# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 21:31:37 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: 2-{4-[5-chloro-6-methyl-2-(pyridin-2-yl)pyrimidin-4-yl]piperazin-1-yl}ethanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc(nc(N2CCN(CCO)CC2)c1Cl)c3ccccn3
#
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
 PVP  PVP  2-{4-[5-chloro-6-methyl-2-(pyridin-2-yl)pyrimidin-4-yl]piperazin-1-yl}ethanol  ligand  43  23  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PVP
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
 PVP  CL   CL  CL    0  -0.093   0.5091  -3.1141  -0.4723
 PVP  C8   C   CR6   0  -0.227  -0.6061  -1.7962  -0.4328
 PVP  C9   C   CR6   0   0.330  -1.9613  -2.0561  -0.5660
 PVP  C16  C   CH3   0  -0.736  -2.4800  -3.4174  -0.8965
 PVP  N3   N   N     0  -0.466  -2.8551  -1.0887  -0.3668
 PVP  C6   C   CR6   0   0.358  -2.3980   0.0999  -0.0057
 PVP  C5   C   CR6   0   0.144  -3.4148   1.1359   0.3191
 PVP  N23  N   N     0  -0.404  -2.9682   2.2976   0.7867
 PVP  C1   C   CR16  0  -0.085  -3.8512   3.2343   1.0968
 PVP  C2   C   CR16  0  -0.312  -5.2230   3.0710   0.9568
 PVP  C3   C   CR16  0  -0.152  -5.6875   1.8611   0.4667
 PVP  C4   C   CR16  0  -0.296  -4.7713   0.8738   0.1423
 PVP  N2   N   N     0  -0.448  -1.1268   0.4434   0.0813
 PVP  C7   C   CR6   0   0.606  -0.1949  -0.4739  -0.1644
 PVP  N4   N   NT    0  -0.502   1.1098  -0.0937  -0.0828
 PVP  C13  C   CH2   0  -0.316   2.0680  -0.4098  -1.1357
 PVP  C12  C   CH2   0  -0.284   3.4687  -0.4723  -0.5635
 PVP  N5   N   NT    0  -0.417   3.8121   0.7818   0.0769
 PVP  C11  C   CH2   0  -0.282   2.8448   1.0981   1.1093
 PVP  C10  C   CH2   0  -0.304   1.4331   1.1712   0.5570
 PVP  C14  C   CH2   0  -0.293   5.1599   0.7933   0.6120
 PVP  C15  C   CH2   0  -0.178   6.2534   0.7574  -0.4346
 PVP  O1   O   OH1   0  -0.669   6.1325   1.8768  -1.2820
 PVP  H1   H   HCH3  0   0.264  -2.2780  -4.1192  -0.0854
 PVP  H2   H   HCH3  0   0.262  -3.5548  -3.3753  -1.0529
 PVP  H3   H   HCH3  0   0.260  -2.0067  -3.8186  -1.7927
 PVP  H4   H   HCR6  0   0.263  -3.4503   4.1668   1.4784
 PVP  H5   H   HCR6  0   0.274  -5.8995   3.8702   1.2263
 PVP  H6   H   HCR6  0   0.276  -6.7474   1.6851   0.3393
 PVP  H7   H   HCR6  0   0.272  -5.0961  -0.0827  -0.2396
 PVP  H8   H   HCH2  0   0.260   1.8302  -1.3508  -1.6198
 PVP  H9   H   HCH2  0   0.239   2.0223   0.3709  -1.9057
 PVP  H10  H   HCH2  0   0.196   3.5348  -1.3239   0.1363
 PVP  H11  H   HCH2  0   0.246   4.1595  -0.6729  -1.3837
 PVP  H13  H   HCH2  0   0.195   2.8636   0.3602   1.9309
 PVP  H14  H   HCH2  0   0.243   3.0957   2.0680   1.5451
 PVP  H15  H   HCH2  0   0.226   1.3442   2.0048  -0.1507
 PVP  H16  H   HCH2  0   0.261   0.7387   1.3584   1.3728
 PVP  H17  H   HCH2  0   0.234   5.2760   1.7058   1.2040
 PVP  H18  H   HCH2  0   0.197   5.3336  -0.0469   1.3066
 PVP  H19  H   HCH2  0   0.208   7.2112   0.7528   0.1014
 PVP  H20  H   HCH2  0   0.197   6.2181  -0.1823  -1.0007
 PVP  H21  H   HOH1  0   0.452   6.8786   1.8705  -1.8877

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
 PVP  C1   C2   aromatic  1.389  0.020  1.389
 PVP  C1   N23  aromatic  1.324  0.020  1.324
 PVP  C2   C3   aromatic  1.386  0.020  1.386
 PVP  N23  C5   aromatic  1.329  0.020  1.329
 PVP  C3   C4   aromatic  1.385  0.020  1.385
 PVP  C5   C4   aromatic  1.393  0.020  1.393
 PVP  C5   C6   single    1.488  0.020  1.488
 PVP  N3   C6   aromatic  1.324  0.020  1.324
 PVP  N3   C9   aromatic  1.332  0.020  1.332
 PVP  C6   N2   aromatic  1.320  0.020  1.320
 PVP  C16  C9   single    1.494  0.020  1.494
 PVP  C9   C8   aromatic  1.386  0.020  1.386
 PVP  N2   C7   aromatic  1.330  0.020  1.330
 PVP  C8   C7   aromatic  1.410  0.020  1.410
 PVP  C8   CL   single    1.727  0.020  1.727
 PVP  C7   N4   single    1.361  0.020  1.361
 PVP  C13  N4   single    1.458  0.020  1.458
 PVP  C13  C12  single    1.514  0.020  1.514
 PVP  N4   C10  single    1.454  0.020  1.454
 PVP  C10  C11  single    1.518  0.020  1.518
 PVP  C12  N5   single    1.449  0.020  1.449
 PVP  C11  N5   single    1.450  0.020  1.450
 PVP  N5   C14  single    1.450  0.020  1.450
 PVP  O1   C15  single    1.409  0.020  1.409
 PVP  C14  C15  single    1.514  0.020  1.514
 PVP  C16  H1   single    0.970  0.020  1.090
 PVP  C16  H2   single    0.970  0.020  1.090
 PVP  C16  H3   single    0.970  0.020  1.090
 PVP  C1   H4   single    0.930  0.020  1.080
 PVP  C2   H5   single    0.930  0.020  1.080
 PVP  C3   H6   single    0.930  0.020  1.080
 PVP  C4   H7   single    0.930  0.020  1.080
 PVP  C13  H8   single    0.970  0.020  1.090
 PVP  C13  H9   single    0.970  0.020  1.090
 PVP  C12  H10  single    0.970  0.020  1.090
 PVP  C12  H11  single    0.970  0.020  1.090
 PVP  C11  H13  single    0.970  0.020  1.090
 PVP  C11  H14  single    0.970  0.020  1.090
 PVP  C10  H15  single    0.970  0.020  1.090
 PVP  C10  H16  single    0.970  0.020  1.090
 PVP  C14  H17  single    0.970  0.020  1.090
 PVP  C14  H18  single    0.970  0.020  1.090
 PVP  C15  H19  single    0.970  0.020  1.090
 PVP  C15  H20  single    0.970  0.020  1.090
 PVP  O1   H21  single    0.850  0.020  0.980

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
 PVP  C7   C8   C9   118.62  3.000
 PVP  C7   C8   CL   122.11  3.000
 PVP  C9   C8   CL   119.08  3.000
 PVP  N3   C9   C16  117.51  3.000
 PVP  C16  C9   C8   122.11  3.000
 PVP  N3   C9   C8   120.35  3.000
 PVP  H3   C16  H2   108.98  3.000
 PVP  H3   C16  H1   107.10  3.000
 PVP  H2   C16  H1   108.36  3.000
 PVP  H3   C16  C9   111.50  3.000
 PVP  H2   C16  C9   109.87  3.000
 PVP  H1   C16  C9   110.93  3.000
 PVP  C6   N3   C9   117.47  3.000
 PVP  N2   C6   C5   117.57  3.000
 PVP  N2   C6   N3   125.76  3.000
 PVP  C5   C6   N3   116.67  3.000
 PVP  C4   C5   N23  122.43  3.000
 PVP  C4   C5   C6   120.46  3.000
 PVP  N23  C5   C6   117.11  3.000
 PVP  C1   N23  C5   118.46  3.000
 PVP  H4   C1   C2   120.12  3.000
 PVP  H4   C1   N23  116.38  3.000
 PVP  C2   C1   N23  123.50  3.000
 PVP  H5   C2   C3   121.59  3.000
 PVP  H5   C2   C1   120.41  3.000
 PVP  C3   C2   C1   118.01  3.000
 PVP  H6   C3   C4   120.29  3.000
 PVP  H6   C3   C2   120.81  3.000
 PVP  C4   C3   C2   118.91  3.000
 PVP  H7   C4   C3   121.01  3.000
 PVP  H7   C4   C5   120.30  3.000
 PVP  C3   C4   C5   118.70  3.000
 PVP  C7   N2   C6   118.88  3.000
 PVP  N4   C7   N2   117.88  3.000
 PVP  N4   C7   C8   123.54  3.000
 PVP  N2   C7   C8   118.51  3.000
 PVP  C10  N4   C13  111.11  3.000
 PVP  C10  N4   C7   118.84  3.000
 PVP  C13  N4   C7   121.73  3.000
 PVP  H9   C13  H8   107.14  3.000
 PVP  H9   C13  C12  109.45  3.000
 PVP  H8   C13  C12  109.61  3.000
 PVP  H9   C13  N4   108.97  3.000
 PVP  H8   C13  N4   111.48  3.000
 PVP  C12  C13  N4   110.12  3.000
 PVP  H11  C12  H10  107.27  3.000
 PVP  H11  C12  N5   109.95  3.000
 PVP  H10  C12  N5   111.90  3.000
 PVP  H11  C12  C13  108.02  3.000
 PVP  H10  C12  C13  109.07  3.000
 PVP  N5   C12  C13  110.51  3.000
 PVP  C14  N5   C11  110.83  3.000
 PVP  C14  N5   C12  112.96  3.000
 PVP  C11  N5   C12  110.20  3.000
 PVP  H14  C11  H13  107.01  3.000
 PVP  H14  C11  C10  108.42  3.000
 PVP  H13  C11  C10  108.59  3.000
 PVP  H14  C11  N5   108.93  3.000
 PVP  H13  C11  N5   111.88  3.000
 PVP  C10  C11  N5   111.84  3.000
 PVP  H16  C10  H15  107.54  3.000
 PVP  H16  C10  C11  109.21  3.000
 PVP  H15  C10  C11  110.28  3.000
 PVP  H16  C10  N4   109.75  3.000
 PVP  H15  C10  N4   111.05  3.000
 PVP  C11  C10  N4   108.97  3.000
 PVP  H18  C14  H17  106.12  3.000
 PVP  H18  C14  C15  107.66  3.000
 PVP  H17  C14  C15  108.49  3.000
 PVP  H18  C14  N5   111.86  3.000
 PVP  H17  C14  N5   107.75  3.000
 PVP  C15  C14  N5   114.58  3.000
 PVP  H20  C15  H19  106.04  3.000
 PVP  H20  C15  O1   111.55  3.000
 PVP  H19  C15  O1   111.83  3.000
 PVP  H20  C15  C14  110.70  3.000
 PVP  H19  C15  C14  107.02  3.000
 PVP  O1   C15  C14  109.57  3.000
 PVP  H21  O1   C15  107.89  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
 PVP  CONST_01  C6   N3   C9   C8      0.00   0.0  0
 PVP  CONST_02  C6   N2   C7   C8      0.00   0.0  0
 PVP  CONST_03  C5   C6   N3   C9    180.00   0.0  0
 PVP  CONST_04  N2   C6   N3   C9      0.00   0.0  0
 PVP  CONST_05  N2   C7   C8   C9      0.00   0.0  0
 PVP  CONST_06  N23  C5   C6   N3    180.00   0.0  0
 PVP  CONST_07  C4   C5   C6   N3      0.00   0.0  0
 PVP  CONST_08  C7   N2   C6   N3      0.00   0.0  0
 PVP  CONST_09  C7   C8   C9   N3      0.00   0.0  0
 PVP  CONST_10  C1   N23  C5   C6    180.00   0.0  0
 PVP  CONST_11  C3   C4   C5   C6    180.00   0.0  0
 PVP  CONST_12  C2   C1   N23  C5      0.00   0.0  0
 PVP  CONST_13  C2   C3   C4   C5      0.00   0.0  0
 PVP  CONST_14  C7   N2   C6   C5    180.00   0.0  0
 PVP  CONST_15  C3   C2   C1   N23     0.00   0.0  0
 PVP  CONST_16  C3   C4   C5   N23     0.00   0.0  0
 PVP  CONST_17  N2   C6   C5   N23     0.00   0.0  0
 PVP  CONST_18  C4   C3   C2   C1      0.00   0.0  0
 PVP  CONST_19  C4   C5   N23  C1      0.00   0.0  0
 PVP  CONST_20  N2   C6   C5   C4    180.00   0.0  0
 PVP  CONST_21  N4   C7   C8   C9    180.00   0.0  0
 PVP  CONST_22  N4   C7   N2   C6    180.00   0.0  0
 PVP  CONST_23  N3   C9   C8   CL    180.00   0.0  0
 PVP  CONST_24  N2   C7   C8   CL    180.00   0.0  0
 PVP  CONST_25  N4   C7   C8   CL      0.00   0.0  0
 PVP  CONST_26  C6   N3   C9   C16   180.00   0.0  0
 PVP  CONST_27  C7   C8   C9   C16   180.00   0.0  0
 PVP  CONST_28  H7   C4   C5   C6      0.00   0.0  0
 PVP  CONST_29  H4   C1   N23  C5    180.00   0.0  0
 PVP  CONST_30  H6   C3   C4   C5    180.00   0.0  0
 PVP  CONST_31  H5   C2   C1   N23   180.00   0.0  0
 PVP  Var_01    C13  N4   C7   C8     51.67  30.0  2
 PVP  Var_02    C12  C13  N4   C7   -153.81  30.0  1
 PVP  Var_03    C11  C10  N4   C7    153.75  30.0  1
 PVP  Var_04    N5   C12  C13  N4    -57.60  30.0  1
 PVP  Var_05    N5   C11  C10  N4     57.18  30.0  1
 PVP  Var_06    C11  N5   C12  C13    57.05  30.0  1
 PVP  Var_07    C10  C11  N5   C12   -57.51  30.0  1
 PVP  Var_08    C15  C14  N5   C12    67.75  30.0  3
 PVP  Var_09    H1   C16  C9   C8     66.01  30.0  2
 PVP  Var_10    O1   C15  C14  N5     59.52  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
 PVP  plan-1  CL   0.020
 PVP  plan-1  C8   0.020
 PVP  plan-1  C9   0.020
 PVP  plan-1  C16  0.020
 PVP  plan-1  N3   0.020
 PVP  plan-1  C6   0.020
 PVP  plan-1  C5   0.020
 PVP  plan-1  N2   0.020
 PVP  plan-1  C7   0.020
 PVP  plan-1  N4   0.020
 PVP  plan-2  C6   0.020
 PVP  plan-2  C5   0.020
 PVP  plan-2  N23  0.020
 PVP  plan-2  C1   0.020
 PVP  plan-2  C2   0.020
 PVP  plan-2  C3   0.020
 PVP  plan-2  C4   0.020
 PVP  plan-2  H4   0.020
 PVP  plan-2  H5   0.020
 PVP  plan-2  H6   0.020
 PVP  plan-2  H7   0.020

