# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 11:14:52 2021
#   Inital geometry file: a 43 line input string
#   Ligand name: 6,7-dihydro-5H-pyrrolo[2,3-d]pyrimidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1Cc2cncnc2N1
#
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
 WOY  WOY  6,7-dihydro-5H-pyrrolo[2,3-d]pyrimidine  ligand  16  9  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_WOY
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
 WOY  N1  N  N     0  -0.434  -0.9389  15.0955   1.6512
 WOY  C4  C  CR56  0   0.366  -2.1005  15.0813   1.0144
 WOY  C5  C  CH2   0  -0.286  -4.3815  15.0433   0.6300
 WOY  C   C  CH2   0  -0.572  -3.6761  14.8963  -0.7392
 WOY  N2  N  NR15  0  -0.607  -3.2967  15.3527   1.5556
 WOY  C1  C  CR56  0   0.093  -2.2297  14.7821  -0.3567
 WOY  C3  C  CR16  0   0.038   0.1118  14.8033   0.8819
 WOY  N   N  N     0  -0.319   0.1199  14.5094  -0.4008
 WOY  C2  C  CR16  0  -0.093  -1.0780  14.5026  -1.0265
 WOY  H1  H  HCH2  0   0.260  -5.1269  15.8370   0.6265
 WOY  H2  H  HCH2  0   0.173  -4.8805  14.1160   0.9217
 WOY  H3  H  HCH2  0   0.285  -3.8412  15.7752  -1.3660
 WOY  H4  H  HCH2  0   0.244  -4.0453  14.0331  -1.2916
 WOY  H5  H  HNR5  0   0.390  -3.4382  15.3928   2.5515
 WOY  H6  H  HCR6  0   0.190   1.0740  14.8074   1.3849
 WOY  H7  H  HCR6  0   0.273  -1.0794  14.2607  -2.0842

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
 WOY  C2  N   aromatic  1.351  0.020  1.351
 WOY  C2  C1  aromatic  1.361  0.020  1.361
 WOY  C   C1  single    1.500  0.020  1.500
 WOY  C   C5  single    1.547  0.020  1.547
 WOY  N   C3  aromatic  1.316  0.020  1.316
 WOY  C1  C4  aromatic  1.409  0.020  1.409
 WOY  C5  N2  single    1.459  0.020  1.459
 WOY  C3  N1  aromatic  1.335  0.020  1.335
 WOY  C4  N2  single    1.341  0.020  1.341
 WOY  C4  N1  aromatic  1.325  0.020  1.325
 WOY  C5  H1  single    0.970  0.020  1.090
 WOY  C5  H2  single    0.970  0.020  1.090
 WOY  C   H3  single    0.970  0.020  1.090
 WOY  C   H4  single    0.970  0.020  1.090
 WOY  N2  H5  single    0.890  0.020  1.040
 WOY  C3  H6  single    0.930  0.020  1.080
 WOY  C2  H7  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
 WOY  C3  N1  C4  114.26  3.000
 WOY  C1  C4  N2  110.73  3.000
 WOY  N2  C4  N1  125.88  3.000
 WOY  C1  C4  N1  123.39  3.000
 WOY  H2  C5  H1  107.86  3.000
 WOY  H2  C5  N2  110.49  3.000
 WOY  H1  C5  N2  110.88  3.000
 WOY  H2  C5  C   111.34  3.000
 WOY  H1  C5  C   112.24  3.000
 WOY  N2  C5  C   104.04  3.000
 WOY  H4  C   H3  107.19  3.000
 WOY  H4  C   C1  113.31  3.000
 WOY  H3  C   C1  110.69  3.000
 WOY  H4  C   C5  111.68  3.000
 WOY  H3  C   C5  111.25  3.000
 WOY  C1  C   C5  102.77  3.000
 WOY  H5  N2  C5  122.11  3.000
 WOY  H5  N2  C4  122.20  3.000
 WOY  C5  N2  C4  111.36  3.000
 WOY  C2  C1  C   134.89  3.000
 WOY  C   C1  C4  108.68  3.000
 WOY  C2  C1  C4  116.40  3.000
 WOY  H6  C3  N   116.55  3.000
 WOY  H6  C3  N1  115.45  3.000
 WOY  N   C3  N1  128.00  3.000
 WOY  C2  N   C3  116.54  3.000
 WOY  H7  C2  N   116.97  3.000
 WOY  H7  C2  C1  121.62  3.000
 WOY  N   C2  C1  121.41  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
 WOY  CONST_01  C2  N   C3  N1     0.00   0.0  0
 WOY  CONST_02  C2  C1  C4  N1     0.00   0.0  0
 WOY  CONST_03  N   C2  C1  C4     0.00   0.0  0
 WOY  CONST_04  N   C3  N1  C4     0.00   0.0  0
 WOY  CONST_05  C3  N   C2  C1     0.00   0.0  0
 WOY  CONST_06  C3  N1  C4  C1     0.00   0.0  0
 WOY  CONST_07  H7  C2  C1  C4   180.00   0.0  0
 WOY  CONST_08  H6  C3  N1  C4   180.00   0.0  0
 WOY  Var_01    C5  N2  C4  N1  -171.12  30.0  1
 WOY  Var_02    C5  C   C1  C4    -9.90  30.0  1
 WOY  Var_03    C   C5  N2  C4   -15.26  30.0  1
 WOY  Var_04    C1  C   C5  N2    14.54  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
 WOY  plan-1  N1  0.020
 WOY  plan-1  C4  0.020
 WOY  plan-1  C   0.020
 WOY  plan-1  N2  0.020
 WOY  plan-1  C1  0.020
 WOY  plan-1  C3  0.020
 WOY  plan-1  N   0.020
 WOY  plan-1  C2  0.020
 WOY  plan-1  H6  0.020
 WOY  plan-1  H7  0.020

