# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 02:42:48 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: [1-(pyrimidin-2-yl)piperidin-4-yl]methanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCC1CCN(CC1)c2ncccn2
#
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
 NXS  NXS  '[1-(pyrimidin-2-yl)piperidin-4-yl]methanol'  ligand  29  14  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NXS
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
 NXS  N1   N  NT    0  -0.480  -0.2813   0.0462   0.9860
 NXS  N3   N  N     0  -0.471  -2.1169  -1.1127   0.2036
 NXS  C4   C  CH2   0  -0.319   0.5869   1.2096   1.0154
 NXS  C5   C  CH2   0  -0.317   0.4189  -1.1899   1.2814
 NXS  C6   C  CH2   0  -0.428   1.5512  -1.4187   0.2860
 NXS  C7   C  CR6   0   0.633  -1.4783   0.0571   0.3536
 NXS  C8   C  CR16  0  -0.011  -3.1429   1.2380  -0.6406
 NXS  C10  C  CR16  0  -0.011  -3.2992  -1.0815  -0.3837
 NXS  C2   C  CH1   0  -0.281   2.5066  -0.2265   0.2459
 NXS  C3   C  CH2   0  -0.415   1.7224   1.0639   0.0078
 NXS  C9   C  CR16  0  -0.402  -3.8876   0.0866  -0.8413
 NXS  N2   N  N     0  -0.471  -1.9581   1.2402  -0.0574
 NXS  H1   H  HCH2  0   0.266   0.0064   2.1071   0.8264
 NXS  H2   H  HCH2  0   0.235   1.0015   1.2942   2.0252
 NXS  H3   H  HCH2  0   0.236   0.8288  -1.1143   2.2938
 NXS  H4   H  HCH2  0   0.268  -0.2801  -2.0199   1.2746
 NXS  H5   H  HCH2  0   0.237   2.0891  -2.3293   0.5620
 NXS  H6   H  HCH2  0   0.221   1.1247  -1.5886  -0.7090
 NXS  H7   H  HCR6  0   0.266  -3.5182   2.2027  -0.9664
 NXS  H8   H  HCR6  0   0.266  -3.8027  -2.0361  -0.4977
 NXS  H11  H  HCH1  0   0.221   2.9950  -0.1574   1.2277
 NXS  H12  H  HCH2  0   0.216   1.3056   1.0583  -1.0062
 NXS  H13  H  HCH2  0   0.239   2.3771   1.9342   0.0801
 NXS  H14  H  HCR6  0   0.268  -4.8532   0.0980  -1.3235
 NXS  H15  H  HOH1  0   0.453   5.1727   0.4515  -1.4437
 NXS  C1   C  CH2   0  -0.126   3.5838  -0.4546  -0.7994
 NXS  O1   O  OH1   0  -0.674   4.5120   0.6068  -0.7631
 NXS  H9   H  HCH2  0   0.198   4.0727  -1.4188  -0.6033
 NXS  H10  H  HCH2  0   0.184   3.1078  -0.5377  -1.7874

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
 NXS  C3   C2   single    1.529  0.020  1.529
 NXS  C3   C4   single    1.525  0.020  1.525
 NXS  C2   C6   single    1.528  0.020  1.528
 NXS  C2   C1   single    1.518  0.020  1.518
 NXS  C4   N1   single    1.452  0.020  1.452
 NXS  C5   C6   single    1.525  0.020  1.525
 NXS  C5   N1   single    1.451  0.020  1.451
 NXS  C1   O1   single    1.410  0.020  1.410
 NXS  N1   C7   single    1.354  0.020  1.354
 NXS  C7   N3   aromatic  1.341  0.020  1.341
 NXS  C7   N2   aromatic  1.341  0.020  1.341
 NXS  N3   C10  aromatic  1.321  0.020  1.321
 NXS  N2   C8   aromatic  1.321  0.020  1.321
 NXS  C10  C9   aromatic  1.386  0.020  1.386
 NXS  C8   C9   aromatic  1.386  0.020  1.386
 NXS  C4   H1   single    0.970  0.020  1.090
 NXS  C4   H2   single    0.970  0.020  1.090
 NXS  C5   H3   single    0.970  0.020  1.090
 NXS  C5   H4   single    0.970  0.020  1.090
 NXS  C6   H5   single    0.970  0.020  1.090
 NXS  C6   H6   single    0.970  0.020  1.090
 NXS  C8   H7   single    0.930  0.020  1.080
 NXS  C10  H8   single    0.930  0.020  1.080
 NXS  C1   H9   single    0.970  0.020  1.090
 NXS  C1   H10  single    0.970  0.020  1.090
 NXS  C2   H11  single    0.970  0.020  1.090
 NXS  C3   H12  single    0.970  0.020  1.090
 NXS  C3   H13  single    0.970  0.020  1.090
 NXS  C9   H14  single    0.930  0.020  1.080
 NXS  O1   H15  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
 NXS  C7   N1   C5   121.92  3.000
 NXS  C7   N1   C4   122.12  3.000
 NXS  C5   N1   C4   112.95  3.000
 NXS  C10  N3   C7   117.09  3.000
 NXS  H2   C4   H1   107.41  3.000
 NXS  H2   C4   C3   109.56  3.000
 NXS  H1   C4   C3   111.23  3.000
 NXS  H2   C4   N1   107.88  3.000
 NXS  H1   C4   N1   109.83  3.000
 NXS  C3   C4   N1   110.81  3.000
 NXS  H4   C5   H3   107.44  3.000
 NXS  H4   C5   C6   111.07  3.000
 NXS  H3   C5   C6   109.63  3.000
 NXS  H4   C5   N1   109.85  3.000
 NXS  H3   C5   N1   108.07  3.000
 NXS  C6   C5   N1   110.68  3.000
 NXS  H6   C6   H5   106.95  3.000
 NXS  H6   C6   C2   109.90  3.000
 NXS  H5   C6   C2   110.42  3.000
 NXS  H6   C6   C5   109.08  3.000
 NXS  H5   C6   C5   109.00  3.000
 NXS  C2   C6   C5   111.36  3.000
 NXS  N2   C7   N3   124.39  3.000
 NXS  N2   C7   N1   117.81  3.000
 NXS  N3   C7   N1   117.78  3.000
 NXS  H7   C8   N2   116.19  3.000
 NXS  H7   C8   C9   120.62  3.000
 NXS  N2   C8   C9   123.19  3.000
 NXS  H8   C10  C9   120.65  3.000
 NXS  H8   C10  N3   116.19  3.000
 NXS  C9   C10  N3   123.16  3.000
 NXS  H11  C2   C3   108.31  3.000
 NXS  H11  C2   C1   108.01  3.000
 NXS  C3   C2   C1   112.55  3.000
 NXS  H11  C2   C6   107.67  3.000
 NXS  C1   C2   C6   110.15  3.000
 NXS  C3   C2   C6   109.99  3.000
 NXS  H13  C3   H12  107.06  3.000
 NXS  H13  C3   C2   110.80  3.000
 NXS  H12  C3   C2   109.56  3.000
 NXS  H13  C3   C4   109.06  3.000
 NXS  H12  C3   C4   109.18  3.000
 NXS  C2   C3   C4   111.08  3.000
 NXS  H14  C9   C10  122.43  3.000
 NXS  H14  C9   C8   122.45  3.000
 NXS  C10  C9   C8   115.11  3.000
 NXS  C8   N2   C7   117.05  3.000
 NXS  H10  C1   H9   106.66  3.000
 NXS  H10  C1   O1   111.40  3.000
 NXS  H9   C1   O1   111.28  3.000
 NXS  H10  C1   C2   108.83  3.000
 NXS  H9   C1   C2   108.95  3.000
 NXS  O1   C1   C2   109.64  3.000
 NXS  H15  O1   C1   108.21  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
 NXS  CONST_01  C8   N2   C7   N3     0.00   0.0  0
 NXS  CONST_02  C8   C9   C10  N3     0.00   0.0  0
 NXS  CONST_03  C9   C10  N3   C7     0.00   0.0  0
 NXS  CONST_04  C9   C8   N2   C7     0.00   0.0  0
 NXS  CONST_05  N2   C7   N3   C10    0.00   0.0  0
 NXS  CONST_06  N2   C8   C9   C10    0.00   0.0  0
 NXS  CONST_07  C10  N3   C7   N1   180.00   0.0  0
 NXS  CONST_08  C8   N2   C7   N1   180.00   0.0  0
 NXS  CONST_09  H14  C9   C10  N3   180.00   0.0  0
 NXS  CONST_10  H8   C10  N3   C7   180.00   0.0  0
 NXS  CONST_11  H7   C8   N2   C7   180.00   0.0  0
 NXS  Var_01    C2   C3   C4   N1   -55.48  30.0  1
 NXS  Var_02    C2   C6   C5   N1    55.23  30.0  1
 NXS  Var_03    C4   N1   C7   N3   170.05  30.0  1
 NXS  Var_04    C6   C5   N1   C4   -58.64  30.0  1
 NXS  Var_05    C3   C4   N1   C5    58.90  30.0  1

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
 NXS  chir_01  C2  C3  C6  C1  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
 NXS  plan-1  N1   0.020
 NXS  plan-1  N3   0.020
 NXS  plan-1  C7   0.020
 NXS  plan-1  C8   0.020
 NXS  plan-1  C10  0.020
 NXS  plan-1  C9   0.020
 NXS  plan-1  N2   0.020
 NXS  plan-1  H7   0.020
 NXS  plan-1  H8   0.020
 NXS  plan-1  H14  0.020

