# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 18:18:17 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: N-carbamoyl-D-valine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@@H](NC(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
 CDV  CDV  'N-carbamoyl-D-valine     '  L-peptide  23  11  .  2022-03-15  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_CDV
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
 CDV  NT    N  NH2   0  -0.846   0.5926  -0.3600  -3.2278
 CDV  CT    C  C     0   0.686  -0.0210   0.1064  -2.1092
 CDV  OT    O  O     0  -0.542  -1.1261   0.6415  -2.1260
 CDV  N     N  NH1   0  -0.678   0.6843  -0.0221  -0.9574
 CDV  CA    C  CH1   0  -0.108   0.1773   0.5179   0.2730
 CDV  CB    C  CH1   0  -0.307   1.2123   0.3168   1.4012
 CDV  CG1   C  CH3   0  -0.653   0.8327   1.0845   2.6620
 CDV  CG2   C  CH3   0  -0.656   1.5013  -1.1466   1.7263
 CDV  C     C  C     0   0.535  -1.1746  -0.0689   0.6421
 CDV  O     O  O     0  -0.447  -2.0203   0.5491   1.2412
 CDV  OXT   O  OH1   0  -0.583  -1.3122  -1.3377   0.2891
 CDV  HT1   H  HNH2  0   0.397   0.0229  -0.4758  -4.0487
 CDV  HT2   H  HNH2  0   0.396   1.3766  -0.9869  -3.1565
 CDV  HN1   H  HNH1  0   0.399   1.6019  -0.4366  -0.9654
 CDV  HA    H  HCH1  0   0.279   0.0166   1.5964   0.1763
 CDV  HB    H  HCH1  0   0.257   2.1334   0.7658   1.0131
 CDV  HG11  H  HCH3  0   0.236   1.6520   1.0387   3.3793
 CDV  HG12  H  HCH3  0   0.234   0.6341   2.1359   2.4514
 CDV  HG13  H  HCH3  0   0.226  -0.0492   0.6660   3.1485
 CDV  HG21  H  HCH3  0   0.227   0.6494  -1.6333   2.2024
 CDV  HG22  H  HCH3  0   0.230   1.7697  -1.7328   0.8464
 CDV  HG23  H  HCH3  0   0.238   2.3400  -1.2075   2.4204
 CDV  HXT   H  HOH1  0   0.479  -2.1790  -1.6631   0.5753

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
 CDV  NT   CT    single  1.358  0.020  1.358
 CDV  NT   HT1   single  0.890  0.020  1.040
 CDV  NT   HT2   single  0.890  0.020  1.040
 CDV  CT   OT    double  1.228  0.020  1.228
 CDV  CT   N     single  1.357  0.020  1.357
 CDV  N    CA    single  1.458  0.019  1.458
 CDV  N    HN1   single  0.860  0.020  1.020
 CDV  CA   CB    single  1.521  0.033  1.521
 CDV  CA   C     single  1.525  0.021  1.525
 CDV  CA   HA    single  0.970  0.020  0.970
 CDV  CB   CG1   single  1.524  0.020  1.524
 CDV  CB   CG2   single  1.527  0.020  1.527
 CDV  CB   HB    single  0.970  0.020  1.090
 CDV  CG1  HG11  single  0.970  0.020  1.090
 CDV  CG1  HG12  single  0.970  0.020  1.090
 CDV  CG1  HG13  single  0.970  0.020  1.090
 CDV  CG2  HG21  single  0.970  0.020  1.090
 CDV  CG2  HG22  single  0.970  0.020  1.090
 CDV  CG2  HG23  single  0.970  0.020  1.090
 CDV  C    O     double  1.231  0.020  1.231
 CDV  C    OXT   single  1.324  0.020  1.324
 CDV  OXT  HXT   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
 CDV  HT2   NT   HT1   115.30  3.000
 CDV  HT2   NT   CT    120.50  3.000
 CDV  HT1   NT   CT    117.11  3.000
 CDV  N     CT   OT    121.38  3.000
 CDV  N     CT   NT    115.57  3.000
 CDV  OT    CT   NT    123.02  3.000
 CDV  HN1   N    CA    118.90  3.000
 CDV  HN1   N    CT    120.40  3.000
 CDV  CA    N    CT    120.54  3.000
 CDV  HA    CA   C     110.00  3.000
 CDV  HA    CA   CB    109.00  3.000
 CDV  C     CA   CB    110.50  1.500
 CDV  HA    CA   N     110.00  3.000
 CDV  C     CA   N     111.00  2.800
 CDV  CB    CA   N     110.40  1.500
 CDV  HB    CB   CG2   108.01  3.000
 CDV  HB    CB   CG1   107.21  3.000
 CDV  CG2   CB   CG1   110.72  3.000
 CDV  HB    CB   CA    104.56  3.000
 CDV  CG2   CB   CA    114.03  3.000
 CDV  CG1   CB   CA    111.83  3.000
 CDV  HG13  CG1  HG12  107.99  3.000
 CDV  HG13  CG1  HG11  107.35  3.000
 CDV  HG12  CG1  HG11  107.73  3.000
 CDV  HG13  CG1  CB    112.15  3.000
 CDV  HG12  CG1  CB    111.79  3.000
 CDV  HG11  CG1  CB    109.63  3.000
 CDV  HG23  CG2  HG22  107.10  3.000
 CDV  HG23  CG2  HG21  107.34  3.000
 CDV  HG22  CG2  HG21  107.73  3.000
 CDV  HG23  CG2  CB    109.56  3.000
 CDV  HG22  CG2  CB    112.95  3.000
 CDV  HG21  CG2  CB    111.89  3.000
 CDV  OXT   C    O     123.39  3.000
 CDV  OXT   C    CA    120.80  1.700
 CDV  O     C    CA    120.80  1.700
 CDV  HXT   OXT  C     109.63  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
 CDV  CONST_01  CA    N    CT  OT     0.00   0.0  0
 CDV  CONST_02  CA    N    CT  NT   180.00   0.0  0
 CDV  CONST_05  HN1   N    CT  OT   180.00   0.0  0
 CDV  CONST_06  HXT   OXT  C   CA   180.00   0.0  0
 CDV  Var_01    HG11  CG1  CB  CA  -171.73  30.0  3
 CDV  Var_02    HG21  CG2  CB  CA   -69.38  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
 CDV  chir_01  CA  N  CB  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
 CDV  plan-1  NT   0.020
 CDV  plan-1  CT   0.020
 CDV  plan-1  OT   0.020
 CDV  plan-1  N    0.020
 CDV  plan-1  CA   0.020
 CDV  plan-1  HT1  0.020
 CDV  plan-1  HT2  0.020
 CDV  plan-1  HN1  0.020
 CDV  plan-2  CA   0.020
 CDV  plan-2  C    0.020
 CDV  plan-2  O    0.020
 CDV  plan-2  OXT  0.020
 CDV  plan-2  HXT  0.020

