# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 03:07:01 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 8-[4-[2-[(4-fluorophenyl)methyl-methyl-amino]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(CCc1cnn(c1)c2nccc3C(=O)NC=Nc23)Cc4ccc(F)cc4
#
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
 5U8  5U8  8-[4-[2-[(4-fluorophenyl)methyl-methyl-amino]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one  ligand  47  28  .  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_5U8
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
 5U8  C8   C  CH2   0  -0.254   1.9516   0.7473  -0.3177
 5U8  N4   N  NR16  0  -0.659  -6.4767   1.0777   1.7653
 5U8  C2   C  CR6   0   0.079   5.4609   0.2797   0.8653
 5U8  C3   C  CR16  0  -0.295   6.5032   1.0862   1.3056
 5U8  C4   C  CR16  0  -0.398   7.8139   0.6229   1.3314
 5U8  C5   C  CR6   0   0.508   8.0632  -0.6642   0.9028
 5U8  C6   C  CR16  0  -0.398   7.0542  -1.4965   0.4528
 5U8  C1   C  CH2   0  -0.326   4.0369   0.7701   0.8638
 5U8  C7   C  CR16  0  -0.265   5.7551  -1.0139   0.4373
 5U8  C9   C  CH2   0  -0.546   1.1923   0.1911  -1.5229
 5U8  N1   N  NR5   0  -0.371  -2.4031   0.0298  -0.9041
 5U8  C10  C  CR5   0  -0.143  -0.2814   0.3494  -1.3500
 5U8  C11  C  CR15  0   0.026  -1.2027  -0.5996  -0.9968
 5U8  N2   N  N     0  -0.267  -2.3169   1.3307  -1.1979
 5U8  C12  C  CR15  0  -0.063  -1.0468   1.5342  -1.4630
 5U8  C13  C  CR6   0   0.444  -3.6375  -0.5883  -0.6575
 5U8  C15  C  CR16  0   0.152  -5.2518   1.6400   1.6062
 5U8  C14  C  CR66  0   0.155  -4.5993   0.0109   0.1890
 5U8  C16  C  CR6   0   0.580  -6.8627  -0.0981   1.1689
 5U8  N3   N  N     0  -0.430  -4.3216   1.1720   0.8599
 5U8  C17  C  CR66  0  -0.018  -5.8109  -0.6756   0.3258
 5U8  C18  C  CR16  0  -0.356  -5.9999  -1.9019  -0.3077
 5U8  O    O  O     0  -0.434  -7.9613  -0.5848   1.3408
 5U8  C19  C  CR16  0  -0.063  -4.9613  -2.4077  -1.0535
 5U8  N5   N  N     0  -0.402  -3.8132  -1.7503  -1.2323
 5U8  N    N  NT    0  -0.410   3.3884   0.5724  -0.4195
 5U8  C    C  CH3   0  -0.532   3.9718   1.4237  -1.4364
 5U8  F    F  F     0  -0.319   9.3268  -1.1244   0.9180
 5U8  H1   H  HCH2  0   0.196   1.6773   1.8067  -0.1712
 5U8  H2   H  HCH2  0   0.237   1.6051   0.2151   0.5721
 5U8  H3   H  HNR6  0   0.440  -7.1403   1.5366   2.3767
 5U8  H4   H  HCR6  0   0.260   6.2968   2.0986   1.6314
 5U8  H5   H  HCR6  0   0.276   8.6228   1.2570   1.6702
 5U8  H6   H  HCR6  0   0.276   7.2804  -2.5018   0.1217
 5U8  H7   H  HCH2  0   0.252   3.4741   0.2074   1.6142
 5U8  H8   H  HCH2  0   0.213   4.0110   1.8244   1.1864
 5U8  H9   H  HCR6  0   0.256   4.9562  -1.6514   0.0790
 5U8  H10  H  HCH2  0   0.248   1.5023   0.6979  -2.4398
 5U8  H11  H  HCH2  0   0.244   1.4449  -0.8639  -1.6474
 5U8  H12  H  HCR5  0   0.293  -1.0963  -1.6533  -0.7962
 5U8  H13  H  HCR5  0   0.263  -0.7013   2.5197  -1.7403
 5U8  H14  H  HCR6  0   0.307  -5.0878   2.5493   2.1706
 5U8  H15  H  HCR6  0   0.286  -6.9282  -2.4463  -0.2088
 5U8  H16  H  HCR6  0   0.282  -5.0463  -3.3684  -1.5451
 5U8  H18  H  HCH3  0   0.241   5.0505   1.2740  -1.4806
 5U8  H19  H  HCH3  0   0.239   3.5772   1.1805  -2.4221
 5U8  H20  H  HCH3  0   0.195   3.7883   2.4942  -1.2529

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
 5U8  F    C5   single    1.345  0.020  1.345
 5U8  C5   C4   aromatic  1.379  0.020  1.379
 5U8  C5   C6   aromatic  1.383  0.020  1.383
 5U8  C4   C3   aromatic  1.390  0.020  1.390
 5U8  C6   C7   aromatic  1.386  0.020  1.386
 5U8  C3   C2   aromatic  1.390  0.020  1.390
 5U8  C7   C2   aromatic  1.394  0.020  1.394
 5U8  C2   C1   single    1.506  0.020  1.506
 5U8  C1   N    single    1.451  0.020  1.451
 5U8  N    C    single    1.449  0.020  1.449
 5U8  N    C8   single    1.451  0.020  1.451
 5U8  C8   C9   single    1.529  0.020  1.529
 5U8  C9   C10  single    1.492  0.020  1.492
 5U8  C10  C12  aromatic  1.415  0.020  1.415
 5U8  C10  C11  aromatic  1.369  0.020  1.369
 5U8  C12  N2   aromatic  1.313  0.020  1.313
 5U8  C11  N1   aromatic  1.359  0.020  1.359
 5U8  N2   N1   aromatic  1.336  0.020  1.336
 5U8  N1   C13  single    1.402  0.020  1.402
 5U8  N3   C15  double    1.281  0.020  1.281
 5U8  N3   C14  single    1.369  0.020  1.369
 5U8  C15  N4   single    1.357  0.020  1.357
 5U8  C13  C14  aromatic  1.414  0.020  1.414
 5U8  C13  N5   aromatic  1.308  0.020  1.308
 5U8  C14  C17  aromatic  1.399  0.020  1.399
 5U8  N4   C16  single    1.374  0.020  1.374
 5U8  N5   C19  aromatic  1.335  0.020  1.335
 5U8  C17  C16  single    1.466  0.020  1.466
 5U8  C17  C18  aromatic  1.393  0.020  1.393
 5U8  C16  O    double    1.214  0.020  1.214
 5U8  C19  C18  aromatic  1.375  0.020  1.375
 5U8  C8   H1   single    0.970  0.020  1.090
 5U8  C8   H2   single    0.970  0.020  1.090
 5U8  N4   H3   single    0.860  0.020  1.020
 5U8  C3   H4   single    0.930  0.020  1.080
 5U8  C4   H5   single    0.930  0.020  1.080
 5U8  C6   H6   single    0.930  0.020  1.080
 5U8  C1   H7   single    0.970  0.020  1.090
 5U8  C1   H8   single    0.970  0.020  1.090
 5U8  C7   H9   single    0.930  0.020  1.080
 5U8  C9   H10  single    0.970  0.020  1.090
 5U8  C9   H11  single    0.970  0.020  1.090
 5U8  C11  H12  single    0.930  0.020  1.080
 5U8  C12  H13  single    0.930  0.020  1.080
 5U8  C15  H14  single    0.930  0.020  1.080
 5U8  C18  H15  single    0.930  0.020  1.080
 5U8  C19  H16  single    0.930  0.020  1.080
 5U8  C    H18  single    0.970  0.020  1.090
 5U8  C    H19  single    0.970  0.020  1.090
 5U8  C    H20  single    0.970  0.020  1.090

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
 5U8  H2   C8   H1   106.29  3.000
 5U8  H2   C8   N    108.19  3.000
 5U8  H1   C8   N    111.78  3.000
 5U8  H2   C8   C9   107.88  3.000
 5U8  H1   C8   C9   109.28  3.000
 5U8  N    C8   C9   113.11  3.000
 5U8  H3   N4   C16  117.77  3.000
 5U8  H3   N4   C15  118.34  3.000
 5U8  C16  N4   C15  123.87  3.000
 5U8  C7   C2   C1   120.09  3.000
 5U8  C1   C2   C3   121.37  3.000
 5U8  C7   C2   C3   118.53  3.000
 5U8  H4   C3   C4   119.04  3.000
 5U8  H4   C3   C2   119.65  3.000
 5U8  C4   C3   C2   121.31  3.000
 5U8  H5   C4   C5   120.59  3.000
 5U8  H5   C4   C3   121.01  3.000
 5U8  C5   C4   C3   118.40  3.000
 5U8  F    C5   C6   118.89  3.000
 5U8  C6   C5   C4   122.05  3.000
 5U8  F    C5   C4   119.06  3.000
 5U8  H6   C6   C7   121.06  3.000
 5U8  H6   C6   C5   120.39  3.000
 5U8  C7   C6   C5   118.55  3.000
 5U8  H8   C1   H7   106.20  3.000
 5U8  H8   C1   N    112.23  3.000
 5U8  H7   C1   N    107.85  3.000
 5U8  H8   C1   C2   109.47  3.000
 5U8  H7   C1   C2   108.56  3.000
 5U8  N    C1   C2   112.27  3.000
 5U8  H9   C7   C6   119.35  3.000
 5U8  H9   C7   C2   119.48  3.000
 5U8  C6   C7   C2   121.17  3.000
 5U8  H11  C9   H10  106.67  3.000
 5U8  H11  C9   C10  110.13  3.000
 5U8  H10  C9   C10  109.16  3.000
 5U8  H11  C9   C8   109.05  3.000
 5U8  H10  C9   C8   110.60  3.000
 5U8  C10  C9   C8   111.13  3.000
 5U8  C13  N1   N2   121.63  3.000
 5U8  C13  N1   C11  125.84  3.000
 5U8  N2   N1   C11  112.27  3.000
 5U8  C12  C10  C11  103.71  3.000
 5U8  C11  C10  C9   128.39  3.000
 5U8  C12  C10  C9   127.86  3.000
 5U8  H12  C11  C10  131.24  3.000
 5U8  H12  C11  N1   121.83  3.000
 5U8  C10  C11  N1   106.92  3.000
 5U8  C12  N2   N1   104.93  3.000
 5U8  H13  C12  N2   120.16  3.000
 5U8  H13  C12  C10  127.67  3.000
 5U8  N2   C12  C10  112.17  3.000
 5U8  N5   C13  C14  123.23  3.000
 5U8  N5   C13  N1   115.62  3.000
 5U8  C14  C13  N1   121.13  3.000
 5U8  H14  C15  N3   120.04  3.000
 5U8  H14  C15  N4   115.06  3.000
 5U8  N3   C15  N4   124.90  3.000
 5U8  C17  C14  N3   122.93  3.000
 5U8  C17  C14  C13  116.07  3.000
 5U8  N3   C14  C13  120.97  3.000
 5U8  O    C16  C17  124.94  3.000
 5U8  O    C16  N4   122.41  3.000
 5U8  C17  C16  N4   112.65  3.000
 5U8  C14  N3   C15  116.61  3.000
 5U8  C18  C17  C16  120.71  3.000
 5U8  C18  C17  C14  120.32  3.000
 5U8  C16  C17  C14  118.95  3.000
 5U8  H15  C18  C19  120.87  3.000
 5U8  H15  C18  C17  121.22  3.000
 5U8  C19  C18  C17  117.91  3.000
 5U8  H16  C19  N5   116.34  3.000
 5U8  H16  C19  C18  120.89  3.000
 5U8  N5   C19  C18  122.75  3.000
 5U8  C19  N5   C13  119.60  3.000
 5U8  C    N    C1   111.14  3.000
 5U8  C    N    C8   112.15  3.000
 5U8  C1   N    C8   111.34  3.000
 5U8  H20  C    H19  107.91  3.000
 5U8  H20  C    H18  107.77  3.000
 5U8  H19  C    H18  106.93  3.000
 5U8  H20  C    N    112.77  3.000
 5U8  H19  C    N    110.98  3.000
 5U8  H18  C    N    110.26  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
 5U8  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 5U8  CONST_02  C5   C6   C7   C2      0.00   0.0  0
 5U8  CONST_03  C6   C5   C4   C3      0.00   0.0  0
 5U8  CONST_04  C6   C7   C2   C3      0.00   0.0  0
 5U8  CONST_05  C7   C6   C5   C4      0.00   0.0  0
 5U8  CONST_06  C7   C2   C3   C4      0.00   0.0  0
 5U8  CONST_07  C12  C10  C11  N1      0.00   0.0  0
 5U8  CONST_08  C10  C12  N2   N1      0.00   0.0  0
 5U8  CONST_09  C17  C14  C13  N1    180.00   0.0  0
 5U8  CONST_10  C19  N5   C13  N1    180.00   0.0  0
 5U8  CONST_11  N2   N1   C11  C10     0.00   0.0  0
 5U8  CONST_12  C13  N1   C11  C10   180.00   0.0  0
 5U8  CONST_13  N2   C12  C10  C11     0.00   0.0  0
 5U8  CONST_14  C12  N2   N1   C11     0.00   0.0  0
 5U8  CONST_19  C13  N1   N2   C12   180.00   0.0  0
 5U8  CONST_20  C18  C17  C14  C13     0.00   0.0  0
 5U8  CONST_21  C18  C19  N5   C13     0.00   0.0  0
 5U8  CONST_22  C19  N5   C13  C14     0.00   0.0  0
 5U8  CONST_23  C19  C18  C17  C14     0.00   0.0  0
 5U8  CONST_24  N5   C13  C14  C17     0.00   0.0  0
 5U8  CONST_25  N5   C19  C18  C17     0.00   0.0  0
 5U8  CONST_26  N3   C14  C13  N1      0.00   0.0  0
 5U8  CONST_27  C14  N3   C15  N4      0.00   0.0  0
 5U8  CONST_28  C17  C16  N4   C15     0.00   0.0  0
 5U8  CONST_29  N3   C15  N4   C16     0.00   0.0  0
 5U8  CONST_30  F    C5   C4   C3    180.00   0.0  0
 5U8  CONST_31  C1   C2   C3   C4    180.00   0.0  0
 5U8  CONST_32  C1   C2   C7   C6    180.00   0.0  0
 5U8  CONST_33  F    C5   C6   C7    180.00   0.0  0
 5U8  CONST_34  N2   C12  C10  C9    180.00   0.0  0
 5U8  CONST_35  N1   C11  C10  C9    180.00   0.0  0
 5U8  CONST_36  O    C16  N4   C15   180.00   0.0  0
 5U8  CONST_37  H5   C4   C3   C2    180.00   0.0  0
 5U8  CONST_38  H6   C6   C7   C2    180.00   0.0  0
 5U8  CONST_39  H9   C7   C2   C3    180.00   0.0  0
 5U8  CONST_40  H4   C3   C4   C5    180.00   0.0  0
 5U8  CONST_41  H13  C12  N2   N1    180.00   0.0  0
 5U8  CONST_42  H12  C11  N1   N2    180.00   0.0  0
 5U8  CONST_43  H16  C19  N5   C13   180.00   0.0  0
 5U8  CONST_44  H15  C18  C17  C14   180.00   0.0  0
 5U8  CONST_45  H14  C15  N3   C14   180.00   0.0  0
 5U8  CONST_46  H3   N4   C15  N3    180.00   0.0  0
 5U8  Var_01    C12  C10  C9   C8     74.70  30.0  2
 5U8  Var_02    N    C1   C2   C3    128.99  30.0  2
 5U8  Var_03    C2   C1   N    C8    166.33  30.0  1
 5U8  Var_04    N    C8   C9   C10   177.94  30.0  1
 5U8  Var_05    C9   C8   N    C1   -164.48  30.0  3
 5U8  Var_06    H18  C    N    C8    179.51  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
 5U8  plan-1  C9   0.020
 5U8  plan-1  N1   0.020
 5U8  plan-1  C10  0.020
 5U8  plan-1  C11  0.020
 5U8  plan-1  N2   0.020
 5U8  plan-1  C12  0.020
 5U8  plan-1  C13  0.020
 5U8  plan-1  H12  0.020
 5U8  plan-1  H13  0.020
 5U8  plan-2  C2   0.020
 5U8  plan-2  C3   0.020
 5U8  plan-2  C4   0.020
 5U8  plan-2  C5   0.020
 5U8  plan-2  C6   0.020
 5U8  plan-2  C1   0.020
 5U8  plan-2  C7   0.020
 5U8  plan-2  F    0.020
 5U8  plan-2  H4   0.020
 5U8  plan-2  H5   0.020
 5U8  plan-2  H6   0.020
 5U8  plan-2  H9   0.020
 5U8  plan-3  N4   0.020
 5U8  plan-3  N1   0.020
 5U8  plan-3  C13  0.020
 5U8  plan-3  C15  0.020
 5U8  plan-3  C14  0.020
 5U8  plan-3  C16  0.020
 5U8  plan-3  N3   0.020
 5U8  plan-3  C17  0.020
 5U8  plan-3  C18  0.020
 5U8  plan-3  O    0.020
 5U8  plan-3  C19  0.020
 5U8  plan-3  N5   0.020
 5U8  plan-3  H3   0.020
 5U8  plan-3  H14  0.020
 5U8  plan-3  H15  0.020
 5U8  plan-3  H16  0.020

