# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 07:52:32 2020
#   Inital geometry file: a 44 line input string
#   Ligand name: 5H-pyrrolo[3,2-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2cc[nH]c12
#
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
 9DA  9DA  5H-pyrrolo[3,2-d]pyrimidin-4-amine  ligand  16  10  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_9DA
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
 9DA  N1    N  N     0  -0.472  -0.3026   0.0201   1.9668
 9DA  C2    C  CR16  0   0.010  -1.5341  -0.0062   1.4462
 9DA  N3    N  N     0  -0.455  -1.8851  -0.0223   0.1826
 9DA  C4    C  CR56  0   0.186  -0.8428  -0.0066  -0.6752
 9DA  C5    C  CR56  0   0.197   0.4873   0.0230  -0.2372
 9DA  C6    C  CR6   0   0.457   0.7417   0.0363   1.1435
 9DA  N6    N  NH2   0  -0.825   1.9805   0.1028   1.6688
 9DA  N7    N  NR15  0  -0.667   1.2934   0.0372  -1.3398
 9DA  C8    C  CR15  0  -0.016   0.5125   0.0172  -2.4506
 9DA  C9    C  CR15  0  -0.417  -0.8118  -0.0104  -2.0957
 9DA  HC2   H  HCR6  0   0.239  -2.3394  -0.0177   2.1741
 9DA  HN61  H  HNH2  0   0.401   2.7858  -0.1248   1.1121
 9DA  HN62  H  HNH2  0   0.397   2.0772  -0.0507   2.6589
 9DA  HN7   H  HNR5  0   0.418   2.2992   0.0637  -1.3538
 9DA  HC8   H  HCR5  0   0.290   0.9607   0.0262  -3.4310
 9DA  HC9   H  HCR5  0   0.255  -1.6528  -0.0298  -2.7695

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
 9DA  N1  C2    aromatic  1.337  0.020  1.337
 9DA  N1  C6    aromatic  1.330  0.020  1.330
 9DA  C2  N3    aromatic  1.312  0.020  1.312
 9DA  C2  HC2   single    0.930  0.020  1.080
 9DA  N3  C4    aromatic  1.350  0.020  1.350
 9DA  C4  C5    aromatic  1.401  0.020  1.401
 9DA  C4  C9    aromatic  1.421  0.020  1.421
 9DA  C5  C6    aromatic  1.404  0.020  1.404
 9DA  C5  N7    aromatic  1.366  0.020  1.366
 9DA  C6  N6    single    1.347  0.020  1.347
 9DA  N6  HN61  single    0.890  0.020  1.040
 9DA  N6  HN62  single    0.890  0.020  1.040
 9DA  N7  C8    aromatic  1.358  0.020  1.358
 9DA  N7  HN7   single    0.860  0.020  1.020
 9DA  C8  C9    aromatic  1.371  0.020  1.371
 9DA  C8  HC8   single    0.930  0.020  1.080
 9DA  C9  HC9   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
 9DA  C6    N1  C2    118.84  3.000
 9DA  HC2   C2  N3    116.58  3.000
 9DA  HC2   C2  N1    114.98  3.000
 9DA  N3    C2  N1    128.44  3.000
 9DA  C4    N3  C2    113.92  3.000
 9DA  C9    C4  C5    106.98  3.000
 9DA  C9    C4  N3    130.70  3.000
 9DA  C5    C4  N3    122.33  3.000
 9DA  N7    C5  C6    133.37  3.000
 9DA  N7    C5  C4    107.96  3.000
 9DA  C6    C5  C4    118.67  3.000
 9DA  N6    C6  C5    123.40  3.000
 9DA  N6    C6  N1    118.77  3.000
 9DA  C5    C6  N1    117.80  3.000
 9DA  HN62  N6  HN61  115.68  3.000
 9DA  HN62  N6  C6    117.67  3.000
 9DA  HN61  N6  C6    120.64  3.000
 9DA  HN7   N7  C8    124.32  3.000
 9DA  HN7   N7  C5    126.98  3.000
 9DA  C8    N7  C5    108.71  3.000
 9DA  HC8   C8  C9    129.57  3.000
 9DA  HC8   C8  N7    120.31  3.000
 9DA  C9    C8  N7    110.12  3.000
 9DA  HC9   C9  C8    126.31  3.000
 9DA  HC9   C9  C4    127.44  3.000
 9DA  C8    C9  C4    106.24  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
 9DA  CONST_01  C4    N3  C2  N1    0.00  0.0  0
 9DA  CONST_02  C4    C5  C6  N1    0.00  0.0  0
 9DA  CONST_03  N7    C5  C6  N1  180.00  0.0  0
 9DA  CONST_04  C5    C6  N1  C2    0.00  0.0  0
 9DA  CONST_05  C5    C4  N3  C2    0.00  0.0  0
 9DA  CONST_06  C9    C4  N3  C2  180.00  0.0  0
 9DA  CONST_07  C6    N1  C2  N3    0.00  0.0  0
 9DA  CONST_08  C6    C5  C4  N3    0.00  0.0  0
 9DA  CONST_09  N7    C5  C4  N3  180.00  0.0  0
 9DA  CONST_10  C8    C9  C4  N3  180.00  0.0  0
 9DA  CONST_11  C8    N7  C5  C4    0.00  0.0  0
 9DA  CONST_12  N7    C8  C9  C4    0.00  0.0  0
 9DA  CONST_13  C8    C9  C4  C5    0.00  0.0  0
 9DA  CONST_14  C9    C8  N7  C5    0.00  0.0  0
 9DA  CONST_15  C9    C4  C5  C6  180.00  0.0  0
 9DA  CONST_16  C8    N7  C5  C6  180.00  0.0  0
 9DA  CONST_17  C9    C4  C5  N7    0.00  0.0  0
 9DA  CONST_18  N6    C6  N1  C2  180.00  0.0  0
 9DA  CONST_19  N6    C6  C5  C4  180.00  0.0  0
 9DA  CONST_20  N7    C5  C6  N6    0.00  0.0  0
 9DA  CONST_21  HC9   C9  C4  N3    0.00  0.0  0
 9DA  CONST_22  HC2   C2  N3  C4  180.00  0.0  0
 9DA  CONST_23  HN7   N7  C5  C4  180.00  0.0  0
 9DA  CONST_24  HC8   C8  C9  C4  180.00  0.0  0
 9DA  CONST_26  HN62  N6  C6  N1    0.00  0.0  0

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
 9DA  plan-1  N1    0.020
 9DA  plan-1  C2    0.020
 9DA  plan-1  N3    0.020
 9DA  plan-1  C4    0.020
 9DA  plan-1  C5    0.020
 9DA  plan-1  C6    0.020
 9DA  plan-1  N6    0.020
 9DA  plan-1  N7    0.020
 9DA  plan-1  C8    0.020
 9DA  plan-1  C9    0.020
 9DA  plan-1  HC2   0.020
 9DA  plan-1  HN7   0.020
 9DA  plan-1  HC8   0.020
 9DA  plan-1  HC9   0.020
 9DA  plan-2  C6    0.020
 9DA  plan-2  N6    0.020
 9DA  plan-2  HN61  0.020
 9DA  plan-2  HN62  0.020

