# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 20:06:19 2020
#   Inital geometry file: a 51 line input string
#   Ligand name: 5-(aminomethyl)-2-methylpyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CN)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
 NSP  NSP  5-(aminomethyl)-2-methylpyrimidin-4-amine  ligand  20  10  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_NSP
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
 NSP  N     N  NH2   0  -0.798   1.2119   0.0328  -3.0542
 NSP  CA    C  CH2   0  -0.344  -0.0680   0.0134  -2.3730
 NSP  CP    C  CR6   0  -0.072   0.0829   0.0007  -0.8777
 NSP  CQ1   C  CR16  0  -0.085   1.2898  -0.1042  -0.2347
 NSP  CQ2   C  CR6   0   0.458  -1.0412   0.0983  -0.0232
 NSP  NR1   N  N     0  -0.450   1.4348  -0.1111   1.0981
 NSP  NQ2   N  NH2   0  -0.833  -2.2883   0.2244  -0.5148
 NSP  NR2   N  N     0  -0.468  -0.9051   0.0927   1.3010
 NSP  CS    C  CR6   0   0.344   0.3212  -0.0094   1.8036
 NSP  CS1   C  CH3   0  -0.728   0.4335  -0.0006   3.2971
 NSP  HN1   H  HNH2  0   0.360   1.0640  -0.1416  -4.0392
 NSP  HN2   H  HNH2  0   0.348   1.6149   0.9596  -2.9951
 NSP  HCA1  H  HCH2  0   0.247  -0.6023  -0.8916  -2.6822
 NSP  HCA2  H  HCH2  0   0.218  -0.7221   0.8531  -2.6539
 NSP  HQ1   H  HCR6  0   0.257   2.1988  -0.1903  -0.8197
 NSP  HQ21  H  HNH2  0   0.395  -3.0636   0.1522   0.1223
 NSP  HQ22  H  HNH2  0   0.410  -2.4869   0.0390  -1.4819
 NSP  HS11  H  HCH3  0   0.251   0.1464   0.9737   3.6969
 NSP  HS12  H  HCH3  0   0.248  -0.2366  -0.7373   3.7404
 NSP  HS13  H  HCH3  0   0.242   1.4515  -0.2143   3.6137

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
 NSP  N    CA    single    1.450  0.020  1.450
 NSP  N    HN1   single    0.890  0.020  1.040
 NSP  N    HN2   single    0.890  0.020  1.040
 NSP  CA   CP    single    1.503  0.020  1.503
 NSP  CA   HCA1  single    0.970  0.020  1.090
 NSP  CA   HCA2  single    0.970  0.020  1.090
 NSP  CP   CQ1   aromatic  1.372  0.020  1.372
 NSP  CP   CQ2   aromatic  1.415  0.020  1.415
 NSP  CQ1  NR1   aromatic  1.341  0.020  1.341
 NSP  CQ1  HQ1   single    0.930  0.020  1.080
 NSP  CQ2  NQ2   single    1.346  0.020  1.346
 NSP  CQ2  NR2   aromatic  1.331  0.020  1.331
 NSP  NR1  CS    aromatic  1.322  0.020  1.322
 NSP  NQ2  HQ21  single    0.890  0.020  1.040
 NSP  NQ2  HQ22  single    0.890  0.020  1.040
 NSP  NR2  CS    aromatic  1.329  0.020  1.329
 NSP  CS   CS1   single    1.498  0.020  1.498
 NSP  CS1  HS11  single    0.970  0.020  1.090
 NSP  CS1  HS12  single    0.970  0.020  1.090
 NSP  CS1  HS13  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
 NSP  HN2   N    HN1   105.84  3.000
 NSP  HN2   N    CA    109.65  3.000
 NSP  HN1   N    CA    109.04  3.000
 NSP  HCA2  CA   HCA1  105.57  3.000
 NSP  HCA2  CA   CP    108.66  3.000
 NSP  HCA1  CA   CP    108.83  3.000
 NSP  HCA2  CA   N     113.22  3.000
 NSP  HCA1  CA   N     108.00  3.000
 NSP  CP    CA   N     112.26  3.000
 NSP  CQ2   CP   CQ1   114.90  3.000
 NSP  CQ2   CP   CA    121.36  3.000
 NSP  CQ1   CP   CA    123.74  3.000
 NSP  HQ1   CQ1  NR1   116.44  3.000
 NSP  HQ1   CQ1  CP    119.39  3.000
 NSP  NR1   CQ1  CP    124.17  3.000
 NSP  NR2   CQ2  NQ2   117.28  3.000
 NSP  NR2   CQ2  CP    121.27  3.000
 NSP  NQ2   CQ2  CP    121.44  3.000
 NSP  CS    NR1  CQ1   116.04  3.000
 NSP  HQ22  NQ2  HQ21  116.36  3.000
 NSP  HQ22  NQ2  CQ2   121.15  3.000
 NSP  HQ21  NQ2  CQ2   118.42  3.000
 NSP  CS    NR2  CQ2   118.09  3.000
 NSP  CS1   CS   NR2   116.48  3.000
 NSP  CS1   CS   NR1   118.00  3.000
 NSP  NR2   CS   NR1   125.53  3.000
 NSP  HS13  CS1  HS12  108.92  3.000
 NSP  HS13  CS1  HS11  108.37  3.000
 NSP  HS12  CS1  HS11  107.02  3.000
 NSP  HS13  CS1  CS    111.06  3.000
 NSP  HS12  CS1  CS    110.82  3.000
 NSP  HS11  CS1  CS    110.53  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
 NSP  CONST_01  CS    NR1  CQ1  CP     0.00   0.0  0
 NSP  CONST_02  CS    NR2  CQ2  CP     0.00   0.0  0
 NSP  CONST_03  NR2   CQ2  CP   CQ1    0.00   0.0  0
 NSP  CONST_04  NR2   CS   NR1  CQ1    0.00   0.0  0
 NSP  CONST_05  NR1   CQ1  CP   CQ2    0.00   0.0  0
 NSP  CONST_06  NR1   CS   NR2  CQ2    0.00   0.0  0
 NSP  CONST_07  NR1   CQ1  CP   CA   180.00   0.0  0
 NSP  CONST_08  NR2   CQ2  CP   CA   180.00   0.0  0
 NSP  CONST_09  NQ2   CQ2  CP   CQ1  180.00   0.0  0
 NSP  CONST_10  CS1   CS   NR1  CQ1  180.00   0.0  0
 NSP  CONST_11  CS1   CS   NR2  CQ2  180.00   0.0  0
 NSP  CONST_12  CS    NR2  CQ2  NQ2  180.00   0.0  0
 NSP  CONST_13  HQ1   CQ1  CP   CQ2  180.00   0.0  0
 NSP  CONST_14  HQ21  NQ2  CQ2  CP   180.00   0.0  0
 NSP  CONST_15  HQ22  NQ2  CQ2  CP     0.00   0.0  0
 NSP  Var_01    CQ1   CP   CA   N     -5.58  30.0  2
 NSP  Var_02    HS11  CS1  CS   NR1  112.84  30.0  2
 NSP  Var_03    HN1   N    CA   CP   169.01  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
 NSP  plan-1  CA    0.020
 NSP  plan-1  CP    0.020
 NSP  plan-1  CQ1   0.020
 NSP  plan-1  CQ2   0.020
 NSP  plan-1  NR1   0.020
 NSP  plan-1  NQ2   0.020
 NSP  plan-1  NR2   0.020
 NSP  plan-1  CS    0.020
 NSP  plan-1  CS1   0.020
 NSP  plan-1  HQ1   0.020
 NSP  plan-2  CQ2   0.020
 NSP  plan-2  NQ2   0.020
 NSP  plan-2  HQ21  0.020
 NSP  plan-2  HQ22  0.020

