# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:43:40 2022
#   Inital geometry file: a 54 line input string
#   Ligand name: [(2~{S})-4-azanyl-1,4-bis(oxidanylidene)butan-2-yl]carbamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)C[C@H](NC(O)=O)C=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
 5VV  5VV  '[(2~{S})-4-azanyl-1,4-bis(oxidanylidene)butan-2-yl]carbamic acid'  L-peptide  18  11  .  2019-03-22  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_5VV
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
 5VV  N    N  NH1    0  -0.679  -13.2664  -15.6659  37.6465
 5VV  C9   C  C      0   0.524  -12.2874  -16.5176  38.1995
 5VV  O10  O  OC    -1  -0.613  -12.1914  -16.4709  39.4508
 5VV  O11  O  O      0  -0.619  -11.6519  -17.2414  37.4158
 5VV  CA   C  CH1    0  -0.130  -13.7121  -14.5702  38.4637
 5VV  CB   C  CH2    0  -0.605  -14.9233  -13.8772  37.8412
 5VV  CG   C  C      0   0.523  -14.6194  -13.1774  36.5280
 5VV  ND2  N  NH2    0  -0.802  -15.6958  -12.9379  35.7643
 5VV  OD1  O  O      0  -0.482  -13.4896  -12.8372  36.2111
 5VV  C    C  C1     0   0.187  -14.1672  -15.1172  39.7989
 5VV  O    O  O      0  -0.415  -14.1166  -14.4981  40.8360
 5VV  H1   H  HNH1   0   0.356  -13.1288  -15.4521  36.6707
 5VV  H3   H  HCH1   0   0.228  -12.9352  -13.8177  38.6540
 5VV  H4   H  HCH2   0   0.290  -15.2958  -13.1118  38.5298
 5VV  H5   H  HCH2   0   0.265  -15.7382  -14.5938  37.7055
 5VV  H6   H  HNH2   0   0.398  -15.6055  -12.4218  34.9042
 5VV  H7   H  HNH2   0   0.407  -16.6200  -13.2191  36.0428
 5VV  H8   H  H      0   0.166  -14.7183  -16.0725  39.7208

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
 5VV  ND2  CG   single  1.341  0.020  1.341
 5VV  OD1  CG   double  1.222  0.020  1.222
 5VV  CG   CB   single  1.519  0.020  1.519
 5VV  O11  C9   deloc   1.242  0.020  1.242
 5VV  CB   CA   single  1.530  0.020  1.530
 5VV  N    C9   single  1.411  0.020  1.411
 5VV  N    CA   single  1.458  0.019  1.458
 5VV  C9   O10  deloc   1.256  0.020  1.256
 5VV  CA   C    single  1.525  0.021  1.525
 5VV  C    O    double  1.231  0.020  1.231
 5VV  N    H1   single  0.890  0.020  1.040
 5VV  CA   H3   single  0.970  0.020  1.090
 5VV  CB   H4   single  0.970  0.020  1.090
 5VV  CB   H5   single  0.970  0.020  1.090
 5VV  ND2  H6   single  0.860  0.020  1.020
 5VV  ND2  H7   single  0.860  0.020  1.020
 5VV  C    H8   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
 5VV  H1   N    CA   115.51  3.000
 5VV  H1   N    C9   114.37  3.000
 5VV  CA   N    C9   116.91  3.000
 5VV  O11  C9   O10  127.69  3.000
 5VV  O10  C9   N    114.91  3.000
 5VV  O11  C9   N    117.37  3.000
 5VV  H3   CA   C    107.92  3.000
 5VV  H3   CA   CB   108.70  3.000
 5VV  C    CA   CB   110.10  1.900
 5VV  H3   CA   N    113.66  3.000
 5VV  C    CA   N    111.00  2.800
 5VV  CB   CA   N    110.50  1.700
 5VV  H5   CB   H4   106.42  3.000
 5VV  H5   CB   CG   110.11  3.000
 5VV  H4   CB   CG   106.84  3.000
 5VV  H5   CB   CA   110.12  3.000
 5VV  H4   CB   CA   109.30  3.000
 5VV  CG   CB   CA   113.74  3.000
 5VV  OD1  CG   ND2  123.00  3.000
 5VV  OD1  CG   CB   122.53  3.000
 5VV  ND2  CG   CB   114.45  3.000
 5VV  H7   ND2  H6   117.53  3.000
 5VV  H7   ND2  CG   122.01  3.000
 5VV  H6   ND2  CG   120.39  3.000
 5VV  H8   C    O    121.60  3.000
 5VV  H8   C    CA   113.58  3.000
 5VV  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
 5VV  CONST_01  H6   ND2  CG  CB   180.00   0.0  0
 5VV  CONST_02  H7   ND2  CG  CB     0.00   0.0  0
 5VV  Var_01    CA   N    C9  O10   19.67  30.0  2
 5VV  Var_02    ND2  CG   CB  CA   159.87  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
 5VV  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
 5VV  plan-1  CB   0.020
 5VV  plan-1  CG   0.020
 5VV  plan-1  ND2  0.020
 5VV  plan-1  OD1  0.020
 5VV  plan-1  H6   0.020
 5VV  plan-1  H7   0.020
 5VV  plan-2  N    0.020
 5VV  plan-2  C9   0.020
 5VV  plan-2  O10  0.020
 5VV  plan-2  O11  0.020
 5VV  plan-3  CA   0.020
 5VV  plan-3  C    0.020
 5VV  plan-3  O    0.020
 5VV  plan-3  H8   0.020

