# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 08:30:04 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: 1-(9H-purin-6-yl)piperidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1CCN(CC1)c2ncnc3[nH]cnc23
#
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
 M02  M02  1-(9H-purin-6-yl)piperidin-4-amine  ligand  30  16  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_M02
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
 M02  CAK   C  CH2   0  -0.437   8.8227   8.8419   5.1760
 M02  CAM   C  CH1   0  -0.067   9.7180   8.3981   4.0237
 M02  CAP   C  CH2   0  -0.328   8.1196  10.1530   4.8456
 M02  CAO   C  CH2   0  -0.430   8.9020   8.3382   2.7368
 M02  C7    C  CH2   0  -0.348   8.1909   9.6614   2.4760
 M02  N6    N  NT    0  -0.468   7.3591  10.0227   3.6124
 M02  C6    C  CR6   0   0.524   6.0167   9.9750   3.6097
 M02  C5    C  CR56  0  -0.011   5.2020   9.7426   2.4705
 M02  N7    N  N     0  -0.459   5.4582   9.4940   1.1414
 M02  C4    C  CR56  0   0.456   3.8248   9.7647   2.6897
 M02  N9    N  NR15  0  -0.646   3.2667   9.5257   1.4741
 M02  C8    C  CR15  0   0.116   4.2867   9.3726   0.5905
 M02  N10   N  NH2   0  -0.802  10.2967   7.0950   4.3114
 M02  N3    N  N     0  -0.450   3.1943   9.9770   3.8437
 M02  C2    C  CR16  0   0.042   4.0529  10.1767   4.8259
 M02  N1    N  N     0  -0.497   5.3773  10.1834   4.7712
 M02  HAM   H  HCH1  0   0.192  10.4858   9.1789   3.8879
 M02  HAO1  H  HCH2  0   0.238   9.5507   8.1110   1.8860
 M02  HAO2  H  HCH2  0   0.223   8.1649   7.5326   2.8105
 M02  HAK1  H  HCH2  0   0.224   8.0769   8.0668   5.3779
 M02  HAK2  H  HCH2  0   0.238   9.4133   8.9713   6.0873
 M02  H101  H  HNH2  0   0.342  10.9412   6.8440   3.5708
 M02  H102  H  HNH2  0   0.342  10.8621   7.1562   5.1500
 M02  H7C1  H  HCH2  0   0.240   8.9307  10.4571   2.3360
 M02  H7C2  H  HCH2  0   0.290   7.5949   9.6091   1.5714
 M02  HAP1  H  HCH2  0   0.274   7.4619  10.4610   5.6514
 M02  HAP2  H  HCH2  0   0.239   8.8604  10.9456   4.6988
 M02  H2    H  HCR6  0   0.247   3.6265  10.3571   5.8076
 M02  H9    H  HNR5  0   0.425   2.2814   9.4736   1.2658
 M02  H8    H  HCR5  0   0.290   4.1056   9.1714  -0.4541

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
 M02  CAM  CAO   single    1.525  0.020  1.525
 M02  CAM  CAK   single    1.525  0.020  1.525
 M02  CAM  N10   single    1.455  0.020  1.455
 M02  CAO  C7    single    1.525  0.020  1.525
 M02  CAK  CAP   single    1.524  0.020  1.524
 M02  CAP  N6    single    1.455  0.020  1.455
 M02  N6   C6    single    1.343  0.020  1.343
 M02  N6   C7    single    1.454  0.020  1.454
 M02  C6   N1    aromatic  1.342  0.020  1.342
 M02  C6   C5    aromatic  1.420  0.020  1.420
 M02  N1   C2    aromatic  1.326  0.020  1.326
 M02  C2   N3    aromatic  1.320  0.020  1.320
 M02  N3   C4    aromatic  1.332  0.020  1.332
 M02  C4   C5    aromatic  1.395  0.020  1.395
 M02  C4   N9    aromatic  1.359  0.020  1.359
 M02  C5   N7    aromatic  1.376  0.020  1.376
 M02  N7   C8    aromatic  1.300  0.020  1.300
 M02  C8   N9    aromatic  1.358  0.020  1.358
 M02  CAM  HAM   single    0.970  0.020  1.090
 M02  CAO  HAO1  single    0.970  0.020  1.090
 M02  CAO  HAO2  single    0.970  0.020  1.090
 M02  CAK  HAK1  single    0.970  0.020  1.090
 M02  CAK  HAK2  single    0.970  0.020  1.090
 M02  N10  H101  single    0.890  0.020  1.040
 M02  N10  H102  single    0.890  0.020  1.040
 M02  C7   H7C1  single    0.970  0.020  1.090
 M02  C7   H7C2  single    0.970  0.020  1.090
 M02  CAP  HAP1  single    0.970  0.020  1.090
 M02  CAP  HAP2  single    0.970  0.020  1.090
 M02  C2   H2    single    0.930  0.020  1.080
 M02  N9   H9    single    0.860  0.020  1.020
 M02  C8   H8    single    0.930  0.020  1.080

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
 M02  HAK2  CAK  HAK1  107.34  3.000
 M02  HAK2  CAK  CAP   109.14  3.000
 M02  HAK1  CAK  CAP   109.57  3.000
 M02  HAK2  CAK  CAM   110.30  3.000
 M02  HAK1  CAK  CAM   109.47  3.000
 M02  CAP   CAK  CAM   110.94  3.000
 M02  HAM   CAM  N10   112.42  3.000
 M02  HAM   CAM  CAO   107.23  3.000
 M02  N10   CAM  CAO   110.16  3.000
 M02  HAM   CAM  CAK   107.19  3.000
 M02  N10   CAM  CAK   110.17  3.000
 M02  CAO   CAM  CAK   109.56  3.000
 M02  HAP2  CAP  HAP1  107.72  3.000
 M02  HAP2  CAP  N6    107.75  3.000
 M02  HAP1  CAP  N6    109.76  3.000
 M02  HAP2  CAP  CAK   109.86  3.000
 M02  HAP1  CAP  CAK   111.28  3.000
 M02  N6    CAP  CAK   110.36  3.000
 M02  HAO2  CAO  HAO1  107.39  3.000
 M02  HAO2  CAO  C7    109.65  3.000
 M02  HAO1  CAO  C7    108.90  3.000
 M02  HAO2  CAO  CAM   109.42  3.000
 M02  HAO1  CAO  CAM   110.32  3.000
 M02  C7    CAO  CAM   111.09  3.000
 M02  H7C2  C7   H7C1  107.43  3.000
 M02  H7C2  C7   N6    110.46  3.000
 M02  H7C1  C7   N6    107.81  3.000
 M02  H7C2  C7   CAO   110.92  3.000
 M02  H7C1  C7   CAO   109.71  3.000
 M02  N6    C7   CAO   110.42  3.000
 M02  C6    N6   C7    124.15  3.000
 M02  C7    N6   CAP   112.69  3.000
 M02  C6    N6   CAP   121.83  3.000
 M02  N1    C6   C5    116.51  3.000
 M02  C5    C6   N6    125.51  3.000
 M02  N1    C6   N6    117.96  3.000
 M02  C4    C5   N7    109.78  3.000
 M02  N7    C5   C6    134.24  3.000
 M02  C4    C5   C6    115.97  3.000
 M02  C8    N7   C5    104.98  3.000
 M02  N3    C4   N9    127.49  3.000
 M02  N9    C4   C5    105.20  3.000
 M02  N3    C4   C5    127.31  3.000
 M02  H9    N9   C8    126.41  3.000
 M02  H9    N9   C4    126.52  3.000
 M02  C8    N9   C4    107.07  3.000
 M02  H8    C8   N9    121.65  3.000
 M02  H8    C8   N7    125.37  3.000
 M02  N9    C8   N7    112.98  3.000
 M02  H102  N10  H101  105.36  3.000
 M02  H102  N10  CAM   109.36  3.000
 M02  H101  N10  CAM   109.29  3.000
 M02  C2    N3   C4    111.16  3.000
 M02  H2    C2   N1    115.40  3.000
 M02  H2    C2   N3    116.28  3.000
 M02  N1    C2   N3    128.32  3.000
 M02  C2    N1   C6    120.73  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
 M02  CONST_01  N3   C2   N1   C6     0.00   0.0  0
 M02  CONST_02  N3   C4   C5   C6     0.00   0.0  0
 M02  CONST_03  N9   C4   C5   C6   180.00   0.0  0
 M02  CONST_04  C8   N7   C5   C6   180.00   0.0  0
 M02  CONST_05  C2   N1   C6   C5     0.00   0.0  0
 M02  CONST_06  C2   N3   C4   C5     0.00   0.0  0
 M02  CONST_07  C8   N9   C4   C5     0.00   0.0  0
 M02  CONST_08  N9   C8   N7   C5     0.00   0.0  0
 M02  CONST_09  N1   C6   C5   N7   180.00   0.0  0
 M02  CONST_10  N3   C4   C5   N7   180.00   0.0  0
 M02  CONST_11  N9   C4   C5   N7     0.00   0.0  0
 M02  CONST_12  C4   N9   C8   N7     0.00   0.0  0
 M02  CONST_13  N1   C2   N3   C4     0.00   0.0  0
 M02  CONST_14  N1   C6   C5   C4     0.00   0.0  0
 M02  CONST_15  C8   N7   C5   C4     0.00   0.0  0
 M02  CONST_16  C2   N3   C4   N9   180.00   0.0  0
 M02  CONST_17  N3   C4   N9   C8   180.00   0.0  0
 M02  CONST_18  C2   N1   C6   N6   180.00   0.0  0
 M02  CONST_19  C4   C5   C6   N6   180.00   0.0  0
 M02  CONST_20  N7   C5   C6   N6     0.00   0.0  0
 M02  CONST_21  H2   C2   N1   C6   180.00   0.0  0
 M02  CONST_22  H9   N9   C4   C5   180.00   0.0  0
 M02  CONST_23  H8   C8   N7   C5   180.00   0.0  0
 M02  Var_01    C6   N6   CAP  CAK  108.10  30.0  1
 M02  Var_02    N6   C7   CAO  CAM  -56.02  30.0  1
 M02  Var_03    N6   CAP  CAK  CAM   56.45  30.0  1
 M02  Var_04    N1   C6   N6   CAP    6.45  30.0  2
 M02  Var_05    CAO  C7   N6   CAP   58.97  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
 M02  chir_01  CAM  CAO  CAK  N10  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
 M02  plan-1  N6  0.020
 M02  plan-1  C6  0.020
 M02  plan-1  C5  0.020
 M02  plan-1  N7  0.020
 M02  plan-1  C4  0.020
 M02  plan-1  N9  0.020
 M02  plan-1  C8  0.020
 M02  plan-1  N3  0.020
 M02  plan-1  C2  0.020
 M02  plan-1  N1  0.020
 M02  plan-1  H2  0.020
 M02  plan-1  H9  0.020
 M02  plan-1  H8  0.020

