# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 05:56:35 2020
#   Inital geometry file: a 156 line input string
#   Ligand name: 2-({4-[2-(diethylamino)ethoxy]phenyl}amino)-6-(4-fluorophenoxy)-8-methylpyrido[2,3-d]pyrimidin-7(8H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN(CC)CCOc1ccc(Nc2ncc3C=C(Oc4ccc(F)cc4)C(=O)N(C)c3n2)cc1
#
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
 04K  04K  2-({4-[2-(diethylamino)ethoxy]phenyl}amino)-6-(4-fluorophenoxy)-8-methylpyrido[2,3-d]pyrimidin-7(8H)-one  ligand  63  35  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_04K
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
 04K  N1    N  N     0  -0.460    0.1166   0.0458  -0.9818
 04K  C2    C  CR6   0   0.608    0.1132  -0.9548  -0.0907
 04K  N3    N  N     0  -0.507    1.1880  -1.6004   0.3600
 04K  C4    C  CR16  0  -0.027    1.2935   0.4125  -1.4350
 04K  C5    C  CR66  0  -0.122    2.4909  -0.1773  -1.0378
 04K  C6    C  CR66  0   0.568    2.3638  -1.2209  -0.1017
 04K  N7    N  NR6   0  -0.590    3.4892  -1.8610   0.3459
 04K  C8    C  CR6   0   0.536    4.7651  -1.5134  -0.0708
 04K  C9    C  CR6   0   0.137    4.8619  -0.4218  -1.0370
 04K  C10   C  CR16  0  -0.227    3.7750   0.2197  -1.4978
 04K  O11   O  O2    0  -0.497    6.1104  -0.1284  -1.4900
 04K  C12   C  CR6   0   0.367    6.9946   0.4651  -0.6322
 04K  N13   N  NH1   0  -0.753   -1.0644  -1.3803   0.4144
 04K  C14   C  CR6   0   0.325   -2.3627  -0.9188   0.1541
 04K  C15   C  CR16  0  -0.311   -3.4045  -1.8473   0.2104
 04K  C16   C  CR16  0  -0.343   -4.7151  -1.4596   0.0163
 04K  C17   C  CR6   0   0.378   -5.0273  -0.1267  -0.2572
 04K  C18   C  CR16  0  -0.384   -3.9929   0.8036  -0.3098
 04K  C19   C  CR16  0  -0.271   -2.6765   0.4117  -0.0962
 04K  O20   O  O2    0  -0.461   -6.3283   0.1585  -0.4496
 04K  C21   C  CH2   0  -0.188   -6.6935   1.4907  -0.7603
 04K  C22   C  CH2   0  -0.315   -8.1901   1.5333  -0.9766
 04K  N23   N  NT    0  -0.405   -8.9516   1.2180   0.2178
 04K  C24   C  CH2   0  -0.282   -9.0629   2.3670   1.1023
 04K  C25   C  CH3   0  -0.668   -9.4115   1.9917   2.5334
 04K  C26   C  CH2   0  -0.289  -10.2402   0.6239  -0.1069
 04K  C27   C  CH3   0  -0.658  -10.1183  -0.8362  -0.5141
 04K  O28   O  O     0  -0.455    5.7439  -2.0981   0.3567
 04K  C29   C  CH3   0  -0.544    3.4000  -2.9536   1.3079
 04K  C30   C  CR16  0  -0.315    8.3371   0.4020  -0.9846
 04K  C31   C  CR16  0  -0.401    9.2920   1.0214  -0.1941
 04K  C32   C  CR6   0   0.508    8.8860   1.6939   0.9434
 04K  C33   C  CR16  0  -0.401    7.5577   1.7625   1.3090
 04K  C34   C  CR16  0  -0.322    6.6022   1.1458   0.5120
 04K  F35   F  F     0  -0.319    9.8085   2.3006   1.7117
 04K  H4    H  HCR6  0   0.283    1.3119   1.2209  -2.1593
 04K  H10   H  HCR6  0   0.294    3.8648   1.0263  -2.2159
 04K  HN13  H  HNH1  0   0.409   -0.9921  -2.2007   0.9971
 04K  H15   H  HCR6  0   0.270   -3.1860  -2.8902   0.4073
 04K  H16   H  HCR6  0   0.263   -5.5080  -2.1953   0.0642
 04K  H18   H  HCR6  0   0.279   -4.1837   1.8497  -0.5064
 04K  H19   H  HCR6  0   0.270   -1.9027   1.1626  -0.1279
 04K  H21   H  HCH2  0   0.221   -6.3898   2.1691   0.0452
 04K  H21A  H  HCH2  0   0.227   -6.1891   1.8253  -1.6740
 04K  H22   H  HCH2  0   0.214   -8.4448   2.5261  -1.3817
 04K  H22A  H  HCH2  0   0.242   -8.4376   0.8185  -1.7638
 04K  H24   H  HCH2  0   0.225   -8.0979   2.8784   1.1176
 04K  H24A  H  HCH2  0   0.193   -9.7865   3.1058   0.7188
 04K  H25   H  HCH3  0   0.224  -10.4044   1.5503   2.6216
 04K  H25A  H  HCH3  0   0.221   -8.6892   1.2770   2.9290
 04K  H25B  H  HCH3  0   0.227   -9.3951   2.8778   3.1685
 04K  H26   H  HCH2  0   0.230  -10.8812   0.6798   0.7736
 04K  H26A  H  HCH2  0   0.194  -10.7602   1.1935  -0.8949
 04K  H27   H  HCH3  0   0.221   -9.4738  -0.9698  -1.3841
 04K  H27A  H  HCH3  0   0.220   -9.7002  -1.4273   0.3010
 04K  H27B  H  HCH3  0   0.222  -11.0970  -1.2459  -0.7657
 04K  H29   H  HCH3  0   0.260    3.8858  -3.8415   0.9108
 04K  H29A  H  HCH3  0   0.259    3.8829  -2.6731   2.2419
 04K  H29B  H  HCH3  0   0.278    2.3572  -3.1722   1.4977
 04K  H30   H  HCR6  0   0.281    8.6371  -0.1267  -1.8799
 04K  H31   H  HCR6  0   0.285   10.3386   0.9791  -0.4653
 04K  H33   H  HCR6  0   0.286    7.2595   2.2941   2.2030
 04K  H34   H  HCR6  0   0.286    5.5603   1.2180   0.7953

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
 04K  C2   N1    aromatic  1.340  0.020  1.340
 04K  N1   C4    aromatic  1.313  0.020  1.313
 04K  N13  C2    single    1.350  0.020  1.350
 04K  C2   N3    aromatic  1.332  0.020  1.332
 04K  N3   C6    aromatic  1.319  0.020  1.319
 04K  C4   C5    aromatic  1.393  0.020  1.393
 04K  C4   H4    single    0.930  0.020  1.080
 04K  C6   C5    aromatic  1.408  0.020  1.408
 04K  C5   C10   single    1.421  0.020  1.421
 04K  C6   N7    single    1.370  0.020  1.370
 04K  C29  N7    single    1.459  0.020  1.459
 04K  N7   C8    single    1.386  0.020  1.386
 04K  C8   C9    single    1.461  0.020  1.461
 04K  C8   O28   double    1.218  0.020  1.218
 04K  C10  C9    double    1.344  0.020  1.344
 04K  C9   O11   single    1.360  0.020  1.360
 04K  C10  H10   single    0.930  0.020  1.080
 04K  O11  C12   single    1.367  0.020  1.367
 04K  C34  C12   aromatic  1.388  0.020  1.388
 04K  C12  C30   aromatic  1.389  0.020  1.389
 04K  C14  N13   single    1.402  0.020  1.402
 04K  N13  HN13  single    0.860  0.020  1.020
 04K  C15  C14   aromatic  1.397  0.020  1.397
 04K  C14  C19   aromatic  1.390  0.020  1.390
 04K  C16  C15   aromatic  1.381  0.020  1.381
 04K  C15  H15   single    0.930  0.020  1.080
 04K  C16  C17   aromatic  1.396  0.020  1.396
 04K  C16  H16   single    0.930  0.020  1.080
 04K  O20  C17   single    1.346  0.020  1.346
 04K  C17  C18   aromatic  1.392  0.020  1.392
 04K  C18  C19   aromatic  1.390  0.020  1.390
 04K  C18  H18   single    0.930  0.020  1.080
 04K  C19  H19   single    0.930  0.020  1.080
 04K  O20  C21   single    1.416  0.020  1.416
 04K  C22  C21   single    1.513  0.020  1.513
 04K  C21  H21   single    0.970  0.020  1.090
 04K  C21  H21A  single    0.970  0.020  1.090
 04K  N23  C22   single    1.451  0.020  1.451
 04K  C22  H22   single    0.970  0.020  1.090
 04K  C22  H22A  single    0.970  0.020  1.090
 04K  C24  N23   single    1.454  0.020  1.454
 04K  N23  C26   single    1.456  0.020  1.456
 04K  C25  C24   single    1.520  0.020  1.520
 04K  C24  H24   single    0.970  0.020  1.090
 04K  C24  H24A  single    0.970  0.020  1.090
 04K  C25  H25   single    0.970  0.020  1.090
 04K  C25  H25A  single    0.970  0.020  1.090
 04K  C25  H25B  single    0.970  0.020  1.090
 04K  C27  C26   single    1.521  0.020  1.521
 04K  C26  H26   single    0.970  0.020  1.090
 04K  C26  H26A  single    0.970  0.020  1.090
 04K  C27  H27   single    0.970  0.020  1.090
 04K  C27  H27A  single    0.970  0.020  1.090
 04K  C27  H27B  single    0.970  0.020  1.090
 04K  C29  H29   single    0.970  0.020  1.090
 04K  C29  H29A  single    0.970  0.020  1.090
 04K  C29  H29B  single    0.970  0.020  1.090
 04K  C30  C31   aromatic  1.386  0.020  1.386
 04K  C30  H30   single    0.930  0.020  1.080
 04K  C32  C31   aromatic  1.382  0.020  1.382
 04K  C31  H31   single    0.930  0.020  1.080
 04K  C33  C32   aromatic  1.379  0.020  1.379
 04K  C32  F35   single    1.345  0.020  1.345
 04K  C34  C33   aromatic  1.389  0.020  1.389
 04K  C33  H33   single    0.930  0.020  1.080
 04K  C34  H34   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
 04K  C4    N1   C2    116.12  3.000
 04K  N13   C2   N3    115.11  3.000
 04K  N3    C2   N1    125.79  3.000
 04K  N13   C2   N1    119.10  3.000
 04K  C6    N3   C2    117.47  3.000
 04K  H4    C4   C5    119.41  3.000
 04K  H4    C4   N1    116.96  3.000
 04K  C5    C4   N1    123.63  3.000
 04K  C10   C5   C6    120.27  3.000
 04K  C10   C5   C4    124.51  3.000
 04K  C6    C5   C4    115.22  3.000
 04K  N7    C6   C5    119.31  3.000
 04K  N7    C6   N3    118.92  3.000
 04K  C5    C6   N3    121.77  3.000
 04K  C29   N7   C8    116.25  3.000
 04K  C8    N7   C6    122.73  3.000
 04K  C29   N7   C6    121.01  3.000
 04K  O28   C8   C9    122.52  3.000
 04K  O28   C8   N7    120.92  3.000
 04K  C9    C8   N7    116.55  3.000
 04K  O11   C9   C10   121.69  3.000
 04K  O11   C9   C8    116.25  3.000
 04K  C10   C9   C8    122.01  3.000
 04K  H10   C10  C9    121.04  3.000
 04K  H10   C10  C5    119.83  3.000
 04K  C9    C10  C5    119.12  3.000
 04K  C12   O11  C9    118.57  3.000
 04K  C34   C12  C30   120.29  3.000
 04K  C30   C12  O11   116.49  3.000
 04K  C34   C12  O11   123.17  3.000
 04K  HN13  N13  C14   116.18  3.000
 04K  HN13  N13  C2    114.19  3.000
 04K  C14   N13  C2    129.38  3.000
 04K  C19   C14  C15   118.38  3.000
 04K  C19   C14  N13   123.89  3.000
 04K  C15   C14  N13   117.67  3.000
 04K  H15   C15  C16   119.16  3.000
 04K  H15   C15  C14   119.79  3.000
 04K  C16   C15  C14   121.05  3.000
 04K  H16   C16  C17   119.58  3.000
 04K  H16   C16  C15   119.89  3.000
 04K  C17   C16  C15   120.53  3.000
 04K  O20   C17  C18   124.84  3.000
 04K  C18   C17  C16   118.64  3.000
 04K  O20   C17  C16   116.52  3.000
 04K  H18   C18  C19   117.89  3.000
 04K  H18   C18  C17   121.48  3.000
 04K  C19   C18  C17   120.63  3.000
 04K  H19   C19  C18   118.59  3.000
 04K  H19   C19  C14   120.65  3.000
 04K  C18   C19  C14   120.76  3.000
 04K  C21   O20  C17   118.70  3.000
 04K  H21A  C21  H21   107.23  3.000
 04K  H21A  C21  C22   109.12  3.000
 04K  H21   C21  C22   111.21  3.000
 04K  H21A  C21  O20   110.58  3.000
 04K  H21   C21  O20   110.47  3.000
 04K  C22   C21  O20   108.24  3.000
 04K  H22A  C22  H22   105.80  3.000
 04K  H22A  C22  N23   109.41  3.000
 04K  H22   C22  N23   112.15  3.000
 04K  H22A  C22  C21   108.00  3.000
 04K  H22   C22  C21   107.85  3.000
 04K  N23   C22  C21   113.29  3.000
 04K  C26   N23  C24   112.98  3.000
 04K  C26   N23  C22   111.69  3.000
 04K  C24   N23  C22   111.66  3.000
 04K  H24A  C24  H24   105.72  3.000
 04K  H24A  C24  C25   110.02  3.000
 04K  H24   C24  C25   107.76  3.000
 04K  H24A  C24  N23   111.59  3.000
 04K  H24   C24  N23   108.11  3.000
 04K  C25   C24  N23   113.27  3.000
 04K  H25B  C25  H25A  108.14  3.000
 04K  H25B  C25  H25   107.19  3.000
 04K  H25A  C25  H25   107.97  3.000
 04K  H25B  C25  C24   110.14  3.000
 04K  H25A  C25  C24   110.58  3.000
 04K  H25   C25  C24   112.65  3.000
 04K  H26A  C26  H26   105.86  3.000
 04K  H26A  C26  C27   110.03  3.000
 04K  H26   C26  C27   108.21  3.000
 04K  H26A  C26  N23   111.47  3.000
 04K  H26   C26  N23   108.62  3.000
 04K  C27   C26  N23   112.38  3.000
 04K  H27B  C27  H27A  108.24  3.000
 04K  H27B  C27  H27   107.47  3.000
 04K  H27A  C27  H27   107.66  3.000
 04K  H27B  C27  C26   110.52  3.000
 04K  H27A  C27  C26   110.55  3.000
 04K  H27   C27  C26   112.24  3.000
 04K  H29B  C29  H29A  109.22  3.000
 04K  H29B  C29  H29   109.25  3.000
 04K  H29A  C29  H29   109.01  3.000
 04K  H29B  C29  N7    109.02  3.000
 04K  H29A  C29  N7    110.23  3.000
 04K  H29   C29  N7    110.09  3.000
 04K  H30   C30  C31   119.95  3.000
 04K  H30   C30  C12   119.99  3.000
 04K  C31   C30  C12   120.06  3.000
 04K  H31   C31  C32   120.62  3.000
 04K  H31   C31  C30   120.40  3.000
 04K  C32   C31  C30   118.97  3.000
 04K  F35   C32  C33   119.11  3.000
 04K  F35   C32  C31   119.21  3.000
 04K  C33   C32  C31   121.68  3.000
 04K  H33   C33  C34   120.18  3.000
 04K  H33   C33  C32   120.59  3.000
 04K  C34   C33  C32   119.23  3.000
 04K  H34   C34  C33   118.86  3.000
 04K  H34   C34  C12   121.38  3.000
 04K  C33   C34  C12   119.76  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
 04K  CONST_01  C6   N3   C2   N1      0.00   0.0  0
 04K  CONST_02  C6   C5   C4   N1      0.00   0.0  0
 04K  CONST_03  C5   C4   N1   C2      0.00   0.0  0
 04K  CONST_04  C5   C6   N3   C2      0.00   0.0  0
 04K  CONST_05  C4   N1   C2   N3      0.00   0.0  0
 04K  CONST_06  C4   C5   C6   N3      0.00   0.0  0
 04K  CONST_07  C32  C33  C34  C12     0.00   0.0  0
 04K  CONST_08  C32  C31  C30  C12     0.00   0.0  0
 04K  CONST_09  C17  C16  C15  C14     0.00   0.0  0
 04K  CONST_10  C17  C18  C19  C14     0.00   0.0  0
 04K  CONST_11  C18  C19  C14  C15     0.00   0.0  0
 04K  CONST_12  C18  C17  C16  C15     0.00   0.0  0
 04K  CONST_13  C19  C14  C15  C16     0.00   0.0  0
 04K  CONST_14  C19  C18  C17  C16     0.00   0.0  0
 04K  CONST_15  C33  C34  C12  C30     0.00   0.0  0
 04K  CONST_16  C33  C32  C31  C30     0.00   0.0  0
 04K  CONST_17  C34  C12  C30  C31     0.00   0.0  0
 04K  CONST_18  C34  C33  C32  C31     0.00   0.0  0
 04K  CONST_19  C9   C8   N7   C6      0.00   0.0  0
 04K  CONST_20  N13  C2   N1   C4    180.00   0.0  0
 04K  CONST_21  N13  C2   N3   C6    180.00   0.0  0
 04K  CONST_22  C33  C34  C12  O11   180.00   0.0  0
 04K  CONST_23  C31  C30  C12  O11   180.00   0.0  0
 04K  CONST_24  C16  C15  C14  N13   180.00   0.0  0
 04K  CONST_25  C18  C19  C14  N13   180.00   0.0  0
 04K  CONST_26  O20  C17  C16  C15   180.00   0.0  0
 04K  CONST_27  O20  C17  C18  C19   180.00   0.0  0
 04K  CONST_28  F35  C32  C31  C30   180.00   0.0  0
 04K  CONST_29  F35  C32  C33  C34   180.00   0.0  0
 04K  CONST_30  O28  C8   N7   C6    180.00   0.0  0
 04K  CONST_31  C29  N7   C8   C9    180.00   0.0  0
 04K  CONST_32  H4   C4   N1   C2    180.00   0.0  0
 04K  CONST_33  H33  C33  C34  C12   180.00   0.0  0
 04K  CONST_34  H31  C31  C30  C12   180.00   0.0  0
 04K  CONST_35  H16  C16  C15  C14   180.00   0.0  0
 04K  CONST_36  H18  C18  C19  C14   180.00   0.0  0
 04K  CONST_37  H19  C19  C14  C15   180.00   0.0  0
 04K  CONST_38  H15  C15  C16  C17   180.00   0.0  0
 04K  CONST_39  H34  C34  C12  C30   180.00   0.0  0
 04K  CONST_40  H30  C30  C31  C32   180.00   0.0  0
 04K  CONST_41  C29  N7   C8   O28     0.00   0.0  0
 04K  Var_01    C14  N13  C2   N1     -0.43  30.0  1
 04K  Var_02    C15  C14  N13  C2    148.00  30.0  2
 04K  Var_03    C34  C12  O11  C9    -20.19  30.0  2
 04K  Var_04    H29  C29  N7   C6    124.19  30.0  3
 04K  Var_05    C22  C21  O20  C17   177.92  30.0  3
 04K  Var_06    N23  C22  C21  O20    64.66  30.0  1
 04K  Var_07    C24  N23  C22  C21    80.91  30.0  1
 04K  Var_08    C25  C24  N23  C22  -160.15  30.0  1
 04K  Var_09    C27  C26  N23  C22    76.91  30.0  3
 04K  Var_10    H25  C25  C24  N23   -65.39  30.0  3
 04K  Var_11    H27  C27  C26  N23   -59.13  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
 04K  plan-1  N13  0.020
 04K  plan-1  C14  0.020
 04K  plan-1  C15  0.020
 04K  plan-1  C16  0.020
 04K  plan-1  C17  0.020
 04K  plan-1  C18  0.020
 04K  plan-1  C19  0.020
 04K  plan-1  O20  0.020
 04K  plan-1  H15  0.020
 04K  plan-1  H16  0.020
 04K  plan-1  H18  0.020
 04K  plan-1  H19  0.020
 04K  plan-2  O11  0.020
 04K  plan-2  C12  0.020
 04K  plan-2  C30  0.020
 04K  plan-2  C31  0.020
 04K  plan-2  C32  0.020
 04K  plan-2  C33  0.020
 04K  plan-2  C34  0.020
 04K  plan-2  F35  0.020
 04K  plan-2  H30  0.020
 04K  plan-2  H31  0.020
 04K  plan-2  H33  0.020
 04K  plan-2  H34  0.020
 04K  plan-3  N1   0.020
 04K  plan-3  C2   0.020
 04K  plan-3  N3   0.020
 04K  plan-3  C4   0.020
 04K  plan-3  C5   0.020
 04K  plan-3  C6   0.020
 04K  plan-3  N7   0.020
 04K  plan-3  C8   0.020
 04K  plan-3  C9   0.020
 04K  plan-3  C10  0.020
 04K  plan-3  O11  0.020
 04K  plan-3  N13  0.020
 04K  plan-3  O28  0.020
 04K  plan-3  C29  0.020
 04K  plan-3  H4   0.020
 04K  plan-3  H10  0.020

