# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 10:35:23 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 4-cycloheptyl-6-(3-piperidin-1-ylpropyl)pyrimidine-2-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N#Cc1nc(CCCN2CCCCC2)cc(n1)C3CCCCCC3
#
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
 KX1  KX1  4-cycloheptyl-6-(3-piperidin-1-ylpropyl)pyrimidine-2-carbonitrile  ligand  54  24  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_KX1
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
 KX1  N1    N  N     0  -0.413  -2.3218   1.9474   0.0789
 KX1  C2    C  CR6   0   0.338  -2.4809   0.6425   0.2988
 KX1  C3    C  CR16  0  -0.380  -1.4068  -0.1267   0.7369
 KX1  C4    C  CR6   0   0.318  -0.1862   0.4942   0.9610
 KX1  N5    N  N     0  -0.411  -0.0461   1.8038   0.7423
 KX1  C6    C  CR6   0   0.344  -1.1181   2.4348   0.3122
 KX1  C7    C  CH2   0  -0.502   1.0184  -0.2489   1.4434
 KX1  C8    C  CH2   0  -0.451   2.1448  -0.2510   0.4086
 KX1  C9    C  CH2   0  -0.255   3.4006  -0.9061   0.9696
 KX1  C10   C  CH1   0  -0.324  -3.8360   0.0593   0.0179
 KX1  C11   C  CH2   0  -0.421  -3.8370  -0.4669  -1.4246
 KX1  C12   C  CH2   0  -0.441  -5.1519  -1.0786  -1.9043
 KX1  C13   C  CH2   0  -0.439  -4.2596  -0.9650   1.0763
 KX1  C14   C  CH2   0  -0.442  -5.4597  -2.4409  -1.2828
 KX1  C15   C  CH2   0  -0.446  -5.7544  -1.2832   1.0226
 KX1  C16   C  CH2   0  -0.424  -6.1642  -2.4115   0.0761
 KX1  C17   C  CSP   0   0.042  -0.9589   3.8534   0.0707
 KX1  N18   N  NT    0  -0.421   4.5017  -0.9456   0.0256
 KX1  N19   N  NS    0  -0.224  -0.8347   4.9813  -0.1142
 KX1  C20   C  CH2   0  -0.278   5.5213  -1.8896   0.4554
 KX1  C21   C  CH2   0  -0.438   6.6346  -2.0208  -0.5734
 KX1  C22   C  CH2   0  -0.439   7.2565  -0.6641  -0.8777
 KX1  C23   C  CH2   0  -0.435   6.1671   0.3287  -1.2601
 KX1  C24   C  CH2   0  -0.285   5.0805   0.3702  -0.1969
 KX1  H3    H  HCR6  0   0.282  -1.5177  -1.1880   0.9111
 KX1  H7    H  HCH2  0   0.263   1.3708   0.2311   2.3614
 KX1  H7A   H  HCH2  0   0.256   0.7382  -1.2711   1.7037
 KX1  H8    H  HCH2  0   0.235   1.8261  -0.7875  -0.4888
 KX1  H8A   H  HCH2  0   0.241   2.3454   0.7798   0.1112
 KX1  H9    H  HCH2  0   0.188   3.6884  -0.3982   1.9077
 KX1  H9A   H  HCH2  0   0.229   3.1564  -1.9365   1.2435
 KX1  H10   H  HCH1  0   0.252  -4.5424   0.8951   0.0638
 KX1  H11   H  HCH2  0   0.240  -3.5666   0.3617  -2.0856
 KX1  H11A  H  HCH2  0   0.225  -3.0445  -1.2159  -1.5352
 KX1  H12   H  HCH2  0   0.221  -5.9798  -0.3800  -1.7440
 KX1  H12A  H  HCH2  0   0.234  -5.0722  -1.2003  -2.9873
 KX1  H13   H  HCH2  0   0.228  -3.6660  -1.8816   0.9948
 KX1  H13A  H  HCH2  0   0.243  -4.0282  -0.5484   2.0605
 KX1  H14   H  HCH2  0   0.230  -6.0811  -3.0191  -1.9711
 KX1  H14A  H  HCH2  0   0.215  -4.5217  -2.9995  -1.2046
 KX1  H15   H  HCH2  0   0.236  -6.0998  -1.5416   2.0261
 KX1  H15A  H  HCH2  0   0.220  -6.2909  -0.3671   0.7578
 KX1  H16   H  HCH2  0   0.220  -7.2442  -2.3410  -0.0798
 KX1  H16A  H  HCH2  0   0.219  -5.9966  -3.3733   0.5685
 KX1  H20   H  HCH2  0   0.180   5.9597  -1.5909   1.4257
 KX1  H20A  H  HCH2  0   0.232   5.0496  -2.8628   0.6135
 KX1  H21   H  HCH2  0   0.229   7.3879  -2.7186  -0.2007
 KX1  H21A  H  HCH2  0   0.214   6.2259  -2.4530  -1.4920
 KX1  H22   H  HCH2  0   0.209   7.7803  -0.2976   0.0118
 KX1  H22A  H  HCH2  0   0.230   8.0033  -0.7486  -1.6700
 KX1  H23   H  HCH2  0   0.229   6.5820   1.3308  -1.3897
 KX1  H23A  H  HCH2  0   0.214   5.7222   0.0410  -2.2176
 KX1  H24   H  HCH2  0   0.236   4.2963   1.0617  -0.5085
 KX1  H24A  H  HCH2  0   0.181   5.5043   0.7769   0.7405

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
 KX1  N1   C2    aromatic  1.333  0.020  1.333
 KX1  N1   C6    aromatic  1.319  0.020  1.319
 KX1  C2   C3    aromatic  1.392  0.020  1.392
 KX1  C2   C10   single    1.502  0.020  1.502
 KX1  C3   C4    aromatic  1.388  0.020  1.388
 KX1  C4   N5    aromatic  1.335  0.020  1.335
 KX1  C4   C7    single    1.495  0.020  1.495
 KX1  N5   C6    aromatic  1.316  0.020  1.316
 KX1  C6   C17   single    1.448  0.020  1.448
 KX1  C7   C8    single    1.530  0.020  1.530
 KX1  C8   C9    single    1.523  0.020  1.523
 KX1  C9   N18   single    1.451  0.020  1.451
 KX1  C10  C11   single    1.536  0.020  1.536
 KX1  C10  C13   single    1.533  0.020  1.533
 KX1  C11  C12   single    1.527  0.020  1.527
 KX1  C12  C14   single    1.529  0.020  1.529
 KX1  C13  C15   single    1.529  0.020  1.529
 KX1  C14  C16   single    1.531  0.020  1.531
 KX1  C15  C16   single    1.529  0.020  1.529
 KX1  C17  N19   triple    1.150  0.020  1.150
 KX1  N18  C20   single    1.454  0.020  1.454
 KX1  N18  C24   single    1.455  0.020  1.455
 KX1  C20  C21   single    1.522  0.020  1.522
 KX1  C21  C22   single    1.523  0.020  1.523
 KX1  C22  C23   single    1.523  0.020  1.523
 KX1  C23  C24   single    1.521  0.020  1.521
 KX1  C3   H3    single    0.930  0.020  1.080
 KX1  C7   H7    single    0.970  0.020  1.090
 KX1  C7   H7A   single    0.970  0.020  1.090
 KX1  C8   H8    single    0.970  0.020  1.090
 KX1  C8   H8A   single    0.970  0.020  1.090
 KX1  C9   H9    single    0.970  0.020  1.090
 KX1  C9   H9A   single    0.970  0.020  1.090
 KX1  C10  H10   single    0.970  0.020  1.090
 KX1  C11  H11   single    0.970  0.020  1.090
 KX1  C11  H11A  single    0.970  0.020  1.090
 KX1  C12  H12   single    0.970  0.020  1.090
 KX1  C12  H12A  single    0.970  0.020  1.090
 KX1  C13  H13   single    0.970  0.020  1.090
 KX1  C13  H13A  single    0.970  0.020  1.090
 KX1  C14  H14   single    0.970  0.020  1.090
 KX1  C14  H14A  single    0.970  0.020  1.090
 KX1  C15  H15   single    0.970  0.020  1.090
 KX1  C15  H15A  single    0.970  0.020  1.090
 KX1  C16  H16   single    0.970  0.020  1.090
 KX1  C16  H16A  single    0.970  0.020  1.090
 KX1  C20  H20   single    0.970  0.020  1.090
 KX1  C20  H20A  single    0.970  0.020  1.090
 KX1  C21  H21   single    0.970  0.020  1.090
 KX1  C21  H21A  single    0.970  0.020  1.090
 KX1  C22  H22   single    0.970  0.020  1.090
 KX1  C22  H22A  single    0.970  0.020  1.090
 KX1  C23  H23   single    0.970  0.020  1.090
 KX1  C23  H23A  single    0.970  0.020  1.090
 KX1  C24  H24   single    0.970  0.020  1.090
 KX1  C24  H24A  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
 KX1  C6    N1   C2   116.20  3.000
 KX1  C10   C2   C3   122.73  3.000
 KX1  C10   C2   N1   117.20  3.000
 KX1  C3    C2   N1   120.06  3.000
 KX1  H3    C3   C4   120.22  3.000
 KX1  H3    C3   C2   120.94  3.000
 KX1  C4    C3   C2   118.84  3.000
 KX1  C7    C4   N5   117.11  3.000
 KX1  C7    C4   C3   122.57  3.000
 KX1  N5    C4   C3   120.32  3.000
 KX1  C6    N5   C4   115.99  3.000
 KX1  C17   C6   N5   115.76  3.000
 KX1  C17   C6   N1   115.65  3.000
 KX1  N5    C6   N1   128.59  3.000
 KX1  H7A   C7   H7   107.06  3.000
 KX1  H7A   C7   C8   110.43  3.000
 KX1  H7    C7   C8   109.33  3.000
 KX1  H7A   C7   C4   109.61  3.000
 KX1  H7    C7   C4   108.19  3.000
 KX1  C8    C7   C4   112.07  3.000
 KX1  H8A   C8   H8   107.06  3.000
 KX1  H8A   C8   C9   110.79  3.000
 KX1  H8    C8   C9   109.37  3.000
 KX1  H8A   C8   C7   108.57  3.000
 KX1  H8    C8   C7   109.96  3.000
 KX1  C9    C8   C7   111.01  3.000
 KX1  H9A   C9   H9   106.18  3.000
 KX1  H9A   C9   N18  107.86  3.000
 KX1  H9    C9   N18  111.54  3.000
 KX1  H9A   C9   C8   108.25  3.000
 KX1  H9    C9   C8   109.26  3.000
 KX1  N18   C9   C8   113.43  3.000
 KX1  H10   C10  C13  107.63  3.000
 KX1  H10   C10  C11  107.48  3.000
 KX1  C13   C10  C11  114.81  3.000
 KX1  H10   C10  C2   106.13  3.000
 KX1  C13   C10  C2   112.32  3.000
 KX1  C11   C10  C2   108.02  3.000
 KX1  H11A  C11  H11  106.14  3.000
 KX1  H11A  C11  C12  108.49  3.000
 KX1  H11   C11  C12  109.05  3.000
 KX1  H11A  C11  C10  109.18  3.000
 KX1  H11   C11  C10  107.93  3.000
 KX1  C12   C11  C10  115.65  3.000
 KX1  H12A  C12  H12  105.74  3.000
 KX1  H12A  C12  C14  108.56  3.000
 KX1  H12   C12  C14  110.90  3.000
 KX1  H12A  C12  C11  107.04  3.000
 KX1  H12   C12  C11  110.45  3.000
 KX1  C14   C12  C11  113.74  3.000
 KX1  H13A  C13  H13  105.73  3.000
 KX1  H13A  C13  C15  108.53  3.000
 KX1  H13   C13  C15  110.68  3.000
 KX1  H13A  C13  C10  107.97  3.000
 KX1  H13   C13  C10  110.99  3.000
 KX1  C15   C13  C10  112.65  3.000
 KX1  H14A  C14  H14  105.21  3.000
 KX1  H14A  C14  C16  109.93  3.000
 KX1  H14   C14  C16  107.91  3.000
 KX1  H14A  C14  C12  108.13  3.000
 KX1  H14   C14  C12  109.26  3.000
 KX1  C16   C14  C12  115.88  3.000
 KX1  H15A  C15  H15  105.39  3.000
 KX1  H15A  C15  C16  109.67  3.000
 KX1  H15   C15  C16  108.03  3.000
 KX1  H15A  C15  C13  108.27  3.000
 KX1  H15   C15  C13  109.03  3.000
 KX1  C16   C15  C13  115.94  3.000
 KX1  H16A  C16  H16  105.81  3.000
 KX1  H16A  C16  C15  109.23  3.000
 KX1  H16   C16  C15  107.79  3.000
 KX1  H16A  C16  C14  108.20  3.000
 KX1  H16   C16  C14  109.22  3.000
 KX1  C15   C16  C14  116.13  3.000
 KX1  N19   C17  C6   180.00  3.000
 KX1  C24   N18  C20  110.69  3.000
 KX1  C24   N18  C9   112.14  3.000
 KX1  C20   N18  C9   110.94  3.000
 KX1  H20A  C20  H20  106.53  3.000
 KX1  H20A  C20  C21  109.68  3.000
 KX1  H20   C20  C21  109.06  3.000
 KX1  H20A  C20  N18  108.55  3.000
 KX1  H20   C20  N18  111.22  3.000
 KX1  C21   C20  N18  111.66  3.000
 KX1  H21A  C21  H21  106.95  3.000
 KX1  H21A  C21  C22  109.67  3.000
 KX1  H21   C21  C22  110.83  3.000
 KX1  H21A  C21  C20  109.17  3.000
 KX1  H21   C21  C20  109.21  3.000
 KX1  C22   C21  C20  110.92  3.000
 KX1  H22A  C22  H22  106.74  3.000
 KX1  H22A  C22  C23  110.94  3.000
 KX1  H22   C22  C23  109.14  3.000
 KX1  H22A  C22  C21  110.81  3.000
 KX1  H22   C22  C21  109.33  3.000
 KX1  C23   C22  C21  109.81  3.000
 KX1  H23A  C23  H23  106.97  3.000
 KX1  H23A  C23  C24  109.17  3.000
 KX1  H23   C23  C24  109.23  3.000
 KX1  H23A  C23  C22  109.82  3.000
 KX1  H23   C23  C22  110.87  3.000
 KX1  C24   C23  C22  110.69  3.000
 KX1  H24A  C24  H24  106.52  3.000
 KX1  H24A  C24  C23  109.19  3.000
 KX1  H24   C24  C23  109.34  3.000
 KX1  H24A  C24  N18  110.82  3.000
 KX1  H24   C24  N18  109.33  3.000
 KX1  C23   C24  N18  111.50  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
 KX1  CONST_01  C4   C3   C2   N1      0.00   0.0  0
 KX1  CONST_02  C4   N5   C6   N1      0.00   0.0  0
 KX1  CONST_03  N5   C6   N1   C2      0.00   0.0  0
 KX1  CONST_04  N5   C4   C3   C2      0.00   0.0  0
 KX1  CONST_05  C6   N1   C2   C3      0.00   0.0  0
 KX1  CONST_06  C6   N5   C4   C3      0.00   0.0  0
 KX1  CONST_07  C10  C2   C3   C4    180.00   0.0  0
 KX1  CONST_08  C10  C2   N1   C6    180.00   0.0  0
 KX1  CONST_09  C17  C6   N1   C2    180.00   0.0  0
 KX1  CONST_10  C7   C4   C3   C2    180.00   0.0  0
 KX1  CONST_11  C17  C6   N5   C4    180.00   0.0  0
 KX1  CONST_12  C7   C4   N5   C6    180.00   0.0  0
 KX1  CONST_13  H3   C3   C2   N1    180.00   0.0  0
 KX1  Var_01    C22  C21  C20  N18    56.22  30.0  1
 KX1  Var_02    C22  C23  C24  N18   -57.08  30.0  1
 KX1  Var_03    C23  C24  N18  C20    59.52  30.0  1
 KX1  Var_04    C23  C22  C21  C20   -52.84  30.0  1
 KX1  Var_05    C24  N18  C20  C21   -59.06  30.0  1
 KX1  Var_06    C24  C23  C22  C21    53.23  30.0  1
 KX1  Var_07    C8   C7   C4   C3    115.46  30.0  2
 KX1  Var_08    C20  N18  C9   C8   -163.98  30.0  3
 KX1  Var_09    C9   C8   C7   C4    175.00  30.0  3
 KX1  Var_10    N18  C9   C8   C7    179.55  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
 KX1  chir_01  C10  C2  C11  C13  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
 KX1  plan-1  N1   0.020
 KX1  plan-1  C2   0.020
 KX1  plan-1  C3   0.020
 KX1  plan-1  C4   0.020
 KX1  plan-1  N5   0.020
 KX1  plan-1  C6   0.020
 KX1  plan-1  C7   0.020
 KX1  plan-1  C10  0.020
 KX1  plan-1  C17  0.020
 KX1  plan-1  N19  0.020
 KX1  plan-1  H3   0.020

