# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 13:34:48 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 6-(2,4-difluorophenoxy)-8-methyl-2-{[(1S)-1-methyl-2-(methylsulfonyl)ethyl]amino}pyrido[2,3-d]pyrimidin-7(8H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](C[S](C)(=O)=O)Nc1ncc2C=C(Oc3ccc(F)cc3F)C(=O)N(C)c2n1
#
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
 891  891  6-(2,4-difluorophenoxy)-8-methyl-2-{[(1S)-1-methyl-2-(methylsulfonyl)ethyl]amino}pyrido[2,3-d]pyrimidin-7(8H)-one  ligand  47  29  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_891
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
 891  C16   C  CR6   0   0.629  -2.3847   0.6943   0.0115
 891  C13   C  CR66  0  -0.116   0.0573   0.2184   0.9999
 891  C11   C  CR16  0  -0.223   1.3712  -0.0442   1.4686
 891  C12   C  CR66  0   0.558  -0.2846  -0.0762  -0.3323
 891  C10   C  CR6   0   0.132   2.2635  -0.5970   0.6299
 891  C1    C  CH1   0  -0.090  -4.6880   1.5561   0.2203
 891  C2    C  CH3   0  -0.645  -4.6416   3.0754   0.0941
 891  C5    C  CH3   0  -0.790  -7.9074  -1.0450  -0.2852
 891  N8    N  NR6   0  -0.587   0.6480  -0.6291  -1.1680
 891  C3    C  CH2   0  -0.631  -6.0238   1.0353  -0.2939
 891  C25   C  CR6   0   0.528   6.8710   0.9308  -0.4229
 891  C24   C  CR16  0  -0.415   5.6668   1.5926  -0.5310
 891  C23   C  CR16  0  -0.315   4.5176   0.9788  -0.0482
 891  C26   C  CR16  0  -0.558   6.9691  -0.3252   0.1483
 891  C27   C  CR6   0   0.487   5.8116  -0.9142   0.6086
 891  F28   F  F     0  -0.301   5.8689  -2.1307   1.1594
 891  C21   C  CR6   0   0.221   4.5765  -0.2822   0.5221
 891  O20   O  O2    0  -0.489   3.5120  -0.9423   1.0533
 891  C9    C  CR6   0   0.529   1.9374  -0.9339  -0.7548
 891  O18   O  O     0  -0.452   2.7510  -1.4494  -1.5000
 891  C14   C  CR16  0  -0.030  -0.9647   0.7773   1.7639
 891  N15   N  N     0  -0.469  -2.1673   1.0207   1.2979
 891  N17   N  N     0  -0.501  -1.4872   0.1592  -0.8189
 891  C22   C  CH3   0  -0.537   0.2544  -0.9283  -2.5399
 891  N19   N  NH1   0  -0.650  -3.6069   0.9131  -0.4939
 891  S4    S  S     0   1.202  -6.1593  -0.7523  -0.1335
 891  O6    O  OS    0  -0.682  -5.7357  -1.1279   1.2162
 891  O7    O  OS    0  -0.682  -5.4929  -1.3948  -1.2672
 891  H11   H  HCR6  0   0.294   1.6379   0.1915   2.4920
 891  H1    H  HCH1  0   0.278  -4.5938   1.2899   1.2725
 891  H2    H  HCH3  0   0.232  -4.7386   3.3874  -0.9466
 891  H2A   H  HCH3  0   0.239  -5.4477   3.5347   0.6667
 891  H2B   H  HCH3  0   0.248  -3.6953   3.4536   0.4797
 891  H5    H  HCH3  0   0.295  -8.2525  -0.6789  -1.2497
 891  H5A   H  HCH3  0   0.311  -8.0555  -2.1220  -0.2211
 891  H5B   H  HCH3  0   0.294  -8.4360  -0.5483   0.5246
 891  H3    H  HCH2  0   0.318  -6.8356   1.4758   0.2867
 891  H3A   H  HCH2  0   0.309  -6.1877   1.2770  -1.3466
 891  H24   H  HCR6  0   0.290   5.6135   2.5748  -0.9807
 891  H23   H  HCR6  0   0.298   3.5742   1.5045  -0.1213
 891  H26   H  HCR6  0   0.309   7.9188  -0.8377   0.2308
 891  H14   H  HCR6  0   0.283  -0.7758   1.0356   2.8015
 891  H22   H  HCH3  0   0.261  -0.0753  -0.0213  -3.0409
 891  H22A  H  HCH3  0   0.271   1.1040  -1.3407  -3.0695
 891  H22B  H  HCH3  0   0.261  -0.5598  -1.6493  -2.5503
 891  HN19  H  HNH1  0   0.400  -3.7158   0.7379  -1.4813
 891  F29   F  F     0  -0.312   7.9875   1.5142  -0.8825

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
 891  C16  N15   aromatic  1.345  0.020  1.345
 891  C16  N17   aromatic  1.335  0.020  1.335
 891  C16  N19   single    1.341  0.020  1.341
 891  C13  C11   single    1.419  0.020  1.419
 891  C13  C12   aromatic  1.407  0.020  1.407
 891  C13  C14   aromatic  1.393  0.020  1.393
 891  C11  C10   double    1.344  0.020  1.344
 891  C12  N8    single    1.369  0.020  1.369
 891  C12  N17   aromatic  1.318  0.020  1.318
 891  C10  O20   single    1.363  0.020  1.363
 891  C10  C9    single    1.462  0.020  1.462
 891  C1   C2    single    1.525  0.020  1.525
 891  C1   C3    single    1.523  0.020  1.523
 891  C1   N19   single    1.446  0.020  1.446
 891  C5   S4    single    1.779  0.020  1.779
 891  N8   C9    single    1.388  0.020  1.388
 891  N8   C22   single    1.458  0.020  1.458
 891  C3   S4    single    1.800  0.020  1.800
 891  F29  C25   single    1.341  0.020  1.341
 891  C25  C24   aromatic  1.378  0.020  1.378
 891  C25  C26   aromatic  1.383  0.020  1.383
 891  C24  C23   aromatic  1.389  0.020  1.389
 891  C23  C21   aromatic  1.385  0.020  1.385
 891  C26  C27   aromatic  1.378  0.020  1.378
 891  C27  F28   single    1.337  0.020  1.337
 891  C27  C21   aromatic  1.390  0.020  1.390
 891  C21  O20   single    1.361  0.020  1.361
 891  C9   O18   double    1.218  0.020  1.218
 891  C14  N15   aromatic  1.312  0.020  1.312
 891  S4   O6    double    1.464  0.020  1.464
 891  S4   O7    double    1.464  0.020  1.464
 891  C11  H11   single    0.930  0.020  1.080
 891  C1   H1    single    0.970  0.020  1.090
 891  C2   H2    single    0.970  0.020  1.090
 891  C2   H2A   single    0.970  0.020  1.090
 891  C2   H2B   single    0.970  0.020  1.090
 891  C5   H5    single    0.970  0.020  1.090
 891  C5   H5A   single    0.970  0.020  1.090
 891  C5   H5B   single    0.970  0.020  1.090
 891  C3   H3    single    0.970  0.020  1.090
 891  C3   H3A   single    0.970  0.020  1.090
 891  C24  H24   single    0.930  0.020  1.080
 891  C23  H23   single    0.930  0.020  1.080
 891  C26  H26   single    0.930  0.020  1.080
 891  C14  H14   single    0.930  0.020  1.080
 891  C22  H22   single    0.970  0.020  1.090
 891  C22  H22A  single    0.970  0.020  1.090
 891  C22  H22B  single    0.970  0.020  1.090
 891  N19  HN19  single    0.860  0.020  1.020

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
 891  N19   C16  N17   116.36  3.000
 891  N19   C16  N15   117.93  3.000
 891  N17   C16  N15   125.71  3.000
 891  C14   C13  C12   115.16  3.000
 891  C14   C13  C11   124.91  3.000
 891  C12   C13  C11   119.93  3.000
 891  H11   C11  C10   121.03  3.000
 891  H11   C11  C13   119.97  3.000
 891  C10   C11  C13   119.00  3.000
 891  N17   C12  N8    117.92  3.000
 891  N17   C12  C13   122.27  3.000
 891  N8    C12  C13   119.82  3.000
 891  C9    C10  O20   116.12  3.000
 891  C9    C10  C11   122.54  3.000
 891  O20   C10  C11   121.25  3.000
 891  H1    C1   N19   107.68  3.000
 891  H1    C1   C3    108.57  3.000
 891  N19   C1   C3    109.68  3.000
 891  H1    C1   C2    108.70  3.000
 891  N19   C1   C2    112.29  3.000
 891  C3    C1   C2    109.84  3.000
 891  H2B   C2   H2A   108.07  3.000
 891  H2B   C2   H2    108.40  3.000
 891  H2A   C2   H2    108.35  3.000
 891  H2B   C2   C1    110.05  3.000
 891  H2A   C2   C1    110.71  3.000
 891  H2    C2   C1    111.17  3.000
 891  H5B   C5   H5A   109.99  3.000
 891  H5B   C5   H5    110.63  3.000
 891  H5A   C5   H5    109.99  3.000
 891  H5B   C5   S4    109.82  3.000
 891  H5A   C5   S4    106.94  3.000
 891  H5    C5   S4    109.39  3.000
 891  C22   N8   C9    119.07  3.000
 891  C22   N8   C12   118.25  3.000
 891  C9    N8   C12   122.67  3.000
 891  H3A   C3   H3    108.18  3.000
 891  H3A   C3   S4    107.12  3.000
 891  H3    C3   S4    107.32  3.000
 891  H3A   C3   C1    112.41  3.000
 891  H3    C3   C1    109.56  3.000
 891  S4    C3   C1    112.06  3.000
 891  C26   C25  C24   122.03  3.000
 891  C26   C25  F29   118.52  3.000
 891  C24   C25  F29   119.45  3.000
 891  H24   C24  C23   120.33  3.000
 891  H24   C24  C25   120.77  3.000
 891  C23   C24  C25   118.90  3.000
 891  H23   C23  C21   120.46  3.000
 891  H23   C23  C24   118.87  3.000
 891  C21   C23  C24   120.66  3.000
 891  H26   C26  C27   120.62  3.000
 891  H26   C26  C25   121.58  3.000
 891  C27   C26  C25   117.80  3.000
 891  C21   C27  F28   118.52  3.000
 891  C21   C27  C26   122.09  3.000
 891  F28   C27  C26   119.39  3.000
 891  O20   C21  C27   116.77  3.000
 891  O20   C21  C23   124.69  3.000
 891  C27   C21  C23   118.51  3.000
 891  C21   O20  C10   118.20  3.000
 891  O18   C9   N8    122.10  3.000
 891  O18   C9   C10   121.88  3.000
 891  N8    C9   C10   116.02  3.000
 891  H14   C14  N15   117.04  3.000
 891  H14   C14  C13   119.46  3.000
 891  N15   C14  C13   123.50  3.000
 891  C14   N15  C16   116.28  3.000
 891  C12   N17  C16   117.08  3.000
 891  H22B  C22  H22A  109.29  3.000
 891  H22B  C22  H22   108.76  3.000
 891  H22A  C22  H22   109.28  3.000
 891  H22B  C22  N8    110.31  3.000
 891  H22A  C22  N8    109.06  3.000
 891  H22   C22  N8    110.13  3.000
 891  HN19  N19  C1    118.68  3.000
 891  HN19  N19  C16   116.04  3.000
 891  C1    N19  C16   124.60  3.000
 891  O7    S4   O6    118.03  3.000
 891  O7    S4   C3    109.43  3.000
 891  O6    S4   C3    108.37  3.000
 891  O7    S4   C5    108.01  3.000
 891  O6    S4   C5    108.72  3.000
 891  C3    S4   C5    103.28  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
 891  CONST_01  C13   C14  N15  C16    0.00   0.0  0
 891  CONST_02  C13   C12  N17  C16    0.00   0.0  0
 891  CONST_03  N15   C14  C13  C12    0.00   0.0  0
 891  CONST_04  N15   C16  N17  C12    0.00   0.0  0
 891  CONST_05  C21   C23  C24  C25    0.00   0.0  0
 891  CONST_06  C21   C27  C26  C25    0.00   0.0  0
 891  CONST_07  C27   C26  C25  C24    0.00   0.0  0
 891  CONST_08  C27   C21  C23  C24    0.00   0.0  0
 891  CONST_09  C26   C25  C24  C23    0.00   0.0  0
 891  CONST_10  C26   C27  C21  C23    0.00   0.0  0
 891  CONST_11  N17   C12  C13  C14    0.00   0.0  0
 891  CONST_12  N17   C16  N15  C14    0.00   0.0  0
 891  CONST_13  C10   C9   N8   C12    0.00   0.0  0
 891  CONST_14  N19   C16  N17  C12  180.00   0.0  0
 891  CONST_15  C23   C24  C25  F29  180.00   0.0  0
 891  CONST_16  C27   C26  C25  F29  180.00   0.0  0
 891  CONST_17  F28   C27  C26  C25  180.00   0.0  0
 891  CONST_18  O20   C21  C23  C24  180.00   0.0  0
 891  CONST_19  F28   C27  C21  C23  180.00   0.0  0
 891  CONST_20  O20   C21  C27  C26  180.00   0.0  0
 891  CONST_21  N19   C16  N15  C14  180.00   0.0  0
 891  CONST_22  O18   C9   N8   C12  180.00   0.0  0
 891  CONST_23  C22   N8   C9   C10  180.00   0.0  0
 891  CONST_24  H14   C14  N15  C16  180.00   0.0  0
 891  CONST_25  H23   C23  C24  C25  180.00   0.0  0
 891  CONST_26  H26   C26  C25  C24  180.00   0.0  0
 891  CONST_27  H24   C24  C25  C26  180.00   0.0  0
 891  CONST_28  N15   C16  N19  C1     0.00   0.0  0
 891  CONST_29  N17   C16  N19  C1   180.00   0.0  0
 891  CONST_30  C22   N8   C9   O18    0.00   0.0  0
 891  CONST_31  HN19  N19  C16  N15  180.00   0.0  0
 891  Var_01    C23   C21  O20  C10   23.12  30.0  3
 891  Var_02    C9    C10  O20  C21   68.39  30.0  2
 891  Var_03    H22   C22  N8   C12   59.07  30.0  3
 891  Var_04    C5    S4   C3   C1   162.57  30.0  3
 891  Var_05    H5    C5   S4   C3    59.52  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
 891  chir_01  C1  C2  C3  N19  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
 891  plan-1  C25   0.020
 891  plan-1  C24   0.020
 891  plan-1  C23   0.020
 891  plan-1  C26   0.020
 891  plan-1  C27   0.020
 891  plan-1  F28   0.020
 891  plan-1  C21   0.020
 891  plan-1  O20   0.020
 891  plan-1  H24   0.020
 891  plan-1  H23   0.020
 891  plan-1  H26   0.020
 891  plan-1  F29   0.020
 891  plan-2  C16   0.020
 891  plan-2  C13   0.020
 891  plan-2  C11   0.020
 891  plan-2  C12   0.020
 891  plan-2  C10   0.020
 891  plan-2  N8    0.020
 891  plan-2  O20   0.020
 891  plan-2  C9    0.020
 891  plan-2  O18   0.020
 891  plan-2  C14   0.020
 891  plan-2  N15   0.020
 891  plan-2  N17   0.020
 891  plan-2  C22   0.020
 891  plan-2  N19   0.020
 891  plan-2  H11   0.020
 891  plan-2  H14   0.020
 891  plan-3  C16   0.020
 891  plan-3  C1    0.020
 891  plan-3  N19   0.020
 891  plan-3  HN19  0.020

