# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 01:23:52 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  22  11  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.848   0.5105  -0.5632  -3.1342
 CDV  CT    C  C      0   0.659   0.0599   0.1951  -2.0904
 CDV  OT    O  O      0  -0.549  -0.9130   0.9349  -2.1971
 CDV  N     N  NH1    0  -0.657   0.7695   0.0735  -0.9392
 CDV  CA    C  CH1    0  -0.132   0.1848   0.5034   0.3147
 CDV  CB    C  CH1    0  -0.272   1.2281   0.3209   1.4342
 CDV  CG1   C  CH3    0  -0.647   0.8643   1.1009   2.6924
 CDV  CG2   C  CH3    0  -0.659   1.4970  -1.1427   1.7816
 CDV  C     C  C      0   0.406  -1.1405  -0.2288   0.6341
 CDV  O     O  O      0  -0.613  -1.9267   0.3731   1.3947
 CDV  OXT   O  OC    -1  -0.606  -1.2989  -1.3577   0.1359
 CDV  HT1   H  HNH2   0   0.387   0.1971  -0.2934  -4.0513
 CDV  HT2   H  HNH2   0   0.388   1.4404  -0.9480  -3.1087
 CDV  HN1   H  HNH1   0   0.375   1.4054  -0.7066  -0.8861
 CDV  HA    H  HCH1   0   0.221  -0.0205   1.5750   0.2409
 CDV  HB    H  HCH1   0   0.223   2.1616   0.7479   1.0478
 CDV  HG11  H  HCH3   0   0.216   1.6718   1.0343   3.4230
 CDV  HG12  H  HCH3   0   0.219   0.7015   2.1576   2.4741
 CDV  HG13  H  HCH3   0   0.223  -0.0423   0.7139   3.1562
 CDV  HG21  H  HCH3   0   0.222   0.6245  -1.6134   2.2359
 CDV  HG22  H  HCH3   0   0.219   1.7777  -1.7459   0.9158
 CDV  HG23  H  HCH3   0   0.225   2.3193  -1.2129   2.4953

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  1.367  0.020  1.367
 CDV  NT   HT1   single  0.890  0.020  1.040
 CDV  NT   HT2   single  0.890  0.020  1.040
 CDV  CT   OT    double  1.227  0.020  1.227
 CDV  CT   N     single  1.358  0.020  1.358
 CDV  N    CA    single  1.458  0.019  1.458
 CDV  N    HN1   single  0.890  0.020  1.040
 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  1.528  0.020  1.528
 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     deloc   1.231  0.020  1.231
 CDV  C    OXT   deloc   1.244  0.020  1.244

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   114.42  3.000
 CDV  HT2   NT   CT    119.83  3.000
 CDV  HT1   NT   CT    116.40  3.000
 CDV  N     CT   OT    122.83  3.000
 CDV  N     CT   NT    115.18  3.000
 CDV  OT    CT   NT    121.98  3.000
 CDV  HN1   N    CA    116.02  3.000
 CDV  HN1   N    CT    116.35  3.000
 CDV  CA    N    CT    119.76  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   107.65  3.000
 CDV  HB    CB   CG1   107.14  3.000
 CDV  CG2   CB   CG1   110.15  3.000
 CDV  HB    CB   CA    105.91  3.000
 CDV  CG2   CB   CA    113.43  3.000
 CDV  CG1   CB   CA    112.17  3.000
 CDV  HG13  CG1  HG12  107.76  3.000
 CDV  HG13  CG1  HG11  108.01  3.000
 CDV  HG12  CG1  HG11  107.67  3.000
 CDV  HG13  CG1  CB    111.60  3.000
 CDV  HG12  CG1  CB    111.47  3.000
 CDV  HG11  CG1  CB    110.17  3.000
 CDV  HG23  CG2  HG22  106.82  3.000
 CDV  HG23  CG2  HG21  107.62  3.000
 CDV  HG22  CG2  HG21  107.32  3.000
 CDV  HG23  CG2  CB    110.05  3.000
 CDV  HG22  CG2  CB    113.20  3.000
 CDV  HG21  CG2  CB    111.55  3.000
 CDV  OXT   C    O     126.96  3.000
 CDV  OXT   C    CA    117.11  3.000
 CDV  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
 CDV  CONST_05  HN1   N    CT  OT   180.00   0.0  0
 CDV  Var_01    HG11  CG1  CB  CA  -174.08  30.0  3
 CDV  Var_02    HG21  CG2  CB  CA   -66.96  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

