# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 04:49:38 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: (2R,5R)-4-[2-(6-chloro-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(Cl)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
 4YL  4YL  (2R,5R)-4-[2-(6-chloro-3,3-dimethyl-2,3-dihydro-1H-pyrrolo[3,2-c]pyridin-1-yl)-2-oxoethyl]-5-(methoxymethyl)-2-methylpiperazin-1-ium  ligand  53  25  .  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_4YL
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
 4YL  C1   C   CH3   0  -0.397   2.5332   2.0480   3.4387
 4YL  C3   C   CH2   0  -0.202   2.8378   1.9621   1.1272
 4YL  C5   C   C     0  -0.298   4.6024   0.5299   0.1593
 4YL  C7   C   CR16  0  -0.143   4.0512  -1.4916  -1.1762
 4YL  C8   C   CH3   0  -0.675   4.4746  -2.2968  -2.3852
 4YL  C11  C   CH2   0  -0.430   0.8896   0.1172  -0.0594
 4YL  C12  C   C     0   0.554   0.1596  -1.1062   0.4693
 4YL  C15  C   CH2   0  -0.261  -1.9393  -2.2862   0.9185
 4YL  C16  C   CR5   0  -0.181  -3.3802  -2.1085   0.4067
 4YL  C19  C   CR56  0  -0.019  -3.4127  -0.6281   0.1396
 4YL  C22  C   CR6   0   0.144  -3.1108   1.9669  -0.4060
 4YL  C24  C   CR16  0  -0.312  -1.9456   1.2478  -0.1595
 4YL  C25  C   CR56  0   0.517  -2.1170  -0.1005   0.1188
 4YL  O2   O   O2    0  -0.477   2.7697   1.2321   2.3184
 4YL  C4   C   CR16  0  -0.099   3.1770   1.0325  -0.0268
 4YL  N6   N   N     1  -0.656   4.9969  -0.3495  -0.9708
 4YL  C9   C   C     0  -0.281   2.6529  -0.9200  -1.3006
 4YL  N10  N   NR6   0  -0.430   2.3037  -0.1268  -0.1391
 4YL  O13  O   O     0  -0.443   0.7463  -2.0738   0.9040
 4YL  N14  N   NR5   0  -0.614  -1.2107  -1.1013   0.4377
 4YL  C18  C   CH3   0  -0.645  -4.4010  -2.5591   1.4449
 4YL  C20  C   CR16  0  -0.123  -4.4769   0.1968  -0.1221
 4YL  N21  N   N     0  -0.404  -4.3299   1.4984  -0.3943
 4YL  CL   CL  CL    0  -0.104  -2.9419   3.6622  -0.7523
 4YL  H26  H   HCH3  0   0.208   3.3291   2.7883   3.5825
 4YL  H27  H   HCH3  0   0.207   1.5818   2.5870   3.3601
 4YL  H28  H   HCH3  0   0.238   2.4940   1.4072   4.3182
 4YL  H29  H   HCH2  0   0.231   1.8975   2.4956   0.9290
 4YL  H30  H   HCH2  0   0.242   3.6130   2.7409   1.1726
 4YL  H32  H   H     0   0.304   5.3105   1.3552   0.1850
 4YL  H33  H   H     0   0.299   4.6957  -0.0566   1.0706
 4YL  H36  H   HCR6  0   0.306   4.1155  -2.0915  -0.2678
 4YL  H38  H   HCH3  0   0.264   5.4777  -2.7038  -2.2610
 4YL  H37  H   HCH3  0   0.267   3.7907  -3.1335  -2.5164
 4YL  H39  H   HCH3  0   0.247   4.4534  -1.6961  -3.2954
 4YL  H42  H   HCH2  0   0.267   0.4546   0.4277  -1.0213
 4YL  H43  H   HCH2  0   0.294   0.6886   0.9223   0.6482
 4YL  H45  H   HCH2  0   0.269  -1.9037  -2.3106   2.0109
 4YL  H44  H   HCH2  0   0.269  -1.4759  -3.1969   0.5444
 4YL  H53  H   HCR6  0   0.291  -0.9981   1.7572  -0.1832
 4YL  H31  H   HCR6  0   0.251   3.1473   1.6555  -0.9381
 4YL  H35  H   H     0   0.460   5.0586   0.2042  -1.8287
 4YL  H34  H   H     0   0.477   5.9404  -0.7044  -0.8091
 4YL  H40  H   H     0   0.230   2.5741  -0.3393  -2.2361
 4YL  H41  H   H     0   0.283   1.9703  -1.7638  -1.3911
 4YL  H48  H   HCH3  0   0.239  -3.5137  -3.9412  -0.7460
 4YL  H46  H   HCH3  0   0.238  -4.5715  -2.6514  -1.3268
 4YL  H47  H   HCH3  0   0.238  -2.8395  -2.5871  -1.6562
 4YL  H50  H   HCH3  0   0.239  -4.2888  -2.0065   2.3783
 4YL  H49  H   HCH3  0   0.238  -5.4204  -2.4147   1.0844
 4YL  H51  H   HCH3  0   0.242  -4.2783  -3.6214   1.6626
 4YL  H52  H   HCR6  0   0.273  -5.4939  -0.1793  -0.1163
 4YL  C17  C   CH3   0  -0.634  -3.5862  -2.8647  -0.9103

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
 4YL  C20  N21  aromatic  1.338  0.020  1.338
 4YL  C20  C19  aromatic  1.372  0.020  1.372
 4YL  N21  C22  aromatic  1.306  0.020  1.306
 4YL  C17  C16  single    1.533  0.020  1.533
 4YL  C18  C16  single    1.524  0.020  1.524
 4YL  C19  C16  single    1.505  0.020  1.505
 4YL  C19  C25  aromatic  1.399  0.020  1.399
 4YL  C16  C15  single    1.539  0.020  1.539
 4YL  C22  CL   single    1.739  0.020  1.739
 4YL  C22  C24  aromatic  1.391  0.020  1.391
 4YL  C25  C24  aromatic  1.387  0.020  1.387
 4YL  C25  N14  single    1.387  0.020  1.387
 4YL  C15  N14  single    1.472  0.020  1.472
 4YL  N14  C12  single    1.371  0.020  1.371
 4YL  C12  O13  double    1.212  0.020  1.212
 4YL  C12  C11  single    1.520  0.020  1.520
 4YL  C11  N10  single    1.437  0.020  1.437
 4YL  C1   O2   single    1.406  0.020  1.406
 4YL  O2   C3   single    1.399  0.020  1.399
 4YL  N10  C9   single    1.449  0.020  1.449
 4YL  N10  C4   single    1.456  0.020  1.456
 4YL  C3   C4   single    1.520  0.020  1.520
 4YL  C9   C7   single    1.516  0.020  1.516
 4YL  C4   C5   single    1.523  0.020  1.523
 4YL  C7   N6   single    1.497  0.020  1.497
 4YL  C7   C8   single    1.513  0.020  1.513
 4YL  C5   N6   single    1.485  0.020  1.485
 4YL  C1   H26  single    0.970  0.020  1.090
 4YL  C1   H27  single    0.970  0.020  1.090
 4YL  C1   H28  single    0.970  0.020  1.090
 4YL  C3   H29  single    0.970  0.020  1.090
 4YL  C3   H30  single    0.970  0.020  1.090
 4YL  C5   H32  single    0.970  0.020  1.090
 4YL  C5   H33  single    0.970  0.020  1.090
 4YL  C7   H36  single    0.970  0.020  1.090
 4YL  C8   H38  single    0.970  0.020  1.090
 4YL  C8   H37  single    0.970  0.020  1.090
 4YL  C8   H39  single    0.970  0.020  1.090
 4YL  C11  H42  single    0.970  0.020  1.090
 4YL  C11  H43  single    0.970  0.020  1.090
 4YL  C15  H45  single    0.970  0.020  1.090
 4YL  C15  H44  single    0.970  0.020  1.090
 4YL  C24  H53  single    0.930  0.020  1.080
 4YL  C4   H31  single    0.970  0.020  1.090
 4YL  N6   H35  single    0.890  0.020  1.040
 4YL  N6   H34  single    0.890  0.020  1.040
 4YL  C9   H40  single    0.970  0.020  1.090
 4YL  C9   H41  single    0.970  0.020  1.090
 4YL  C17  H48  single    0.970  0.020  1.090
 4YL  C17  H46  single    0.970  0.020  1.090
 4YL  C17  H47  single    0.970  0.020  1.090
 4YL  C18  H50  single    0.970  0.020  1.090
 4YL  C18  H49  single    0.970  0.020  1.090
 4YL  C18  H51  single    0.970  0.020  1.090
 4YL  C20  H52  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
 4YL  H28  C1   H27  108.42  3.000
 4YL  H28  C1   H26  108.52  3.000
 4YL  H27  C1   H26  107.90  3.000
 4YL  H28  C1   O2   107.95  3.000
 4YL  H27  C1   O2   111.97  3.000
 4YL  H26  C1   O2   111.98  3.000
 4YL  H30  C3   H29  105.47  3.000
 4YL  H30  C3   C4   107.88  3.000
 4YL  H29  C3   C4   110.54  3.000
 4YL  H30  C3   O2   111.64  3.000
 4YL  H29  C3   O2   111.42  3.000
 4YL  C4   C3   O2   109.77  3.000
 4YL  H33  C5   H32  109.48  3.000
 4YL  H33  C5   N6   107.19  3.000
 4YL  H32  C5   N6   107.11  3.000
 4YL  H33  C5   C4   111.13  3.000
 4YL  H32  C5   C4   111.21  3.000
 4YL  N6   C5   C4   110.55  3.000
 4YL  H36  C7   C9   109.28  3.000
 4YL  H36  C7   N6   105.56  3.000
 4YL  C9   C7   N6   107.84  3.000
 4YL  H36  C7   C8   110.87  3.000
 4YL  N6   C7   C8   109.81  3.000
 4YL  C9   C7   C8   113.16  3.000
 4YL  H39  C8   H37  108.09  3.000
 4YL  H39  C8   H38  108.58  3.000
 4YL  H37  C8   H38  107.76  3.000
 4YL  H39  C8   C7   111.61  3.000
 4YL  H37  C8   C7   109.24  3.000
 4YL  H38  C8   C7   111.43  3.000
 4YL  H43  C11  H42  106.62  3.000
 4YL  H43  C11  N10  110.04  3.000
 4YL  H42  C11  N10  112.85  3.000
 4YL  H43  C11  C12  106.27  3.000
 4YL  H42  C11  C12  109.96  3.000
 4YL  N10  C11  C12  110.81  3.000
 4YL  N14  C12  O13  119.67  3.000
 4YL  O13  C12  C11  122.33  3.000
 4YL  N14  C12  C11  117.99  3.000
 4YL  H44  C15  H45  108.12  3.000
 4YL  H44  C15  N14  110.53  3.000
 4YL  H45  C15  N14  109.16  3.000
 4YL  H44  C15  C16  112.39  3.000
 4YL  H45  C15  C16  111.43  3.000
 4YL  N14  C15  C16  105.17  3.000
 4YL  C18  C16  C17  110.45  3.000
 4YL  C18  C16  C19  113.41  3.000
 4YL  C17  C16  C19  109.27  3.000
 4YL  C19  C16  C15  101.12  3.000
 4YL  C18  C16  C15  111.48  3.000
 4YL  C17  C16  C15  110.77  3.000
 4YL  C20  C19  C25  119.27  3.000
 4YL  C25  C19  C16  110.71  3.000
 4YL  C20  C19  C16  129.96  3.000
 4YL  CL   C22  N21  116.25  3.000
 4YL  CL   C22  C24  117.25  3.000
 4YL  N21  C22  C24  126.50  3.000
 4YL  H53  C24  C25  124.98  3.000
 4YL  H53  C24  C22  119.27  3.000
 4YL  C25  C24  C22  115.75  3.000
 4YL  N14  C25  C24  131.80  3.000
 4YL  N14  C25  C19  109.24  3.000
 4YL  C24  C25  C19  118.93  3.000
 4YL  C3   O2   C1   112.58  3.000
 4YL  H31  C4   N10  111.68  3.000
 4YL  H31  C4   C5   108.19  3.000
 4YL  N10  C4   C5   107.94  3.000
 4YL  H31  C4   C3   105.99  3.000
 4YL  C5   C4   C3   108.54  3.000
 4YL  N10  C4   C3   114.31  3.000
 4YL  H34  N6   H35  105.38  3.000
 4YL  H34  N6   C7   109.90  3.000
 4YL  H35  N6   C7   109.63  3.000
 4YL  H34  N6   C5   109.32  3.000
 4YL  H35  N6   C5   109.49  3.000
 4YL  C7   N6   C5   112.85  3.000
 4YL  H41  C9   H40  107.00  3.000
 4YL  H41  C9   N10  109.86  3.000
 4YL  H40  C9   N10  111.97  3.000
 4YL  H41  C9   C7   107.03  3.000
 4YL  H40  C9   C7   109.50  3.000
 4YL  N10  C9   C7   111.28  3.000
 4YL  C9   N10  C4   110.68  3.000
 4YL  C4   N10  C11  116.79  3.000
 4YL  C9   N10  C11  111.99  3.000
 4YL  C25  N14  C15  109.42  3.000
 4YL  C15  N14  C12  118.98  3.000
 4YL  C25  N14  C12  131.37  3.000
 4YL  H51  C18  H49  107.44  3.000
 4YL  H51  C18  H50  108.12  3.000
 4YL  H49  C18  H50  108.18  3.000
 4YL  H51  C18  C16  110.39  3.000
 4YL  H49  C18  C16  111.20  3.000
 4YL  H50  C18  C16  111.37  3.000
 4YL  H52  C20  N21  116.21  3.000
 4YL  H52  C20  C19  121.21  3.000
 4YL  N21  C20  C19  122.59  3.000
 4YL  C20  N21  C22  116.96  3.000
 4YL  H47  C17  H46  107.90  3.000
 4YL  H47  C17  H48  107.96  3.000
 4YL  H46  C17  H48  108.09  3.000
 4YL  H47  C17  C16  111.70  3.000
 4YL  H46  C17  C16  110.68  3.000
 4YL  H48  C17  C16  110.39  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
 4YL  CONST_01  C22  N21  C20  C19     0.00   0.0  0
 4YL  CONST_02  C22  C24  C25  C19     0.00   0.0  0
 4YL  CONST_03  C20  N21  C22  C24     0.00   0.0  0
 4YL  CONST_04  C20  C19  C25  C24     0.00   0.0  0
 4YL  CONST_05  N21  C20  C19  C25     0.00   0.0  0
 4YL  CONST_06  N21  C22  C24  C25     0.00   0.0  0
 4YL  CONST_07  CL   C22  C24  C25   180.00   0.0  0
 4YL  CONST_08  CL   C22  N21  C20   180.00   0.0  0
 4YL  CONST_09  H52  C20  C19  C16     0.00   0.0  0
 4YL  CONST_10  H53  C24  C25  C19   180.00   0.0  0
 4YL  CONST_11  C25  N14  C12  C11     0.00   0.0  0
 4YL  CONST_12  C15  N14  C12  C11   180.00   0.0  0
 4YL  CONST_13  O13  C12  N14  C15     0.00   0.0  0
 4YL  CONST_14  O13  C12  N14  C25   180.00   0.0  0
 4YL  Var_01    C4   N10  C9   C7     63.60  30.0  1
 4YL  Var_02    C4   C5   N6   C7    -55.19  30.0  1
 4YL  Var_03    C20  C19  C16  C15  -167.85  30.0  1
 4YL  Var_04    C19  C25  N14  C15   -10.16  30.0  1
 4YL  Var_05    C25  N14  C15  C16    19.45  30.0  1
 4YL  Var_06    N14  C15  C16  C19   -20.00  30.0  1
 4YL  Var_07    C9   N10  C11  C12    78.07  30.0  3
 4YL  Var_08    N14  C12  C11  N10  -171.45  30.0  2
 4YL  Var_09    H48  C17  C16  C15    66.48  30.0  3
 4YL  Var_10    H50  C18  C16  C15    58.27  30.0  3
 4YL  Var_11    C4   C3   O2   C1    176.63  30.0  3
 4YL  Var_12    H26  C1   O2   C3    -60.65  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
 4YL  chir_01  C7  C9   N6  C8  positiv
 4YL  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
 4YL  plan-1  C11  0.020
 4YL  plan-1  C12  0.020
 4YL  plan-1  C15  0.020
 4YL  plan-1  C25  0.020
 4YL  plan-1  O13  0.020
 4YL  plan-1  N14  0.020
 4YL  plan-2  C16  0.020
 4YL  plan-2  C19  0.020
 4YL  plan-2  C22  0.020
 4YL  plan-2  C24  0.020
 4YL  plan-2  C25  0.020
 4YL  plan-2  N14  0.020
 4YL  plan-2  C20  0.020
 4YL  plan-2  N21  0.020
 4YL  plan-2  CL   0.020
 4YL  plan-2  H53  0.020
 4YL  plan-2  H52  0.020

