# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 10:04:48 2021
#   Inital geometry file: a 73 line input string
#   Ligand name: 6-[(1s,4s)-2-azabicyclo[2.2.2]octan-2-yl]-5-chloropyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc(N2CC3CCC2CC3)c1Cl
#
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
 W51  W51  6-[(1s,4s)-2-azabicyclo[2.2.2]octan-2-yl]-5-chloropyrimidin-4-amine  ligand  31  16  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_W51
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
 W51  C10   C   CH2   0  -0.434  -45.2866  -32.2595   1.4440
 W51  C13   C   CH2   0  -0.427  -45.2733  -29.2820   1.1191
 W51  C15   C   CR6   0  -0.285  -46.6016  -29.4670   5.1971
 W51  C02   C   CR6   0   0.533  -46.5913  -28.8566   6.4582
 W51  C04   C   CR16  0   0.058  -44.3440  -29.0263   6.4806
 W51  C06   C   CR6   0   0.601  -45.3728  -29.7618   4.5808
 W51  C08   C   CH2   0  -0.255  -43.9172  -30.8497   2.9744
 W51  C09   C   CH1   0  -0.308  -44.0344  -31.3872   1.5506
 W51  C11   C   CH2   0  -0.417  -46.5354  -31.3739   1.6341
 W51  C12   C   CH1   0  -0.155  -46.0808  -30.0264   2.1868
 W51  C14   C   CH2   0  -0.434  -44.1549  -30.2009   0.5938
 W51  N03   N   N     0  -0.474  -45.4347  -28.6155   7.0941
 W51  N05   N   N     0  -0.488  -44.2418  -29.5683   5.2881
 W51  N07   N   NT    0  -0.480  -45.2095  -30.2676   3.3413
 W51  CL16  CL  CL    0  -0.117  -48.1413  -29.9586   4.5584
 W51  H102  H   HCH2  0   0.237  -45.3110  -32.7638   0.4757
 W51  H101  H   HCH2  0   0.231  -45.2518  -33.0451   2.2032
 W51  H132  H   HCH2  0   0.239  -44.8644  -28.3667   1.5525
 W51  H131  H   HCH2  0   0.241  -45.9471  -28.9750   0.3168
 W51  H041  H   HCR6  0   0.252  -43.4127  -28.8881   7.0220
 W51  H081  H   HCH2  0   0.243  -43.6694  -31.6548   3.6705
 W51  H082  H   HCH2  0   0.233  -43.1105  -30.1118   3.0360
 W51  H091  H   HCH1  0   0.245  -43.1407  -31.9740   1.3298
 W51  H112  H   HCH2  0   0.228  -47.0538  -31.2130   0.6863
 W51  H111  H   HCH2  0   0.236  -47.2503  -31.8408   2.3128
 W51  H121  H   HCH1  0   0.257  -46.9219  -29.4088   2.4824
 W51  H142  H   HCH2  0   0.232  -44.3774  -30.5589  -0.4140
 W51  H141  H   HCH2  0   0.237  -43.2064  -29.6634   0.5353
 W51  H012  H   HNH2  0   0.399  -47.6296  -27.9810   7.9496
 W51  H011  H   HNH2  0   0.397  -48.6016  -28.4824   6.6343
 W51  N01   N   NH2   0  -0.824  -47.7200  -28.5326   7.1134

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
 W51  C14   C13   single    1.540  0.020  1.540
 W51  C14   C09   single    1.529  0.020  1.529
 W51  C13   C12   single    1.532  0.020  1.532
 W51  C09   C10   single    1.530  0.020  1.530
 W51  C09   C08   single    1.526  0.020  1.526
 W51  C11   C10   single    1.543  0.020  1.543
 W51  C11   C12   single    1.526  0.020  1.526
 W51  C12   N07   single    1.466  0.020  1.466
 W51  C08   N07   single    1.464  0.020  1.464
 W51  N07   C06   single    1.349  0.020  1.349
 W51  CL16  C15   single    1.738  0.020  1.738
 W51  C06   C15   aromatic  1.406  0.020  1.406
 W51  C06   N05   aromatic  1.348  0.020  1.348
 W51  C15   C02   aromatic  1.401  0.020  1.401
 W51  N05   C04   aromatic  1.314  0.020  1.314
 W51  C02   N01   single    1.345  0.020  1.345
 W51  C02   N03   aromatic  1.342  0.020  1.342
 W51  C04   N03   aromatic  1.317  0.020  1.317
 W51  C10   H102  single    0.970  0.020  1.090
 W51  C10   H101  single    0.970  0.020  1.090
 W51  C13   H132  single    0.970  0.020  1.090
 W51  C13   H131  single    0.970  0.020  1.090
 W51  C04   H041  single    0.930  0.020  1.080
 W51  C08   H081  single    0.970  0.020  1.090
 W51  C08   H082  single    0.970  0.020  1.090
 W51  C09   H091  single    0.970  0.020  1.090
 W51  C11   H112  single    0.970  0.020  1.090
 W51  C11   H111  single    0.970  0.020  1.090
 W51  C12   H121  single    0.970  0.020  1.090
 W51  C14   H142  single    0.970  0.020  1.090
 W51  C14   H141  single    0.970  0.020  1.090
 W51  N01   H012  single    0.890  0.020  1.040
 W51  N01   H011  single    0.890  0.020  1.040

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
 W51  H101  C10  H102  106.54  3.000
 W51  H101  C10  C11   110.65  3.000
 W51  H102  C10  C11   110.87  3.000
 W51  H101  C10  C09   109.60  3.000
 W51  H102  C10  C09   110.09  3.000
 W51  C11   C10  C09   109.06  3.000
 W51  H131  C13  H132  106.68  3.000
 W51  H131  C13  C14   111.43  3.000
 W51  H132  C13  C14   111.32  3.000
 W51  H131  C13  C12   108.88  3.000
 W51  H132  C13  C12   109.15  3.000
 W51  C14   C13  C12   109.31  3.000
 W51  CL16  C15  C06   123.64  3.000
 W51  C06   C15  C02   118.65  3.000
 W51  CL16  C15  C02   117.42  3.000
 W51  N03   C02  N01   116.70  3.000
 W51  N03   C02  C15   120.75  3.000
 W51  N01   C02  C15   122.50  3.000
 W51  H041  C04  N05   115.99  3.000
 W51  H041  C04  N03   115.99  3.000
 W51  N05   C04  N03   128.02  3.000
 W51  N07   C06  N05   115.76  3.000
 W51  N05   C06  C15   118.24  3.000
 W51  N07   C06  C15   125.97  3.000
 W51  H082  C08  H081  107.08  3.000
 W51  H082  C08  N07   111.61  3.000
 W51  H081  C08  N07   109.48  3.000
 W51  H082  C08  C09   110.26  3.000
 W51  H081  C08  C09   110.62  3.000
 W51  N07   C08  C09   107.81  3.000
 W51  H091  C09  C14   110.79  3.000
 W51  H091  C09  C08   108.37  3.000
 W51  C14   C09  C08   108.46  3.000
 W51  H091  C09  C10   110.45  3.000
 W51  C08   C09  C10   109.19  3.000
 W51  C14   C09  C10   109.53  3.000
 W51  H111  C11  H112  106.97  3.000
 W51  H111  C11  C12   110.36  3.000
 W51  H112  C11  C12   109.01  3.000
 W51  H111  C11  C10   111.19  3.000
 W51  H112  C11  C10   111.21  3.000
 W51  C12   C11  C10   108.09  3.000
 W51  H121  C12  N07   109.87  3.000
 W51  H121  C12  C11   111.75  3.000
 W51  N07   C12  C11   108.48  3.000
 W51  H121  C12  C13   108.79  3.000
 W51  N07   C12  C13   108.39  3.000
 W51  C11   C12  C13   109.50  3.000
 W51  H141  C14  H142  106.78  3.000
 W51  H141  C14  C09   110.31  3.000
 W51  H142  C14  C09   109.82  3.000
 W51  H141  C14  C13   110.83  3.000
 W51  H142  C14  C13   111.25  3.000
 W51  C09   C14  C13   107.87  3.000
 W51  C04   N03  C02   115.91  3.000
 W51  C06   N05  C04   118.05  3.000
 W51  C12   N07  C08   113.12  3.000
 W51  C08   N07  C06   119.10  3.000
 W51  C12   N07  C06   126.15  3.000
 W51  H011  N01  H012  116.61  3.000
 W51  H011  N01  C02   121.08  3.000
 W51  H012  N01  C02   117.50  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
 W51  CONST_01  C04   N05  C06  C15    0.00   0.0  0
 W51  CONST_02  C04   N03  C02  C15    0.00   0.0  0
 W51  CONST_03  N05   C06  C15  C02    0.00   0.0  0
 W51  CONST_04  N05   C04  N03  C02    0.00   0.0  0
 W51  CONST_05  N03   C02  C15  C06    0.00   0.0  0
 W51  CONST_06  N03   C04  N05  C06    0.00   0.0  0
 W51  CONST_07  N07   C06  C15  C02  180.00   0.0  0
 W51  CONST_08  N07   C06  N05  C04  180.00   0.0  0
 W51  CONST_09  N01   C02  N03  C04  180.00   0.0  0
 W51  CONST_10  N01   C02  C15  C06  180.00   0.0  0
 W51  CONST_11  CL16  C15  C02  N03  180.00   0.0  0
 W51  CONST_12  CL16  C15  C06  N05  180.00   0.0  0
 W51  CONST_13  CL16  C15  C06  N07    0.00   0.0  0
 W51  CONST_14  H041  C04  N03  C02  180.00   0.0  0
 W51  CONST_15  H012  N01  C02  C15  180.00   0.0  0
 W51  Var_01    C12   N07  C06  C15   31.83  30.0  1
 W51  Var_02    C09   C08  N07  C06  177.80  30.0  1
 W51  Var_03    C12   C13  C14  C09  -13.54  30.0  3
 W51  Var_04    C12   C11  C10  C09  -13.35  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
 W51  chir_01  C09  C14  C10  C08  positiv
 W51  chir_02  C12  N07  C11  C13  positiv

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
 W51  plan-1  C15   0.020
 W51  plan-1  C02   0.020
 W51  plan-1  C04   0.020
 W51  plan-1  C06   0.020
 W51  plan-1  N03   0.020
 W51  plan-1  N05   0.020
 W51  plan-1  N07   0.020
 W51  plan-1  CL16  0.020
 W51  plan-1  H041  0.020
 W51  plan-1  N01   0.020
 W51  plan-2  C02   0.020
 W51  plan-2  H012  0.020
 W51  plan-2  H011  0.020
 W51  plan-2  N01   0.020

