# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 06:19:10 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: 6-piperidin-1-ylpyrimidine-2,4-diamine 3-oxide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cc(nc(N)[n+]1[O-])N2CCCCC2
#
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
 MXD  MXD  '6-piperidin-1-ylpyrimidine-2,4-diamine 3-oxide'  ligand  30  15  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_MXD
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
 MXD  NAO   N  NH2    0  -0.836  -2.8950   2.1466   0.0433
 MXD  CAE   C  CR6    0   0.603  -2.0489   1.1095  -0.0005
 MXD  CAF   C  CR16   0  -0.545  -0.6796   1.2060   0.2131
 MXD  NAC   N  NR6    1  -0.195  -2.6062  -0.0932  -0.2926
 MXD  OAN   O  O     -1  -0.671  -3.9059  -0.2077  -0.4751
 MXD  CAA   C  CR6    0   0.626  -1.7947  -1.1786  -0.3578
 MXD  NAM   N  NH2    0  -0.823  -2.3988  -2.3371  -0.6645
 MXD  NAB   N  N      0  -0.542  -0.4953  -1.1328  -0.1696
 MXD  CAD   C  CR6    0   0.580   0.0901   0.0420   0.1053
 MXD  NAI   N  NT     0  -0.502   1.4403   0.0297   0.2532
 MXD  CAG   C  CH2    0  -0.301   2.1571  -1.2176   0.4783
 MXD  CAK   C  CH2    0  -0.296   2.1887   1.2226   0.6065
 MXD  CAL   C  CH2    0  -0.434   3.5409   1.2553  -0.0956
 MXD  CAJ   C  CH2    0  -0.443   4.3350  -0.0193   0.1470
 MXD  CAH   C  CH2    0  -0.438   3.4969  -1.2289  -0.2416
 MXD  HAO1  H  HNH2   0   0.406  -2.5867   3.0129   0.4483
 MXD  HAO2  H  HNH2   0   0.397  -3.8800   1.9375   0.0655
 MXD  HAF   H  HCR6   0   0.278  -0.2764   2.1705   0.4756
 MXD  HAM1  H  HNH2   0   0.400  -1.8871  -3.1880  -0.5082
 MXD  HAM2  H  HNH2   0   0.397  -3.4031  -2.3664  -0.6001
 MXD  HAG1  H  HCH2   0   0.219   2.3241  -1.3475   1.5565
 MXD  HAG2  H  HCH2   0   0.269   1.5387  -2.0447   0.1452
 MXD  HAK1  H  HCH2   0   0.258   1.6345   2.1118   0.3195
 MXD  HAK2  H  HCH2   0   0.225   2.3324   1.2678   1.6943
 MXD  HAL1  H  HCH2   0   0.239   4.0892   2.1313   0.2568
 MXD  HAL2  H  HCH2   0   0.223   3.3790   1.3908  -1.1689
 MXD  HAJ1  H  HCH2   0   0.215   4.6074  -0.0875   1.2056
 MXD  HAJ2  H  HCH2   0   0.236   5.2690   0.0007  -0.4181
 MXD  HAH1  H  HCH2   0   0.236   4.0148  -2.1581   0.0045
 MXD  HAH2  H  HCH2   0   0.221   3.3271  -1.2328  -1.3224

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
 MXD  NAO  CAE   single    1.339  0.020  1.339
 MXD  NAO  HAO1  single    0.890  0.020  1.040
 MXD  NAO  HAO2  single    0.890  0.020  1.040
 MXD  CAE  CAF   aromatic  1.389  0.020  1.389
 MXD  CAE  NAC   aromatic  1.357  0.020  1.357
 MXD  CAF  CAD   aromatic  1.400  0.020  1.400
 MXD  CAF  HAF   single    0.930  0.020  1.080
 MXD  NAC  OAN   single    1.317  0.020  1.317
 MXD  NAC  CAA   aromatic  1.357  0.020  1.357
 MXD  CAA  NAM   single    1.342  0.020  1.342
 MXD  CAA  NAB   aromatic  1.314  0.020  1.314
 MXD  NAM  HAM1  single    0.890  0.020  1.040
 MXD  NAM  HAM2  single    0.890  0.020  1.040
 MXD  NAB  CAD   aromatic  1.341  0.020  1.341
 MXD  CAD  NAI   single    1.358  0.020  1.358
 MXD  NAI  CAG   single    1.456  0.020  1.456
 MXD  NAI  CAK   single    1.452  0.020  1.452
 MXD  CAG  CAH   single    1.521  0.020  1.521
 MXD  CAG  HAG1  single    0.970  0.020  1.090
 MXD  CAG  HAG2  single    0.970  0.020  1.090
 MXD  CAK  CAL   single    1.524  0.020  1.524
 MXD  CAK  HAK1  single    0.970  0.020  1.090
 MXD  CAK  HAK2  single    0.970  0.020  1.090
 MXD  CAL  CAJ   single    1.521  0.020  1.521
 MXD  CAL  HAL1  single    0.970  0.020  1.090
 MXD  CAL  HAL2  single    0.970  0.020  1.090
 MXD  CAJ  CAH   single    1.522  0.020  1.522
 MXD  CAJ  HAJ1  single    0.970  0.020  1.090
 MXD  CAJ  HAJ2  single    0.970  0.020  1.090
 MXD  CAH  HAH1  single    0.970  0.020  1.090
 MXD  CAH  HAH2  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
 MXD  HAO2  NAO  HAO1  118.05  3.000
 MXD  HAO2  NAO  CAE   117.25  3.000
 MXD  HAO1  NAO  CAE   119.14  3.000
 MXD  NAC   CAE  CAF   119.96  3.000
 MXD  NAC   CAE  NAO   115.71  3.000
 MXD  CAF   CAE  NAO   124.33  3.000
 MXD  HAF   CAF  CAD   123.86  3.000
 MXD  HAF   CAF  CAE   117.93  3.000
 MXD  CAD   CAF  CAE   118.19  3.000
 MXD  CAA   NAC  OAN   120.92  3.000
 MXD  CAA   NAC  CAE   118.27  3.000
 MXD  OAN   NAC  CAE   120.79  3.000
 MXD  NAB   CAA  NAM   120.53  3.000
 MXD  NAB   CAA  NAC   123.83  3.000
 MXD  NAM   CAA  NAC   115.62  3.000
 MXD  HAM2  NAM  HAM1  118.25  3.000
 MXD  HAM2  NAM  CAA   117.35  3.000
 MXD  HAM1  NAM  CAA   117.77  3.000
 MXD  CAD   NAB  CAA   119.45  3.000
 MXD  NAI   CAD  NAB   116.64  3.000
 MXD  NAI   CAD  CAF   123.08  3.000
 MXD  NAB   CAD  CAF   120.28  3.000
 MXD  CAK   NAI  CAG   114.36  3.000
 MXD  CAK   NAI  CAD   122.10  3.000
 MXD  CAG   NAI  CAD   120.92  3.000
 MXD  HAG2  CAG  HAG1  107.33  3.000
 MXD  HAG2  CAG  CAH   110.55  3.000
 MXD  HAG1  CAG  CAH   109.25  3.000
 MXD  HAG2  CAG  NAI   108.96  3.000
 MXD  HAG1  CAG  NAI   109.13  3.000
 MXD  CAH   CAG  NAI   111.52  3.000
 MXD  HAK2  CAK  HAK1  107.14  3.000
 MXD  HAK2  CAK  CAL   109.84  3.000
 MXD  HAK1  CAK  CAL   108.26  3.000
 MXD  HAK2  CAK  NAI   110.02  3.000
 MXD  HAK1  CAK  NAI   110.20  3.000
 MXD  CAL   CAK  NAI   111.28  3.000
 MXD  HAL2  CAL  HAL1  106.95  3.000
 MXD  HAL2  CAL  CAJ   109.72  3.000
 MXD  HAL1  CAL  CAJ   111.02  3.000
 MXD  HAL2  CAL  CAK   108.87  3.000
 MXD  HAL1  CAL  CAK   108.31  3.000
 MXD  CAJ   CAL  CAK   111.82  3.000
 MXD  HAJ2  CAJ  HAJ1  106.77  3.000
 MXD  HAJ2  CAJ  CAH   110.70  3.000
 MXD  HAJ1  CAJ  CAH   109.52  3.000
 MXD  HAJ2  CAJ  CAL   110.41  3.000
 MXD  HAJ1  CAJ  CAL   109.64  3.000
 MXD  CAH   CAJ  CAL   109.74  3.000
 MXD  HAH2  CAH  HAH1  107.05  3.000
 MXD  HAH2  CAH  CAJ   109.91  3.000
 MXD  HAH1  CAH  CAJ   110.95  3.000
 MXD  HAH2  CAH  CAG   109.32  3.000
 MXD  HAH1  CAH  CAG   108.51  3.000
 MXD  CAJ   CAH  CAG   111.00  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
 MXD  CONST_01  NAB   CAD  CAF  CAE     0.00   0.0  0
 MXD  CONST_02  NAB   CAA  NAC  CAE     0.00   0.0  0
 MXD  CONST_03  CAA   NAC  CAE  CAF     0.00   0.0  0
 MXD  CONST_04  CAA   NAB  CAD  CAF     0.00   0.0  0
 MXD  CONST_05  CAD   CAF  CAE  NAC     0.00   0.0  0
 MXD  CONST_06  CAD   NAB  CAA  NAC     0.00   0.0  0
 MXD  CONST_07  NAI   CAD  CAF  CAE   180.00   0.0  0
 MXD  CONST_08  NAI   CAD  NAB  CAA   180.00   0.0  0
 MXD  CONST_09  CAD   CAF  CAE  NAO   180.00   0.0  0
 MXD  CONST_10  CAA   NAC  CAE  NAO   180.00   0.0  0
 MXD  CONST_11  NAM   CAA  NAC  CAE   180.00   0.0  0
 MXD  CONST_12  OAN   NAC  CAE  CAF   180.00   0.0  0
 MXD  CONST_13  NAB   CAA  NAC  OAN   180.00   0.0  0
 MXD  CONST_14  CAD   NAB  CAA  NAM   180.00   0.0  0
 MXD  CONST_15  HAF   CAF  CAE  NAC   180.00   0.0  0
 MXD  CONST_16  HAO1  NAO  CAE  CAF     0.00   0.0  0
 MXD  CONST_17  HAO2  NAO  CAE  CAF   180.00   0.0  0
 MXD  CONST_18  HAM1  NAM  CAA  NAC   180.00   0.0  0
 MXD  CONST_19  HAM2  NAM  CAA  NAC     0.00   0.0  0
 MXD  Var_01    CAG   NAI  CAD  CAF   163.93  30.0  2
 MXD  Var_02    CAH   CAG  NAI  CAD   142.80  30.0  1
 MXD  Var_03    CAL   CAK  NAI  CAD  -144.02  30.0  1
 MXD  Var_04    CAJ   CAH  CAG  NAI    54.71  30.0  1
 MXD  Var_05    CAJ   CAL  CAK  NAI   -53.43  30.0  1
 MXD  Var_06    CAL   CAJ  CAH  CAG   -54.39  30.0  1
 MXD  Var_07    CAH   CAJ  CAL  CAK    54.00  30.0  1

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
 MXD  plan-1  NAO   0.020
 MXD  plan-1  CAE   0.020
 MXD  plan-1  CAF   0.020
 MXD  plan-1  NAC   0.020
 MXD  plan-1  OAN   0.020
 MXD  plan-1  CAA   0.020
 MXD  plan-1  NAM   0.020
 MXD  plan-1  NAB   0.020
 MXD  plan-1  CAD   0.020
 MXD  plan-1  NAI   0.020
 MXD  plan-1  HAF   0.020
 MXD  plan-2  NAO   0.020
 MXD  plan-2  CAE   0.020
 MXD  plan-2  HAO1  0.020
 MXD  plan-2  HAO2  0.020
 MXD  plan-3  CAA   0.020
 MXD  plan-3  NAM   0.020
 MXD  plan-3  HAM1  0.020
 MXD  plan-3  HAM2  0.020

