# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 08:15:49 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: 1-[1-(9H-purin-6-yl)piperidin-4-yl]methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCC1CCN(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
 M01  M01  1-[1-(9H-purin-6-yl)piperidin-4-yl]methanamine  ligand  33  17  .  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_M01
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
 M01  N1    N  N     0  -0.496   5.2250  10.0394   4.8233
 M01  C2    C  CR16  0   0.041   3.9175   9.8631   4.9501
 M01  N3    N  N     0  -0.449   3.0279   9.6274   4.0039
 M01  C4    C  CR56  0   0.456   3.6038   9.5782   2.8041
 M01  C5    C  CR56  0  -0.009   4.9568   9.7446   2.5085
 M01  C7    C  CR6   0   0.519   5.8089   9.9962   3.6158
 M01  C9    C  CH2   0  -0.275  10.3204   7.3601   3.9114
 M01  N7    N  N     0  -0.458   5.1556   9.6246   1.1521
 M01  C8    C  CR15  0   0.115   3.9744   9.3971   0.6583
 M01  N9    N  NR15  0  -0.646   3.0021   9.3575   1.6059
 M01  C10   C  CH1   0  -0.260   9.5969   8.6949   3.7196
 M01  C15   C  CH2   0  -0.423   8.7457   9.0283   4.9443
 M01  C14   C  CH2   0  -0.324   7.9526  10.3144   4.7450
 M01  C12   C  CH2   0  -0.343   7.9272  10.0034   2.3488
 M01  N10   N  NH2   0  -0.795  11.2379   6.9547   2.8599
 M01  C11   C  CH2   0  -0.423   8.7288   8.7110   2.4617
 M01  N6    N  NT    0  -0.464   7.1325  10.2183   3.5468
 M01  H2    H  HCR6  0   0.247   3.5362   9.9187   5.9648
 M01  H9    H  HNR5  0   0.425   2.0183   9.2031   1.4467
 M01  H9C1  H  HCH2  0   0.221  10.8784   7.3976   4.8519
 M01  H9C2  H  HCH2  0   0.210   9.5727   6.5691   4.0343
 M01  H10   H  HCH1  0   0.215  10.3572   9.4822   3.6142
 M01  H101  H  HNH2  0   0.343  10.7444   6.8669   1.9806
 M01  H102  H  HNH2  0   0.339  11.9343   7.6760   2.7162
 M01  H8    H  HCR5  0   0.290   3.7523   9.2499  -0.3873
 M01  H111  H  HCH2  0   0.232   9.3435   8.6104   1.5638
 M01  H112  H  HCH2  0   0.220   8.0400   7.8584   2.4766
 M01  H151  H  HCH2  0   0.221   8.0454   8.2091   5.1419
 M01  H152  H  HCH2  0   0.236   9.3789   9.1282   5.8300
 M01  H121  H  HCH2  0   0.239   8.6125  10.8517   2.2490
 M01  H122  H  HCH2  0   0.288   7.2925   9.9917   1.4688
 M01  H141  H  HCH2  0   0.270   7.3242  10.5285   5.6037
 M01  H142  H  HCH2  0   0.239   8.6377  11.1573   4.6113

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
 M01  N1   C2    aromatic  1.325  0.020  1.325
 M01  N1   C7    aromatic  1.342  0.020  1.342
 M01  C2   N3    aromatic  1.320  0.020  1.320
 M01  N3   C4    aromatic  1.332  0.020  1.332
 M01  C4   C5    aromatic  1.395  0.020  1.395
 M01  C4   N9    aromatic  1.359  0.020  1.359
 M01  C5   N7    aromatic  1.376  0.020  1.376
 M01  C5   C7    aromatic  1.420  0.020  1.420
 M01  C9   C10   single    1.530  0.020  1.530
 M01  C9   N10   single    1.453  0.020  1.453
 M01  N7   C8    aromatic  1.300  0.020  1.300
 M01  C8   N9    aromatic  1.358  0.020  1.358
 M01  C10  C11   single    1.528  0.020  1.528
 M01  C10  C15   single    1.528  0.020  1.528
 M01  C11  C12   single    1.525  0.020  1.525
 M01  C12  N6    single    1.454  0.020  1.454
 M01  C14  C15   single    1.524  0.020  1.524
 M01  C14  N6    single    1.455  0.020  1.455
 M01  N6   C7    single    1.344  0.020  1.344
 M01  C2   H2    single    0.930  0.020  1.080
 M01  N9   H9    single    0.860  0.020  1.020
 M01  C9   H9C1  single    0.970  0.020  1.090
 M01  C9   H9C2  single    0.970  0.020  1.090
 M01  C10  H10   single    0.970  0.020  1.090
 M01  N10  H101  single    0.890  0.020  1.040
 M01  N10  H102  single    0.890  0.020  1.040
 M01  C8   H8    single    0.930  0.020  1.080
 M01  C11  H111  single    0.970  0.020  1.090
 M01  C11  H112  single    0.970  0.020  1.090
 M01  C15  H151  single    0.970  0.020  1.090
 M01  C15  H152  single    0.970  0.020  1.090
 M01  C12  H121  single    0.970  0.020  1.090
 M01  C12  H122  single    0.970  0.020  1.090
 M01  C14  H141  single    0.970  0.020  1.090
 M01  C14  H142  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
 M01  C7    N1   C2    120.73  3.000
 M01  H2    C2   N3    116.27  3.000
 M01  H2    C2   N1    115.41  3.000
 M01  N3    C2   N1    128.32  3.000
 M01  C4    N3   C2    111.16  3.000
 M01  N9    C4   C5    105.19  3.000
 M01  N9    C4   N3    127.51  3.000
 M01  C5    C4   N3    127.30  3.000
 M01  N7    C5   C7    134.23  3.000
 M01  C7    C5   C4    115.98  3.000
 M01  N7    C5   C4    109.79  3.000
 M01  N6    C7   C5    125.48  3.000
 M01  N6    C7   N1    118.00  3.000
 M01  C5    C7   N1    116.51  3.000
 M01  H9C2  C9   H9C1  106.04  3.000
 M01  H9C2  C9   N10   108.10  3.000
 M01  H9C1  C9   N10   108.03  3.000
 M01  H9C2  C9   C10   108.73  3.000
 M01  H9C1  C9   C10   108.60  3.000
 M01  N10   C9   C10   116.82  3.000
 M01  C8    N7   C5    104.97  3.000
 M01  H8    C8   N9    121.65  3.000
 M01  H8    C8   N7    125.36  3.000
 M01  N9    C8   N7    112.99  3.000
 M01  H9    N9   C8    126.34  3.000
 M01  H9    N9   C4    126.59  3.000
 M01  C8    N9   C4    107.06  3.000
 M01  H10   C10  C11   107.84  3.000
 M01  H10   C10  C15   107.80  3.000
 M01  C11   C10  C15   109.93  3.000
 M01  H10   C10  C9    108.04  3.000
 M01  C15   C10  C9    110.68  3.000
 M01  C11   C10  C9    112.39  3.000
 M01  H152  C15  H151  107.00  3.000
 M01  H152  C15  C14   109.28  3.000
 M01  H151  C15  C14   108.78  3.000
 M01  H152  C15  C10   110.27  3.000
 M01  H151  C15  C10   109.72  3.000
 M01  C14   C15  C10   111.66  3.000
 M01  H142  C14  H141  107.89  3.000
 M01  H142  C14  N6    107.65  3.000
 M01  H141  C14  N6    109.77  3.000
 M01  H142  C14  C15   109.88  3.000
 M01  H141  C14  C15   111.36  3.000
 M01  N6    C14  C15   110.20  3.000
 M01  H122  C12  H121  107.49  3.000
 M01  H122  C12  N6    110.50  3.000
 M01  H121  C12  N6    107.62  3.000
 M01  H122  C12  C11   111.00  3.000
 M01  H121  C12  C11   109.53  3.000
 M01  N6    C12  C11   110.59  3.000
 M01  H102  N10  H101  105.88  3.000
 M01  H102  N10  C9    109.75  3.000
 M01  H101  N10  C9    110.18  3.000
 M01  H112  C11  H111  107.04  3.000
 M01  H112  C11  C12   109.26  3.000
 M01  H111  C11  C12   108.23  3.000
 M01  H112  C11  C10   109.73  3.000
 M01  H111  C11  C10   110.84  3.000
 M01  C12   C11  C10   111.62  3.000
 M01  C12   N6   C14   112.35  3.000
 M01  C14   N6   C7    121.58  3.000
 M01  C12   N6   C7    123.80  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
 M01  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 M01  CONST_02  C4    C5   C7   N1      0.00   0.0  0
 M01  CONST_03  N7    C5   C7   N1    180.00   0.0  0
 M01  CONST_04  C5    C7   N1   C2      0.00   0.0  0
 M01  CONST_05  C5    C4   N3   C2      0.00   0.0  0
 M01  CONST_06  N9    C4   N3   C2    180.00   0.0  0
 M01  CONST_07  C7    N1   C2   N3      0.00   0.0  0
 M01  CONST_08  N7    C5   C4   N3    180.00   0.0  0
 M01  CONST_09  C7    C5   C4   N3      0.00   0.0  0
 M01  CONST_10  C8    N9   C4   N3    180.00   0.0  0
 M01  CONST_11  C8    N7   C5   C4      0.00   0.0  0
 M01  CONST_12  N7    C8   N9   C4      0.00   0.0  0
 M01  CONST_13  C8    N9   C4   C5      0.00   0.0  0
 M01  CONST_14  N9    C8   N7   C5      0.00   0.0  0
 M01  CONST_15  N9    C4   C5   C7    180.00   0.0  0
 M01  CONST_16  C8    N7   C5   C7    180.00   0.0  0
 M01  CONST_17  N9    C4   C5   N7      0.00   0.0  0
 M01  CONST_18  N6    C7   N1   C2    180.00   0.0  0
 M01  CONST_19  N6    C7   C5   C4    180.00   0.0  0
 M01  CONST_20  N6    C7   C5   N7      0.00   0.0  0
 M01  CONST_21  H9    N9   C4   N3      0.00   0.0  0
 M01  CONST_22  H2    C2   N3   C4    180.00   0.0  0
 M01  CONST_23  H8    C8   N9   C4    180.00   0.0  0
 M01  Var_01    C12   N6   C7   N1    170.23  30.0  1
 M01  Var_02    C11   C12  N6   C7   -103.25  30.0  1
 M01  Var_03    C15   C14  N6   C7    103.42  30.0  1
 M01  Var_04    N6    C12  C11  C10   -55.28  30.0  1
 M01  Var_05    N6    C14  C15  C10    56.00  30.0  1
 M01  Var_06    H101  N10  C9   C10   -59.95  30.0  3

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
 M01  chir_01  C10  C9  C11  C15  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
 M01  plan-1  N1  0.020
 M01  plan-1  C2  0.020
 M01  plan-1  N3  0.020
 M01  plan-1  C4  0.020
 M01  plan-1  C5  0.020
 M01  plan-1  C7  0.020
 M01  plan-1  N7  0.020
 M01  plan-1  C8  0.020
 M01  plan-1  N9  0.020
 M01  plan-1  N6  0.020
 M01  plan-1  H2  0.020
 M01  plan-1  H9  0.020
 M01  plan-1  H8  0.020

