# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 17:19:11 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: (6S)-1-chloro-3-[(4-fluorobenzyl)oxy]-6-(pyrrolidin-1-ylcarbonyl)pyrrolo[1,2-a]pyrazin-4(6H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc(COC2=NC(=C3C=C[C@H](N3C2=O)C(=O)N4CCCC4)Cl)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
 552  552  (6S)-1-chloro-3-[(4-fluorobenzyl)oxy]-6-(pyrrolidin-1-ylcarbonyl)pyrrolo[1,2-a]pyrazin-4(6H)-one  ligand  44  27  .  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_552
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
 552  CL11  CL  CL    0  -0.100  -0.5393  -4.4896   0.5182
 552  C10   C   CR6   0  -0.009  -0.5403  -2.8119   0.1234
 552  N09   N   N     0  -0.401   0.6536  -2.1888   0.0793
 552  C12   C   CR56  0   0.506  -1.6951  -2.1568  -0.1263
 552  N23   N   N     0  -0.581  -1.6146  -0.8210  -0.4477
 552  C15   C   CR15  0  -0.269  -2.9280  -0.2468  -0.6443
 552  C16   C   C     0   0.580  -3.2172   0.7862   0.4622
 552  N18   N   NR5   0  -0.471  -4.1397   1.7024   0.1760
 552  C22   C   CH2   0  -0.290  -4.8832   1.8346  -1.0777
 552  C21   C   CH2   0  -0.472  -6.0181   2.7796  -0.7034
 552  C20   C   CH2   0  -0.488  -5.3774   3.6852   0.3423
 552  C19   C   CH2   0  -0.262  -4.5153   2.7246   1.1528
 552  O17   O   O     0  -0.481  -2.6449   0.7039   1.5364
 552  C14   C   CR15  0  -0.194  -3.8126  -1.4481  -0.4787
 552  C13   C   CR15  0  -0.305  -3.0912  -2.5268  -0.1625
 552  C24   C   CR6   0   0.490  -0.4692  -0.0985  -0.5118
 552  O25   O   O     0  -0.462  -0.4372   1.0857  -0.7946
 552  C08   C   CR6   0   0.399   0.7087  -0.9371  -0.2089
 552  O07   O   O2    0  -0.444   1.8460  -0.2700  -0.2581
 552  C06   C   CH2   0  -0.254   3.0509  -0.9877   0.0432
 552  C05   C   CR6   0   0.071   4.1708   0.0035   0.0096
 552  C04   C   CR16  0  -0.273   4.9307   0.1801  -1.1421
 552  C03   C   CR16  0  -0.398   5.9534   1.1168  -1.1869
 552  C26   C   CR16  0  -0.267   4.4476   0.7874   1.1263
 552  C27   C   CR16  0  -0.398   5.4629   1.7311   1.1021
 552  C02   C   CR6   0   0.522   6.1974   1.8771  -0.0598
 552  F01   F   F     0  -0.313   7.1836   2.7862  -0.0916
 552  H15   H   HCR5  0   0.339  -2.9983   0.1956  -1.6422
 552  H22   H   HCH2  0   0.257  -4.2515   2.2708  -1.8567
 552  H22A  H   HCH2  0   0.262  -5.2517   0.8742  -1.4369
 552  H21   H   HCH2  0   0.258  -6.4019   3.3166  -1.5693
 552  H21A  H   HCH2  0   0.244  -6.8431   2.2165  -0.2623
 552  H20   H   HCH2  0   0.243  -4.7510   4.4364  -0.1432
 552  H20A  H   HCH2  0   0.257  -6.1030   4.2070   0.9644
 552  H19   H   HCH2  0   0.245  -5.0807   2.2733   1.9723
 552  H19A  H   HCH2  0   0.255  -3.6318   3.2003   1.5771
 552  H14   H   HCR5  0   0.302  -4.8852  -1.4028  -0.5888
 552  H13   H   HCR5  0   0.287  -3.4594  -3.5218   0.0322
 552  H06   H   HCH2  0   0.256   2.9636  -1.4541   1.0272
 552  H06A  H   HCH2  0   0.257   3.1985  -1.7821  -0.6916
 552  H04   H   HCR6  0   0.268   4.7300  -0.4233  -2.0188
 552  H03   H   HCR6  0   0.283   6.5491   1.2502  -2.0804
 552  H26   H   HCR6  0   0.268   3.8686   0.6604   2.0328
 552  H27   H   HCR6  0   0.283   5.6803   2.3394   1.9702

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
 552  C10  CL11  single    1.723  0.020  1.723
 552  C12  C10   double    1.351  0.020  1.351
 552  N09  C10   single    1.348  0.020  1.348
 552  C08  N09   double    1.286  0.020  1.286
 552  N23  C12   single    1.376  0.020  1.376
 552  C13  C12   single    1.445  0.020  1.445
 552  C15  N23   single    1.447  0.020  1.447
 552  C24  N23   single    1.356  0.020  1.356
 552  C16  C15   single    1.541  0.020  1.541
 552  C15  C14   single    1.501  0.020  1.501
 552  C15  H15   single    0.970  0.020  1.090
 552  N18  C16   single    1.331  0.020  1.331
 552  C16  O17   double    1.220  0.020  1.220
 552  C22  N18   single    1.464  0.020  1.464
 552  C19  N18   single    1.463  0.020  1.463
 552  C21  C22   single    1.524  0.020  1.524
 552  C22  H22   single    0.970  0.020  1.090
 552  C22  H22A  single    0.970  0.020  1.090
 552  C21  C20   single    1.525  0.020  1.525
 552  C21  H21   single    0.970  0.020  1.090
 552  C21  H21A  single    0.970  0.020  1.090
 552  C20  C19   single    1.524  0.020  1.524
 552  C20  H20   single    0.970  0.020  1.090
 552  C20  H20A  single    0.970  0.020  1.090
 552  C19  H19   single    0.970  0.020  1.090
 552  C19  H19A  single    0.970  0.020  1.090
 552  C14  C13   double    1.336  0.020  1.336
 552  C14  H14   single    0.930  0.020  1.080
 552  C13  H13   single    0.930  0.020  1.080
 552  O25  C24   double    1.218  0.020  1.218
 552  C24  C08   single    1.477  0.020  1.477
 552  O07  C08   single    1.319  0.020  1.319
 552  O07  C06   single    1.434  0.020  1.434
 552  C06  C05   single    1.496  0.020  1.496
 552  C06  H06   single    0.970  0.020  1.090
 552  C06  H06A  single    0.970  0.020  1.090
 552  C04  C05   aromatic  1.391  0.020  1.391
 552  C05  C26   aromatic  1.392  0.020  1.392
 552  C04  C03   aromatic  1.388  0.020  1.388
 552  C04  H04   single    0.930  0.020  1.080
 552  C03  C02   aromatic  1.381  0.020  1.381
 552  C03  H03   single    0.930  0.020  1.080
 552  C26  C27   aromatic  1.386  0.020  1.386
 552  C26  H26   single    0.930  0.020  1.080
 552  C02  C27   aromatic  1.382  0.020  1.382
 552  C27  H27   single    0.930  0.020  1.080
 552  C02  F01   single    1.342  0.020  1.342

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
 552  C12   C10  N09   121.81  3.000
 552  N09   C10  CL11  117.20  3.000
 552  C12   C10  CL11  120.99  3.000
 552  C08   N09  C10   119.70  3.000
 552  C13   C12  N23   107.41  3.000
 552  C13   C12  C10   134.94  3.000
 552  N23   C12  C10   117.64  3.000
 552  C24   N23  C15   123.29  3.000
 552  C24   N23  C12   125.29  3.000
 552  C15   N23  C12   111.34  3.000
 552  H15   C15  C14   112.74  3.000
 552  H15   C15  C16   111.83  3.000
 552  C14   C15  C16   110.28  3.000
 552  H15   C15  N23   110.05  3.000
 552  C14   C15  N23   101.67  3.000
 552  C16   C15  N23   109.80  3.000
 552  O17   C16  N18   124.11  3.000
 552  O17   C16  C15   119.93  3.000
 552  N18   C16  C15   115.91  3.000
 552  C19   N18  C22   112.24  3.000
 552  C19   N18  C16   121.01  3.000
 552  C22   N18  C16   126.75  3.000
 552  H22A  C22  H22   108.18  3.000
 552  H22A  C22  C21   112.07  3.000
 552  H22   C22  C21   110.97  3.000
 552  H22A  C22  N18   112.00  3.000
 552  H22   C22  N18   110.65  3.000
 552  C21   C22  N18   102.94  3.000
 552  H21A  C21  H21   108.02  3.000
 552  H21A  C21  C20   110.29  3.000
 552  H21   C21  C20   113.62  3.000
 552  H21A  C21  C22   110.01  3.000
 552  H21   C21  C22   111.91  3.000
 552  C20   C21  C22   102.94  3.000
 552  H20A  C20  H20   107.86  3.000
 552  H20A  C20  C19   112.04  3.000
 552  H20   C20  C19   110.22  3.000
 552  H20A  C20  C21   113.35  3.000
 552  H20   C20  C21   110.17  3.000
 552  C19   C20  C21   103.18  3.000
 552  H19A  C19  H19   107.92  3.000
 552  H19A  C19  C20   112.99  3.000
 552  H19   C19  C20   111.49  3.000
 552  H19A  C19  N18   110.91  3.000
 552  H19   C19  N18   110.18  3.000
 552  C20   C19  N18   103.33  3.000
 552  H14   C14  C13   126.51  3.000
 552  H14   C14  C15   122.74  3.000
 552  C13   C14  C15   110.74  3.000
 552  H13   C13  C14   127.11  3.000
 552  H13   C13  C12   124.17  3.000
 552  C14   C13  C12   108.73  3.000
 552  C08   C24  O25   125.35  3.000
 552  C08   C24  N23   111.18  3.000
 552  O25   C24  N23   123.46  3.000
 552  O07   C08  C24   113.12  3.000
 552  O07   C08  N09   122.51  3.000
 552  C24   C08  N09   124.37  3.000
 552  C06   O07  C08   117.60  3.000
 552  H06A  C06  H06   107.84  3.000
 552  H06A  C06  C05   111.45  3.000
 552  H06   C06  C05   111.28  3.000
 552  H06A  C06  O07   109.64  3.000
 552  H06   C06  O07   109.62  3.000
 552  C05   C06  O07   107.01  3.000
 552  C26   C05  C04   118.94  3.000
 552  C26   C05  C06   120.26  3.000
 552  C04   C05  C06   120.78  3.000
 552  H04   C04  C03   119.11  3.000
 552  H04   C04  C05   119.88  3.000
 552  C03   C04  C05   121.00  3.000
 552  H03   C03  C02   120.57  3.000
 552  H03   C03  C04   121.04  3.000
 552  C02   C03  C04   118.39  3.000
 552  H26   C26  C27   119.07  3.000
 552  H26   C26  C05   119.93  3.000
 552  C27   C26  C05   120.99  3.000
 552  H27   C27  C02   120.55  3.000
 552  H27   C27  C26   121.05  3.000
 552  C02   C27  C26   118.40  3.000
 552  F01   C02  C27   118.82  3.000
 552  F01   C02  C03   118.91  3.000
 552  C27   C02  C03   122.27  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
 552  CONST_01  C02  C03  C04  C05     0.00   0.0  0
 552  CONST_02  C02  C27  C26  C05     0.00   0.0  0
 552  CONST_03  C27  C26  C05  C04     0.00   0.0  0
 552  CONST_04  C27  C02  C03  C04     0.00   0.0  0
 552  CONST_05  C26  C05  C04  C03     0.00   0.0  0
 552  CONST_06  C26  C27  C02  C03     0.00   0.0  0
 552  CONST_07  C08  C24  N23  C12     0.00   0.0  0
 552  CONST_08  C08  C24  N23  C15   180.00   0.0  0
 552  CONST_09  C03  C04  C05  C06   180.00   0.0  0
 552  CONST_10  C27  C26  C05  C06   180.00   0.0  0
 552  CONST_11  F01  C02  C03  C04   180.00   0.0  0
 552  CONST_12  F01  C02  C27  C26   180.00   0.0  0
 552  CONST_13  C22  N18  C16  C15     0.00   0.0  0
 552  CONST_14  C19  N18  C16  C15   180.00   0.0  0
 552  CONST_15  O25  C24  N23  C12   180.00   0.0  0
 552  CONST_16  O25  C24  N23  C15     0.00   0.0  0
 552  CONST_17  H03  C03  C04  C05   180.00   0.0  0
 552  CONST_18  H27  C27  C26  C05   180.00   0.0  0
 552  CONST_19  H26  C26  C05  C04   180.00   0.0  0
 552  CONST_20  H04  C04  C05  C26   180.00   0.0  0
 552  CONST_21  O17  C16  N18  C22   180.00   0.0  0
 552  CONST_22  O17  C16  N18  C19     0.00   0.0  0
 552  Var_01    C20  C21  C22  N18    32.89  30.0  1
 552  Var_02    C21  C20  C19  N18    30.33  30.0  1
 552  Var_03    C20  C19  N18  C22    -9.99  30.0  1
 552  Var_04    C19  C20  C21  C22   -39.45  30.0  1
 552  Var_05    C19  N18  C22  C21   -14.47  30.0  1
 552  Var_06    C05  C06  O07  C08  -176.21  30.0  3
 552  Var_07    C04  C05  C06  O07   -95.00  30.0  2

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
 552  chir_01  C15  N23  C16  C14  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
 552  plan-1  C06   0.020
 552  plan-1  C05   0.020
 552  plan-1  C04   0.020
 552  plan-1  C03   0.020
 552  plan-1  C26   0.020
 552  plan-1  C27   0.020
 552  plan-1  C02   0.020
 552  plan-1  F01   0.020
 552  plan-1  H04   0.020
 552  plan-1  H03   0.020
 552  plan-1  H26   0.020
 552  plan-1  H27   0.020
 552  plan-2  C15   0.020
 552  plan-2  C16   0.020
 552  plan-2  N18   0.020
 552  plan-2  C22   0.020
 552  plan-2  C19   0.020
 552  plan-2  O17   0.020
 552  plan-3  CL11  0.020
 552  plan-3  C10   0.020
 552  plan-3  N09   0.020
 552  plan-3  C12   0.020
 552  plan-3  N23   0.020
 552  plan-3  C15   0.020
 552  plan-3  C16   0.020
 552  plan-3  C14   0.020
 552  plan-3  C13   0.020
 552  plan-3  C24   0.020
 552  plan-3  O25   0.020
 552  plan-3  C08   0.020
 552  plan-3  O07   0.020
 552  plan-3  H15   0.020
 552  plan-3  H14   0.020
 552  plan-3  H13   0.020

