# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 08:22:55 2020
#   Inital geometry file: a 153 line input string
#   Ligand name: (2R,5R)-4-[2-(6-benzyl-3,3-dimethyl-2,3-dihydro-1H-pyrrolo[3,2-c]pyridin-1-yl)-2-oxoethyl]-5-(methoxymethyl)-2-methylpiperazin-1-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC[C@H]1C[NH2+][C@H](C)CN1CC(=O)N2CC(C)(C)c3cnc(Cc4ccccc4)cc23
#
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
 4YN  4YN  (2R,5R)-4-[2-(6-benzyl-3,3-dimethyl-2,3-dihydro-1H-pyrrolo[3,2-c]pyridin-1-yl)-2-oxoethyl]-5-(methoxymethyl)-2-methylpiperazin-1-ium  ligand  66  31  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_4YN
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
 4YN  C1   C  CH3   0  -0.396  -3.4330   0.1141  -3.9046
 4YN  C3   C  CH2   0  -0.199  -3.1460   1.5164  -2.0629
 4YN  C5   C  C     0  -0.299  -4.9522   1.7767  -0.3999
 4YN  C7   C  CR16  0  -0.142  -4.7261   0.9061   1.9155
 4YN  C8   C  CH3   0  -0.674  -5.0498   1.2129   3.3616
 4YN  C11  C  CH2   0  -0.425  -1.6185   0.1244   0.0256
 4YN  C12  C  C     0   0.554  -1.4607  -1.3500   0.3572
 4YN  C15  C  CH2   0  -0.257  -0.0877  -3.3492   0.5444
 4YN  C16  C  CR5   0  -0.177   1.4009  -3.7037   0.3247
 4YN  C19  C  CR56  0  -0.018   1.9577  -2.4037  -0.1866
 4YN  C22  C  CR6   0   0.263   2.6816   0.0524  -1.0563
 4YN  C23  C  CH2   0  -0.599   3.1380   1.4143  -1.5160
 4YN  C24  C  CR6   0   0.143   4.0485   2.0485  -0.4961
 4YN  C25  C  CR16  0  -0.309   5.4305   1.9172  -0.5947
 4YN  C26  C  CR16  0  -0.241   6.2660   2.4726   0.3657
 4YN  C27  C  CR16  0  -0.271   5.7277   3.1644   1.4428
 4YN  C28  C  CR16  0  -0.241   4.3491   3.2988   1.5509
 4YN  C31  C  CR56  0   0.509   0.9897  -1.4031  -0.2178
 4YN  O2   O  O2    0  -0.477  -3.6229   0.2847  -2.5219
 4YN  C4   C  CR16  0  -0.101  -3.4441   1.6641  -0.5794
 4YN  N6   N  N     1  -0.656  -5.2935   1.9731   1.0324
 4YN  C9   C  C     0  -0.280  -3.2391   0.8146   1.6417
 4YN  N10  N  NR6   0  -0.429  -2.9731   0.5575   0.2405
 4YN  O13  O  O     0  -0.452  -2.3953  -2.0304   0.7290
 4YN  N14  N  NR5   0  -0.618  -0.2230  -1.9177   0.2280
 4YN  C18  C  CH3   0  -0.645   1.5505  -4.8217  -0.7076
 4YN  C20  C  CR16  0  -0.135   3.2376  -2.1087  -0.5972
 4YN  N21  N  N     0  -0.418   3.6021  -0.9032  -1.0282
 4YN  C29  C  CR16  0  -0.296   3.5176   2.7440   0.5876
 4YN  C30  C  CR16  0  -0.406   1.3574  -0.1390  -0.6645
 4YN  H32  H  HCH3  0   0.207  -2.3723   0.1473  -4.1798
 4YN  H33  H  HCH3  0   0.237  -3.8299  -0.8620  -4.1793
 4YN  H34  H  HCH3  0   0.208  -3.9569   0.8798  -4.4884
 4YN  H35  H  HCH2  0   0.231  -2.0688   1.6260  -2.2501
 4YN  H36  H  HCH2  0   0.240  -3.6229   2.3580  -2.5865
 4YN  H39  H  H     0   0.304  -5.3490   2.6305  -0.9449
 4YN  H38  H  H     0   0.300  -5.4581   0.8710  -0.7281
 4YN  H42  H  HCR6  0   0.305  -5.2085  -0.0193   1.5987
 4YN  H44  H  HCH3  0   0.263  -6.1243   1.3089   3.5159
 4YN  H43  H  HCH3  0   0.267  -4.6952   0.3980   3.9905
 4YN  H45  H  HCH3  0   0.247  -4.5652   2.1314   3.6939
 4YN  H48  H  HCH2  0   0.264  -0.8898   0.7103   0.6058
 4YN  H49  H  HCH2  0   0.291  -1.3421   0.2464  -1.0215
 4YN  H51  H  HCH2  0   0.264  -0.7418  -3.9296  -0.1077
 4YN  H50  H  HCH2  0   0.264  -0.4041  -3.5296   1.5721
 4YN  H60  H  HCH2  0   0.273   3.6629   1.3101  -2.4677
 4YN  H59  H  HCH2  0   0.269   2.2727   2.0551  -1.6935
 4YN  H61  H  HCR6  0   0.246   5.8568   1.3804  -1.4331
 4YN  H62  H  HCR6  0   0.254   7.3392   2.3655   0.2711
 4YN  H63  H  HCR6  0   0.254   6.3771   3.5986   2.1919
 4YN  H64  H  HCR6  0   0.254   3.9199   3.8377   2.3858
 4YN  H37  H  HCR6  0   0.251  -2.9892   2.6232  -0.2731
 4YN  H41  H  H     0   0.460  -4.9604   2.8901   1.3395
 4YN  H40  H  H     0   0.477  -6.3086   2.0057   1.1375
 4YN  H46  H  H     0   0.229  -2.7404   1.7352   1.9913
 4YN  H47  H  H     0   0.282  -2.8541  -0.0036   2.2484
 4YN  H54  H  HCH3  0   0.237   1.9808  -3.3158   2.3886
 4YN  H52  H  HCH3  0   0.238   1.6094  -5.0086   2.0437
 4YN  H53  H  HCH3  0   0.236   3.1321  -4.3100   1.4930
 4YN  H56  H  HCH3  0   0.235   2.6012  -5.0480  -0.8942
 4YN  H55  H  HCH3  0   0.239   1.0720  -5.7367  -0.3538
 4YN  H57  H  HCH3  0   0.237   1.0911  -4.5451  -1.6574
 4YN  H58  H  HCR6  0   0.259   4.0092  -2.8723  -0.5829
 4YN  H65  H  HCR6  0   0.246   2.4431   2.8554   0.6788
 4YN  H66  H  HCR6  0   0.271   0.6840   0.6990  -0.7245
 4YN  C17  C  CH3   0  -0.643   2.0707  -4.1049   1.6409

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
 4YN  C28  C29  aromatic  1.388  0.020  1.388
 4YN  C28  C27  aromatic  1.389  0.020  1.389
 4YN  C20  N21  aromatic  1.331  0.020  1.331
 4YN  C20  C19  aromatic  1.376  0.020  1.376
 4YN  C29  C24  aromatic  1.393  0.020  1.393
 4YN  N21  C22  aromatic  1.327  0.020  1.327
 4YN  C17  C16  single    1.530  0.020  1.530
 4YN  C18  C16  single    1.529  0.020  1.529
 4YN  C27  C26  aromatic  1.389  0.020  1.389
 4YN  C16  C19  single    1.504  0.020  1.504
 4YN  C16  C15  single    1.546  0.020  1.546
 4YN  C19  C31  aromatic  1.393  0.020  1.393
 4YN  C24  C23  single    1.507  0.020  1.507
 4YN  C24  C25  aromatic  1.392  0.020  1.392
 4YN  C22  C23  single    1.508  0.020  1.508
 4YN  C22  C30  aromatic  1.394  0.020  1.394
 4YN  C26  C25  aromatic  1.389  0.020  1.389
 4YN  C31  C30  aromatic  1.390  0.020  1.390
 4YN  C31  N14  single    1.391  0.020  1.391
 4YN  C15  N14  single    1.472  0.020  1.472
 4YN  N14  C12  single    1.368  0.020  1.368
 4YN  C12  O13  double    1.214  0.020  1.214
 4YN  C12  C11  single    1.519  0.020  1.519
 4YN  C11  N10  single    1.438  0.020  1.438
 4YN  C1   O2   single    1.406  0.020  1.406
 4YN  O2   C3   single    1.398  0.020  1.398
 4YN  N10  C9   single    1.449  0.020  1.449
 4YN  N10  C4   single    1.456  0.020  1.456
 4YN  C3   C4   single    1.520  0.020  1.520
 4YN  C9   C7   single    1.515  0.020  1.515
 4YN  C4   C5   single    1.523  0.020  1.523
 4YN  C7   N6   single    1.497  0.020  1.497
 4YN  C7   C8   single    1.513  0.020  1.513
 4YN  C5   N6   single    1.486  0.020  1.486
 4YN  C1   H32  single    0.970  0.020  1.090
 4YN  C1   H33  single    0.970  0.020  1.090
 4YN  C1   H34  single    0.970  0.020  1.090
 4YN  C3   H35  single    0.970  0.020  1.090
 4YN  C3   H36  single    0.970  0.020  1.090
 4YN  C5   H39  single    0.970  0.020  1.090
 4YN  C5   H38  single    0.970  0.020  1.090
 4YN  C7   H42  single    0.970  0.020  1.090
 4YN  C8   H44  single    0.970  0.020  1.090
 4YN  C8   H43  single    0.970  0.020  1.090
 4YN  C8   H45  single    0.970  0.020  1.090
 4YN  C11  H48  single    0.970  0.020  1.090
 4YN  C11  H49  single    0.970  0.020  1.090
 4YN  C15  H51  single    0.970  0.020  1.090
 4YN  C15  H50  single    0.970  0.020  1.090
 4YN  C23  H60  single    0.970  0.020  1.090
 4YN  C23  H59  single    0.970  0.020  1.090
 4YN  C25  H61  single    0.930  0.020  1.080
 4YN  C26  H62  single    0.930  0.020  1.080
 4YN  C27  H63  single    0.930  0.020  1.080
 4YN  C28  H64  single    0.930  0.020  1.080
 4YN  C4   H37  single    0.970  0.020  1.090
 4YN  N6   H41  single    0.890  0.020  1.040
 4YN  N6   H40  single    0.890  0.020  1.040
 4YN  C9   H46  single    0.970  0.020  1.090
 4YN  C9   H47  single    0.970  0.020  1.090
 4YN  C17  H54  single    0.970  0.020  1.090
 4YN  C17  H52  single    0.970  0.020  1.090
 4YN  C17  H53  single    0.970  0.020  1.090
 4YN  C18  H56  single    0.970  0.020  1.090
 4YN  C18  H55  single    0.970  0.020  1.090
 4YN  C18  H57  single    0.970  0.020  1.090
 4YN  C20  H58  single    0.930  0.020  1.080
 4YN  C29  H65  single    0.930  0.020  1.080
 4YN  C30  H66  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
 4YN  H34  C1   H33  108.52  3.000
 4YN  H34  C1   H32  107.92  3.000
 4YN  H33  C1   H32  108.45  3.000
 4YN  H34  C1   O2   111.98  3.000
 4YN  H33  C1   O2   107.92  3.000
 4YN  H32  C1   O2   111.96  3.000
 4YN  H36  C3   H35  105.52  3.000
 4YN  H36  C3   C4   107.77  3.000
 4YN  H35  C3   C4   110.41  3.000
 4YN  H36  C3   O2   111.70  3.000
 4YN  H35  C3   O2   111.49  3.000
 4YN  C4   C3   O2   109.82  3.000
 4YN  H38  C5   H39  109.43  3.000
 4YN  H38  C5   N6   107.10  3.000
 4YN  H39  C5   N6   107.19  3.000
 4YN  H38  C5   C4   111.30  3.000
 4YN  H39  C5   C4   111.11  3.000
 4YN  N6   C5   C4   110.55  3.000
 4YN  H42  C7   C9   109.30  3.000
 4YN  H42  C7   N6   105.42  3.000
 4YN  C9   C7   N6   107.98  3.000
 4YN  H42  C7   C8   110.79  3.000
 4YN  N6   C7   C8   109.77  3.000
 4YN  C9   C7   C8   113.26  3.000
 4YN  H45  C8   H43  108.04  3.000
 4YN  H45  C8   H44  108.72  3.000
 4YN  H43  C8   H44  107.78  3.000
 4YN  H45  C8   C7   111.52  3.000
 4YN  H43  C8   C7   109.31  3.000
 4YN  H44  C8   C7   111.35  3.000
 4YN  H49  C11  H48  106.20  3.000
 4YN  H49  C11  N10  110.41  3.000
 4YN  H48  C11  N10  112.62  3.000
 4YN  H49  C11  C12  106.97  3.000
 4YN  H48  C11  C12  109.44  3.000
 4YN  N10  C11  C12  110.94  3.000
 4YN  N14  C12  O13  119.52  3.000
 4YN  O13  C12  C11  122.05  3.000
 4YN  N14  C12  C11  118.43  3.000
 4YN  H50  C15  H51  107.54  3.000
 4YN  H50  C15  N14  109.68  3.000
 4YN  H51  C15  N14  109.49  3.000
 4YN  H50  C15  C16  112.05  3.000
 4YN  H51  C15  C16  111.74  3.000
 4YN  N14  C15  C16  106.32  3.000
 4YN  C18  C16  C17  110.25  3.000
 4YN  C18  C16  C19  111.49  3.000
 4YN  C17  C16  C19  110.92  3.000
 4YN  C19  C16  C15  101.92  3.000
 4YN  C18  C16  C15  110.97  3.000
 4YN  C17  C16  C15  111.06  3.000
 4YN  C20  C19  C31  119.07  3.000
 4YN  C31  C19  C16  111.80  3.000
 4YN  C20  C19  C16  129.13  3.000
 4YN  C30  C22  N21  123.64  3.000
 4YN  C30  C22  C23  119.81  3.000
 4YN  N21  C22  C23  116.54  3.000
 4YN  H59  C23  H60  107.18  3.000
 4YN  H59  C23  C24  110.00  3.000
 4YN  H60  C23  C24  109.86  3.000
 4YN  H59  C23  C22  109.87  3.000
 4YN  H60  C23  C22  108.97  3.000
 4YN  C24  C23  C22  110.89  3.000
 4YN  C29  C24  C25  118.73  3.000
 4YN  C25  C24  C23  120.82  3.000
 4YN  C29  C24  C23  120.43  3.000
 4YN  H61  C25  C26  119.78  3.000
 4YN  H61  C25  C24  119.50  3.000
 4YN  C26  C25  C24  120.71  3.000
 4YN  H62  C26  C27  120.09  3.000
 4YN  H62  C26  C25  119.76  3.000
 4YN  C27  C26  C25  120.15  3.000
 4YN  H63  C27  C28  120.18  3.000
 4YN  H63  C27  C26  120.27  3.000
 4YN  C28  C27  C26  119.55  3.000
 4YN  H64  C28  C29  119.78  3.000
 4YN  H64  C28  C27  120.11  3.000
 4YN  C29  C28  C27  120.11  3.000
 4YN  C30  C31  N14  132.07  3.000
 4YN  N14  C31  C19  109.46  3.000
 4YN  C30  C31  C19  118.47  3.000
 4YN  C3   O2   C1   112.56  3.000
 4YN  H37  C4   N10  111.75  3.000
 4YN  H37  C4   C5   108.11  3.000
 4YN  N10  C4   C5   108.07  3.000
 4YN  H37  C4   C3   105.91  3.000
 4YN  C5   C4   C3   108.44  3.000
 4YN  N10  C4   C3   114.36  3.000
 4YN  H40  N6   H41  105.32  3.000
 4YN  H40  N6   C7   109.82  3.000
 4YN  H41  N6   C7   109.79  3.000
 4YN  H40  N6   C5   109.38  3.000
 4YN  H41  N6   C5   109.46  3.000
 4YN  C7   N6   C5   112.80  3.000
 4YN  H47  C9   H46  106.89  3.000
 4YN  H47  C9   N10  109.91  3.000
 4YN  H46  C9   N10  111.79  3.000
 4YN  H47  C9   C7   106.97  3.000
 4YN  H46  C9   C7   109.62  3.000
 4YN  N10  C9   C7   111.45  3.000
 4YN  C9   N10  C4   110.52  3.000
 4YN  C4   N10  C11  116.71  3.000
 4YN  C9   N10  C11  111.76  3.000
 4YN  C31  N14  C15  110.39  3.000
 4YN  C15  N14  C12  117.80  3.000
 4YN  C31  N14  C12  131.74  3.000
 4YN  H57  C18  H55  108.07  3.000
 4YN  H57  C18  H56  108.02  3.000
 4YN  H55  C18  H56  107.68  3.000
 4YN  H57  C18  C16  111.18  3.000
 4YN  H55  C18  C16  110.56  3.000
 4YN  H56  C18  C16  111.19  3.000
 4YN  H58  C20  N21  116.53  3.000
 4YN  H58  C20  C19  120.42  3.000
 4YN  N21  C20  C19  123.05  3.000
 4YN  C20  N21  C22  117.97  3.000
 4YN  H65  C29  C28  119.62  3.000
 4YN  H65  C29  C24  119.64  3.000
 4YN  C28  C29  C24  120.74  3.000
 4YN  H66  C30  C31  124.07  3.000
 4YN  H66  C30  C22  118.13  3.000
 4YN  C31  C30  C22  117.80  3.000
 4YN  H53  C17  H52  107.79  3.000
 4YN  H53  C17  H54  108.00  3.000
 4YN  H52  C17  H54  108.13  3.000
 4YN  H53  C17  C16  111.00  3.000
 4YN  H52  C17  C16  110.45  3.000
 4YN  H54  C17  C16  111.34  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
 4YN  CONST_01  C22  N21  C20  C19     0.00   0.0  0
 4YN  CONST_02  C22  C30  C31  C19     0.00   0.0  0
 4YN  CONST_03  C27  C28  C29  C24     0.00   0.0  0
 4YN  CONST_04  C27  C26  C25  C24     0.00   0.0  0
 4YN  CONST_05  C28  C29  C24  C25     0.00   0.0  0
 4YN  CONST_06  C28  C27  C26  C25     0.00   0.0  0
 4YN  CONST_07  C29  C28  C27  C26     0.00   0.0  0
 4YN  CONST_08  C29  C24  C25  C26     0.00   0.0  0
 4YN  CONST_09  N21  C20  C19  C31     0.00   0.0  0
 4YN  CONST_10  N21  C22  C30  C31     0.00   0.0  0
 4YN  CONST_11  C30  C22  N21  C20     0.00   0.0  0
 4YN  CONST_12  C30  C31  C19  C20     0.00   0.0  0
 4YN  CONST_13  C28  C29  C24  C23   180.00   0.0  0
 4YN  CONST_14  C26  C25  C24  C23   180.00   0.0  0
 4YN  CONST_15  C20  N21  C22  C23   180.00   0.0  0
 4YN  CONST_16  C31  C30  C22  C23   180.00   0.0  0
 4YN  CONST_17  H58  C20  C19  C16     0.00   0.0  0
 4YN  CONST_18  H66  C30  C31  C19   180.00   0.0  0
 4YN  CONST_19  H64  C28  C29  C24   180.00   0.0  0
 4YN  CONST_20  H62  C26  C25  C24   180.00   0.0  0
 4YN  CONST_21  H65  C29  C24  C25   180.00   0.0  0
 4YN  CONST_22  H63  C27  C26  C25   180.00   0.0  0
 4YN  CONST_23  H61  C25  C26  C27   180.00   0.0  0
 4YN  CONST_24  C31  N14  C12  C11     0.00   0.0  0
 4YN  CONST_25  C15  N14  C12  C11   180.00   0.0  0
 4YN  CONST_26  O13  C12  N14  C15     0.00   0.0  0
 4YN  CONST_27  O13  C12  N14  C31   180.00   0.0  0
 4YN  Var_01    C4   N10  C9   C7     63.43  30.0  1
 4YN  Var_02    C4   C5   N6   C7    -55.05  30.0  1
 4YN  Var_03    C20  C19  C16  C15  -177.88  30.0  1
 4YN  Var_04    C19  C31  N14  C15    -1.64  30.0  1
 4YN  Var_05    C31  N14  C15  C16     3.09  30.0  1
 4YN  Var_06    N14  C15  C16  C19    -3.15  30.0  1
 4YN  Var_07    C29  C24  C23  C22   -84.15  30.0  2
 4YN  Var_08    N21  C22  C23  C24   -69.73  30.0  1
 4YN  Var_09    C9   N10  C11  C12    79.88  30.0  3
 4YN  Var_10    N14  C12  C11  N10  -178.92  30.0  2
 4YN  Var_11    H54  C17  C16  C15   -57.01  30.0  3
 4YN  Var_12    H56  C18  C16  C15   177.79  30.0  3
 4YN  Var_13    C4   C3   O2   C1    177.20  30.0  3
 4YN  Var_14    H32  C1   O2   C3     60.82  30.0  3

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
 4YN  chir_01  C7  C9   N6  C8  positiv
 4YN  chir_02  C4  N10  C5  C3  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
 4YN  plan-1  C23  0.020
 4YN  plan-1  C24  0.020
 4YN  plan-1  C25  0.020
 4YN  plan-1  C26  0.020
 4YN  plan-1  C27  0.020
 4YN  plan-1  C28  0.020
 4YN  plan-1  C29  0.020
 4YN  plan-1  H61  0.020
 4YN  plan-1  H62  0.020
 4YN  plan-1  H63  0.020
 4YN  plan-1  H64  0.020
 4YN  plan-1  H65  0.020
 4YN  plan-2  C16  0.020
 4YN  plan-2  C19  0.020
 4YN  plan-2  C22  0.020
 4YN  plan-2  C23  0.020
 4YN  plan-2  C31  0.020
 4YN  plan-2  N14  0.020
 4YN  plan-2  C20  0.020
 4YN  plan-2  N21  0.020
 4YN  plan-2  C30  0.020
 4YN  plan-2  H58  0.020
 4YN  plan-2  H66  0.020
 4YN  plan-3  C11  0.020
 4YN  plan-3  C12  0.020
 4YN  plan-3  C15  0.020
 4YN  plan-3  C31  0.020
 4YN  plan-3  O13  0.020
 4YN  plan-3  N14  0.020

