# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Aug  4 00:36:23 2022
#   Inital geometry file: a 130 line input string
#   Ligand name: N-(3-chloropyridin-4-yl)-2-[5-(3-cyano-4-hydroxyphenyl)-3-methyl-4-oxo-3,4-dihydro-7H-pyrrolo[2,3-d]pyrimidin-7-yl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C=Nc2n(CC(=O)Nc3ccncc3Cl)cc(c4ccc(O)c(c4)C#N)c2C1=O
#
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
 YNA  YNA  "N-(3-chloropyridin-4-yl)-2-[5-(3-cyano-4-hydroxyphenyl)-3-methyl-4-oxo-3,4-dihydro-7H-pyrrolo[2,3-d]pyrimidin-7-yl]acetamide"
  ligand  46  31  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_YNA
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
 YNA  C28   C   CH3   0  -0.515   -4.3390   0.2843  150.2271
 YNA  C29   C   CR16  0   0.154   -4.0448  -1.5018  148.6063
 YNA  C26   C   CR6   0   0.506   -5.3674   0.4519  148.0171
 YNA  C23   C   CR16  0  -0.286   -6.8871   1.9041  143.9524
 YNA  C22   C   CR16  0  -0.319   -7.6499   2.9985  143.5976
 YNA  C14   C   CR5   0   0.017   -6.2061   0.1088  145.5377
 YNA  C15   C   CR6   0   0.033   -7.0102   1.2862  145.2034
 YNA  C16   C   CR16  0  -0.306   -7.9333   1.8122  146.0920
 YNA  C13   C   CR15  0  -0.057   -5.9345  -0.9276  144.6841
 YNA  C02   C   C     0   0.551   -3.1732  -2.7433  144.2521
 YNA  C04   C   CR6   0   0.554   -1.2470  -3.9686  143.3039
 YNA  C05   C   CR6   0  -0.211   -0.7419  -5.2331  142.9745
 YNA  C07   C   CR16  0  -0.039    0.5373  -5.3622  142.4633
 YNA  C09   C   CR16  0  -0.061    0.8731  -3.1296  142.5668
 YNA  C10   C   CR16  0  -0.378   -0.3882  -2.8903  143.0817
 YNA  C17   C   CR6   0  -0.084   -8.7073   2.9237  145.7485
 YNA  C18   C   CSP   0   0.027   -9.6470   3.4382  146.6850
 YNA  C20   C   CR6   0   0.360   -8.5724   3.5337  144.4928
 YNA  C24   C   CR56  0   0.521   -4.9277  -1.4452  146.5840
 YNA  C25   C   CR56  0  -0.182   -5.5562  -0.2220  146.7696
 YNA  N03   N   NH1   0  -0.750   -2.5283  -3.8623  143.8112
 YNA  N08   N   N     0  -0.404    1.3426  -4.3318  142.2583
 YNA  N12   N   NR5   0  -0.497   -5.1785  -1.8745  145.3259
 YNA  N19   N   NS    0  -0.238  -10.4142   3.8686  147.4309
 YNA  N27   N   NR6   0  -0.511   -4.5847  -0.2968  148.9142
 YNA  N30   N   N     0  -0.454   -4.1738  -2.1138  147.4772
 YNA  O01   O   O     0  -0.417   -2.7030  -1.6309  144.2730
 YNA  O21   O   OH1   0  -0.595   -9.2739   4.6010  144.1022
 YNA  CL06  CL  CL    0  -0.097   -1.6958  -6.6573  143.1982
 YNA  H282  H   HCH3  0   0.261   -3.7546  -0.4139  150.8185
 YNA  H283  H   HCH3  0   0.261   -3.7865   1.2172  150.1385
 YNA  H281  H   HCH3  0   0.262   -5.2785   0.4772  150.7397
 YNA  H291  H   HCR6  0   0.294   -3.4591  -1.9655  149.3904
 YNA  H231  H   HCR6  0   0.265   -6.1628   1.5248  143.2424
 YNA  H221  H   HCR6  0   0.280   -7.5277   3.4579  142.6253
 YNA  H161  H   HCR6  0   0.273   -8.0800   1.3608  147.0626
 YNA  H131  H   HCR5  0   0.300   -6.2535  -1.0820  143.6649
 YNA  H112  H   HCH2  0   0.330   -5.2043  -3.3666  143.8924
 YNA  H111  H   HCH2  0   0.318   -4.5762  -3.8526  145.4571
 YNA  H071  H   HCR6  0   0.287    0.9131  -6.3484  142.2137
 YNA  H091  H   HCR6  0   0.274    1.5369  -2.2904  142.3941
 YNA  H101  H   HCR6  0   0.304   -0.6870  -1.8801  143.3022
 YNA  H1    H   HNH1  0   0.421   -3.0429  -4.7299  143.8848
 YNA  H211  H   HOH1  0   0.484   -9.8835   4.9175  144.7803
 YNA  O31   O   O     0  -0.467   -5.7894   1.5481  148.3477
 YNA  C11   C   CH2   0  -0.472   -4.5908  -3.0358  144.7328

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
 YNA  CL06  C05   single    1.729  0.020  1.729
 YNA  C07   N08   aromatic  1.324  0.020  1.324
 YNA  C07   C05   aromatic  1.384  0.020  1.384
 YNA  N08   C09   aromatic  1.327  0.020  1.327
 YNA  C05   C04   aromatic  1.401  0.020  1.401
 YNA  C09   C10   aromatic  1.383  0.020  1.383
 YNA  C04   C10   aromatic  1.396  0.020  1.396
 YNA  C04   N03   single    1.382  0.020  1.382
 YNA  C22   C23   aromatic  1.380  0.020  1.380
 YNA  C22   C20   aromatic  1.392  0.020  1.392
 YNA  N03   C02   single    1.365  0.020  1.365
 YNA  C23   C15   aromatic  1.401  0.020  1.401
 YNA  O21   C20   single    1.336  0.020  1.336
 YNA  C20   C17   aromatic  1.403  0.020  1.403
 YNA  C02   O01   double    1.208  0.020  1.208
 YNA  C02   C11   single    1.525  0.020  1.525
 YNA  C13   N12   aromatic  1.371  0.020  1.371
 YNA  C13   C14   aromatic  1.370  0.020  1.370
 YNA  C15   C14   single    1.464  0.020  1.464
 YNA  C15   C16   aromatic  1.385  0.020  1.385
 YNA  C11   N12   single    1.430  0.020  1.430
 YNA  C17   C16   aromatic  1.397  0.020  1.397
 YNA  C17   C18   single    1.423  0.020  1.423
 YNA  N12   C24   aromatic  1.353  0.020  1.353
 YNA  C14   C25   aromatic  1.432  0.020  1.432
 YNA  C18   N19   triple    1.153  0.020  1.153
 YNA  C24   C25   aromatic  1.388  0.020  1.388
 YNA  C24   N30   single    1.347  0.020  1.347
 YNA  C25   C26   single    1.430  0.020  1.430
 YNA  N30   C29   double    1.291  0.020  1.291
 YNA  C26   O31   double    1.220  0.020  1.220
 YNA  C26   N27   single    1.406  0.020  1.406
 YNA  C29   N27   single    1.356  0.020  1.356
 YNA  N27   C28   single    1.457  0.020  1.457
 YNA  C28   H282  single    0.970  0.020  1.090
 YNA  C28   H283  single    0.970  0.020  1.090
 YNA  C28   H281  single    0.970  0.020  1.090
 YNA  C29   H291  single    0.930  0.020  1.080
 YNA  C23   H231  single    0.930  0.020  1.080
 YNA  C22   H221  single    0.930  0.020  1.080
 YNA  C16   H161  single    0.930  0.020  1.080
 YNA  C13   H131  single    0.930  0.020  1.080
 YNA  C11   H112  single    0.970  0.020  1.090
 YNA  C11   H111  single    0.970  0.020  1.090
 YNA  C07   H071  single    0.930  0.020  1.080
 YNA  C09   H091  single    0.930  0.020  1.080
 YNA  C10   H101  single    0.930  0.020  1.080
 YNA  N03   H1    single    0.860  0.020  1.020
 YNA  O21   H211  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
 YNA  H281  C28  H283  108.97  3.000
 YNA  H281  C28  H282  108.80  3.000
 YNA  H283  C28  H282  108.81  3.000
 YNA  H281  C28  N27   110.48  3.000
 YNA  H283  C28  N27   110.76  3.000
 YNA  H282  C28  N27   108.98  3.000
 YNA  H291  C29  N30   118.98  3.000
 YNA  H291  C29  N27   115.56  3.000
 YNA  N30   C29  N27   125.46  3.000
 YNA  O31   C26  N27   119.86  3.000
 YNA  N27   C26  C25   112.27  3.000
 YNA  O31   C26  C25   127.87  3.000
 YNA  H231  C23  C15   119.33  3.000
 YNA  H231  C23  C22   118.61  3.000
 YNA  C15   C23  C22   122.06  3.000
 YNA  H221  C22  C20   119.29  3.000
 YNA  H221  C22  C23   120.34  3.000
 YNA  C20   C22  C23   120.37  3.000
 YNA  C25   C14  C13   105.75  3.000
 YNA  C25   C14  C15   129.16  3.000
 YNA  C13   C14  C15   125.09  3.000
 YNA  C16   C15  C14   121.65  3.000
 YNA  C16   C15  C23   117.65  3.000
 YNA  C14   C15  C23   120.69  3.000
 YNA  H161  C16  C17   118.55  3.000
 YNA  H161  C16  C15   120.54  3.000
 YNA  C17   C16  C15   120.90  3.000
 YNA  H131  C13  N12   120.42  3.000
 YNA  H131  C13  C14   129.66  3.000
 YNA  N12   C13  C14   109.89  3.000
 YNA  O01   C02  N03   125.22  3.000
 YNA  O01   C02  C11   122.21  3.000
 YNA  N03   C02  C11   112.57  3.000
 YNA  N03   C04  C10   124.69  3.000
 YNA  N03   C04  C05   119.34  3.000
 YNA  C10   C04  C05   115.97  3.000
 YNA  CL06  C05  C07   118.75  3.000
 YNA  C07   C05  C04   120.29  3.000
 YNA  CL06  C05  C04   120.95  3.000
 YNA  H071  C07  N08   117.48  3.000
 YNA  H071  C07  C05   119.36  3.000
 YNA  N08   C07  C05   123.16  3.000
 YNA  H091  C09  N08   116.60  3.000
 YNA  H091  C09  C10   118.93  3.000
 YNA  N08   C09  C10   124.46  3.000
 YNA  H101  C10  C09   119.46  3.000
 YNA  H101  C10  C04   121.43  3.000
 YNA  C09   C10  C04   119.11  3.000
 YNA  C20   C17  C18   119.70  3.000
 YNA  C18   C17  C16   119.45  3.000
 YNA  C20   C17  C16   120.85  3.000
 YNA  N19   C18  C17   180.00  3.000
 YNA  O21   C20  C17   123.98  3.000
 YNA  C17   C20  C22   118.17  3.000
 YNA  O21   C20  C22   117.85  3.000
 YNA  N30   C24  N12   124.27  3.000
 YNA  N30   C24  C25   127.05  3.000
 YNA  N12   C24  C25   108.68  3.000
 YNA  C24   C25  C14   107.11  3.000
 YNA  C24   C25  C26   118.18  3.000
 YNA  C14   C25  C26   134.55  3.000
 YNA  H1    N03  C04   115.62  3.000
 YNA  H1    N03  C02   116.07  3.000
 YNA  C04   N03  C02   128.30  3.000
 YNA  C09   N08  C07   117.00  3.000
 YNA  C24   N12  C11   124.55  3.000
 YNA  C24   N12  C13   108.56  3.000
 YNA  C11   N12  C13   126.38  3.000
 YNA  C26   N27  C29   123.36  3.000
 YNA  C29   N27  C28   119.47  3.000
 YNA  C26   N27  C28   117.16  3.000
 YNA  C24   N30  C29   113.63  3.000
 YNA  H211  O21  C20   112.85  3.000
 YNA  H111  C11  H112  106.95  3.000
 YNA  H111  C11  N12   109.75  3.000
 YNA  H112  C11  N12   109.52  3.000
 YNA  H111  C11  C02   109.89  3.000
 YNA  H112  C11  C02   109.74  3.000
 YNA  N12   C11  C02   110.91  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
 YNA  CONST_01  C17   C20  C22  C23     0.00   0.0  0
 YNA  CONST_04  C17   C16  C15  C23     0.00   0.0  0
 YNA  CONST_05  C14   C15  C23  C22   180.00   0.0  0
 YNA  CONST_06  C16   C15  C23  C22     0.00   0.0  0
 YNA  CONST_07  C16   C17  C20  C22     0.00   0.0  0
 YNA  CONST_08  C24   N12  C13  C14     0.00   0.0  0
 YNA  CONST_09  C17   C16  C15  C14   180.00   0.0  0
 YNA  CONST_10  N12   C24  C25  C14     0.00   0.0  0
 YNA  CONST_11  C20   C22  C23  C15     0.00   0.0  0
 YNA  CONST_12  N12   C13  C14  C15   180.00   0.0  0
 YNA  CONST_13  C24   C25  C14  C15   180.00   0.0  0
 YNA  CONST_14  C20   C17  C16  C15     0.00   0.0  0
 YNA  CONST_17  C25   C24  N12  C13     0.00   0.0  0
 YNA  CONST_18  C24   C25  C14  C13     0.00   0.0  0
 YNA  CONST_19  N08   C07  C05  C04     0.00   0.0  0
 YNA  CONST_20  N08   C09  C10  C04     0.00   0.0  0
 YNA  CONST_21  C09   N08  C07  C05     0.00   0.0  0
 YNA  CONST_22  C09   C10  C04  C05     0.00   0.0  0
 YNA  CONST_23  C10   C09  N08  C07     0.00   0.0  0
 YNA  CONST_24  C10   C04  C05  C07     0.00   0.0  0
 YNA  CONST_25  N12   C13  C14  C25     0.00   0.0  0
 YNA  CONST_26  C15   C14  C25  C26     0.00   0.0  0
 YNA  CONST_27  C25   C26  N27  C29     0.00   0.0  0
 YNA  CONST_28  N30   C29  N27  C26     0.00   0.0  0
 YNA  CONST_29  N27   C29  N30  C24     0.00   0.0  0
 YNA  CONST_30  O21   C20  C22  C23   180.00   0.0  0
 YNA  CONST_31  C18   C17  C20  C22   180.00   0.0  0
 YNA  CONST_32  C11   N12  C13  C14   180.00   0.0  0
 YNA  CONST_33  C18   C17  C16  C15   180.00   0.0  0
 YNA  CONST_34  O21   C20  C17  C16   180.00   0.0  0
 YNA  CONST_35  C25   C24  N12  C11   180.00   0.0  0
 YNA  CONST_36  N30   C24  N12  C11     0.00   0.0  0
 YNA  CONST_37  N03   C04  C05  C07   180.00   0.0  0
 YNA  CONST_38  N03   C04  C10  C09   180.00   0.0  0
 YNA  CONST_39  CL06  C05  C04  C10   180.00   0.0  0
 YNA  CONST_40  CL06  C05  C07  N08   180.00   0.0  0
 YNA  CONST_41  C25   C26  N27  C28   180.00   0.0  0
 YNA  CONST_42  N30   C29  N27  C28   180.00   0.0  0
 YNA  CONST_43  O31   C26  N27  C29   180.00   0.0  0
 YNA  CONST_44  H161  C16  C15  C23   180.00   0.0  0
 YNA  CONST_45  H231  C23  C15  C14     0.00   0.0  0
 YNA  CONST_46  H161  C16  C15  C14     0.00   0.0  0
 YNA  CONST_47  H221  C22  C23  C15   180.00   0.0  0
 YNA  CONST_48  H131  C13  C14  C15     0.00   0.0  0
 YNA  CONST_49  H231  C23  C15  C16   180.00   0.0  0
 YNA  CONST_50  H071  C07  C05  C04   180.00   0.0  0
 YNA  CONST_51  H091  C09  C10  C04   180.00   0.0  0
 YNA  CONST_52  H101  C10  C04  C05   180.00   0.0  0
 YNA  CONST_53  H091  C09  N08  C07   180.00   0.0  0
 YNA  CONST_54  H071  C07  N08  C09   180.00   0.0  0
 YNA  CONST_55  H221  C22  C20  C17   180.00   0.0  0
 YNA  CONST_56  H231  C23  C22  C20   180.00   0.0  0
 YNA  CONST_57  H161  C16  C17  C20   180.00   0.0  0
 YNA  CONST_58  H131  C13  N12  C24   180.00   0.0  0
 YNA  CONST_59  H131  C13  C14  C25   180.00   0.0  0
 YNA  CONST_60  H101  C10  C09  N08   180.00   0.0  0
 YNA  CONST_61  H291  C29  N27  C26   180.00   0.0  0
 YNA  CONST_62  H291  C29  N30  C24   180.00   0.0  0
 YNA  CONST_63  C05   C04  N03  C02   180.00   0.0  0
 YNA  CONST_64  C10   C04  N03  C02     0.00   0.0  0
 YNA  CONST_65  O31   C26  N27  C28     0.00   0.0  0
 YNA  CONST_66  H1    N03  C04  C05     0.00   0.0  0
 YNA  CONST_67  H1    N03  C04  C10   180.00   0.0  0
 YNA  CONST_68  H291  C29  N27  C28     0.00   0.0  0
 YNA  CONST_69  C04   N03  C02  C11   180.00   0.0  0
 YNA  CONST_70  O01   C02  N03  C04     0.00   0.0  0
 YNA  CONST_71  H1    N03  C02  C11     0.00   0.0  0
 YNA  CONST_72  H1    N03  C02  O01   180.00   0.0  0
 YNA  Var_01    C02   C11  N12  C13    91.58  30.0  2
 YNA  Var_02    C24   N12  C11  C02   -79.33  30.0  2
 YNA  Var_03    H282  C28  N27  C29    -2.87  30.0  3
 YNA  Var_04    H283  C28  N27  C29   116.80  30.0  3
 YNA  Var_05    H281  C28  N27  C29  -122.37  30.0  3
 YNA  Var_06    H282  C28  N27  C26   178.10  30.0  3
 YNA  Var_07    H283  C28  N27  C26   -62.23  30.0  3
 YNA  Var_08    H281  C28  N27  C26    58.60  30.0  3
 YNA  Var_09    H112  C11  N12  C13   -29.69  30.0  2
 YNA  Var_10    H111  C11  N12  C13  -146.82  30.0  2
 YNA  Var_11    H112  C11  N12  C24   159.40  30.0  2
 YNA  Var_12    H111  C11  N12  C24    42.27  30.0  2
 YNA  Var_13    N12   C11  C02  N03   173.40  30.0  3
 YNA  Var_14    O01   C02  C11  N12    -6.58  30.0  1
 YNA  Var_15    H112  C11  C02  N03   -65.45  30.0  3
 YNA  Var_16    H111  C11  C02  N03    51.88  30.0  3
 YNA  Var_17    H112  C11  C02  O01   114.56  30.0  3
 YNA  Var_18    H111  C11  C02  O01  -128.11  30.0  3

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
 YNA  plan-1  C23   0.020
 YNA  plan-1  C22   0.020
 YNA  plan-1  C14   0.020
 YNA  plan-1  C15   0.020
 YNA  plan-1  C16   0.020
 YNA  plan-1  C17   0.020
 YNA  plan-1  C18   0.020
 YNA  plan-1  C20   0.020
 YNA  plan-1  N19   0.020
 YNA  plan-1  O21   0.020
 YNA  plan-1  H231  0.020
 YNA  plan-1  H221  0.020
 YNA  plan-1  H161  0.020
 YNA  plan-2  C04   0.020
 YNA  plan-2  C05   0.020
 YNA  plan-2  C07   0.020
 YNA  plan-2  C09   0.020
 YNA  plan-2  C10   0.020
 YNA  plan-2  N03   0.020
 YNA  plan-2  N08   0.020
 YNA  plan-2  CL06  0.020
 YNA  plan-2  H071  0.020
 YNA  plan-2  H091  0.020
 YNA  plan-2  H101  0.020
 YNA  plan-3  C02   0.020
 YNA  plan-3  C04   0.020
 YNA  plan-3  N03   0.020
 YNA  plan-3  O01   0.020
 YNA  plan-3  H1    0.020
 YNA  plan-3  C11   0.020
 YNA  plan-4  C28   0.020
 YNA  plan-4  C29   0.020
 YNA  plan-4  C26   0.020
 YNA  plan-4  C14   0.020
 YNA  plan-4  C15   0.020
 YNA  plan-4  C13   0.020
 YNA  plan-4  C24   0.020
 YNA  plan-4  C25   0.020
 YNA  plan-4  N12   0.020
 YNA  plan-4  N27   0.020
 YNA  plan-4  N30   0.020
 YNA  plan-4  H291  0.020
 YNA  plan-4  H131  0.020
 YNA  plan-4  O31   0.020
 YNA  plan-4  C11   0.020

