# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 22:47:25 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: 2-[(1S)-1-(3-chlorophenyl)-2-hydroxyethyl]-7-[2-(tetrahydro-2H-pyran-4-ylamino)pyrimidin-4-yl]-3,4-dihydropyrrolo[1,2-a]pyrazin-1(2H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](N1CCn2cc(cc2C1=O)c3ccnc(NC4CCOCC4)n3)c5cccc(Cl)c5
#
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
 4VF  4VF  2-[(1S)-1-(3-chlorophenyl)-2-hydroxyethyl]-7-[2-(tetrahydro-2H-pyran-4-ylamino)pyrimidin-4-yl]-3,4-dihydropyrrolo[1,2-a]pyrazin-1(2H)-one  ligand  59  33  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4VF
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
 4VF  C2   C   CR5   0   0.240  -0.8092   1.1958  -0.2245
 4VF  C3   C   CH2   0  -0.294  -1.5249  -0.9381   0.7411
 4VF  C12  C   CR6   0   0.590   4.9779   0.4927   0.1169
 4VF  C15  C   CR15  0  -0.460   0.3623   1.8412  -0.5402
 4VF  C16  C   CR5   0  -0.015   1.4206   0.9994  -0.1258
 4VF  C17  C   CR15  0  -0.011   0.8406  -0.1371   0.4233
 4VF  C18  C   CH1   0  -0.169  -4.5463   1.1064  -0.0872
 4VF  C19  C   CR6   0   0.085  -5.3255  -0.1732  -0.3269
 4VF  C20  C   CR16  0  -0.259  -6.4986  -0.4753   0.3539
 4VF  C21  C   CR6   0  -0.019  -7.1902  -1.6393   0.0465
 4VF  C22  C   CR16  0  -0.232  -6.7423  -2.5226  -0.9187
 4VF  C23  C   CR16  0  -0.248  -5.5674  -2.2177  -1.5938
 4VF  C24  C   CR16  0  -0.270  -4.8682  -1.0584  -1.3035
 4VF  C25  C   CH1   0  -0.059   7.2088  -0.5231   0.4401
 4VF  C26  C   CH2   0  -0.471   7.8069  -1.5019   1.4439
 4VF  C27  C   CH2   0  -0.183   9.3145  -1.5897   1.2571
 4VF  C29  C   CH2   0  -0.186   9.1857  -1.0159  -1.0067
 4VF  C30  C   CH2   0  -0.457   7.6695  -0.9040  -0.9680
 4VF  CL1  CL  CL    0  -0.130  -8.6531  -1.9949   0.9107
 4VF  O28  O   O2    0  -0.483   9.6682  -1.9459  -0.0610
 4VF  N5   N   NT    0  -0.499  -3.1355   0.8029   0.1237
 4VF  C31  C   CH2   0  -0.180  -5.1032   2.0372   0.9782
 4VF  C8   C   CR6   0   0.256   2.8512   1.2442  -0.2242
 4VF  C6   C   C     0   0.572  -2.1974   1.5895  -0.4651
 4VF  N13  N   N     0  -0.506   3.6601   0.2803   0.1997
 4VF  N14  N   NH1   0  -0.671   5.7707  -0.4955   0.5784
 4VF  C4   C   CH2   0  -0.317  -2.7427  -0.1447   1.1613
 4VF  C10  C   CR16  0  -0.017   4.7369   2.5474  -0.7797
 4VF  O7   O   O     0  -0.490  -2.4646   2.5528  -1.1730
 4VF  C9   C   CR16  0  -0.413   3.3617   2.4390  -0.7401
 4VF  N1   N   NR5   0  -0.480  -0.4915   0.0021   0.3643
 4VF  N11  N   N     0  -0.471   5.5606   1.5964  -0.3632
 4VF  H1   H   HCH2  0   0.283  -1.1746  -1.5487   1.5708
 4VF  H2   H   HCH2  0   0.270  -1.7502  -1.5966  -0.1009
 4VF  H3   H   HCR5  0   0.257   0.4367   2.8095  -1.0097
 4VF  H4   H   HCR5  0   0.293   1.3000  -1.0131   0.8512
 4VF  H5   H   HCH1  0   0.294  -4.5956   1.6810  -1.0154
 4VF  H6   H   HCR6  0   0.278  -6.8807   0.1737   1.1284
 4VF  H7   H   HCR6  0   0.280  -7.2913  -3.4266  -1.1438
 4VF  H8   H   HCR6  0   0.269  -5.2006  -2.8922  -2.3561
 4VF  H9   H   HCR6  0   0.259  -3.9561  -0.8390  -1.8447
 4VF  H10  H   HCH1  0   0.239   7.5848   0.4788   0.6671
 4VF  H11  H   HCH2  0   0.248   7.5858  -1.1891   2.4670
 4VF  H12  H   HCH2  0   0.230   7.3648  -2.4940   1.3017
 4VF  H13  H   HCH2  0   0.199   9.7740  -0.6276   1.5285
 4VF  H14  H   HCH2  0   0.239   9.7354  -2.3492   1.9176
 4VF  H15  H   HCH2  0   0.238   9.5245  -1.3513  -1.9880
 4VF  H16  H   HCH2  0   0.198   9.6291  -0.0248  -0.8268
 4VF  H17  H   HCH2  0   0.224   7.2152  -1.8582  -1.2526
 4VF  H18  H   HCH2  0   0.242   7.3425  -0.1542  -1.6917
 4VF  H19  H   HOH1  0   0.462  -5.3130   2.0678   2.9035
 4VF  H20  H   HCH2  0   0.235  -4.5127   2.9600   0.9526
 4VF  H21  H   HCH2  0   0.214  -6.1289   2.3107   0.6978
 4VF  H22  H   HNH1  0   0.384   5.3029  -1.3528   0.8274
 4VF  H23  H   HCH2  0   0.280  -3.5623  -0.8373   1.3401
 4VF  H24  H   HCH2  0   0.268  -2.5402   0.3728   2.1015
 4VF  H25  H   HCR6  0   0.265   5.2010   3.4474  -1.1693
 4VF  H26  H   HCR6  0   0.259   2.7292   3.2403  -1.0911
 4VF  O32  O   OH1   0  -0.660  -5.0456   1.4230   2.2421

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
 4VF  C22  C23  aromatic  1.389  0.020  1.389
 4VF  C22  C21  aromatic  1.383  0.020  1.383
 4VF  C10  C9   aromatic  1.380  0.020  1.380
 4VF  C10  N11  aromatic  1.325  0.020  1.325
 4VF  C23  C24  aromatic  1.385  0.020  1.385
 4VF  CL1  C21  single    1.736  0.020  1.736
 4VF  C9   C8   aromatic  1.398  0.020  1.398
 4VF  C21  C20  aromatic  1.388  0.020  1.388
 4VF  N11  C12  aromatic  1.337  0.020  1.337
 4VF  C24  C19  aromatic  1.395  0.020  1.395
 4VF  C15  C16  aromatic  1.414  0.020  1.414
 4VF  C15  C2   aromatic  1.374  0.020  1.374
 4VF  O7   C6   double    1.225  0.020  1.225
 4VF  C8   C16  single    1.455  0.020  1.455
 4VF  C8   N13  aromatic  1.328  0.020  1.328
 4VF  C20  C19  aromatic  1.390  0.020  1.390
 4VF  C12  N13  aromatic  1.337  0.020  1.337
 4VF  C12  N14  single    1.348  0.020  1.348
 4VF  C19  C18  single    1.517  0.020  1.517
 4VF  C16  C17  aromatic  1.389  0.020  1.389
 4VF  C6   C2   single    1.463  0.020  1.463
 4VF  C6   N5   single    1.359  0.020  1.359
 4VF  C2   N1   aromatic  1.368  0.020  1.368
 4VF  N14  C25  single    1.445  0.020  1.445
 4VF  C18  N5   single    1.458  0.020  1.458
 4VF  C18  C31  single    1.520  0.020  1.520
 4VF  N5   C4   single    1.459  0.020  1.459
 4VF  C17  N1   aromatic  1.341  0.020  1.341
 4VF  N1   C3   single    1.447  0.020  1.447
 4VF  C25  C26  single    1.524  0.020  1.524
 4VF  C25  C30  single    1.530  0.020  1.530
 4VF  C26  C27  single    1.522  0.020  1.522
 4VF  C4   C3   single    1.513  0.020  1.513
 4VF  C31  O32  single    1.406  0.020  1.406
 4VF  C27  O28  single    1.410  0.020  1.410
 4VF  C30  C29  single    1.521  0.020  1.521
 4VF  C29  O28  single    1.411  0.020  1.411
 4VF  C3   H1   single    0.970  0.020  1.090
 4VF  C3   H2   single    0.970  0.020  1.090
 4VF  C15  H3   single    0.930  0.020  1.080
 4VF  C17  H4   single    0.930  0.020  1.080
 4VF  C18  H5   single    0.970  0.020  1.090
 4VF  C20  H6   single    0.930  0.020  1.080
 4VF  C22  H7   single    0.930  0.020  1.080
 4VF  C23  H8   single    0.930  0.020  1.080
 4VF  C24  H9   single    0.930  0.020  1.080
 4VF  C25  H10  single    0.970  0.020  1.090
 4VF  C26  H11  single    0.970  0.020  1.090
 4VF  C26  H12  single    0.970  0.020  1.090
 4VF  C27  H13  single    0.970  0.020  1.090
 4VF  C27  H14  single    0.970  0.020  1.090
 4VF  C29  H15  single    0.970  0.020  1.090
 4VF  C29  H16  single    0.970  0.020  1.090
 4VF  C30  H17  single    0.970  0.020  1.090
 4VF  C30  H18  single    0.970  0.020  1.090
 4VF  O32  H19  single    0.850  0.020  0.980
 4VF  C31  H20  single    0.970  0.020  1.090
 4VF  C31  H21  single    0.970  0.020  1.090
 4VF  N14  H22  single    0.860  0.020  1.020
 4VF  C4   H23  single    0.970  0.020  1.090
 4VF  C4   H24  single    0.970  0.020  1.090
 4VF  C10  H25  single    0.930  0.020  1.080
 4VF  C9   H26  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
 4VF  N1   C2   C6   121.73  3.000
 4VF  N1   C2   C15  108.10  3.000
 4VF  C6   C2   C15  130.15  3.000
 4VF  H2   C3   H1   108.42  3.000
 4VF  H2   C3   N1   109.77  3.000
 4VF  H1   C3   N1   109.47  3.000
 4VF  H2   C3   C4   111.35  3.000
 4VF  H1   C3   C4   109.98  3.000
 4VF  N1   C3   C4   107.84  3.000
 4VF  N11  C12  N14  118.13  3.000
 4VF  N14  C12  N13  116.22  3.000
 4VF  N11  C12  N13  125.64  3.000
 4VF  H3   C15  C16  127.60  3.000
 4VF  H3   C15  C2   125.48  3.000
 4VF  C16  C15  C2   106.92  3.000
 4VF  C8   C16  C17  125.10  3.000
 4VF  C17  C16  C15  106.88  3.000
 4VF  C8   C16  C15  128.01  3.000
 4VF  H4   C17  N1   121.70  3.000
 4VF  H4   C17  C16  130.09  3.000
 4VF  N1   C17  C16  108.21  3.000
 4VF  H5   C18  C31  104.88  3.000
 4VF  H5   C18  N5   106.02  3.000
 4VF  C31  C18  N5   112.36  3.000
 4VF  H5   C18  C19  106.62  3.000
 4VF  C31  C18  C19  116.03  3.000
 4VF  N5   C18  C19  110.13  3.000
 4VF  C24  C19  C20  118.79  3.000
 4VF  C20  C19  C18  122.66  3.000
 4VF  C24  C19  C18  118.51  3.000
 4VF  H6   C20  C21  119.09  3.000
 4VF  H6   C20  C19  121.28  3.000
 4VF  C21  C20  C19  119.63  3.000
 4VF  CL1  C21  C22  119.31  3.000
 4VF  CL1  C21  C20  118.77  3.000
 4VF  C22  C21  C20  121.91  3.000
 4VF  H7   C22  C23  120.79  3.000
 4VF  H7   C22  C21  120.98  3.000
 4VF  C23  C22  C21  118.23  3.000
 4VF  H8   C23  C24  119.90  3.000
 4VF  H8   C23  C22  119.50  3.000
 4VF  C24  C23  C22  120.60  3.000
 4VF  H9   C24  C23  119.35  3.000
 4VF  H9   C24  C19  119.82  3.000
 4VF  C23  C24  C19  120.83  3.000
 4VF  H10  C25  N14  107.74  3.000
 4VF  H10  C25  C30  108.39  3.000
 4VF  N14  C25  C30  113.11  3.000
 4VF  H10  C25  C26  108.46  3.000
 4VF  C30  C25  C26  109.16  3.000
 4VF  N14  C25  C26  109.86  3.000
 4VF  H12  C26  H11  107.42  3.000
 4VF  H12  C26  C27  109.37  3.000
 4VF  H11  C26  C27  109.39  3.000
 4VF  H12  C26  C25  109.74  3.000
 4VF  H11  C26  C25  110.70  3.000
 4VF  C27  C26  C25  110.17  3.000
 4VF  H14  C27  H13  107.35  3.000
 4VF  H14  C27  O28  107.05  3.000
 4VF  H13  C27  O28  110.29  3.000
 4VF  H14  C27  C26  110.36  3.000
 4VF  H13  C27  C26  109.46  3.000
 4VF  O28  C27  C26  112.20  3.000
 4VF  H16  C29  H15  107.39  3.000
 4VF  H16  C29  O28  110.25  3.000
 4VF  H15  C29  O28  107.09  3.000
 4VF  H16  C29  C30  109.34  3.000
 4VF  H15  C29  C30  110.80  3.000
 4VF  O28  C29  C30  111.85  3.000
 4VF  H18  C30  H17  107.57  3.000
 4VF  H18  C30  C29  109.40  3.000
 4VF  H17  C30  C29  110.06  3.000
 4VF  H18  C30  C25  110.42  3.000
 4VF  H17  C30  C25  109.36  3.000
 4VF  C29  C30  C25  110.00  3.000
 4VF  C29  O28  C27  111.96  3.000
 4VF  C4   N5   C6   119.89  3.000
 4VF  C4   N5   C18  119.90  3.000
 4VF  C6   N5   C18  119.00  3.000
 4VF  H21  C31  H20  106.71  3.000
 4VF  H21  C31  O32  112.13  3.000
 4VF  H20  C31  O32  111.51  3.000
 4VF  H21  C31  C18  108.41  3.000
 4VF  H20  C31  C18  107.56  3.000
 4VF  O32  C31  C18  110.33  3.000
 4VF  C9   C8   N13  121.05  3.000
 4VF  N13  C8   C16  117.09  3.000
 4VF  C9   C8   C16  121.87  3.000
 4VF  O7   C6   N5   123.73  3.000
 4VF  N5   C6   C2   115.35  3.000
 4VF  O7   C6   C2   120.91  3.000
 4VF  C8   N13  C12  117.72  3.000
 4VF  H22  N14  C25  117.99  3.000
 4VF  H22  N14  C12  115.79  3.000
 4VF  C25  N14  C12  124.51  3.000
 4VF  H24  C4   H23  107.45  3.000
 4VF  H24  C4   N5   110.75  3.000
 4VF  H23  C4   N5   109.12  3.000
 4VF  H24  C4   C3   109.77  3.000
 4VF  H23  C4   C3   108.55  3.000
 4VF  N5   C4   C3   111.09  3.000
 4VF  H25  C10  N11  116.24  3.000
 4VF  H25  C10  C9   120.12  3.000
 4VF  N11  C10  C9   123.64  3.000
 4VF  H26  C9   C10  121.08  3.000
 4VF  H26  C9   C8   122.71  3.000
 4VF  C10  C9   C8   116.21  3.000
 4VF  C17  N1   C3   129.10  3.000
 4VF  C3   N1   C2   120.87  3.000
 4VF  C17  N1   C2   109.89  3.000
 4VF  C10  N11  C12  115.73  3.000
 4VF  H19  O32  C31  108.29  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
 4VF  CONST_01  C8   C16  C15  C2    180.00   0.0  0
 4VF  CONST_02  C17  C16  C15  C2      0.00   0.0  0
 4VF  CONST_03  C16  C17  N1   C2      0.00   0.0  0
 4VF  CONST_04  C9   C10  N11  C12     0.00   0.0  0
 4VF  CONST_05  C9   C8   N13  C12     0.00   0.0  0
 4VF  CONST_06  C16  C8   N13  C12   180.00   0.0  0
 4VF  CONST_07  C9   C8   C16  C15     0.00   0.0  0
 4VF  CONST_08  N13  C8   C16  C15   180.00   0.0  0
 4VF  CONST_09  N1   C17  C16  C15     0.00   0.0  0
 4VF  CONST_10  C17  N1   C2   C15     0.00   0.0  0
 4VF  CONST_11  N1   C2   C15  C16     0.00   0.0  0
 4VF  CONST_12  C10  C9   C8   C16   180.00   0.0  0
 4VF  CONST_13  C9   C8   C16  C17   180.00   0.0  0
 4VF  CONST_14  N13  C8   C16  C17     0.00   0.0  0
 4VF  CONST_15  C22  C23  C24  C19     0.00   0.0  0
 4VF  CONST_16  C22  C21  C20  C19     0.00   0.0  0
 4VF  CONST_17  C23  C22  C21  C20     0.00   0.0  0
 4VF  CONST_18  C23  C24  C19  C20     0.00   0.0  0
 4VF  CONST_19  C24  C23  C22  C21     0.00   0.0  0
 4VF  CONST_20  C24  C19  C20  C21     0.00   0.0  0
 4VF  CONST_21  N11  C10  C9   C8      0.00   0.0  0
 4VF  CONST_22  N1   C17  C16  C8    180.00   0.0  0
 4VF  CONST_23  N11  C12  N13  C8      0.00   0.0  0
 4VF  CONST_24  C10  C9   C8   N13     0.00   0.0  0
 4VF  CONST_25  C10  N11  C12  N13     0.00   0.0  0
 4VF  CONST_26  C4   N5   C6   C2      0.00   0.0  0
 4VF  CONST_27  C23  C24  C19  C18   180.00   0.0  0
 4VF  CONST_28  C21  C20  C19  C18   180.00   0.0  0
 4VF  CONST_29  CL1  C21  C20  C19   180.00   0.0  0
 4VF  CONST_30  CL1  C21  C22  C23   180.00   0.0  0
 4VF  CONST_31  N14  C12  N13  C8    180.00   0.0  0
 4VF  CONST_32  C10  N11  C12  N14   180.00   0.0  0
 4VF  CONST_33  N11  C12  N14  C25     0.00   0.0  0
 4VF  CONST_34  N13  C12  N14  C25   180.00   0.0  0
 4VF  CONST_35  C18  N5   C6   C2    180.00   0.0  0
 4VF  CONST_36  O7   C6   N5   C4    180.00   0.0  0
 4VF  CONST_37  H4   C17  N1   C2    180.00   0.0  0
 4VF  CONST_38  H25  C10  N11  C12   180.00   0.0  0
 4VF  CONST_39  H26  C9   C8   C16     0.00   0.0  0
 4VF  CONST_40  H3   C15  C16  C17   180.00   0.0  0
 4VF  CONST_41  H8   C23  C24  C19   180.00   0.0  0
 4VF  CONST_42  H7   C22  C21  C20   180.00   0.0  0
 4VF  CONST_43  H9   C24  C19  C20   180.00   0.0  0
 4VF  CONST_44  H6   C20  C21  C22   180.00   0.0  0
 4VF  CONST_45  O7   C6   N5   C18     0.00   0.0  0
 4VF  CONST_46  H22  N14  C12  N13     0.00   0.0  0
 4VF  Var_01    C4   C3   N1   C2    -33.41  30.0  1
 4VF  Var_02    C6   N5   C4   C3    -46.98  30.0  1
 4VF  Var_03    N5   C6   C2   C15  -172.02  30.0  1
 4VF  Var_04    O28  C27  C26  C25   -56.07  30.0  1
 4VF  Var_05    O28  C29  C30  C25    56.84  30.0  1
 4VF  Var_06    C30  C29  O28  C27   -59.90  30.0  1
 4VF  Var_07    N1   C3   C4   N5     53.75  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
 4VF  chir_01  C18  C19  N5   C31  positiv
 4VF  chir_02  C25  N14  C26  C30  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
 4VF  plan-1  C18  0.020
 4VF  plan-1  C19  0.020
 4VF  plan-1  C20  0.020
 4VF  plan-1  C21  0.020
 4VF  plan-1  C22  0.020
 4VF  plan-1  C23  0.020
 4VF  plan-1  C24  0.020
 4VF  plan-1  CL1  0.020
 4VF  plan-1  H6   0.020
 4VF  plan-1  H7   0.020
 4VF  plan-1  H8   0.020
 4VF  plan-1  H9   0.020
 4VF  plan-2  C2   0.020
 4VF  plan-2  C3   0.020
 4VF  plan-2  C15  0.020
 4VF  plan-2  C16  0.020
 4VF  plan-2  C17  0.020
 4VF  plan-2  C8   0.020
 4VF  plan-2  C6   0.020
 4VF  plan-2  N1   0.020
 4VF  plan-2  H3   0.020
 4VF  plan-2  H4   0.020
 4VF  plan-3  C12  0.020
 4VF  plan-3  C16  0.020
 4VF  plan-3  C8   0.020
 4VF  plan-3  N13  0.020
 4VF  plan-3  N14  0.020
 4VF  plan-3  C10  0.020
 4VF  plan-3  C9   0.020
 4VF  plan-3  N11  0.020
 4VF  plan-3  H25  0.020
 4VF  plan-3  H26  0.020
 4VF  plan-4  C12  0.020
 4VF  plan-4  C25  0.020
 4VF  plan-4  N14  0.020
 4VF  plan-4  H22  0.020
 4VF  plan-5  C2   0.020
 4VF  plan-5  C18  0.020
 4VF  plan-5  N5   0.020
 4VF  plan-5  C6   0.020
 4VF  plan-5  C4   0.020
 4VF  plan-5  O7   0.020

