# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 01:49:14 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: (2R,6S)-2-amino-6-hydroxy-7,9-dimethyl-2,3,6,9-tetrahydro-1H-purin-7-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1c[n+](C)c2[C@H](O)N[C@H](N)Nc12
#
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
 NDM  NDM  (2R,6S)-2-amino-6-hydroxy-7,9-dimethyl-2,3,6,9-tetrahydro-1H-purin-7-ium  ligand  27  13  .  2021-08-15  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NDM
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
 NDM  CN9   C  CH3   0  -0.544   1.4965  -2.2875  -1.0017
 NDM  N9    N  NR5   0  -0.479   1.0056  -1.0591  -1.5976
 NDM  C4    C  CR56  0   0.528   0.7806  -0.8535  -2.9306
 NDM  N3    N  NR16  0  -0.686   1.0149  -1.7276  -3.9526
 NDM  C2    C  CR16  0   0.239   0.3227  -1.2877  -5.1708
 NDM  N2    N  NH2   0  -0.828   0.8603  -2.0140  -6.2889
 NDM  N1    N  NR16  0  -0.658   0.6168   0.1216  -5.3460
 NDM  C6    C  CR16  0   0.119   0.0097   1.0194  -4.3936
 NDM  O6    O  OH1   0  -0.660  -1.3885   1.1819  -4.4785
 NDM  C5    C  CR56  0   0.229   0.3223   0.4172  -3.0733
 NDM  N7    N  NR5   1  -0.455   0.2670   0.9622  -1.8139
 NDM  CN7   C  CH3   0  -0.529  -0.1889   2.3027  -1.4972
 NDM  C8    C  CR15  0   0.223   0.6784   0.0605  -0.9445
 NDM  HN91  H  HCH3  0   0.289   1.6693  -2.1231   0.0568
 NDM  HN92  H  HCH3  0   0.284   2.4314  -2.5747  -1.4759
 NDM  HN93  H  HCH3  0   0.283   0.7623  -3.0806  -1.1233
 NDM  H22   H  HCR6  0   0.212  -0.7600  -1.4571  -5.0314
 NDM  HN21  H  HNH2  0   0.363   0.3133  -1.7923  -7.1136
 NDM  HN22  H  HNH2  0   0.363   0.7189  -3.0070  -6.1419
 NDM  HN11  H  HNR6  0   0.379   0.4428   0.4153  -6.2984
 NDM  H66   H  HCR6  0   0.265   0.5053   1.9896  -4.5132
 NDM  HN71  H  HCH3  0   0.281  -1.2303   2.4120  -1.7873
 NDM  HN72  H  HCH3  0   0.280   0.4169   3.0311  -2.0304
 NDM  HN73  H  HCH3  0   0.284  -0.0902   2.4683  -0.4295
 NDM  HC81  H  HCR5  0   0.358   0.7391   0.1960   0.1219
 NDM  HN1   H  HNR6  0   0.401   0.8345  -2.6989  -3.7289
 NDM  HO1   H  HOH1  0   0.461  -1.5813   1.8027  -5.1898

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
 NDM  CN9  N9    single    1.451  0.020  1.451
 NDM  CN9  HN91  single    0.970  0.020  1.090
 NDM  CN9  HN92  single    0.970  0.020  1.090
 NDM  CN9  HN93  single    0.970  0.020  1.090
 NDM  N9   C4    aromatic  1.367  0.020  1.367
 NDM  N9   C8    aromatic  1.337  0.020  1.337
 NDM  C4   N3    single    1.365  0.020  1.365
 NDM  C4   C5    aromatic  1.358  0.020  1.358
 NDM  N3   C2    single    1.469  0.020  1.469
 NDM  C2   N2    single    1.438  0.020  1.438
 NDM  C2   N1    single    1.450  0.020  1.450
 NDM  C2   H22   single    0.970  0.020  1.090
 NDM  N2   HN21  single    0.890  0.020  1.040
 NDM  N2   HN22  single    0.890  0.020  1.040
 NDM  N1   C6    single    1.443  0.020  1.443
 NDM  N1   HN11  single    0.890  0.020  1.040
 NDM  C6   O6    single    1.410  0.020  1.410
 NDM  C6   C5    single    1.485  0.020  1.485
 NDM  C6   H66   single    0.970  0.020  1.090
 NDM  C5   N7    aromatic  1.373  0.020  1.373
 NDM  N7   CN7   single    1.451  0.020  1.451
 NDM  N7   C8    aromatic  1.318  0.020  1.318
 NDM  CN7  HN71  single    0.970  0.020  1.090
 NDM  CN7  HN72  single    0.970  0.020  1.090
 NDM  CN7  HN73  single    0.970  0.020  1.090
 NDM  C8   HC81  single    0.930  0.020  1.080
 NDM  HN1  N3    single    0.890  0.020  1.040
 NDM  HO1  O6    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
 NDM  HN93  CN9  HN92  109.83  3.000
 NDM  HN93  CN9  HN91  109.10  3.000
 NDM  HN92  CN9  HN91  109.18  3.000
 NDM  HN93  CN9  N9    110.06  3.000
 NDM  HN92  CN9  N9    109.60  3.000
 NDM  HN91  CN9  N9    109.04  3.000
 NDM  C8    N9   C4    108.06  3.000
 NDM  C8    N9   CN9   126.25  3.000
 NDM  C4    N9   CN9   125.69  3.000
 NDM  C5    C4   N3    125.33  3.000
 NDM  C5    C4   N9    107.37  3.000
 NDM  N3    C4   N9    127.25  3.000
 NDM  HN1   N3   C2    112.73  3.000
 NDM  HN1   N3   C4    114.71  3.000
 NDM  C2    N3   C4    110.39  3.000
 NDM  H22   C2   N1    111.28  3.000
 NDM  H22   C2   N2    112.78  3.000
 NDM  N1    C2   N2    108.73  3.000
 NDM  H22   C2   N3    108.14  3.000
 NDM  N1    C2   N3    107.20  3.000
 NDM  N2    C2   N3    108.52  3.000
 NDM  HN22  N2   HN21  104.88  3.000
 NDM  HN22  N2   C2    109.26  3.000
 NDM  HN21  N2   C2    108.69  3.000
 NDM  HN11  N1   C6    111.61  3.000
 NDM  HN11  N1   C2    111.16  3.000
 NDM  C6    N1   C2    116.08  3.000
 NDM  H66   C6   C5    111.16  3.000
 NDM  H66   C6   O6    109.87  3.000
 NDM  C5    C6   O6    108.01  3.000
 NDM  H66   C6   N1    106.77  3.000
 NDM  C5    C6   N1    104.24  3.000
 NDM  O6    C6   N1    116.69  3.000
 NDM  HO1   O6   C6    108.49  3.000
 NDM  N7    C5   C6    130.25  3.000
 NDM  N7    C5   C4    106.77  3.000
 NDM  C6    C5   C4    122.96  3.000
 NDM  C8    N7   CN7   125.87  3.000
 NDM  C8    N7   C5    108.71  3.000
 NDM  CN7   N7   C5    125.41  3.000
 NDM  HN73  CN7  HN72  109.25  3.000
 NDM  HN73  CN7  HN71  109.55  3.000
 NDM  HN72  CN7  HN71  109.62  3.000
 NDM  HN73  CN7  N7    109.10  3.000
 NDM  HN72  CN7  N7    109.69  3.000
 NDM  HN71  CN7  N7    109.62  3.000
 NDM  HC81  C8   N7    125.78  3.000
 NDM  HC81  C8   N9    125.13  3.000
 NDM  N7    C8   N9    109.09  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
 NDM  CONST_01  N7    C5   C4  N9     0.00   0.0  0
 NDM  CONST_02  C5    N7   C8  N9     0.00   0.0  0
 NDM  CONST_03  N7    C8   N9  C4     0.00   0.0  0
 NDM  CONST_04  C8    N7   C5  C4     0.00   0.0  0
 NDM  CONST_05  C8    N9   C4  C5     0.00   0.0  0
 NDM  CONST_06  N3    C4   N9  CN9    0.00   0.0  0
 NDM  CONST_07  C5    C4   N9  CN9  180.00   0.0  0
 NDM  CONST_08  N7    C8   N9  CN9  180.00   0.0  0
 NDM  CONST_09  CN7   N7   C8  N9   180.00   0.0  0
 NDM  CONST_10  CN7   N7   C5  C4   180.00   0.0  0
 NDM  CONST_11  CN7   N7   C5  C6     0.00   0.0  0
 NDM  CONST_12  HC81  C8   N9  C4   180.00   0.0  0
 NDM  Var_01    C2    N3   C4  N9   164.91  30.0  1
 NDM  Var_02    HN91  CN9  N9  C4   174.39  30.0  2
 NDM  Var_03    HN71  CN7  N7  C5    61.96  30.0  2

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
 NDM  chir_01  C2  N3  N2  N1  positiv
 NDM  chir_02  C6  O6  N1  C5  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
 NDM  plan-1  CN9   0.020
 NDM  plan-1  N9    0.020
 NDM  plan-1  C4    0.020
 NDM  plan-1  N3    0.020
 NDM  plan-1  C6    0.020
 NDM  plan-1  C5    0.020
 NDM  plan-1  N7    0.020
 NDM  plan-1  CN7   0.020
 NDM  plan-1  C8    0.020
 NDM  plan-1  HC81  0.020

