# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 22:42:00 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: 1-{4-[7-(naphthalen-1-yl)-5,6,7,8-tetrahydropyrido[3,4-d]pyrimidin-4-yl]piperazin-1-yl}propan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)N1CCN(CC1)c2ncnc3CN(CCc23)c4cccc5ccccc45
#
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
 K9M  K9M  1-{4-[7-(naphthalen-1-yl)-5,6,7,8-tetrahydropyrido[3,4-d]pyrimidin-4-yl]piperazin-1-yl}propan-1-one  ligand  57  30  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_K9M
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
 K9M  C18  C  CR16  0  -0.339  -4.1317   0.7457  -2.1644
 K9M  N5   N  N     0  -0.441   1.5775   0.9752   2.3263
 K9M  C13  C  CH2   0  -0.311   3.9561  -0.4392  -1.4515
 K9M  C12  C  CH2   0  -0.325   3.0749   0.5317  -0.6882
 K9M  C17  C  CR6   0   0.288  -3.7784   0.2136  -0.9479
 K9M  C16  C  CH2   0  -0.286   3.6211  -0.5433   1.3895
 K9M  C15  C  CH2   0  -0.323   4.5072  -1.5226   0.6332
 K9M  N3   N  N     0  -0.436  -0.6717   1.6799   2.3330
 K9M  C10  C  CH2   0  -0.353  -2.2136   1.2317   0.5461
 K9M  C8   C  CH2   0  -0.322  -1.3952   0.2263  -1.4661
 K9M  C22  C  CR66  0   0.071  -4.7850  -0.3809  -0.1254
 K9M  C7   C  CH2   0  -0.494  -0.1025  -0.2507  -0.8263
 K9M  C6   C  CR6   0   0.478   1.4376   0.4728   1.1042
 K9M  C1   C  CR6   0  -0.032   0.1898   0.4859   0.4499
 K9M  C4   C  CR16  0   0.043   0.5196   1.5475   2.8768
 K9M  C19  C  CR16  0  -0.254  -5.4716   0.7363  -2.6017
 K9M  C20  C  CR16  0  -0.334  -6.4586   0.2200  -1.8114
 K9M  C21  C  CR66  0   0.101  -6.1374  -0.3499  -0.5566
 K9M  C2   C  CR6   0   0.224  -0.8343   1.1245   1.1284
 K9M  N9   N  NT    0  -0.511  -2.4522   0.2240  -0.4729
 K9M  N11  N  NT    0  -0.505   2.5448  -0.1107   0.5128
 K9M  N14  N  NT    0  -0.462   5.0143  -0.9235  -0.5860
 K9M  C23  C  CR16  0  -0.316  -7.1369  -0.9144   0.2712
 K9M  C24  C  CR16  0  -0.255  -6.8135  -1.5036   1.4624
 K9M  C25  C  CR16  0  -0.255  -5.4664  -1.5722   1.8706
 K9M  C26  C  CR16  0  -0.314  -4.4781  -1.0277   1.0952
 K9M  C27  C  C     0   0.565   6.3172  -0.6913  -0.8715
 K9M  C28  C  CH2   0  -0.596   7.3468  -1.1681   0.1366
 K9M  O29  O  O     0  -0.503   6.6599  -0.1292  -1.9031
 K9M  C30  C  CH3   0  -0.650   8.7741  -0.8648  -0.2842
 K9M  H1   H  HCR6  0   0.265  -3.3804   1.1979  -2.7992
 K9M  H3   H  HCH2  0   0.270   4.3833   0.0503  -2.3219
 K9M  H4   H  HCH2  0   0.246   3.6652   1.4154  -0.4088
 K9M  H5   H  HCH2  0   0.268   2.2700   0.8823  -1.3298
 K9M  H6   H  HCH2  0   0.260   3.2052  -1.0463   2.2615
 K9M  H7   H  HCH2  0   0.224   4.2260   0.3004   1.7471
 K9M  H8   H  HCH2  0   0.279   5.3183  -1.8472   1.2782
 K9M  H9   H  HCH2  0   0.250   3.9230  -2.4111   0.3741
 K9M  H10  H  HCH2  0   0.275  -2.9401   1.1348   1.3530
 K9M  H11  H  HCH2  0   0.255  -2.3353   2.2508   0.1418
 K9M  H12  H  HCH2  0   0.222  -1.2410   1.2227  -1.9074
 K9M  H13  H  HCH2  0   0.263  -1.6659  -0.4496  -2.2772
 K9M  H14  H  HCH2  0   0.262  -0.1768  -1.3188  -0.6014
 K9M  H15  H  HCH2  0   0.256   0.6943  -0.1513  -1.5596
 K9M  H16  H  HCR6  0   0.254   0.6533   1.9532   3.8744
 K9M  H17  H  HCR6  0   0.257  -5.7141   1.1649  -3.5654
 K9M  H18  H  HCR6  0   0.252  -7.4913   0.2319  -2.1377
 K9M  H19  H  HCR6  0   0.255  -8.1683  -0.8770  -0.0586
 K9M  H20  H  HCR6  0   0.257  -7.5875  -1.9306   2.0870
 K9M  H21  H  HCR6  0   0.257  -5.2116  -2.0664   2.7991
 K9M  H22  H  HCR6  0   0.259  -3.4449  -1.1111   1.4050
 K9M  H23  H  HCH2  0   0.264   7.1416  -0.7050   1.1057
 K9M  H24  H  HCH2  0   0.267   7.2253  -2.2437   0.2930
 K9M  H25  H  HCH3  0   0.227   9.0339  -1.3567  -1.2206
 K9M  H26  H  HCH3  0   0.227   8.9403   0.2044  -0.4086
 K9M  H27  H  HCH3  0   0.231   9.4648  -1.2213   0.4796
 K9M  H2   H  HCH2  0   0.248   3.3561  -1.2867  -1.7985

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
 K9M  C19  C18  aromatic  1.409  0.020  1.409
 K9M  C19  C20  aromatic  1.366  0.020  1.366
 K9M  C18  C17  aromatic  1.374  0.020  1.374
 K9M  C20  C21  aromatic  1.415  0.020  1.415
 K9M  C8   N9   single    1.450  0.020  1.450
 K9M  C8   C7   single    1.519  0.020  1.519
 K9M  C17  N9   single    1.409  0.020  1.409
 K9M  C17  C22  aromatic  1.429  0.020  1.429
 K9M  C21  C22  aromatic  1.420  0.020  1.420
 K9M  C21  C23  aromatic  1.415  0.020  1.415
 K9M  N9   C10  single    1.453  0.020  1.453
 K9M  C10  C2   single    1.501  0.020  1.501
 K9M  C7   C1   single    1.502  0.020  1.502
 K9M  C22  C26  aromatic  1.415  0.020  1.415
 K9M  C2   C1   aromatic  1.385  0.020  1.385
 K9M  C2   N3   aromatic  1.336  0.020  1.336
 K9M  C1   C6   aromatic  1.409  0.020  1.409
 K9M  C23  C24  aromatic  1.368  0.020  1.368
 K9M  C13  C12  single    1.517  0.020  1.517
 K9M  C13  N14  single    1.450  0.020  1.450
 K9M  N3   C4   aromatic  1.316  0.020  1.316
 K9M  C12  N11  single    1.462  0.020  1.462
 K9M  C6   N11  single    1.384  0.020  1.384
 K9M  C6   N5   aromatic  1.329  0.020  1.329
 K9M  N11  C16  single    1.454  0.020  1.454
 K9M  C4   N5   aromatic  1.323  0.020  1.323
 K9M  C26  C25  aromatic  1.369  0.020  1.369
 K9M  C16  C15  single    1.522  0.020  1.522
 K9M  C24  C25  aromatic  1.409  0.020  1.409
 K9M  N14  C27  single    1.354  0.020  1.354
 K9M  N14  C15  single    1.450  0.020  1.450
 K9M  C28  C27  single    1.518  0.020  1.518
 K9M  C28  C30  single    1.519  0.020  1.519
 K9M  C27  O29  double    1.224  0.020  1.224
 K9M  C18  H1   single    0.930  0.020  1.080
 K9M  C13  H2   single    0.970  0.020  1.090
 K9M  C13  H3   single    0.970  0.020  1.090
 K9M  C12  H4   single    0.970  0.020  1.090
 K9M  C12  H5   single    0.970  0.020  1.090
 K9M  C16  H6   single    0.970  0.020  1.090
 K9M  C16  H7   single    0.970  0.020  1.090
 K9M  C15  H8   single    0.970  0.020  1.090
 K9M  C15  H9   single    0.970  0.020  1.090
 K9M  C10  H10  single    0.970  0.020  1.090
 K9M  C10  H11  single    0.970  0.020  1.090
 K9M  C8   H12  single    0.970  0.020  1.090
 K9M  C8   H13  single    0.970  0.020  1.090
 K9M  C7   H14  single    0.970  0.020  1.090
 K9M  C7   H15  single    0.970  0.020  1.090
 K9M  C4   H16  single    0.930  0.020  1.080
 K9M  C19  H17  single    0.930  0.020  1.080
 K9M  C20  H18  single    0.930  0.020  1.080
 K9M  C23  H19  single    0.930  0.020  1.080
 K9M  C24  H20  single    0.930  0.020  1.080
 K9M  C25  H21  single    0.930  0.020  1.080
 K9M  C26  H22  single    0.930  0.020  1.080
 K9M  C28  H23  single    0.970  0.020  1.090
 K9M  C28  H24  single    0.970  0.020  1.090
 K9M  C30  H25  single    0.970  0.020  1.090
 K9M  C30  H26  single    0.970  0.020  1.090
 K9M  C30  H27  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
 K9M  H1   C18  C19  118.73  3.000
 K9M  H1   C18  C17  120.16  3.000
 K9M  C19  C18  C17  121.10  3.000
 K9M  C4   N5   C6   117.53  3.000
 K9M  H3   C13  H2   108.08  3.000
 K9M  H3   C13  N14  109.98  3.000
 K9M  H2   C13  N14  109.30  3.000
 K9M  H3   C13  C12  110.07  3.000
 K9M  H2   C13  C12  109.67  3.000
 K9M  N14  C13  C12  109.71  3.000
 K9M  H5   C12  H4   106.76  3.000
 K9M  H5   C12  N11  110.98  3.000
 K9M  H4   C12  N11  109.84  3.000
 K9M  H5   C12  C13  109.84  3.000
 K9M  H4   C12  C13  109.30  3.000
 K9M  N11  C12  C13  110.05  3.000
 K9M  N9   C17  C22  118.17  3.000
 K9M  C22  C17  C18  119.31  3.000
 K9M  N9   C17  C18  122.53  3.000
 K9M  H7   C16  H6   107.73  3.000
 K9M  H7   C16  N11  112.06  3.000
 K9M  H6   C16  N11  109.72  3.000
 K9M  H7   C16  C15  109.61  3.000
 K9M  H6   C16  C15  108.85  3.000
 K9M  N11  C16  C15  108.83  3.000
 K9M  H9   C15  H8   107.26  3.000
 K9M  H9   C15  N14  108.85  3.000
 K9M  H8   C15  N14  111.20  3.000
 K9M  H9   C15  C16  109.22  3.000
 K9M  H8   C15  C16  109.39  3.000
 K9M  N14  C15  C16  110.83  3.000
 K9M  C2   N3   C4   116.15  3.000
 K9M  H11  C10  H10  106.26  3.000
 K9M  H11  C10  N9   111.44  3.000
 K9M  H10  C10  N9   110.37  3.000
 K9M  H11  C10  C2   108.03  3.000
 K9M  H10  C10  C2   108.60  3.000
 K9M  N9   C10  C2   111.93  3.000
 K9M  H13  C8   H12  107.33  3.000
 K9M  H13  C8   N9   109.12  3.000
 K9M  H12  C8   N9   112.21  3.000
 K9M  H13  C8   C7   109.27  3.000
 K9M  H12  C8   C7   109.51  3.000
 K9M  N9   C8   C7   109.34  3.000
 K9M  C26  C22  C21  118.59  3.000
 K9M  C26  C22  C17  122.26  3.000
 K9M  C21  C22  C17  119.14  3.000
 K9M  H15  C7   H14  106.11  3.000
 K9M  H15  C7   C1   112.67  3.000
 K9M  H14  C7   C1   108.49  3.000
 K9M  H15  C7   C8   108.11  3.000
 K9M  H14  C7   C8   109.60  3.000
 K9M  C1   C7   C8   111.68  3.000
 K9M  N11  C6   C1   120.92  3.000
 K9M  N11  C6   N5   117.91  3.000
 K9M  C1   C6   N5   121.12  3.000
 K9M  C2   C1   C6   115.58  3.000
 K9M  C6   C1   C7   124.21  3.000
 K9M  C2   C1   C7   119.90  3.000
 K9M  H16  C4   N3   116.98  3.000
 K9M  H16  C4   N5   116.47  3.000
 K9M  N3   C4   N5   126.54  3.000
 K9M  H17  C19  C20  120.20  3.000
 K9M  H17  C19  C18  119.12  3.000
 K9M  C20  C19  C18  120.67  3.000
 K9M  H18  C20  C21  119.21  3.000
 K9M  H18  C20  C19  120.70  3.000
 K9M  C21  C20  C19  120.09  3.000
 K9M  C23  C21  C20  121.27  3.000
 K9M  C23  C21  C22  119.10  3.000
 K9M  C20  C21  C22  119.62  3.000
 K9M  C1   C2   C10  121.50  3.000
 K9M  C1   C2   N3   122.92  3.000
 K9M  C10  C2   N3   115.58  3.000
 K9M  C8   N9   C10  111.07  3.000
 K9M  C10  N9   C17  113.34  3.000
 K9M  C8   N9   C17  117.08  3.000
 K9M  C6   N11  C16  117.38  3.000
 K9M  C16  N11  C12  110.96  3.000
 K9M  C6   N11  C12  117.12  3.000
 K9M  C27  N14  C15  125.78  3.000
 K9M  C15  N14  C13  112.62  3.000
 K9M  C27  N14  C13  121.27  3.000
 K9M  H19  C23  C24  120.33  3.000
 K9M  H19  C23  C21  118.72  3.000
 K9M  C24  C23  C21  120.95  3.000
 K9M  H20  C24  C25  119.82  3.000
 K9M  H20  C24  C23  120.23  3.000
 K9M  C25  C24  C23  119.95  3.000
 K9M  H21  C25  C26  119.84  3.000
 K9M  H21  C25  C24  119.72  3.000
 K9M  C26  C25  C24  120.44  3.000
 K9M  H22  C26  C25  119.77  3.000
 K9M  H22  C26  C22  119.30  3.000
 K9M  C25  C26  C22  120.92  3.000
 K9M  O29  C27  C28  120.95  3.000
 K9M  O29  C27  N14  121.73  3.000
 K9M  C28  C27  N14  117.32  3.000
 K9M  H24  C28  H23  105.60  3.000
 K9M  H24  C28  C30  109.91  3.000
 K9M  H23  C28  C30  109.71  3.000
 K9M  H24  C28  C27  109.18  3.000
 K9M  H23  C28  C27  109.16  3.000
 K9M  C30  C28  C27  113.01  3.000
 K9M  H27  C30  H26  107.73  3.000
 K9M  H27  C30  H25  107.68  3.000
 K9M  H26  C30  H25  107.99  3.000
 K9M  H27  C30  C28  109.65  3.000
 K9M  H26  C30  C28  111.78  3.000
 K9M  H25  C30  C28  111.85  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
 K9M  CONST_01  C21  C20  C19  C18     0.00   0.0  0
 K9M  CONST_02  C21  C22  C17  C18     0.00   0.0  0
 K9M  CONST_03  C26  C22  C17  C18   180.00   0.0  0
 K9M  CONST_04  C2   C1   C6   N5      0.00   0.0  0
 K9M  CONST_05  C2   N3   C4   N5      0.00   0.0  0
 K9M  CONST_06  C20  C19  C18  C17     0.00   0.0  0
 K9M  CONST_07  C20  C21  C22  C17     0.00   0.0  0
 K9M  CONST_08  C23  C21  C22  C17   180.00   0.0  0
 K9M  CONST_09  C25  C26  C22  C17   180.00   0.0  0
 K9M  CONST_10  C6   C1   C2   N3      0.00   0.0  0
 K9M  CONST_11  C6   N5   C4   N3      0.00   0.0  0
 K9M  CONST_12  C19  C18  C17  C22     0.00   0.0  0
 K9M  CONST_13  C19  C20  C21  C22     0.00   0.0  0
 K9M  CONST_14  C24  C23  C21  C22     0.00   0.0  0
 K9M  CONST_15  C24  C25  C26  C22     0.00   0.0  0
 K9M  CONST_16  C4   N3   C2   C1      0.00   0.0  0
 K9M  CONST_17  C4   N5   C6   C1      0.00   0.0  0
 K9M  CONST_18  C23  C21  C20  C19   180.00   0.0  0
 K9M  CONST_19  C26  C22  C21  C20   180.00   0.0  0
 K9M  CONST_20  C24  C23  C21  C20   180.00   0.0  0
 K9M  CONST_21  C25  C26  C22  C21     0.00   0.0  0
 K9M  CONST_22  C25  C24  C23  C21     0.00   0.0  0
 K9M  CONST_23  C26  C22  C21  C23     0.00   0.0  0
 K9M  CONST_24  C26  C25  C24  C23     0.00   0.0  0
 K9M  CONST_25  N11  C6   C1   C7      0.00   0.0  0
 K9M  CONST_26  N11  C6   N5   C4    180.00   0.0  0
 K9M  CONST_27  N9   C17  C18  C19   180.00   0.0  0
 K9M  CONST_28  N9   C17  C22  C21   180.00   0.0  0
 K9M  CONST_29  N11  C6   C1   C2    180.00   0.0  0
 K9M  CONST_30  C26  C22  C17  N9      0.00   0.0  0
 K9M  CONST_31  H18  C20  C19  C18   180.00   0.0  0
 K9M  CONST_32  H17  C19  C18  C17   180.00   0.0  0
 K9M  CONST_33  H22  C26  C22  C17     0.00   0.0  0
 K9M  CONST_34  H1   C18  C17  C22   180.00   0.0  0
 K9M  CONST_35  H19  C23  C21  C22   180.00   0.0  0
 K9M  CONST_36  H21  C25  C26  C22   180.00   0.0  0
 K9M  CONST_37  H16  C4   N5   C6    180.00   0.0  0
 K9M  CONST_38  H20  C24  C23  C21   180.00   0.0  0
 K9M  CONST_39  C28  C27  N14  C13   180.00   0.0  0
 K9M  CONST_40  O29  C27  N14  C13     0.00   0.0  0
 K9M  CONST_41  C28  C27  N14  C15     0.00   0.0  0
 K9M  CONST_42  O29  C27  N14  C15   180.00   0.0  0
 K9M  Var_01    C8   N9   C17  C18   -27.77  30.0  2
 K9M  Var_02    C12  N11  C6   N5   -115.45  30.0  2
 K9M  Var_03    C6   N11  C12  C13  -161.52  30.0  1
 K9M  Var_04    C16  C15  N14  C13   -56.21  30.0  1
 K9M  Var_05    C15  N14  C13  C12    55.56  30.0  1
 K9M  Var_06    C15  C16  N11  C12   -59.23  30.0  1
 K9M  Var_07    C7   C8   N9   C17  -160.10  30.0  1
 K9M  Var_08    C2   C10  N9   C17   174.21  30.0  1
 K9M  Var_09    N9   C10  C2   N3   -158.63  30.0  1
 K9M  Var_10    C2   C1   C7   C8     21.00  30.0  1
 K9M  Var_11    N9   C8   C7   C1    -50.18  30.0  1
 K9M  Var_12    N14  C13  C12  N11   -56.50  30.0  1
 K9M  Var_13    N14  C15  C16  N11    56.69  30.0  1
 K9M  Var_14    C30  C28  C27  N14   179.68  30.0  1
 K9M  Var_15    H25  C30  C28  C27   -61.11  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
 K9M  plan-1  N5   0.020
 K9M  plan-1  N3   0.020
 K9M  plan-1  C10  0.020
 K9M  plan-1  C7   0.020
 K9M  plan-1  C6   0.020
 K9M  plan-1  C1   0.020
 K9M  plan-1  C4   0.020
 K9M  plan-1  C2   0.020
 K9M  plan-1  N11  0.020
 K9M  plan-1  H16  0.020
 K9M  plan-2  C18  0.020
 K9M  plan-2  C17  0.020
 K9M  plan-2  C22  0.020
 K9M  plan-2  C19  0.020
 K9M  plan-2  C20  0.020
 K9M  plan-2  C21  0.020
 K9M  plan-2  N9   0.020
 K9M  plan-2  C23  0.020
 K9M  plan-2  C24  0.020
 K9M  plan-2  C25  0.020
 K9M  plan-2  C26  0.020
 K9M  plan-2  H1   0.020
 K9M  plan-2  H17  0.020
 K9M  plan-2  H18  0.020
 K9M  plan-2  H19  0.020
 K9M  plan-2  H20  0.020
 K9M  plan-2  H21  0.020
 K9M  plan-2  H22  0.020
 K9M  plan-3  C13  0.020
 K9M  plan-3  C15  0.020
 K9M  plan-3  N14  0.020
 K9M  plan-3  C27  0.020
 K9M  plan-3  C28  0.020
 K9M  plan-3  O29  0.020

