# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 19:34:27 2022
#   Inital geometry file: a 110 line input string
#   Ligand name: (5R)-6-(5-chloropyridin-2-yl)-7-oxo-6,7-dihydro-5H-pyrrolo[3,4-b]pyrazin-5-yl 4-methylpiperazine-1-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CC1)C(=O)O[C@H]2N(C(=O)c3nccnc23)c4ccc(Cl)cn4
#
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
 ZPC  ZPC  '(5R)-6-(5-chloropyridin-2-yl)-7-oxo-6,7-dihydro-5H-pyrrolo[3,4-b]pyrazin-5-yl 4-methylpiperazine-1-carboxylate'  ligand  44  27  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_ZPC
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
 ZPC  C01   C   CH3   0  -0.516  -3.7652   3.4176   1.0868
 ZPC  N02   N   NT    0  -0.412  -3.8922   2.0023   0.8235
 ZPC  C03   C   CH2   0  -0.279  -3.9509   1.7238  -0.5988
 ZPC  C04   C   CH2   0  -0.329  -4.1427   0.2362  -0.8434
 ZPC  N05   N   NT    0  -0.482  -3.0692  -0.5051  -0.2008
 ZPC  C06   C   CH2   0  -0.334  -3.0046  -0.2424   1.2302
 ZPC  C07   C   CH2   0  -0.278  -2.8348   1.2495   1.4676
 ZPC  C08   C   C     0   0.777  -2.0505  -0.9659  -0.9414
 ZPC  O09   O   O     0  -0.500  -1.9884  -0.9561  -2.1517
 ZPC  O10   O   O2    0  -0.488  -1.0733  -1.5028  -0.1647
 ZPC  C11   C   CR15  0   0.195   0.1833  -1.7321  -0.7392
 ZPC  N12   N   NR5   0  -0.648   1.1654  -0.8478  -0.1313
 ZPC  C13   C   CR5   0   0.566   2.1899  -1.5016   0.5178
 ZPC  O14   O   O     0  -0.412   3.1408  -1.0068   1.0665
 ZPC  C15   C   CR56  0   0.064   1.8793  -2.9449   0.3550
 ZPC  N16   N   N     0  -0.346   2.5791  -3.9682   0.8077
 ZPC  C17   C   CR16  0  -0.104   2.0475  -5.1501   0.5291
 ZPC  C18   C   CR16  0  -0.099   0.8498  -5.2868  -0.1828
 ZPC  N19   N   N     0  -0.354   0.1656  -4.2452  -0.6409
 ZPC  C20   C   CR56  0   0.187   0.7096  -3.0801  -0.3548
 ZPC  C21   C   CR6   0   0.481   0.9608   0.5402  -0.1184
 ZPC  N22   N   N     0  -0.397   1.1562   1.1615   1.0312
 ZPC  C23   C   CR16  0  -0.042   0.9317   2.4632   1.0984
 ZPC  C24   C   CR6   0  -0.106   0.4650   3.1908   0.0134
 ZPC  CL    CL  CL    0  -0.099   0.1327   4.8723   0.1837
 ZPC  C26   C   CR16  0  -0.103   0.2583   2.5456  -1.1940
 ZPC  C27   C   CR16  0  -0.348   0.5291   1.1917  -1.2690
 ZPC  H01   H   HCH3  0   0.236  -4.5909   3.9605   0.6247
 ZPC  H01A  H   HCH3  0   0.235  -3.8053   3.6021   2.1613
 ZPC  H01B  H   HCH3  0   0.187  -2.8245   3.8490   0.7086
 ZPC  H03   H   HCH2  0   0.248  -4.7905   2.2707  -1.0338
 ZPC  H03A  H   HCH2  0   0.197  -3.0382   2.0587  -1.1243
 ZPC  H04   H   HCH2  0   0.255  -5.0901  -0.0923  -0.4099
 ZPC  H04A  H   HCH2  0   0.273  -4.1696   0.0209  -1.9078
 ZPC  H06   H   HCH2  0   0.255  -3.9405  -0.5849   1.6777
 ZPC  H06A  H   HCH2  0   0.279  -2.1952  -0.7941   1.6972
 ZPC  H07   H   HCH2  0   0.194  -1.8367   1.5582   1.1080
 ZPC  H07A  H   HCH2  0   0.249  -2.8600   1.4426   2.5425
 ZPC  H11   H   HCR5  0   0.307   0.1470  -1.6117  -1.8253
 ZPC  H17   H   HCR6  0   0.294   2.5741  -6.0312   0.8727
 ZPC  H18   H   HCR6  0   0.296   0.4492  -6.2725  -0.3809
 ZPC  H23   H   HCR6  0   0.295   1.1096   2.9463   2.0520
 ZPC  H26   H   HCR6  0   0.307  -0.0933   3.0828  -2.0640
 ZPC  H27   H   HCR6  0   0.299   0.4034   0.6656  -2.2047

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
 ZPC  C01  N02   single    1.445  0.020  1.445
 ZPC  N02  C03   single    1.450  0.020  1.450
 ZPC  N02  C07   single    1.449  0.020  1.449
 ZPC  C03  C04   single    1.520  0.020  1.520
 ZPC  C04  N05   single    1.454  0.020  1.454
 ZPC  N05  C06   single    1.456  0.020  1.456
 ZPC  N05  C08   single    1.341  0.020  1.341
 ZPC  C06  C07   single    1.520  0.020  1.520
 ZPC  C08  O09   double    1.212  0.020  1.212
 ZPC  C08  O10   single    1.359  0.020  1.359
 ZPC  O10  C11   single    1.401  0.020  1.401
 ZPC  C11  N12   single    1.455  0.020  1.455
 ZPC  C11  C20   single    1.497  0.020  1.497
 ZPC  N12  C13   single    1.378  0.020  1.378
 ZPC  N12  C21   single    1.403  0.020  1.403
 ZPC  C13  O14   double    1.204  0.020  1.204
 ZPC  C13  C15   single    1.485  0.020  1.485
 ZPC  C15  N16   aromatic  1.320  0.020  1.320
 ZPC  C15  C20   aromatic  1.375  0.020  1.375
 ZPC  N16  C17   aromatic  1.326  0.020  1.326
 ZPC  C17  C18   aromatic  1.400  0.020  1.400
 ZPC  C18  N19   aromatic  1.328  0.020  1.328
 ZPC  N19  C20   aromatic  1.317  0.020  1.317
 ZPC  C21  N22   aromatic  1.321  0.020  1.321
 ZPC  C21  C27   aromatic  1.391  0.020  1.391
 ZPC  N22  C23   aromatic  1.323  0.020  1.323
 ZPC  C23  C24   aromatic  1.387  0.020  1.387
 ZPC  C24  CL    single    1.722  0.020  1.722
 ZPC  C24  C26   aromatic  1.385  0.020  1.385
 ZPC  C26  C27   aromatic  1.383  0.020  1.383
 ZPC  C01  H01   single    0.970  0.020  1.090
 ZPC  C01  H01A  single    0.970  0.020  1.090
 ZPC  C01  H01B  single    0.970  0.020  1.090
 ZPC  C03  H03   single    0.970  0.020  1.090
 ZPC  C03  H03A  single    0.970  0.020  1.090
 ZPC  C04  H04   single    0.970  0.020  1.090
 ZPC  C04  H04A  single    0.970  0.020  1.090
 ZPC  C06  H06   single    0.970  0.020  1.090
 ZPC  C06  H06A  single    0.970  0.020  1.090
 ZPC  C07  H07   single    0.970  0.020  1.090
 ZPC  C07  H07A  single    0.970  0.020  1.090
 ZPC  C11  H11   single    0.970  0.020  1.090
 ZPC  C17  H17   single    0.930  0.020  1.080
 ZPC  C18  H18   single    0.930  0.020  1.080
 ZPC  C23  H23   single    0.930  0.020  1.080
 ZPC  C26  H26   single    0.930  0.020  1.080
 ZPC  C27  H27   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
 ZPC  H01B  C01  H01A  107.65  3.000
 ZPC  H01B  C01  H01   107.82  3.000
 ZPC  H01A  C01  H01   107.77  3.000
 ZPC  H01B  C01  N02   113.33  3.000
 ZPC  H01A  C01  N02   109.99  3.000
 ZPC  H01   C01  N02   110.10  3.000
 ZPC  C07   N02  C03   111.44  3.000
 ZPC  C07   N02  C01   111.33  3.000
 ZPC  C03   N02  C01   111.73  3.000
 ZPC  H03A  C03  H03   107.08  3.000
 ZPC  H03A  C03  C04   108.92  3.000
 ZPC  H03   C03  C04   109.21  3.000
 ZPC  H03A  C03  N02   112.01  3.000
 ZPC  H03   C03  N02   108.99  3.000
 ZPC  C04   C03  N02   110.54  3.000
 ZPC  H04A  C04  H04   107.92  3.000
 ZPC  H04A  C04  N05   110.50  3.000
 ZPC  H04   C04  N05   108.15  3.000
 ZPC  H04A  C04  C03   110.79  3.000
 ZPC  H04   C04  C03   109.88  3.000
 ZPC  N05   C04  C03   109.55  3.000
 ZPC  C08   N05  C06   124.81  3.000
 ZPC  C08   N05  C04   119.46  3.000
 ZPC  C06   N05  C04   112.02  3.000
 ZPC  H06A  C06  H06   107.65  3.000
 ZPC  H06A  C06  C07   110.39  3.000
 ZPC  H06   C06  C07   109.84  3.000
 ZPC  H06A  C06  N05   111.36  3.000
 ZPC  H06   C06  N05   107.93  3.000
 ZPC  C07   C06  N05   109.60  3.000
 ZPC  H07A  C07  H07   106.96  3.000
 ZPC  H07A  C07  C06   108.94  3.000
 ZPC  H07   C07  C06   108.92  3.000
 ZPC  H07A  C07  N02   109.19  3.000
 ZPC  H07   C07  N02   111.68  3.000
 ZPC  C06   C07  N02   111.04  3.000
 ZPC  O10   C08  O09   122.49  3.000
 ZPC  O10   C08  N05   111.50  3.000
 ZPC  O09   C08  N05   125.99  3.000
 ZPC  C11   O10  C08   118.39  3.000
 ZPC  H11   C11  C20   111.46  3.000
 ZPC  H11   C11  N12   111.75  3.000
 ZPC  C20   C11  N12   101.70  3.000
 ZPC  H11   C11  O10   111.07  3.000
 ZPC  C20   C11  O10   110.94  3.000
 ZPC  N12   C11  O10   109.55  3.000
 ZPC  C21   N12  C13   125.00  3.000
 ZPC  C21   N12  C11   120.45  3.000
 ZPC  C13   N12  C11   114.23  3.000
 ZPC  C15   C13  O14   127.91  3.000
 ZPC  C15   C13  N12   104.71  3.000
 ZPC  O14   C13  N12   127.36  3.000
 ZPC  C20   C15  N16   123.50  3.000
 ZPC  C20   C15  C13   109.27  3.000
 ZPC  N16   C15  C13   127.22  3.000
 ZPC  C17   N16  C15   113.99  3.000
 ZPC  H17   C17  C18   119.88  3.000
 ZPC  H17   C17  N16   117.64  3.000
 ZPC  C18   C17  N16   122.48  3.000
 ZPC  H18   C18  N19   117.43  3.000
 ZPC  H18   C18  C17   119.91  3.000
 ZPC  N19   C18  C17   122.67  3.000
 ZPC  C20   N19  C18   113.96  3.000
 ZPC  N19   C20  C15   123.40  3.000
 ZPC  N19   C20  C11   126.54  3.000
 ZPC  C15   C20  C11   110.06  3.000
 ZPC  C27   C21  N22   123.05  3.000
 ZPC  C27   C21  N12   120.07  3.000
 ZPC  N22   C21  N12   116.84  3.000
 ZPC  C23   N22  C21   118.81  3.000
 ZPC  H23   C23  C24   120.64  3.000
 ZPC  H23   C23  N22   117.10  3.000
 ZPC  C24   C23  N22   122.24  3.000
 ZPC  C26   C24  CL    120.82  3.000
 ZPC  C26   C24  C23   119.21  3.000
 ZPC  CL    C24  C23   119.97  3.000
 ZPC  H26   C26  C27   120.43  3.000
 ZPC  H26   C26  C24   121.25  3.000
 ZPC  C27   C26  C24   118.32  3.000
 ZPC  H27   C27  C26   120.05  3.000
 ZPC  H27   C27  C21   121.62  3.000
 ZPC  C26   C27  C21   118.33  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
 ZPC  CONST_01  C18  C17  N16  C15    0.00   0.0  0
 ZPC  CONST_02  C18  N19  C20  C15    0.00   0.0  0
 ZPC  CONST_03  N19  C20  C15  N16    0.00   0.0  0
 ZPC  CONST_04  N19  C18  C17  N16    0.00   0.0  0
 ZPC  CONST_05  C20  C15  N16  C17    0.00   0.0  0
 ZPC  CONST_06  C20  N19  C18  C17    0.00   0.0  0
 ZPC  CONST_07  C24  C23  N22  C21    0.00   0.0  0
 ZPC  CONST_08  C24  C26  C27  C21    0.00   0.0  0
 ZPC  CONST_09  C26  C27  C21  N22    0.00   0.0  0
 ZPC  CONST_10  C26  C24  C23  N22    0.00   0.0  0
 ZPC  CONST_11  C27  C21  N22  C23    0.00   0.0  0
 ZPC  CONST_12  C27  C26  C24  C23    0.00   0.0  0
 ZPC  CONST_13  C23  N22  C21  N12  180.00   0.0  0
 ZPC  CONST_14  C26  C27  C21  N12  180.00   0.0  0
 ZPC  CONST_15  C15  C13  N12  C11    0.00   0.0  0
 ZPC  CONST_16  C21  N12  C13  C15  180.00   0.0  0
 ZPC  CONST_17  CL   C24  C23  N22  180.00   0.0  0
 ZPC  CONST_18  C27  C26  C24  CL   180.00   0.0  0
 ZPC  CONST_19  O14  C13  N12  C11  180.00   0.0  0
 ZPC  CONST_20  C21  N12  C13  O14    0.00   0.0  0
 ZPC  CONST_21  H27  C27  C21  N12    0.00   0.0  0
 ZPC  CONST_22  H17  C17  N16  C15  180.00   0.0  0
 ZPC  CONST_23  H18  C18  C17  N16  180.00   0.0  0
 ZPC  CONST_24  H23  C23  N22  C21  180.00   0.0  0
 ZPC  CONST_25  H26  C26  C27  C21  180.00   0.0  0
 ZPC  Var_01    N05  C04  C03  N02  -56.84  30.0  1
 ZPC  Var_02    N05  C06  C07  N02   55.68  30.0  1
 ZPC  Var_03    C06  C07  N02  C03  -56.67  30.0  1
 ZPC  Var_04    C06  N05  C04  C03   57.77  30.0  1
 ZPC  Var_05    C07  N02  C03  C04   57.12  30.0  1
 ZPC  Var_06    C07  C06  N05  C04  -57.08  30.0  1
 ZPC  Var_07    N22  C21  N12  C11  132.58  30.0  2
 ZPC  Var_08    O09  C08  N05  C04   -8.58  30.0  2
 ZPC  Var_09    H01  C01  N02  C03   56.80  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
 ZPC  chir_01  C11  O10  N12  C20  negativ

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
 ZPC  plan-1  N12  0.020
 ZPC  plan-1  C21  0.020
 ZPC  plan-1  N22  0.020
 ZPC  plan-1  C23  0.020
 ZPC  plan-1  C24  0.020
 ZPC  plan-1  CL   0.020
 ZPC  plan-1  C26  0.020
 ZPC  plan-1  C27  0.020
 ZPC  plan-1  H23  0.020
 ZPC  plan-1  H26  0.020
 ZPC  plan-1  H27  0.020
 ZPC  plan-2  C11  0.020
 ZPC  plan-2  N12  0.020
 ZPC  plan-2  C13  0.020
 ZPC  plan-2  O14  0.020
 ZPC  plan-2  C15  0.020
 ZPC  plan-2  N16  0.020
 ZPC  plan-2  C17  0.020
 ZPC  plan-2  C18  0.020
 ZPC  plan-2  N19  0.020
 ZPC  plan-2  C20  0.020
 ZPC  plan-2  C21  0.020
 ZPC  plan-2  H17  0.020
 ZPC  plan-2  H18  0.020
 ZPC  plan-3  N05  0.020
 ZPC  plan-3  C08  0.020
 ZPC  plan-3  O09  0.020
 ZPC  plan-3  O10  0.020

