# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 08:40:51 2020
#   Inital geometry file: a 149 line input string
#   Ligand name: 2-[(1S)-1-(3-chlorophenyl)-2-hydroxyethyl]-8-[2-(tetrahydro-2H-pyran-4-ylamino)pyrimidin-4-yl]-2,3,4,5-tetrahydro-1H-pyrrolo[1,2-a][1,4]diazepin-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](N1CCCn2cc(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
 4VG  4VG  2-[(1S)-1-(3-chlorophenyl)-2-hydroxyethyl]-8-[2-(tetrahydro-2H-pyran-4-ylamino)pyrimidin-4-yl]-2,3,4,5-tetrahydro-1H-pyrrolo[1,2-a][1,4]diazepin-1-one  ligand  62  34  .  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_4VG
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
 4VG  C1   C   CR5   0   0.217    0.9081  -0.3012  -0.0582
 4VG  C3   C   C     0   0.560    2.3816  -0.1897  -0.0085
 4VG  C12  C   CR6   0   0.587   -4.8666   0.5673  -0.3118
 4VG  C15  C   CH2   0  -0.329    0.8629  -2.7497   0.4256
 4VG  C16  C   CH2   0  -0.437    1.6729  -3.2736  -0.7534
 4VG  C17  C   CH2   0  -0.357    2.4091  -2.1497  -1.4739
 4VG  C19  C   CH1   0  -0.180    4.5009  -1.3868  -0.3188
 4VG  C20  C   CR6   0   0.151    5.3066  -0.1090  -0.4575
 4VG  C21  C   CR16  0  -0.267    6.1009   0.3912   0.5657
 4VG  C22  C   CR6   0  -0.024    6.8718   1.5219   0.3424
 4VG  C23  C   CR16  0  -0.238    6.8725   2.1793  -0.8754
 4VG  C24  C   CR16  0  -0.254    6.0775   1.6719  -1.8949
 4VG  C25  C   CR16  0  -0.277    5.3080   0.5389  -1.6899
 4VG  C26  C   CH2   0  -0.170    4.7164  -2.1906   0.9562
 4VG  C28  C   CH1   0  -0.062   -7.3079   0.1909  -0.1531
 4VG  C29  C   CH2   0  -0.468   -8.2447  -0.9287  -0.5924
 4VG  C30  C   CH2   0  -0.184   -9.6944  -0.5052  -0.4088
 4VG  N2   N   NR5   0  -0.457    0.2256  -1.4809   0.1195
 4VG  C8   C   CR6   0   0.253   -2.5928   0.7552  -0.2887
 4VG  C6   C   CR15  0  -0.022   -1.0973  -1.2451   0.0641
 4VG  C5   C   CR5   0  -0.015   -1.2977   0.1076  -0.1588
 4VG  N13  N   N     0  -0.506   -3.6693  -0.0179  -0.2024
 4VG  N14  N   NH1   0  -0.669   -5.9360  -0.2532  -0.2479
 4VG  C4   C   CR15  0  -0.460   -0.0138   0.7026  -0.2185
 4VG  C32  C   CH2   0  -0.185   -9.1714   0.9757   1.3239
 4VG  C10  C   CR16  0  -0.018   -3.9960   2.6287  -0.5849
 4VG  O7   O   O     0  -0.461    2.8965   0.7807   0.5204
 4VG  O31  O   O2    0  -0.483   -9.9728  -0.1123   0.9167
 4VG  C9   C   CR16  0  -0.414   -2.7114   2.1340  -0.4914
 4VG  N18  N   NT    0  -0.481    3.0804  -1.1980  -0.5955
 4VG  CL1  CL  CL    0  -0.137    7.8569   2.1336   1.6366
 4VG  C33  C   CH2   0  -0.458   -7.6890   0.6435   1.2564
 4VG  N11  N   N     0  -0.472   -5.0822   1.8737  -0.4958
 4VG  O27  O   OH1   0  -0.655    4.1067  -1.5619   2.0532
 4VG  H1   H   HCH2  0   0.282    0.0875  -3.4564   0.7136
 4VG  H2   H   HCH2  0   0.269    1.5068  -2.6048   1.2942
 4VG  H3   H   HCH2  0   0.250    2.3684  -4.0275  -0.3802
 4VG  H4   H   HCH2  0   0.256    1.0216  -3.7709  -1.4748
 4VG  H5   H   HCH2  0   0.280    3.1539  -2.5727  -2.1471
 4VG  H6   H   HCH2  0   0.273    1.7119  -1.6045  -2.1120
 4VG  H7   H   HCH1  0   0.282    4.8709  -2.0424  -1.1125
 4VG  H8   H   HCR6  0   0.271    6.1089  -0.0739   1.5413
 4VG  H9   H   HCR6  0   0.276    7.4776   3.0620  -1.0302
 4VG  H10  H   HCR6  0   0.264    6.0696   2.1653  -2.8580
 4VG  H11  H   HCR6  0   0.253    4.6989   0.1548  -2.4995
 4VG  H12  H   HCH2  0   0.230    4.2982  -3.1905   0.7880
 4VG  H13  H   HCH2  0   0.216    5.7965  -2.3276   1.0998
 4VG  H14  H   HCH1  0   0.241   -7.4332   1.0361  -0.8349
 4VG  H16  H   HCH2  0   0.229   -8.0456  -1.8295  -0.0015
 4VG  H17  H   HCH2  0   0.199   -9.9256   0.3139  -1.1063
 4VG  H18  H   HCH2  0   0.239  -10.3658  -1.3321  -0.6457
 4VG  H19  H   HCR5  0   0.291   -1.8139  -2.0386   0.2007
 4VG  H20  H   HNH1  0   0.382   -5.7360  -1.2066   0.0113
 4VG  H21  H   HCR5  0   0.255    0.2211   1.7424  -0.3842
 4VG  H22  H   HCH2  0   0.198   -9.3834   1.8586   0.7020
 4VG  H23  H   HCH2  0   0.238   -9.4626   1.2223   2.3460
 4VG  H24  H   HCR6  0   0.265   -4.1615   3.6906  -0.7351
 4VG  H25  H   HCR6  0   0.258   -1.8553   2.7874  -0.5637
 4VG  H26  H   HCH2  0   0.224   -7.4579  -0.1554   1.9684
 4VG  H27  H   HCH2  0   0.242   -7.1061   1.5202   1.5473
 4VG  H28  H   HOH1  0   0.461    4.1695  -2.1556   2.8071
 4VG  H15  H   HCH2  0   0.248   -8.0733  -1.1825  -1.6411

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
 4VG  C23  C24  aromatic  1.389  0.020  1.389
 4VG  C23  C22  aromatic  1.384  0.020  1.384
 4VG  C24  C25  aromatic  1.385  0.020  1.385
 4VG  C10  C9   aromatic  1.380  0.020  1.380
 4VG  C10  N11  aromatic  1.326  0.020  1.326
 4VG  CL1  C22  single    1.738  0.020  1.738
 4VG  C9   C8   aromatic  1.399  0.020  1.399
 4VG  C22  C21  aromatic  1.387  0.020  1.387
 4VG  N11  C12  aromatic  1.337  0.020  1.337
 4VG  C25  C20  aromatic  1.392  0.020  1.392
 4VG  C4   C5   aromatic  1.416  0.020  1.416
 4VG  C4   C1   aromatic  1.372  0.020  1.372
 4VG  O7   C3   double    1.219  0.020  1.219
 4VG  C21  C20  aromatic  1.389  0.020  1.389
 4VG  C8   C5   single    1.454  0.020  1.454
 4VG  C8   N13  aromatic  1.328  0.020  1.328
 4VG  C20  C19  single    1.517  0.020  1.517
 4VG  C12  N13  aromatic  1.337  0.020  1.337
 4VG  C12  N14  single    1.349  0.020  1.349
 4VG  C5   C6   aromatic  1.385  0.020  1.385
 4VG  C3   C1   single    1.479  0.020  1.479
 4VG  C3   N18  single    1.360  0.020  1.360
 4VG  C1   N2   aromatic  1.374  0.020  1.374
 4VG  N14  C28  single    1.445  0.020  1.445
 4VG  C19  N18  single    1.459  0.020  1.459
 4VG  C19  C26  single    1.523  0.020  1.523
 4VG  N18  C17  single    1.459  0.020  1.459
 4VG  C6   N2   aromatic  1.345  0.020  1.345
 4VG  C28  C29  single    1.525  0.020  1.525
 4VG  C28  C33  single    1.529  0.020  1.529
 4VG  N2   C15  single    1.453  0.020  1.453
 4VG  C17  C16  single    1.524  0.020  1.524
 4VG  C29  C30  single    1.521  0.020  1.521
 4VG  C26  O27  single    1.404  0.020  1.404
 4VG  C15  C16  single    1.523  0.020  1.523
 4VG  C33  C32  single    1.521  0.020  1.521
 4VG  C30  O31  single    1.410  0.020  1.410
 4VG  C32  O31  single    1.411  0.020  1.411
 4VG  C15  H1   single    0.970  0.020  1.090
 4VG  C15  H2   single    0.970  0.020  1.090
 4VG  C16  H3   single    0.970  0.020  1.090
 4VG  C16  H4   single    0.970  0.020  1.090
 4VG  C17  H5   single    0.970  0.020  1.090
 4VG  C17  H6   single    0.970  0.020  1.090
 4VG  C19  H7   single    0.970  0.020  1.090
 4VG  C21  H8   single    0.930  0.020  1.080
 4VG  C23  H9   single    0.930  0.020  1.080
 4VG  C24  H10  single    0.930  0.020  1.080
 4VG  C25  H11  single    0.930  0.020  1.080
 4VG  C26  H12  single    0.970  0.020  1.090
 4VG  C26  H13  single    0.970  0.020  1.090
 4VG  C28  H14  single    0.970  0.020  1.090
 4VG  C29  H15  single    0.970  0.020  1.090
 4VG  C29  H16  single    0.970  0.020  1.090
 4VG  C30  H17  single    0.970  0.020  1.090
 4VG  C30  H18  single    0.970  0.020  1.090
 4VG  C6   H19  single    0.930  0.020  1.080
 4VG  N14  H20  single    0.860  0.020  1.020
 4VG  C4   H21  single    0.930  0.020  1.080
 4VG  C32  H22  single    0.970  0.020  1.090
 4VG  C32  H23  single    0.970  0.020  1.090
 4VG  C10  H24  single    0.930  0.020  1.080
 4VG  C9   H25  single    0.930  0.020  1.080
 4VG  C33  H26  single    0.970  0.020  1.090
 4VG  C33  H27  single    0.970  0.020  1.090
 4VG  O27  H28  single    0.850  0.020  0.980

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
 4VG  C4   C1   N2   108.02  3.000
 4VG  N2   C1   C3   123.73  3.000
 4VG  C4   C1   C3   128.19  3.000
 4VG  N18  C3   O7   124.08  3.000
 4VG  N18  C3   C1   116.21  3.000
 4VG  O7   C3   C1   119.70  3.000
 4VG  N11  C12  N14  118.23  3.000
 4VG  N14  C12  N13  116.08  3.000
 4VG  N11  C12  N13  125.68  3.000
 4VG  H2   C15  H1   107.23  3.000
 4VG  H2   C15  N2   108.10  3.000
 4VG  H1   C15  N2   108.09  3.000
 4VG  H2   C15  C16  110.37  3.000
 4VG  H1   C15  C16  111.13  3.000
 4VG  N2   C15  C16  111.75  3.000
 4VG  H4   C16  H3   106.94  3.000
 4VG  H4   C16  C17  108.16  3.000
 4VG  H3   C16  C17  111.29  3.000
 4VG  H4   C16  C15  110.54  3.000
 4VG  H3   C16  C15  108.16  3.000
 4VG  C17  C16  C15  111.65  3.000
 4VG  H6   C17  H5   105.63  3.000
 4VG  H6   C17  N18  108.68  3.000
 4VG  H5   C17  N18  108.11  3.000
 4VG  H6   C17  C16  109.64  3.000
 4VG  H5   C17  C16  109.63  3.000
 4VG  N18  C17  C16  114.75  3.000
 4VG  H7   C19  N18  105.62  3.000
 4VG  H7   C19  C26  104.09  3.000
 4VG  N18  C19  C26  111.40  3.000
 4VG  H7   C19  C20  105.00  3.000
 4VG  C26  C19  C20  116.49  3.000
 4VG  N18  C19  C20  112.99  3.000
 4VG  C25  C20  C21  118.95  3.000
 4VG  C21  C20  C19  122.68  3.000
 4VG  C25  C20  C19  118.26  3.000
 4VG  H8   C21  C22  119.48  3.000
 4VG  H8   C21  C20  120.95  3.000
 4VG  C22  C21  C20  119.55  3.000
 4VG  CL1  C22  C23  119.20  3.000
 4VG  CL1  C22  C21  118.84  3.000
 4VG  C23  C22  C21  121.96  3.000
 4VG  H9   C23  C24  120.90  3.000
 4VG  H9   C23  C22  120.93  3.000
 4VG  C24  C23  C22  118.17  3.000
 4VG  H10  C24  C25  120.05  3.000
 4VG  H10  C24  C23  119.40  3.000
 4VG  C25  C24  C23  120.55  3.000
 4VG  H11  C25  C24  119.46  3.000
 4VG  H11  C25  C20  119.72  3.000
 4VG  C24  C25  C20  120.82  3.000
 4VG  H13  C26  H12  106.34  3.000
 4VG  H13  C26  O27  112.39  3.000
 4VG  H12  C26  O27  111.26  3.000
 4VG  H13  C26  C19  108.34  3.000
 4VG  H12  C26  C19  107.39  3.000
 4VG  O27  C26  C19  110.88  3.000
 4VG  H14  C28  C33  108.52  3.000
 4VG  H14  C28  N14  107.79  3.000
 4VG  C33  C28  N14  112.84  3.000
 4VG  H14  C28  C29  108.52  3.000
 4VG  C33  C28  C29  109.26  3.000
 4VG  N14  C28  C29  109.80  3.000
 4VG  H16  C29  H15  107.36  3.000
 4VG  H16  C29  C30  109.69  3.000
 4VG  H15  C29  C30  109.27  3.000
 4VG  H16  C29  C28  109.68  3.000
 4VG  H15  C29  C28  110.53  3.000
 4VG  C30  C29  C28  110.26  3.000
 4VG  H18  C30  H17  107.29  3.000
 4VG  H18  C30  O31  107.08  3.000
 4VG  H17  C30  O31  110.30  3.000
 4VG  H18  C30  C29  110.44  3.000
 4VG  H17  C30  C29  109.32  3.000
 4VG  O31  C30  C29  112.28  3.000
 4VG  C6   N2   C15  126.40  3.000
 4VG  C15  N2   C1   123.99  3.000
 4VG  C6   N2   C1   109.43  3.000
 4VG  C9   C8   N13  120.96  3.000
 4VG  N13  C8   C5   117.19  3.000
 4VG  C9   C8   C5   121.85  3.000
 4VG  H19  C6   C5   130.02  3.000
 4VG  H19  C6   N2   121.30  3.000
 4VG  C5   C6   N2   108.67  3.000
 4VG  C4   C5   C6   106.61  3.000
 4VG  C6   C5   C8   125.32  3.000
 4VG  C4   C5   C8   128.07  3.000
 4VG  C8   N13  C12  117.76  3.000
 4VG  H20  N14  C28  117.53  3.000
 4VG  H20  N14  C12  115.47  3.000
 4VG  C28  N14  C12  124.65  3.000
 4VG  H21  C4   C5   127.50  3.000
 4VG  H21  C4   C1   125.22  3.000
 4VG  C5   C4   C1   107.27  3.000
 4VG  H23  C32  H22  107.26  3.000
 4VG  H23  C32  C33  110.56  3.000
 4VG  H22  C32  C33  109.75  3.000
 4VG  H23  C32  O31  107.03  3.000
 4VG  H22  C32  O31  110.25  3.000
 4VG  C33  C32  O31  111.86  3.000
 4VG  H24  C10  N11  116.21  3.000
 4VG  H24  C10  C9   120.15  3.000
 4VG  N11  C10  C9   123.64  3.000
 4VG  C32  O31  C30  111.95  3.000
 4VG  H25  C9   C10  121.12  3.000
 4VG  H25  C9   C8   122.63  3.000
 4VG  C10  C9   C8   116.25  3.000
 4VG  C19  N18  C17  118.53  3.000
 4VG  C17  N18  C3   120.47  3.000
 4VG  C19  N18  C3   120.95  3.000
 4VG  H27  C33  H26  107.45  3.000
 4VG  H27  C33  C32  109.45  3.000
 4VG  H26  C33  C32  109.65  3.000
 4VG  H27  C33  C28  110.50  3.000
 4VG  H26  C33  C28  109.33  3.000
 4VG  C32  C33  C28  110.41  3.000
 4VG  C10  N11  C12  115.70  3.000
 4VG  H28  O27  C26  107.93  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
 4VG  CONST_01  C8   C5   C4   C1   180.00   0.0  0
 4VG  CONST_02  C6   C5   C4   C1     0.00   0.0  0
 4VG  CONST_03  C9   C10  N11  C12    0.00   0.0  0
 4VG  CONST_04  C9   C8   N13  C12    0.00   0.0  0
 4VG  CONST_05  C5   C8   N13  C12  180.00   0.0  0
 4VG  CONST_06  C23  C24  C25  C20    0.00   0.0  0
 4VG  CONST_07  C23  C22  C21  C20    0.00   0.0  0
 4VG  CONST_08  C24  C23  C22  C21    0.00   0.0  0
 4VG  CONST_09  C24  C25  C20  C21    0.00   0.0  0
 4VG  CONST_10  C25  C24  C23  C22    0.00   0.0  0
 4VG  CONST_11  C25  C20  C21  C22    0.00   0.0  0
 4VG  CONST_12  C4   C5   C6   N2     0.00   0.0  0
 4VG  CONST_13  C8   C5   C6   N2   180.00   0.0  0
 4VG  CONST_14  N11  C10  C9   C8     0.00   0.0  0
 4VG  CONST_15  N11  C12  N13  C8     0.00   0.0  0
 4VG  CONST_16  C9   C8   C5   C6   180.00   0.0  0
 4VG  CONST_17  N13  C8   C5   C6     0.00   0.0  0
 4VG  CONST_18  C10  C9   C8   C5   180.00   0.0  0
 4VG  CONST_19  C10  C9   C8   N13    0.00   0.0  0
 4VG  CONST_20  C4   C5   C8   N13  180.00   0.0  0
 4VG  CONST_21  C10  N11  C12  N13    0.00   0.0  0
 4VG  CONST_22  C9   C8   C5   C4     0.00   0.0  0
 4VG  CONST_23  C24  C25  C20  C19  180.00   0.0  0
 4VG  CONST_24  C22  C21  C20  C19  180.00   0.0  0
 4VG  CONST_25  CL1  C22  C21  C20  180.00   0.0  0
 4VG  CONST_26  CL1  C22  C23  C24  180.00   0.0  0
 4VG  CONST_27  N14  C12  N13  C8   180.00   0.0  0
 4VG  CONST_28  C10  N11  C12  N14  180.00   0.0  0
 4VG  CONST_29  N11  C12  N14  C28    0.00   0.0  0
 4VG  CONST_30  N13  C12  N14  C28  180.00   0.0  0
 4VG  CONST_31  H24  C10  N11  C12  180.00   0.0  0
 4VG  CONST_32  H10  C24  C25  C20  180.00   0.0  0
 4VG  CONST_33  H9   C23  C22  C21  180.00   0.0  0
 4VG  CONST_34  H11  C25  C20  C21  180.00   0.0  0
 4VG  CONST_35  H8   C21  C22  C23  180.00   0.0  0
 4VG  CONST_36  H21  C4   C5   C8     0.00   0.0  0
 4VG  CONST_37  H19  C6   C5   C8     0.00   0.0  0
 4VG  CONST_38  H25  C9   C8   C5     0.00   0.0  0
 4VG  CONST_39  H20  N14  C12  N13    0.00   0.0  0
 4VG  Var_01    O31  C30  C29  C28  -56.00  30.0  1
 4VG  Var_02    O31  C32  C33  C28   56.31  30.0  1
 4VG  Var_03    C33  C32  O31  C30  -59.70  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
 4VG  chir_01  C19  C20  N18  C26  positiv
 4VG  chir_02  C28  N14  C29  C33  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
 4VG  plan-1  C19  0.020
 4VG  plan-1  C20  0.020
 4VG  plan-1  C21  0.020
 4VG  plan-1  C22  0.020
 4VG  plan-1  C23  0.020
 4VG  plan-1  C24  0.020
 4VG  plan-1  C25  0.020
 4VG  plan-1  CL1  0.020
 4VG  plan-1  H8   0.020
 4VG  plan-1  H9   0.020
 4VG  plan-1  H10  0.020
 4VG  plan-1  H11  0.020
 4VG  plan-2  C1   0.020
 4VG  plan-2  C3   0.020
 4VG  plan-2  C15  0.020
 4VG  plan-2  N2   0.020
 4VG  plan-2  C8   0.020
 4VG  plan-2  C6   0.020
 4VG  plan-2  C5   0.020
 4VG  plan-2  C4   0.020
 4VG  plan-2  H19  0.020
 4VG  plan-2  H21  0.020
 4VG  plan-3  C12  0.020
 4VG  plan-3  C8   0.020
 4VG  plan-3  C5   0.020
 4VG  plan-3  N13  0.020
 4VG  plan-3  N14  0.020
 4VG  plan-3  C10  0.020
 4VG  plan-3  C9   0.020
 4VG  plan-3  N11  0.020
 4VG  plan-3  H24  0.020
 4VG  plan-3  H25  0.020
 4VG  plan-4  C1   0.020
 4VG  plan-4  C3   0.020
 4VG  plan-4  C17  0.020
 4VG  plan-4  C19  0.020
 4VG  plan-4  O7   0.020
 4VG  plan-4  N18  0.020
 4VG  plan-5  C12  0.020
 4VG  plan-5  C28  0.020
 4VG  plan-5  N14  0.020
 4VG  plan-5  H20  0.020

