# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 23:03:35 2022
#   Inital geometry file: a 56 line input string
#   Ligand name: 3-(N''-hydroxycarbamimidamido)-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CN\C(N)=N\O)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
 DIR  DIR  3-(N''-hydroxycarbamimidamido)-L-alanine  L-peptide  20  11  .  2012-08-28  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_DIR
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
 DIR  CA    C  CH1    0  -0.237  -5.1342  47.6452   9.8994
 DIR  CB    C  CH2    0  -0.252  -4.1406  46.5321   9.5620
 DIR  N     N  NH2    0  -0.812  -5.0035  48.6876   8.8943
 DIR  C     C  C      0   0.432  -4.9378  48.2205  11.3249
 DIR  NG    N  NH1    0  -0.669  -4.3635  45.3668  10.3882
 DIR  CD    C  C      0   0.585  -3.6135  44.2379  10.1981
 DIR  OXT   O  OC    -1  -0.585  -5.0747  49.4467  11.4707
 DIR  O     O  O      0  -0.601  -4.6959  47.3901  12.2325
 DIR  NH1   N  N      0  -0.305  -2.8468  44.1486   9.1665
 DIR  NH2   N  NH2    0  -0.842  -3.7425  43.2826  11.1762
 DIR  OH1   O  OH1    0  -0.605  -2.2445  42.8796   9.1115
 DIR  HA    H  HCH1   0   0.204  -6.1392  47.1875   9.9019
 DIR  HB2   H  HCH2   0   0.218  -4.2716  46.2538   8.5135
 DIR  HB3   H  HCH2   0   0.198  -3.1159  46.9182   9.6527
 DIR  H     H  HNH2   0   0.336  -5.4215  49.5347   9.2552
 DIR  H2    H  HNH2   0   0.333  -5.5214  48.4312   8.0640
 DIR  HG    H  HNH1   0   0.379  -4.4826  45.6540  11.3568
 DIR  HH21  H  HNH2   0   0.384  -3.4367  42.3586  10.9176
 DIR  HH22  H  HNH2   0   0.381  -4.6305  43.2766  11.6528
 DIR  HH1   H  HOH1   0   0.458  -1.8782  42.8510   8.2243

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
 DIR  CA   CB    single  1.530  0.020  1.530
 DIR  CA   N     single  1.458  0.019  1.458
 DIR  CA   C     single  1.525  0.021  1.525
 DIR  CA   HA    single  0.970  0.020  0.970
 DIR  CB   NG    single  1.446  0.020  1.446
 DIR  CB   HB2   single  0.970  0.020  1.090
 DIR  CB   HB3   single  0.970  0.020  1.090
 DIR  N    H     single  0.860  0.020  0.860
 DIR  N    H2    single  0.890  0.020  1.040
 DIR  C    OXT   deloc   1.242  0.020  1.242
 DIR  C    O     deloc   1.231  0.020  1.231
 DIR  NG   CD    single  1.369  0.020  1.369
 DIR  NG   HG    single  0.890  0.020  1.040
 DIR  CD   NH1   double  1.288  0.020  1.288
 DIR  CD   NH2   single  1.373  0.020  1.373
 DIR  NH1  OH1   single  1.406  0.020  1.406
 DIR  NH2  HH21  single  0.890  0.020  1.040
 DIR  NH2  HH22  single  0.890  0.020  1.040
 DIR  OH1  HH1   single  0.850  0.020  0.980

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
 DIR  HA    CA   C     109.00  3.000
 DIR  HA    CA   N     110.00  3.000
 DIR  C     CA   N     111.00  2.800
 DIR  HA    CA   CB    109.00  3.000
 DIR  C     CA   CB    110.10  1.900
 DIR  N     CA   CB    110.50  1.700
 DIR  HB3   CB   HB2   106.29  3.000
 DIR  HB3   CB   NG    112.32  3.000
 DIR  HB2   CB   NG    108.94  3.000
 DIR  HB3   CB   CA    109.38  3.000
 DIR  HB2   CB   CA    108.61  3.000
 DIR  NG    CB   CA    111.12  3.000
 DIR  H2    N    H     107.07  3.000
 DIR  H2    N    CA    109.86  3.000
 DIR  H     N    CA    114.00  3.000
 DIR  O     C    OXT   126.16  3.000
 DIR  O     C    CA    120.80  1.700
 DIR  OXT   C    CA    117.41  3.000
 DIR  HG    NG   CD    115.43  3.000
 DIR  HG    NG   CB    109.55  3.000
 DIR  CD    NG   CB    120.06  3.000
 DIR  NH2   CD   NH1   125.31  3.000
 DIR  NH2   CD   NG    115.05  3.000
 DIR  NH1   CD   NG    119.64  3.000
 DIR  OH1   NH1  CD    110.42  3.000
 DIR  HH22  NH2  HH21  112.56  3.000
 DIR  HH22  NH2  CD    115.07  3.000
 DIR  HH21  NH2  CD    115.27  3.000
 DIR  HH1   OH1  NH1   103.09  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
 DIR  CONST_01  NH1  CD   NG  CB     0.00   0.0  0
 DIR  CONST_02  NH2  CD   NG  CB   180.00   0.0  0
 DIR  CONST_03  OH1  NH1  CD  NG   180.00   0.0  0
 DIR  CONST_04  OH1  NH1  CD  NH2    0.00   0.0  0
 DIR  Var_01    CD   NG   CB  CA   177.08  30.0  3

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
 DIR  chir_01  CA  CB  N  C  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
 DIR  plan-1  CB    0.020
 DIR  plan-1  NG    0.020
 DIR  plan-1  CD    0.020
 DIR  plan-1  NH1   0.020
 DIR  plan-1  NH2   0.020
 DIR  plan-1  OH1   0.020
 DIR  plan-1  HG    0.020
 DIR  plan-1  HH21  0.020
 DIR  plan-1  HH22  0.020
 DIR  plan-2  CA    0.020
 DIR  plan-2  C     0.020
 DIR  plan-2  OXT   0.020
 DIR  plan-2  O     0.020

