# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 19:00:21 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: 8-[4-(1-methylpiperidin-4-yl)pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCC(CC1)c2cnn(c2)c3nccc4C(=O)NC=Nc34
#
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
 FO2  FO2  8-[4-(1-methylpiperidin-4-yl)pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one  ligand  41  23  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_FO2
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
 FO2  C1   C  CR16  0  -0.063  -2.9844   2.5644   0.4316
 FO2  N1   N  NR16  0  -0.659  -4.9464  -1.6506  -0.4500
 FO2  C2   C  CR6   0   0.440  -1.6780   0.6996   0.2492
 FO2  N2   N  N     0  -0.430  -2.6191  -1.4613  -0.3044
 FO2  C3   C  CR66  0   0.156  -2.7901  -0.1375   0.0016
 FO2  N3   N  NR5   0  -0.370  -0.3748   0.1820   0.2777
 FO2  C4   C  CR66  0  -0.017  -4.0459   0.4785   0.0454
 FO2  N4   N  N     0  -0.268  -0.0747  -0.9230   0.9661
 FO2  C5   C  CR6   0   0.580  -5.2439  -0.3367  -0.1795
 FO2  C6   C  CR16  0   0.152  -3.6832  -2.1423  -0.5168
 FO2  C7   C  CR15  0  -0.082   1.2289  -1.0476   0.8562
 FO2  C8   C  CR5   0  -0.080   1.8008  -0.0084   0.0834
 FO2  C9   C  CR15  0   0.009   0.7265   0.7691  -0.2578
 FO2  C10  C  CH1   0  -0.360   3.2384   0.2214  -0.2514
 FO2  C11  C  CH2   0  -0.413   4.0319   0.7124   0.9623
 FO2  O    O  O     0  -0.434  -6.3843   0.0769  -0.1398
 FO2  C    C  CR16  0  -0.356  -4.1481   1.8497   0.2698
 FO2  N    N  N     0  -0.400  -1.7789   1.9905   0.4357
 FO2  C14  C  CH2   0  -0.416   3.9220  -1.0211  -0.8223
 FO2  C13  C  CH2   0  -0.280   5.3878  -0.7414  -1.1153
 FO2  N5   N  NT    0  -0.408   6.0900  -0.2832   0.0694
 FO2  C15  C  CH3   0  -0.518   7.4976  -0.0979  -0.1969
 FO2  C12  C  CH2   0  -0.280   5.4927   0.9271   0.6011
 FO2  H1   H  HCR6  0   0.282  -3.0067   3.6363   0.5801
 FO2  H2   H  HNR6  0   0.440  -5.7173  -2.2823  -0.6274
 FO2  H3   H  HCR6  0   0.307  -3.6126  -3.1918  -0.7731
 FO2  H4   H  HCR5  0   0.259   1.7309  -1.8753   1.3354
 FO2  H5   H  HCR5  0   0.291   0.6606   1.6718  -0.8432
 FO2  H6   H  HCH1  0   0.234   3.2840   1.0074  -1.0155
 FO2  H7   H  HCH2  0   0.235   3.6080   1.6473   1.3358
 FO2  H8   H  HCH2  0   0.219   3.9580  -0.0211   1.7718
 FO2  H9   H  HCR6  0   0.286  -5.1100   2.3414   0.3041
 FO2  H10  H  HCH2  0   0.218   3.8489  -1.8485  -0.1093
 FO2  H11  H  HCH2  0   0.237   3.4215  -1.3407  -1.7391
 FO2  H12  H  HCH2  0   0.235   5.8723  -1.6520  -1.4763
 FO2  H13  H  HCH2  0   0.183   5.4566  -0.0011  -1.9346
 FO2  H15  H  HCH3  0   0.231   8.0167   0.2020   0.7150
 FO2  H16  H  HCH3  0   0.231   7.9434  -1.0326  -0.5412
 FO2  H17  H  HCH3  0   0.189   7.6967   0.6699  -0.9619
 FO2  H18  H  HCH2  0   0.183   5.5664   1.7620  -0.1211
 FO2  H19  H  HCH2  0   0.235   6.0524   1.2324   1.4890

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
 FO2  C15  N5   single    1.445  0.020  1.445
 FO2  N5   C12  single    1.451  0.020  1.451
 FO2  N5   C13  single    1.451  0.020  1.451
 FO2  C12  C11  single    1.520  0.020  1.520
 FO2  C13  C14  single    1.521  0.020  1.521
 FO2  C11  C10  single    1.531  0.020  1.531
 FO2  C14  C10  single    1.529  0.020  1.529
 FO2  C10  C8   single    1.494  0.020  1.494
 FO2  C8   C7   aromatic  1.416  0.020  1.416
 FO2  C8   C9   aromatic  1.369  0.020  1.369
 FO2  C7   N4   aromatic  1.314  0.020  1.314
 FO2  C9   N3   aromatic  1.358  0.020  1.358
 FO2  N4   N3   aromatic  1.336  0.020  1.336
 FO2  N3   C2   single    1.402  0.020  1.402
 FO2  N2   C3   single    1.369  0.020  1.369
 FO2  N2   C6   double    1.281  0.020  1.281
 FO2  C2   C3   aromatic  1.414  0.020  1.414
 FO2  C2   N    aromatic  1.308  0.020  1.308
 FO2  C3   C4   aromatic  1.399  0.020  1.399
 FO2  C6   N1   single    1.357  0.020  1.357
 FO2  N    C1   aromatic  1.335  0.020  1.335
 FO2  N1   C5   single    1.374  0.020  1.374
 FO2  C4   C5   single    1.466  0.020  1.466
 FO2  C4   C    aromatic  1.393  0.020  1.393
 FO2  C1   C    aromatic  1.375  0.020  1.375
 FO2  C5   O    double    1.214  0.020  1.214
 FO2  C1   H1   single    0.930  0.020  1.080
 FO2  N1   H2   single    0.860  0.020  1.020
 FO2  C6   H3   single    0.930  0.020  1.080
 FO2  C7   H4   single    0.930  0.020  1.080
 FO2  C9   H5   single    0.930  0.020  1.080
 FO2  C10  H6   single    0.970  0.020  1.090
 FO2  C11  H7   single    0.970  0.020  1.090
 FO2  C11  H8   single    0.970  0.020  1.090
 FO2  C    H9   single    0.930  0.020  1.080
 FO2  C14  H10  single    0.970  0.020  1.090
 FO2  C14  H11  single    0.970  0.020  1.090
 FO2  C13  H12  single    0.970  0.020  1.090
 FO2  C13  H13  single    0.970  0.020  1.090
 FO2  C15  H15  single    0.970  0.020  1.090
 FO2  C15  H16  single    0.970  0.020  1.090
 FO2  C15  H17  single    0.970  0.020  1.090
 FO2  C12  H18  single    0.970  0.020  1.090
 FO2  C12  H19  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
 FO2  H1   C1   N    116.35  3.000
 FO2  H1   C1   C    120.89  3.000
 FO2  N    C1   C    122.75  3.000
 FO2  H2   N1   C6   118.30  3.000
 FO2  H2   N1   C5   117.79  3.000
 FO2  C6   N1   C5   123.90  3.000
 FO2  N    C2   N3   115.65  3.000
 FO2  N    C2   C3   123.27  3.000
 FO2  N3   C2   C3   121.07  3.000
 FO2  C6   N2   C3   116.56  3.000
 FO2  C4   C3   N2   123.00  3.000
 FO2  C4   C3   C2   116.09  3.000
 FO2  N2   C3   C2   120.88  3.000
 FO2  C9   N3   N4   112.24  3.000
 FO2  N4   N3   C2   121.63  3.000
 FO2  C9   N3   C2   125.88  3.000
 FO2  C    C4   C5   120.79  3.000
 FO2  C    C4   C3   120.28  3.000
 FO2  C5   C4   C3   118.92  3.000
 FO2  C7   N4   N3   104.96  3.000
 FO2  O    C5   C4   124.97  3.000
 FO2  O    C5   N1   122.40  3.000
 FO2  C4   C5   N1   112.64  3.000
 FO2  H3   C6   N2   120.03  3.000
 FO2  H3   C6   N1   115.06  3.000
 FO2  N2   C6   N1   124.91  3.000
 FO2  H4   C7   C8   128.10  3.000
 FO2  H4   C7   N4   119.77  3.000
 FO2  C8   C7   N4   112.13  3.000
 FO2  C10  C8   C9   127.72  3.000
 FO2  C9   C8   C7   103.64  3.000
 FO2  C10  C8   C7   128.61  3.000
 FO2  H5   C9   C8   131.21  3.000
 FO2  H5   C9   N3   121.77  3.000
 FO2  C8   C9   N3   107.01  3.000
 FO2  H6   C10  C14  107.67  3.000
 FO2  H6   C10  C11  107.51  3.000
 FO2  C14  C10  C11  108.96  3.000
 FO2  H6   C10  C8   107.84  3.000
 FO2  C14  C10  C8   112.89  3.000
 FO2  C11  C10  C8   111.74  3.000
 FO2  H8   C11  H7   107.13  3.000
 FO2  H8   C11  C12  109.58  3.000
 FO2  H7   C11  C12  109.47  3.000
 FO2  H8   C11  C10  109.65  3.000
 FO2  H7   C11  C10  110.14  3.000
 FO2  C12  C11  C10  110.79  3.000
 FO2  H9   C    C4   121.21  3.000
 FO2  H9   C    C1   120.86  3.000
 FO2  C4   C    C1   117.93  3.000
 FO2  C2   N    C1   119.56  3.000
 FO2  H11  C14  H10  107.15  3.000
 FO2  H11  C14  C13  109.50  3.000
 FO2  H10  C14  C13  109.20  3.000
 FO2  H11  C14  C10  110.26  3.000
 FO2  H10  C14  C10  109.95  3.000
 FO2  C13  C14  C10  110.70  3.000
 FO2  H13  C13  H12  106.58  3.000
 FO2  H13  C13  N5   111.29  3.000
 FO2  H12  C13  N5   108.55  3.000
 FO2  H13  C13  C14  109.01  3.000
 FO2  H12  C13  C14  109.73  3.000
 FO2  N5   C13  C14  111.54  3.000
 FO2  C12  N5   C15  111.21  3.000
 FO2  C12  N5   C13  111.31  3.000
 FO2  C15  N5   C13  111.19  3.000
 FO2  H17  C15  H16  107.70  3.000
 FO2  H17  C15  H15  107.62  3.000
 FO2  H16  C15  H15  107.74  3.000
 FO2  H17  C15  N5   113.16  3.000
 FO2  H16  C15  N5   110.26  3.000
 FO2  H15  C15  N5   110.17  3.000
 FO2  H19  C12  H18  106.58  3.000
 FO2  H19  C12  N5   108.66  3.000
 FO2  H18  C12  N5   111.28  3.000
 FO2  H19  C12  C11  109.78  3.000
 FO2  H18  C12  C11  109.01  3.000
 FO2  N5   C12  C11  111.41  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
 FO2  CONST_01  N3   C2   N    C1    180.00   0.0  0
 FO2  CONST_02  C3   C2   N    C1      0.00   0.0  0
 FO2  CONST_03  C3   C4   C    C1      0.00   0.0  0
 FO2  CONST_04  C8   C9   N3   C2    180.00   0.0  0
 FO2  CONST_05  C7   N4   N3   C2    180.00   0.0  0
 FO2  CONST_06  C    C4   C3   C2      0.00   0.0  0
 FO2  CONST_07  C    C1   N    C2      0.00   0.0  0
 FO2  CONST_10  C7   C8   C9   N3      0.00   0.0  0
 FO2  CONST_11  C8   C7   N4   N3      0.00   0.0  0
 FO2  CONST_12  C4   C3   C2   N3    180.00   0.0  0
 FO2  CONST_13  N    C2   C3   C4      0.00   0.0  0
 FO2  CONST_14  N    C1   C    C4      0.00   0.0  0
 FO2  CONST_15  C9   C8   C7   N4      0.00   0.0  0
 FO2  CONST_16  C8   C9   N3   N4      0.00   0.0  0
 FO2  CONST_18  C9   N3   N4   C7      0.00   0.0  0
 FO2  CONST_20  N3   C2   C3   N2      0.00   0.0  0
 FO2  CONST_21  C10  C8   C9   N3    180.00   0.0  0
 FO2  CONST_22  C10  C8   C7   N4    180.00   0.0  0
 FO2  CONST_23  C3   N2   C6   N1      0.00   0.0  0
 FO2  CONST_24  C5   N1   C6   N2      0.00   0.0  0
 FO2  CONST_25  C6   N1   C5   C4      0.00   0.0  0
 FO2  CONST_26  O    C5   N1   C6    180.00   0.0  0
 FO2  CONST_27  H5   C9   N3   C2      0.00   0.0  0
 FO2  CONST_28  H1   C1   N    C2    180.00   0.0  0
 FO2  CONST_29  H9   C    C4   C3    180.00   0.0  0
 FO2  CONST_30  H4   C7   N4   N3    180.00   0.0  0
 FO2  CONST_31  H2   N1   C6   N2    180.00   0.0  0
 FO2  CONST_32  H3   C6   N2   C3    180.00   0.0  0
 FO2  Var_01    N5   C12  C11  C10   -56.98  30.0  1
 FO2  Var_02    N5   C13  C14  C10    56.93  30.0  1
 FO2  Var_03    C13  N5   C12  C11    58.89  30.0  1
 FO2  Var_04    C12  N5   C13  C14   -58.91  30.0  1
 FO2  Var_05    H15  C15  N5   C13  -177.40  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
 FO2  chir_01  C10  C11  C14  C8  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
 FO2  plan-1  C2   0.020
 FO2  plan-1  N3   0.020
 FO2  plan-1  N4   0.020
 FO2  plan-1  C7   0.020
 FO2  plan-1  C8   0.020
 FO2  plan-1  C9   0.020
 FO2  plan-1  C10  0.020
 FO2  plan-1  H4   0.020
 FO2  plan-1  H5   0.020
 FO2  plan-2  C1   0.020
 FO2  plan-2  N1   0.020
 FO2  plan-2  C2   0.020
 FO2  plan-2  N2   0.020
 FO2  plan-2  C3   0.020
 FO2  plan-2  N3   0.020
 FO2  plan-2  C4   0.020
 FO2  plan-2  C5   0.020
 FO2  plan-2  C6   0.020
 FO2  plan-2  O    0.020
 FO2  plan-2  C    0.020
 FO2  plan-2  N    0.020
 FO2  plan-2  H1   0.020
 FO2  plan-2  H2   0.020
 FO2  plan-2  H3   0.020
 FO2  plan-2  H9   0.020

