.000
 OM3  C9    C7   C3    119.44  3.000
 OM3  C14   C8   C12   117.05  3.000
 OM3  C14   C8   C10   126.73  3.000
 OM3  C12   C8   C10   116.22  3.000
 OM3  C23   C9   C7    123.27  3.000
 OM3  C23   C9   C4    117.83  3.000
 OM3  C7    C9   C4    118.86  3.000
 OM3  C24   C10  C8    123.63  3.000
 OM3  C24   C10  C5    116.55  3.000
 OM3  C8    C10  C5    119.81  3.000
 OM3  O31   C11  C12   109.61  3.000
 OM3  O31   C11  C6    128.51  3.000
 OM3  C12   C11  C6    121.88  3.000
 OM3  O32   C12  C11   108.92  3.000
 OM3  O32   C12  C8    128.54  3.000
 OM3  C11   C12  C8    122.53  3.000
 OM3  O29   C13  N26   122.98  3.000
 OM3  O29   C13  C7    121.26  3.000
 OM3  N26   C13  C7    115.74  3.000
 OM3  H152  C15  H151  106.58  3.000
 OM3  H152  C15  C17   109.16  3.000
 OM3  H151  C15  C17   110.36  3.000
 OM3  H152  C15  C16   109.24  3.000
 OM3  H151  C15  C16   110.22  3.000
 OM3  C17   C15  C16   111.16  3.000
 OM3  H162  C16  H161  106.51  3.000
 OM3  H162  C16  C18   109.27  3.000
 OM3  H161  C16  C18   109.91  3.000
 OM3  H162  C16  C15   109.22  3.000
 OM3  H161  C16  C15   110.35  3.000
 OM3  C18   C16  C15   111.46  3.000
 OM3  H172  C17  H171  106.59  3.000
 OM3  H172  C17  C19   110.08  3.000
 OM3  H171  C17  C19   109.12  3.000
 OM3  H172  C17  C15   110.43  3.000
 OM3  H171  C17  C15   109.51  3.000
 OM3  C19   C17  C15   111.00  3.000
 OM3  H182  C18  H181  106.56  3.000
 OM3  H182  C18  C21   109.92  3.000
 OM3  H181  C18  C21   109.19  3.000
 OM3  H182  C18  C16   110.20  3.000
 OM3  H181  C18  C16   109.27  3.000
 OM3  C21   C18  C16   111.57  3.000
 OM3  H192  C19  H191  107.83  3.000
 OM3  H192  C19  C21   108.05  3.000
 OM3  H191  C19  C21   110.42  3.000
 OM3  H192  C19  C17   108.73  3.000
 OM3  H191  C19  C17   110.13  3.000
 OM3  C21   C19  C17   111.57  3.000
 OM3  H202  C20  H201  110.80  3.000
 OM3  H202  C20  O32   109.69  3.000
 OM3  H201  C20  O32   109.61  3.000
 OM3  H202  C20  O31   110.07  3.000
 OM3  H201  C20  O31   110.00  3.000
 OM3  O32   C20  O31   106.58  3.000
 OM3  H21   C21  C25   107.90  3.000
 OM3  H21   C21  C19   108.16  3.000
 OM3  C25   C21  C19   112.56  3.000
 OM3  H21   C21  C18   107.67  3.000
 OM3  C25   C21  C18   110.28  3.000
 OM3  C19   C21  C18   110.11  3.000
 OM3  H223  C22  H222  109.83  3.000
 OM3  H223  C22  H221  109.79  3.000
 OM3  H222  C22  H221  108.89  3.000
 OM3  H223  C22  N27   109.49  3.000
 OM3  H222  C22  N27   109.63  3.000
 OM3  H221  C22  N27   109.18  3.000
 OM3  H232  C23  H231  107.58  3.000
 OM3  H232  C23  N27   106.56  3.000
 OM3  H231  C23  N27   107.74  3.000
 OM3  H232  C23  C9    111.68  3.000
 OM3  H231  C23  C9    110.18  3.000
 OM3  N27   C23  C9    112.85  3.000
 OM3  H242  C24  H241  107.16  3.000
 OM3  H242  C24  N27   106.50  3.000
 OM3  H241  C24  N27   107.68  3.000
 OM3  H242  C24  C10   110.06  3.000
 OM3  H241  C24  C10   112.89  3.000
 OM3  N27   C24  C10   112.22  3.000
 OM3  H26   N26  C25   116.25  3.000
 OM3  H26   N26  C13   117.90  3.000
 OM3  C25   N26  C13   125.85  3.000
 OM3  H227  N27  C24   110.95  3.000
 OM3  H227  N27  C23   102.45  3.000
 OM3  C24   N27  C23   110.62  3.000
 OM3  H227  N27  C22   107.71  3.000
 OM3  C24   N27  C22   111.92  3.000
 OM3  C23   N27  C22   112.77  3.000
 OM3  H28   O28  C14   109.57  3.000
 OM3  C20   O31  C11   106.72  3.000
 OM3  C20   O32  C12   107.25  3.000
 OM3  O30   C14  O28   122.87  3.000
 OM3  O30   C14  C8    123.43  3.000
 OM3  O28   C14  C8    113.66  3.000
 OM3  H252  C25  H251  107.21  3.000
 OM3  H252  C25  N26   107.88  3.000
 OM3  H251  C25  N26   108.82  3.000
 OM3  H252  C25  C21   109.62  3.000
 OM3  H251  C25  C21   110.65  3.000
 OM3  N26   C25  C21   112.48  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
 OM3  CONST_01  C9   C4   C2   C1      0.00   0.0  0
 OM3  CONST_02  C9   C7   C3   C1      0.00   0.0  0
 OM3  CONST_03  C7   C3   C1   C2      0.00   0.0  0
 OM3  CONST_04  C7   C9   C4   C2      0.00   0.0  0
 OM3  CONST_05  C4   C2   C1   C3      0.00   0.0  0
 OM3  CONST_06  C4   C9   C7   C3      0.00   0.0  0
 OM3  CONST_07  C12  C11  C6   C5      0.00   0.0  0
 OM3  CONST_08  O31  C11  C6   C5    180.00   0.0  0
 OM3  CONST_09  C12  C8   C10  C5      0.00   0.0  0
 OM3  CONST_10  C8   C10  C5   C6      0.00   0.0  0
 OM3  CONST_11  C8   C12  C11  C6      0.00   0.0  0
 OM3  CONST_12  O32  C12  C11  C6    180.00   0.0  0
 OM3  CONST_13  O31  C11  C12  C8    180.00   0.0  0
 OM3  CONST_14  C11  C6   C5   C10     0.00   0.0  0
 OM3  CONST_15  C11  C12  C8   C10     0.00   0.0  0
 OM3  CONST_16  O32  C12  C8   C10   180.00   0.0  0
 OM3  CONST_17  O32  C12  C11  O31     0.00   0.0  0
 OM3  CONST_18  C13  C7   C3   C1    180.00   0.0  0
 OM3  CONST_19  C13  C7   C9   C4    180.00   0.0  0
 OM3  CONST_20  C14  C8   C10  C5    180.00   0.0  0
 OM3  CONST_21  C24  C10  C5   C6    180.00   0.0  0
 OM3  CONST_22  C14  C8   C12  C11   180.00   0.0  0
 OM3  CONST_23  C24  C10  C8   C12   180.00   0.0  0
 OM3  CONST_24  O32  C12  C8   C14     0.00   0.0  0
 OM3  CONST_25  C23  C9   C4   C2    180.00   0.0  0
 OM3  CONST_26  C23  C9   C7   C3    180.00   0.0  0
 OM3  CONST_27  H4   C4   C2   C1    180.00   0.0  0
 OM3  CONST_28  H3   C3   C1   C2    180.00   0.0  0
 OM3  CONST_29  H2   C2   C1   C3    180.00   0.0  0
 OM3  CONST_30  H1   C1   C2   C4    180.00   0.0  0
 OM3  CONST_31  H5   C5   C10  C8    180.00   0.0  0
 OM3  CONST_32  H6   C6   C5   C10   180.00   0.0  0
 OM3  CONST_33  C24  C10  C8   C14     0.00   0.0  0
 OM3  CONST_34  C25  N26  C13  C7    180.00   0.0  0
 OM3  CONST_35  H26  N26  C13  C7      0.00   0.0  0
 OM3  CONST_36  H28  O28  C14  C8    180.00   0.0  0
 OM3  CONST_37  O29  C13  N26  C25     0.00   0.0  0
 OM3  Var_01    O32  C20  O31  C11     9.51  30.0  1
 OM3  Var_02    O31  C20  O32  C12    -9.30  30.0  1
 OM3  Var_03    C21  C18  C16  C15   -55.43  30.0  1
 OM3  Var_04    C21  C19  C17  C15    56.44  30.0  1
 OM3  Var_05    C19  C17  C15  C16   -55.09  30.0  1
 OM3  Var_06    C18  C16  C15  C17    54.73  30.0  1
 OM3  Var_07    N26  C13  C7   C3    -42.85  30.0  1
 OM3  Var_08    N27  C23  C9   C4   -111.45  30.0  2
 OM3  Var_09    N27  C24  C10  C5    104.62  30.0  1
 OM3  Var_10    O28  C14  C8   C10   -21.23  30.0  1
 OM3  Var_11    C21  C25  N26  C13   118.46  30.0  1

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
 OM3  chir_01  C21  C18  C19  C25  negativ
 OM3  chir_02  N27  C22  C23  C24  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
 OM3  plan-1  C1   0.020
 OM3  plan-1  C2   0.020
 OM3  plan-1  C3   0.020
 OM3  plan-1  C4   0.020
 OM3  plan-1  C7   0.020
 OM3  plan-1  C9   0.020
 OM3  plan-1  C13  0.020
 OM3  plan-1  C23  0.020
 OM3  plan-1  H1   0.020
 OM3  plan-1  H2   0.020
 OM3  plan-1  H3   0.020
 OM3  plan-1  H4   0.020
 OM3  plan-2  C5   0.020
 OM3  plan-2  C6   0.020
 OM3  plan-2  C8   0.020
 OM3  plan-2  C10  0.020
 OM3  plan-2  C11  0.020
 OM3  plan-2  C12  0.020
 OM3  plan-2  C24  0.020
 OM3  plan-2  O31  0.020
 OM3  plan-2  O32  0.020
 OM3  plan-2  H5   0.020
 OM3  plan-2  H6   0.020
 OM3  plan-2  C14  0.020
 OM3  plan-3  C7   0.020
 OM3  plan-3  C13  0.020
 OM3  plan-3  N26  0.020
 OM3  plan-3  O29  0.020
 OM3  plan-3  H26  0.020
 OM3  plan-3  C25  0.020
 OM3  plan-4  C8   0.020
 OM3  plan-4  O28  0.020
 OM3  plan-4  O30  0.020
 OM3  plan-4  H28  0.020
 OM3  plan-4  C14  0.020

