# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 09:43:15 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: 5-(azidomethyl)-2-methylpyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CN=[N+]=[N-])c(N)n1
#
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
 2QB  2QB  5-(azidomethyl)-2-methylpyrimidin-4-amine  ligand  20  12  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2QB
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
 2QB  NAH  N  N     -1  -0.204  -2.9041  -0.8335  -1.4975
 2QB  NAG  N  N      1   0.374  -2.6771  -0.1111  -0.6683
 2QB  NAF  N  N      0  -0.377  -2.5025   0.7288   0.1985
 2QB  CAE  C  CH2    0  -0.406  -1.5371   0.3521   1.2510
 2QB  C5   C  CR6    0  -0.077  -0.1686   0.0659   0.7217
 2QB  C6   C  CR16   0  -0.070   0.4268  -1.1642   0.8613
 2QB  N1   N  N      0  -0.446   1.6606  -1.4508   0.4421
 2QB  C2   C  CR6    0   0.357   2.3187  -0.4570  -0.1404
 2QB  CAL  C  CH3    0  -0.728   3.7025  -0.7377  -0.6356
 2QB  N3   N  N      0  -0.464   1.8470   0.7654  -0.3505
 2QB  C4   C  CR6    0   0.470   0.6100   1.0444   0.0595
 2QB  NAA  N  NH2    0  -0.822   0.1513   2.2904  -0.1488
 2QB  H2   H  HCH2   0   0.287  -1.5231   1.2031   1.9309
 2QB  H3   H  HCH2   0   0.284  -1.9086  -0.5070   1.8158
 2QB  H4   H  HCR6   0   0.266  -0.1161  -1.9683   1.3500
 2QB  H5   H  HCH3   0   0.258   3.6863  -0.9084  -1.7142
 2QB  H6   H  HCH3   0   0.250   4.3630   0.1083  -0.4525
 2QB  H7   H  HCH3   0   0.246   4.1147  -1.6253  -0.1618
 2QB  H8   H  HNH2   0   0.397   0.6962   2.8988  -0.7373
 2QB  H9   H  HNH2   0   0.405  -0.8373   2.4751  -0.1201

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
 2QB  CAL  C2   single    1.496  0.020  1.496
 2QB  N3   C2   aromatic  1.327  0.020  1.327
 2QB  N3   C4   aromatic  1.333  0.020  1.333
 2QB  C2   N1   aromatic  1.327  0.020  1.327
 2QB  NAF  NAG  double    1.220  0.020  1.220
 2QB  NAF  CAE  single    1.477  0.020  1.477
 2QB  NAG  NAH  double    1.123  0.020  1.123
 2QB  C4   NAA  single    1.344  0.020  1.344
 2QB  C4   C5   aromatic  1.415  0.020  1.415
 2QB  N1   C6   aromatic  1.334  0.020  1.334
 2QB  C5   C6   aromatic  1.374  0.020  1.374
 2QB  C5   CAE  single    1.495  0.020  1.495
 2QB  CAE  H2   single    0.970  0.020  1.090
 2QB  CAE  H3   single    0.970  0.020  1.090
 2QB  C6   H4   single    0.930  0.020  1.080
 2QB  CAL  H5   single    0.970  0.020  1.090
 2QB  CAL  H6   single    0.970  0.020  1.090
 2QB  CAL  H7   single    0.970  0.020  1.090
 2QB  NAA  H8   single    0.890  0.020  1.040
 2QB  NAA  H9   single    0.890  0.020  1.040

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
 2QB  NAF  NAG  NAH  175.45  3.000
 2QB  CAE  NAF  NAG  115.11  3.000
 2QB  H3   CAE  H2   107.21  3.000
 2QB  H3   CAE  C5   110.10  3.000
 2QB  H2   CAE  C5   111.03  3.000
 2QB  H3   CAE  NAF  110.27  3.000
 2QB  H2   CAE  NAF  104.71  3.000
 2QB  C5   CAE  NAF  113.26  3.000
 2QB  C4   C5   C6   115.36  3.000
 2QB  C6   C5   CAE  122.16  3.000
 2QB  C4   C5   CAE  122.48  3.000
 2QB  H4   C6   N1   116.39  3.000
 2QB  H4   C6   C5   119.47  3.000
 2QB  N1   C6   C5   124.14  3.000
 2QB  C2   N1   C6   115.83  3.000
 2QB  N3   C2   CAL  116.69  3.000
 2QB  N3   C2   N1   125.68  3.000
 2QB  CAL  C2   N1   117.61  3.000
 2QB  H7   CAL  H6   109.33  3.000
 2QB  H7   CAL  H5   107.96  3.000
 2QB  H6   CAL  H5   107.25  3.000
 2QB  H7   CAL  C2   111.07  3.000
 2QB  H6   CAL  C2   111.08  3.000
 2QB  H5   CAL  C2   110.03  3.000
 2QB  C4   N3   C2   118.30  3.000
 2QB  NAA  C4   N3   117.59  3.000
 2QB  NAA  C4   C5   121.72  3.000
 2QB  N3   C4   C5   120.66  3.000
 2QB  H9   NAA  H8   115.95  3.000
 2QB  H9   NAA  C4   120.08  3.000
 2QB  H8   NAA  C4   117.79  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
 2QB  CONST_01  C2   N3   C4   C5     0.00   0.0  0
 2QB  CONST_02  C2   N1   C6   C5     0.00   0.0  0
 2QB  CONST_03  N3   C2   N1   C6     0.00   0.0  0
 2QB  CONST_04  N3   C4   C5   C6     0.00   0.0  0
 2QB  CONST_05  C4   N3   C2   N1     0.00   0.0  0
 2QB  CONST_06  C4   C5   C6   N1     0.00   0.0  0
 2QB  CONST_07  N3   C4   C5   CAE  180.00   0.0  0
 2QB  CONST_08  N1   C6   C5   CAE  180.00   0.0  0
 2QB  CONST_09  CAL  C2   N1   C6   180.00   0.0  0
 2QB  CONST_10  NAA  C4   C5   C6   180.00   0.0  0
 2QB  CONST_11  NAA  C4   N3   C2   180.00   0.0  0
 2QB  CONST_12  C4   N3   C2   CAL  180.00   0.0  0
 2QB  CONST_13  H4   C6   N1   C2   180.00   0.0  0
 2QB  CONST_14  H8   NAA  C4   C5   180.00   0.0  0
 2QB  Var_01    C4   C5   CAE  NAF   62.14  30.0  2
 2QB  Var_02    H5   CAL  C2   N1   100.41  30.0  2
 2QB  Var_03    C5   CAE  NAF  NAG   59.67  30.0  3

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
 2QB  plan-1  CAE  0.020
 2QB  plan-1  C5   0.020
 2QB  plan-1  C6   0.020
 2QB  plan-1  N1   0.020
 2QB  plan-1  C2   0.020
 2QB  plan-1  CAL  0.020
 2QB  plan-1  N3   0.020
 2QB  plan-1  C4   0.020
 2QB  plan-1  NAA  0.020
 2QB  plan-1  H4   0.020
 2QB  plan-2  C4   0.020
 2QB  plan-2  NAA  0.020
 2QB  plan-2  H8   0.020
 2QB  plan-2  H9   0.020
 2QB  plan-3  NAH  0.020
 2QB  plan-3  NAG  0.020
 2QB  plan-3  NAF  0.020
 2QB  plan-3  CAE  0.020

