# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 16:31:31 2021
#   Inital geometry file: a 137 line input string
#   Ligand name: (3S)-3-[4-(2-aminopyrimidin-5-yl)-2-(morpholin-4-yl)-5,6-dihydro-7H-pyrrolo[2,3-d]pyrimidin-7-yl]-N-methylpyrrolidine-1-sulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN[S](=O)(=O)N1CC[C@@H](C1)N2CCc3c2nc(nc3c4cnc(N)nc4)N5CCOCC5
#
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
 VY1  VY1  (3S)-3-[4-(2-aminopyrimidin-5-yl)-2-(morpholin-4-yl)-5,6-dihydro-7H-pyrrolo[2,3-d]pyrimidin-7-yl]-N-methylpyrrolidine-1-sulfonamide  ligand  59  32  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_VY1
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
 VY1  C22  C  CR16  0  -0.016  -14.7959   7.5513  24.8736
 VY1  C27  C  CR16  0  -0.053  -16.3738   5.8602  25.2551
 VY1  C21  C  CR6   0  -0.130  -16.0175   7.1931  25.4475
 VY1  C15  C  CR56  0  -0.123  -18.1624   8.0282  26.4471
 VY1  C20  C  CR6   0   0.246  -16.8142   8.1591  26.2118
 VY1  C16  C  CR56  0   0.599  -18.7457   9.0567  27.2082
 VY1  C18  C  CR6   0   0.633  -16.7989  10.1495  27.3613
 VY1  C24  C  CR6   0   0.557  -14.4984   5.4655  24.0520
 VY1  C14  C  CH2   0  -0.554  -19.2345   7.0339  26.1095
 VY1  C8   C  CH2   0  -0.509  -22.3998   9.4114  28.0272
 VY1  C13  C  CH2   0  -0.273  -20.5172   7.8152  26.4448
 VY1  C7   C  CH2   0  -0.271  -23.0045  10.5060  28.8908
 VY1  C29  C  CH2   0  -0.321  -16.6848  12.2172  28.6883
 VY1  C33  C  CH2   0  -0.318  -14.6725  11.3455  27.6449
 VY1  C11  C  CH2   0  -0.261  -20.6120  10.3575  29.2758
 VY1  C30  C  CH2   0  -0.184  -16.2124  13.6099  28.3119
 VY1  C32  C  CH2   0  -0.187  -14.2897  12.7771  27.3151
 VY1  C9   C  CR15  0  -0.080  -20.9556   9.8735  27.8643
 VY1  C1   C  CH3   0  -0.505  -20.3032  14.3513  29.8602
 VY1  N23  N  N     0  -0.448  -14.0435   6.7201  24.1836
 VY1  N26  N  N     0  -0.450  -15.6398   5.0011  24.5754
 VY1  N19  N  N     0  -0.549  -16.1378   9.2303  26.6716
 VY1  N17  N  N     0  -0.535  -18.1068  10.1076  27.6715
 VY1  N12  N  NR5   0  -0.534  -20.0709   8.8370  27.3931
 VY1  N28  N  NT    0  -0.520  -16.1111  11.2439  27.7814
 VY1  N6   N  NR5   0  -0.595  -21.8951  10.8442  29.7972
 VY1  N25  N  NH2   0  -0.814  -13.7576   4.6141  23.3304
 VY1  N2   N  NC1   0  -0.741  -21.3139  13.3813  29.4565
 VY1  O4   O  OS    0  -0.663  -20.9048  12.2273  31.6180
 VY1  O5   O  OS    0  -0.659  -23.2837  12.5808  30.8706
 VY1  O31  O  O2    0  -0.484  -14.8059  13.6899  28.2586
 VY1  S3   S  S     0   1.513  -21.8946  12.2913  30.5583
 VY1  H48  H  HCR6  0   0.272  -14.4265   8.5646  24.9837
 VY1  H51  H  HCR6  0   0.272  -17.2807   5.4563  25.6902
 VY1  H47  H  HCH2  0   0.266  -19.2288   6.7072  25.0692
 VY1  H46  H  HCH2  0   0.261  -19.1627   6.1384  26.7341
 VY1  H40  H  HCH2  0   0.274  -22.9344   9.3014  27.0848
 VY1  H41  H  HCH2  0   0.258  -22.4278   8.4557  28.5555
 VY1  H45  H  HCH2  0   0.242  -20.9326   8.2852  25.5463
 VY1  H44  H  HCH2  0   0.255  -21.2858   7.1808  26.8821
 VY1  H39  H  HCH2  0   0.241  -23.3075  11.3564  28.2726
 VY1  H38  H  HCH2  0   0.269  -23.8743  10.1627  29.4471
 VY1  H52  H  HCH2  0   0.267  -17.7695  12.1779  28.6306
 VY1  H53  H  HCH2  0   0.231  -16.3981  11.9894  29.7230
 VY1  H59  H  HCH2  0   0.273  -14.3309  10.6868  26.8508
 VY1  H58  H  HCH2  0   0.229  -14.1794  11.0299  28.5736
 VY1  H43  H  HCH2  0   0.253  -20.2426   9.5310  29.8863
 VY1  H42  H  HCH2  0   0.267  -19.8530  11.1362  29.2594
 VY1  H54  H  HCH2  0   0.240  -16.5545  14.3292  29.0580
 VY1  H55  H  HCH2  0   0.206  -16.6501  13.8900  27.3434
 VY1  H57  H  HCH2  0   0.241  -13.2037  12.8794  27.3195
 VY1  H56  H  HCH2  0   0.205  -14.6505  13.0244  26.3067
 VY1  H10  H  HCR5  0   0.249  -20.9367  10.7371  27.1835
 VY1  H36  H  HCH3  0   0.259  -20.0965  14.9717  28.9915
 VY1  H34  H  HCH3  0   0.239  -20.6147  15.0019  30.6791
 VY1  H35  H  HCH3  0   0.243  -19.3810  13.8488  30.1408
 VY1  H49  H  HNH2  0   0.402  -12.8426   4.8860  23.0174
 VY1  H50  H  HNH2  0   0.402  -14.0002   3.6398  23.2987
 VY1  H37  H  HNC1  0   0.413  -22.0567  13.7796  28.8952

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
 VY1  N25  C24  single    1.340  0.020  1.340
 VY1  N23  C24  aromatic  1.341  0.020  1.341
 VY1  N23  C22  aromatic  1.316  0.020  1.316
 VY1  C24  N26  aromatic  1.339  0.020  1.339
 VY1  C22  C21  aromatic  1.396  0.020  1.396
 VY1  N26  C27  aromatic  1.319  0.020  1.319
 VY1  C21  C27  aromatic  1.393  0.020  1.393
 VY1  C21  C20  single    1.467  0.020  1.467
 VY1  C14  C15  single    1.501  0.020  1.501
 VY1  C14  C13  single    1.539  0.020  1.539
 VY1  C20  C15  aromatic  1.375  0.020  1.375
 VY1  C20  N19  aromatic  1.348  0.020  1.348
 VY1  C15  C16  aromatic  1.406  0.020  1.406
 VY1  C13  N12  single    1.464  0.020  1.464
 VY1  N19  C18  aromatic  1.326  0.020  1.326
 VY1  C16  N12  single    1.356  0.020  1.356
 VY1  C16  N17  aromatic  1.314  0.020  1.314
 VY1  C18  N28  single    1.359  0.020  1.359
 VY1  C18  N17  aromatic  1.345  0.020  1.345
 VY1  C32  C33  single    1.518  0.020  1.518
 VY1  C32  O31  single    1.411  0.020  1.411
 VY1  N12  C9   single    1.442  0.020  1.442
 VY1  C33  N28  single    1.449  0.020  1.449
 VY1  C9   C8   single    1.525  0.020  1.525
 VY1  C9   C11  single    1.531  0.020  1.531
 VY1  N28  C29  single    1.449  0.020  1.449
 VY1  C8   C7   single    1.520  0.020  1.520
 VY1  O31  C30  single    1.410  0.020  1.410
 VY1  C30  C29  single    1.518  0.020  1.518
 VY1  C7   N6   single    1.472  0.020  1.472
 VY1  C11  N6   single    1.468  0.020  1.468
 VY1  N2   C1   single    1.458  0.020  1.458
 VY1  N2   S3   single    1.655  0.020  1.655
 VY1  N6   S3   single    1.635  0.020  1.635
 VY1  S3   O5   double    1.453  0.020  1.453
 VY1  S3   O4   double    1.451  0.020  1.451
 VY1  C22  H48  single    0.930  0.020  1.080
 VY1  C27  H51  single    0.930  0.020  1.080
 VY1  C14  H47  single    0.970  0.020  1.090
 VY1  C14  H46  single    0.970  0.020  1.090
 VY1  C8   H40  single    0.970  0.020  1.090
 VY1  C8   H41  single    0.970  0.020  1.090
 VY1  C13  H45  single    0.970  0.020  1.090
 VY1  C13  H44  single    0.970  0.020  1.090
 VY1  C7   H39  single    0.970  0.020  1.090
 VY1  C7   H38  single    0.970  0.020  1.090
 VY1  C29  H52  single    0.970  0.020  1.090
 VY1  C29  H53  single    0.970  0.020  1.090
 VY1  C33  H59  single    0.970  0.020  1.090
 VY1  C33  H58  single    0.970  0.020  1.090
 VY1  C11  H43  single    0.970  0.020  1.090
 VY1  C11  H42  single    0.970  0.020  1.090
 VY1  C30  H54  single    0.970  0.020  1.090
 VY1  C30  H55  single    0.970  0.020  1.090
 VY1  C32  H57  single    0.970  0.020  1.090
 VY1  C32  H56  single    0.970  0.020  1.090
 VY1  C9   H10  single    0.970  0.020  1.090
 VY1  C1   H36  single    0.970  0.020  1.090
 VY1  C1   H34  single    0.970  0.020  1.090
 VY1  C1   H35  single    0.970  0.020  1.090
 VY1  N25  H49  single    0.860  0.020  1.020
 VY1  N25  H50  single    0.860  0.020  1.020
 VY1  N2   H37  single    0.890  0.020  1.040

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
 VY1  H48  C22  N23  116.65  3.000
 VY1  H48  C22  C21  119.74  3.000
 VY1  N23  C22  C21  123.61  3.000
 VY1  H51  C27  N26  115.46  3.000
 VY1  H51  C27  C21  121.00  3.000
 VY1  N26  C27  C21  123.52  3.000
 VY1  C20  C21  C27  124.27  3.000
 VY1  C20  C21  C22  121.36  3.000
 VY1  C27  C21  C22  114.35  3.000
 VY1  C14  C15  C16  108.06  3.000
 VY1  C16  C15  C20  115.46  3.000
 VY1  C14  C15  C20  136.48  3.000
 VY1  N19  C20  C15  120.62  3.000
 VY1  N19  C20  C21  115.38  3.000
 VY1  C15  C20  C21  123.99  3.000
 VY1  N12  C16  N17  123.82  3.000
 VY1  N17  C16  C15  125.03  3.000
 VY1  N12  C16  C15  111.15  3.000
 VY1  N28  C18  N17  116.49  3.000
 VY1  N17  C18  N19  125.69  3.000
 VY1  N28  C18  N19  117.82  3.000
 VY1  N25  C24  N26  117.49  3.000
 VY1  N26  C24  N23  125.13  3.000
 VY1  N25  C24  N23  117.38  3.000
 VY1  H46  C14  H47  107.41  3.000
 VY1  H46  C14  C13  110.23  3.000
 VY1  H47  C14  C13  111.36  3.000
 VY1  H46  C14  C15  111.53  3.000
 VY1  H47  C14  C15  114.17  3.000
 VY1  C13  C14  C15  102.12  3.000
 VY1  H41  C8   H40  108.51  3.000
 VY1  H41  C8   C9   109.94  3.000
 VY1  H40  C8   C9   113.77  3.000
 VY1  H41  C8   C7   110.19  3.000
 VY1  H40  C8   C7   111.66  3.000
 VY1  C9   C8   C7   102.67  3.000
 VY1  H44  C13  H45  108.17  3.000
 VY1  H44  C13  N12  111.22  3.000
 VY1  H45  C13  N12  110.33  3.000
 VY1  H44  C13  C14  112.35  3.000
 VY1  H45  C13  C14  110.80  3.000
 VY1  N12  C13  C14  103.97  3.000
 VY1  H38  C7   H39  108.22  3.000
 VY1  H38  C7   N6   111.11  3.000
 VY1  H39  C7   N6   112.21  3.000
 VY1  H38  C7   C8   112.42  3.000
 VY1  H39  C7   C8   110.42  3.000
 VY1  N6   C7   C8   102.44  3.000
 VY1  H53  C29  H52  107.65  3.000
 VY1  H53  C29  N28  110.32  3.000
 VY1  H52  C29  N28  109.74  3.000
 VY1  H53  C29  C30  110.05  3.000
 VY1  H52  C29  C30  109.30  3.000
 VY1  N28  C29  C30  109.75  3.000
 VY1  H58  C33  H59  107.62  3.000
 VY1  H58  C33  N28  110.25  3.000
 VY1  H59  C33  N28  109.79  3.000
 VY1  H58  C33  C32  109.97  3.000
 VY1  H59  C33  C32  109.49  3.000
 VY1  N28  C33  C32  109.69  3.000
 VY1  H42  C11  H43  108.32  3.000
 VY1  H42  C11  N6   112.21  3.000
 VY1  H43  C11  N6   110.37  3.000
 VY1  H42  C11  C9   111.66  3.000
 VY1  H43  C11  C9   110.61  3.000
 VY1  N6   C11  C9   103.66  3.000
 VY1  H55  C30  H54  108.03  3.000
 VY1  H55  C30  O31  110.46  3.000
 VY1  H54  C30  O31  107.53  3.000
 VY1  H55  C30  C29  109.16  3.000
 VY1  H54  C30  C29  109.73  3.000
 VY1  O31  C30  C29  111.83  3.000
 VY1  H56  C32  H57  108.02  3.000
 VY1  H56  C32  O31  110.36  3.000
 VY1  H57  C32  O31  107.52  3.000
 VY1  H56  C32  C33  109.19  3.000
 VY1  H57  C32  C33  109.79  3.000
 VY1  O31  C32  C33  111.88  3.000
 VY1  H10  C9   N12  110.58  3.000
 VY1  H10  C9   C11  108.57  3.000
 VY1  N12  C9   C11  113.00  3.000
 VY1  H10  C9   C8   108.68  3.000
 VY1  C11  C9   C8   102.11  3.000
 VY1  N12  C9   C8   113.46  3.000
 VY1  H35  C1   H34  108.91  3.000
 VY1  H35  C1   H36  107.98  3.000
 VY1  H34  C1   H36  108.28  3.000
 VY1  H35  C1   N2   110.61  3.000
 VY1  H34  C1   N2   113.99  3.000
 VY1  H36  C1   N2   106.87  3.000
 VY1  C24  N23  C22  116.63  3.000
 VY1  C24  N26  C27  116.75  3.000
 VY1  C18  N19  C20  118.58  3.000
 VY1  C18  N17  C16  114.60  3.000
 VY1  C9   N12  C13  121.76  3.000
 VY1  C9   N12  C16  121.86  3.000
 VY1  C13  N12  C16  108.83  3.000
 VY1  C33  N28  C29  113.90  3.000
 VY1  C29  N28  C18  122.28  3.000
 VY1  C33  N28  C18  122.00  3.000
 VY1  S3   N6   C11  117.29  3.000
 VY1  S3   N6   C7   119.36  3.000
 VY1  C11  N6   C7   111.34  3.000
 VY1  H50  N25  H49  118.21  3.000
 VY1  H50  N25  C24  119.99  3.000
 VY1  H49  N25  C24  119.97  3.000
 VY1  H37  N2   S3   111.76  3.000
 VY1  H37  N2   C1   113.59  3.000
 VY1  S3   N2   C1   119.81  3.000
 VY1  C32  O31  C30  110.72  3.000
 VY1  O5   S3   O4   120.25  3.000
 VY1  O4   S3   N2   106.01  3.000
 VY1  O5   S3   N2   110.32  3.000
 VY1  O4   S3   N6   107.52  3.000
 VY1  O5   S3   N6   106.03  3.000
 VY1  N2   S3   N6   105.85  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
 VY1  CONST_01  N26  C24  N23  C22     0.00   0.0  0
 VY1  CONST_02  N26  C27  C21  C22     0.00   0.0  0
 VY1  CONST_05  N23  C24  N26  C27     0.00   0.0  0
 VY1  CONST_06  N23  C22  C21  C27     0.00   0.0  0
 VY1  CONST_09  C24  N23  C22  C21     0.00   0.0  0
 VY1  CONST_10  C24  N26  C27  C21     0.00   0.0  0
 VY1  CONST_11  C16  C15  C20  C21   180.00   0.0  0
 VY1  CONST_12  C18  N19  C20  C21   180.00   0.0  0
 VY1  CONST_13  C18  N19  C20  C15     0.00   0.0  0
 VY1  CONST_14  C18  N17  C16  C15     0.00   0.0  0
 VY1  CONST_15  N23  C22  C21  C20   180.00   0.0  0
 VY1  CONST_16  N26  C27  C21  C20   180.00   0.0  0
 VY1  CONST_17  N17  C16  C15  C20     0.00   0.0  0
 VY1  CONST_18  N17  C18  N19  C20     0.00   0.0  0
 VY1  CONST_19  N19  C20  C15  C16     0.00   0.0  0
 VY1  CONST_20  N19  C18  N17  C16     0.00   0.0  0
 VY1  CONST_21  C14  C15  C20  C21     0.00   0.0  0
 VY1  CONST_22  N28  C18  N19  C20   180.00   0.0  0
 VY1  CONST_23  N28  C18  N17  C16   180.00   0.0  0
 VY1  CONST_24  N25  C24  N23  C22   180.00   0.0  0
 VY1  CONST_25  N25  C24  N26  C27   180.00   0.0  0
 VY1  CONST_26  H51  C27  C21  C22   180.00   0.0  0
 VY1  CONST_27  H48  C22  C21  C27   180.00   0.0  0
 VY1  CONST_28  H49  N25  C24  N23     0.00   0.0  0
 VY1  CONST_29  H50  N25  C24  N23   180.00   0.0  0
 VY1  Var_01    N12  C13  C14  C15   -22.46  30.0  1
 VY1  Var_02    C13  N12  C16  C15   -15.37  30.0  1
 VY1  Var_03    C13  C14  C15  C20  -166.27  30.0  1
 VY1  Var_04    C14  C13  N12  C16    23.86  30.0  1
 VY1  Var_05    C32  C33  N28  C18   143.42  30.0  1
 VY1  Var_06    C30  C29  N28  C18  -143.44  30.0  1
 VY1  Var_07    C11  N6   C7   C8     17.63  30.0  1
 VY1  Var_08    C9   C11  N6   C7      8.47  30.0  1
 VY1  Var_09    N19  C18  N28  C29  -171.57  30.0  1
 VY1  Var_10    N6   C7   C8   C9    -36.60  30.0  1
 VY1  Var_11    O31  C32  C33  N28    54.55  30.0  1
 VY1  Var_12    O31  C30  C29  N28   -54.58  30.0  1
 VY1  Var_13    H57  C32  O31  C30  -179.77  30.0  1
 VY1  Var_14    H54  C30  O31  C32   179.66  30.0  1
 VY1  Var_15    N2   S3   N6   C7    -81.22  30.0  3
 VY1  Var_16    N6   S3   N2   C1   -134.23  30.0  3
 VY1  Var_17    H36  C1   N2   S3   -178.51  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
 VY1  chir_01  C9  N12  C8  C11  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
 VY1  plan-1  C21  0.020
 VY1  plan-1  C15  0.020
 VY1  plan-1  C20  0.020
 VY1  plan-1  C16  0.020
 VY1  plan-1  C18  0.020
 VY1  plan-1  C14  0.020
 VY1  plan-1  N19  0.020
 VY1  plan-1  N17  0.020
 VY1  plan-1  N12  0.020
 VY1  plan-1  N28  0.020
 VY1  plan-2  C22  0.020
 VY1  plan-2  C27  0.020
 VY1  plan-2  C21  0.020
 VY1  plan-2  C20  0.020
 VY1  plan-2  C24  0.020
 VY1  plan-2  N23  0.020
 VY1  plan-2  N26  0.020
 VY1  plan-2  N25  0.020
 VY1  plan-2  H48  0.020
 VY1  plan-2  H51  0.020
 VY1  plan-3  C24  0.020
 VY1  plan-3  N25  0.020
 VY1  plan-3  H49  0.020
 VY1  plan-3  H50  0.020

