# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 15:20:11 2022
#   Inital geometry file: a 54 line input string
#   Ligand name: 3-methyl-D-valine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)[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
 TDD  TDD  '3-methyl-D-valine        '  D-peptide  21  9  .  2016-04-26  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_TDD
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
 TDD  N     N  NH2    0  -0.812  16.2163  -4.4301  -1.4185
 TDD  CA    C  CH1    0  -0.137  16.1976  -5.1707  -0.1604
 TDD  CB    C  CT     0  -0.072  16.1691  -6.7007  -0.4429
 TDD  CG1   C  CH3    0  -0.638  14.8476  -7.1259  -1.0831
 TDD  CG2   C  CH3    0  -0.647  17.3171  -7.0436  -1.3986
 TDD  CG3   C  CH3    0  -0.632  16.3826  -7.5028   0.8421
 TDD  C     C  C      0   0.388  15.0174  -4.7015   0.7286
 TDD  O     O  O      0  -0.605  14.0608  -4.1383   0.1573
 TDD  OXT   O  OC    -1  -0.604  15.1232  -4.9135   1.9542
 TDD  H     H  HNH2   0   0.332  15.8218  -3.5114  -1.2748
 TDD  H2    H  HNH2   0   0.331  17.1697  -4.2933  -1.7249
 TDD  HA    H  HCH1   0   0.179  17.1169  -4.9922   0.4204
 TDD  HG11  H  HCH3   0   0.215  14.0078  -7.0053  -0.3963
 TDD  HG12  H  HCH3   0   0.215  14.6336  -6.5465  -1.9817
 TDD  HG13  H  HCH3   0   0.207  14.8849  -8.1797  -1.3690
 TDD  HG21  H  HCH3   0   0.220  17.1972  -6.5638  -2.3706
 TDD  HG22  H  HCH3   0   0.211  18.2813  -6.7329  -0.9862
 TDD  HG23  H  HCH3   0   0.216  17.3660  -8.1216  -1.5690
 TDD  HG31  H  HCH3   0   0.204  16.4450  -8.5697   0.6153
 TDD  HG32  H  HCH3   0   0.206  17.3154  -7.2178   1.3348
 TDD  HG33  H  HCH3   0   0.223  15.5729  -7.3571   1.5543

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
 TDD  N    CA    single  1.458  0.019  1.458
 TDD  CA   CB    single  1.521  0.033  1.521
 TDD  CA   C     single  1.525  0.021  1.525
 TDD  CB   CG1   single  1.529  0.020  1.529
 TDD  CB   CG2   single  1.533  0.020  1.533
 TDD  CB   CG3   single  1.530  0.020  1.530
 TDD  C    O     deloc   1.231  0.020  1.231
 TDD  C    OXT   deloc   1.248  0.020  1.248
 TDD  N    H     single  0.860  0.020  0.860
 TDD  N    H2    single  0.890  0.020  1.040
 TDD  CA   HA    single  0.970  0.020  0.970
 TDD  CG1  HG11  single  0.970  0.020  1.090
 TDD  CG1  HG12  single  0.970  0.020  1.090
 TDD  CG1  HG13  single  0.970  0.020  1.090
 TDD  CG2  HG21  single  0.970  0.020  1.090
 TDD  CG2  HG22  single  0.970  0.020  1.090
 TDD  CG2  HG23  single  0.970  0.020  1.090
 TDD  CG3  HG31  single  0.970  0.020  1.090
 TDD  CG3  HG32  single  0.970  0.020  1.090
 TDD  CG3  HG33  single  0.970  0.020  1.090

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
 TDD  H2    N    H     106.76  3.000
 TDD  H2    N    CA    109.99  3.000
 TDD  H     N    CA    114.00  3.000
 TDD  HA    CA   C     110.00  3.000
 TDD  HA    CA   CB    109.00  3.000
 TDD  C     CA   CB    110.50  1.500
 TDD  HA    CA   N     110.00  3.000
 TDD  C     CA   N     111.00  2.800
 TDD  CB    CA   N     110.40  1.500
 TDD  CG3   CB   CG2   107.58  3.000
 TDD  CG3   CB   CG1   109.06  3.000
 TDD  CG2   CB   CG1   108.92  3.000
 TDD  CG3   CB   CA    111.13  3.000
 TDD  CG2   CB   CA    108.63  3.000
 TDD  CG1   CB   CA    111.43  3.000
 TDD  HG13  CG1  HG12  107.67  3.000
 TDD  HG13  CG1  HG11  107.31  3.000
 TDD  HG12  CG1  HG11  107.99  3.000
 TDD  HG13  CG1  CB    110.38  3.000
 TDD  HG12  CG1  CB    111.53  3.000
 TDD  HG11  CG1  CB    111.77  3.000
 TDD  HG23  CG2  HG22  107.44  3.000
 TDD  HG23  CG2  HG21  107.46  3.000
 TDD  HG22  CG2  HG21  107.94  3.000
 TDD  HG23  CG2  CB    110.58  3.000
 TDD  HG22  CG2  CB    111.20  3.000
 TDD  HG21  CG2  CB    112.03  3.000
 TDD  HG33  CG3  HG32  107.77  3.000
 TDD  HG33  CG3  HG31  108.01  3.000
 TDD  HG32  CG3  HG31  107.43  3.000
 TDD  HG33  CG3  CB    112.07  3.000
 TDD  HG32  CG3  CB    111.17  3.000
 TDD  HG31  CG3  CB    110.22  3.000
 TDD  OXT   C    O     126.22  3.000
 TDD  OXT   C    CA    120.80  1.700
 TDD  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
 TDD  Var_01  HG11  CG1  CB  CA   -66.53  30.0  3
 TDD  Var_02  HG21  CG2  CB  CA   -63.75  30.0  3
 TDD  Var_03  HG31  CG3  CB  CA  -175.19  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
 TDD  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
 TDD  plan-1  CA   0.020
 TDD  plan-1  C    0.020
 TDD  plan-1  O    0.020
 TDD  plan-1  OXT  0.020

