# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 08:02:16 2022
#   Inital geometry file: a 48 line input string
#   Ligand name: 3-triazan-1-yl-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NNNC[C@H](N)C(O)=O
#
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
 RVJ  RVJ  '3-triazan-1-yl-L-alanine '  L-peptide  18  9  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_RVJ
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
 RVJ  N    N  NH2    0  -0.813  -2.3265  -2.4083   0.0608
 RVJ  CA   C  CH1    0  -0.228  -1.1345  -1.5880   0.2255
 RVJ  CB   C  CH2    0  -0.309  -1.1326  -1.0219   1.6648
 RVJ  NG   N  NH1    0  -0.469  -0.5819   0.3053   1.8886
 RVJ  ND   N  NH1    0  -0.417   0.8028   0.4612   1.6911
 RVJ  NE   N  NH2    0  -0.675   1.4980   0.2039   2.8964
 RVJ  C    C  C      0   0.433   0.1285  -2.4072  -0.1402
 RVJ  O    O  O      0  -0.592   1.2315  -1.9467   0.2382
 RVJ  H1   H  HNH2   0   0.330  -3.1350  -1.8147  -0.0729
 RVJ  H2   H  HNH2   0   0.333  -2.2241  -2.9666  -0.7758
 RVJ  HA   H  HCH1   0   0.202  -1.1315  -0.7184  -0.4581
 RVJ  HB3  H  HCH2   0   0.216  -2.1779  -0.9650   1.9830
 RVJ  HB2  H  HCH2   0   0.218  -0.6528  -1.7237   2.3534
 RVJ  H3   H  HNH1   0   0.336  -1.0478   0.9688   1.2830
 RVJ  H4   H  HNH1   0   0.355   1.1019  -0.2274   0.9992
 RVJ  H5   H  HNH2   0   0.327   1.8111  -0.7620   2.9273
 RVJ  H6   H  HNH2   0   0.343   2.3346   0.7720   2.8879
 RVJ  OXT  O  OC    -1  -0.587  -0.0345  -3.4407  -0.8112

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
 RVJ  N   CA   single  1.458  0.019  1.458
 RVJ  C   CA   single  1.525  0.021  1.525
 RVJ  C   O    deloc   1.231  0.020  1.231
 RVJ  CA  CB   single  1.521  0.033  1.521
 RVJ  CB  NG   single  1.454  0.020  1.454
 RVJ  NG  ND   single  1.407  0.020  1.407
 RVJ  ND  NE   single  1.415  0.020  1.415
 RVJ  N   H1   single  0.890  0.020  1.040
 RVJ  N   H2   single  0.890  0.020  1.040
 RVJ  CA  HA   single  0.970  0.020  0.970
 RVJ  CB  HB3  single  0.970  0.020  1.090
 RVJ  CB  HB2  single  0.970  0.020  1.090
 RVJ  NG  H3   single  0.890  0.020  1.040
 RVJ  ND  H4   single  0.890  0.020  1.040
 RVJ  NE  H5   single  0.890  0.020  1.040
 RVJ  NE  H6   single  0.890  0.020  1.040
 RVJ  C   OXT  deloc   1.243  0.020  1.243

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
 RVJ  H2   N   H1   107.19  3.000
 RVJ  H2   N   CA   108.77  3.000
 RVJ  H1   N   CA   109.79  3.000
 RVJ  HA   CA  C    109.00  3.000
 RVJ  HA   CA  CB   109.00  3.000
 RVJ  C    CA  CB   110.50  1.500
 RVJ  HA   CA  N    110.00  3.000
 RVJ  CB   CA  N    110.40  1.500
 RVJ  C    CA  N    111.00  2.800
 RVJ  HB2  CB  HB3  105.62  3.000
 RVJ  HB2  CB  NG   108.81  3.000
 RVJ  HB3  CB  NG   105.64  3.000
 RVJ  HB2  CB  CA   110.58  3.000
 RVJ  HB3  CB  CA   106.77  3.000
 RVJ  NG   CB  CA   118.54  3.000
 RVJ  H3   NG  ND   107.24  3.000
 RVJ  H3   NG  CB   109.38  3.000
 RVJ  ND   NG  CB   116.88  3.000
 RVJ  H4   ND  NE   108.10  3.000
 RVJ  H4   ND  NG   107.98  3.000
 RVJ  NE   ND  NG   110.11  3.000
 RVJ  H6   NE  H5   106.23  3.000
 RVJ  H6   NE  ND   107.29  3.000
 RVJ  H5   NE  ND   110.50  3.000
 RVJ  OXT  C   O    125.72  3.000
 RVJ  OXT  C   CA   117.40  3.000
 RVJ  O    C   CA   120.80  1.700

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
 RVJ  Var_01  ND  NG  CB  CA  -67.11  30.0  3
 RVJ  Var_02  NE  ND  NG  CB  -89.71  30.0  2
 RVJ  Var_03  H5  NE  ND  NG   94.77  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
 RVJ  chir_01  CA  N  C  CB  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
 RVJ  plan-1  CA   0.020
 RVJ  plan-1  C    0.020
 RVJ  plan-1  O    0.020
 RVJ  plan-1  OXT  0.020

