# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 22:59:12 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: (4R)-2,4-dimethyl-L-norleucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@@H](C)C[C@](C)(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
 66D  66D  (4R)-2,4-dimethyl-L-norleucine  L-peptide  28  11  .  2022-03-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_66D
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
 66D  N    N  NH2   0  -0.774  -0.6868  -1.5924  -0.3631
 66D  CA   C  CT    0  -0.030  -0.8449  -0.3132   0.2975
 66D  CB   C  CH2   0  -0.403   0.1927   0.7044  -0.2303
 66D  CC   C  CH1   0  -0.235   1.6670   0.5302   0.1586
 66D  CD2  C  CH3   0  -0.663   2.4165   1.7921  -0.2707
 66D  CD   C  CH2   0  -0.407   2.3152  -0.7290  -0.4210
 66D  CE   C  CH3   0  -0.671   3.7653  -0.9348   0.0017
 66D  CB2  C  CH3   0  -0.657  -0.7068  -0.5265   1.8061
 66D  C    C  C     0   0.546  -2.2168   0.3477   0.0611
 66D  O    O  O     0  -0.452  -2.6079   1.3192   0.6631
 66D  OXT  O  OH1   0  -0.584  -2.9371  -0.2419  -0.8836
 66D  H1   H  HNH2  0   0.348  -1.4257  -2.2321  -0.0980
 66D  H2   H  HNH2  0   0.346  -0.7298  -1.4941  -1.3692
 66D  H4   H  HCH2  0   0.228   0.1175   0.7406  -1.3247
 66D  H5   H  HCH2  0   0.237  -0.1134   1.6922   0.1222
 66D  H6   H  HCH1  0   0.215   1.7303   0.4688   1.2514
 66D  H7   H  HCH3  0   0.225   1.9706   2.6865   0.1677
 66D  H8   H  HCH3  0   0.232   3.4627   1.7677   0.0331
 66D  H9   H  HCH3  0   0.212   2.3920   1.9091  -1.3575
 66D  H10  H  HCH2  0   0.237   1.7294  -1.5970  -0.1204
 66D  H11  H  HCH2  0   0.197   2.2517  -0.6895  -1.5149
 66D  H12  H  HCH3  0   0.218   4.4334  -0.1706  -0.3964
 66D  H13  H  HCH3  0   0.213   3.8642  -0.9227   1.0897
 66D  H14  H  HCH3  0   0.226   4.1364  -1.8994  -0.3471
 66D  H15  H  HCH3  0   0.235  -0.7622   0.4106   2.3574
 66D  H16  H  HCH3  0   0.240  -1.4938  -1.1846   2.1807
 66D  H17  H  HCH3  0   0.244   0.2487  -0.9980   2.0290
 66D  HXT  H  HOH1  0   0.479  -3.7779   0.2282  -0.9914

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
 66D  CE   CD   single  1.524  0.020  1.524
 66D  CD   CC   single  1.530  0.020  1.530
 66D  O    C    double  1.231  0.020  1.231
 66D  CC   CD2  single  1.529  0.020  1.529
 66D  CC   CB   single  1.535  0.020  1.535
 66D  CB2  CA   single  1.530  0.020  1.530
 66D  C    CA   single  1.525  0.021  1.525
 66D  CA   CB   single  1.540  0.027  1.540
 66D  CA   N    single  1.458  0.019  1.458
 66D  C    OXT  single  1.326  0.020  1.326
 66D  N    H1   single  0.890  0.020  1.040
 66D  N    H2   single  0.890  0.020  1.040
 66D  CB   H4   single  0.970  0.020  1.090
 66D  CB   H5   single  0.970  0.020  1.090
 66D  CC   H6   single  0.970  0.020  1.090
 66D  CD2  H7   single  0.970  0.020  1.090
 66D  CD2  H8   single  0.970  0.020  1.090
 66D  CD2  H9   single  0.970  0.020  1.090
 66D  CD   H10  single  0.970  0.020  1.090
 66D  CD   H11  single  0.970  0.020  1.090
 66D  CE   H12  single  0.970  0.020  1.090
 66D  CE   H13  single  0.970  0.020  1.090
 66D  CE   H14  single  0.970  0.020  1.090
 66D  CB2  H15  single  0.970  0.020  1.090
 66D  CB2  H16  single  0.970  0.020  1.090
 66D  CB2  H17  single  0.970  0.020  1.090
 66D  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
 66D  H2   N    H1   106.90  3.000
 66D  H2   N    CA   111.30  3.000
 66D  H1   N    CA   111.03  3.000
 66D  C    CA   CB2  106.94  3.000
 66D  C    CA   CB   111.60  2.000
 66D  CB2  CA   CB   111.58  3.000
 66D  CB   CA   N    111.50  1.700
 66D  C    CA   N    111.00  2.800
 66D  CB2  CA   N    108.47  3.000
 66D  H5   CB   H4   105.82  3.000
 66D  H5   CB   CC   106.86  3.000
 66D  H4   CB   CC   108.80  3.000
 66D  H5   CB   CA   107.27  3.000
 66D  H4   CB   CA   108.43  3.000
 66D  CC   CB   CA   118.91  3.000
 66D  H6   CC   CD   107.88  3.000
 66D  H6   CC   CD2  107.32  3.000
 66D  CD   CC   CD2  111.41  3.000
 66D  H6   CC   CB   108.32  3.000
 66D  CD2  CC   CB   107.82  3.000
 66D  CD   CC   CB   113.85  3.000
 66D  H9   CD2  H8   107.53  3.000
 66D  H9   CD2  H7   107.60  3.000
 66D  H8   CD2  H7   107.37  3.000
 66D  H9   CD2  CC   110.88  3.000
 66D  H8   CD2  CC   111.95  3.000
 66D  H7   CD2  CC   111.30  3.000
 66D  H11  CD   H10  105.83  3.000
 66D  H11  CD   CE   109.67  3.000
 66D  H10  CD   CE   109.11  3.000
 66D  H11  CD   CC   108.89  3.000
 66D  H10  CD   CC   108.86  3.000
 66D  CE   CD   CC   114.14  3.000
 66D  H14  CE   H13  107.30  3.000
 66D  H14  CE   H12  107.13  3.000
 66D  H13  CE   H12  107.48  3.000
 66D  H14  CE   CD   110.75  3.000
 66D  H13  CE   CD   111.15  3.000
 66D  H12  CE   CD   112.77  3.000
 66D  H17  CB2  H16  107.53  3.000
 66D  H17  CB2  H15  108.29  3.000
 66D  H16  CB2  H15  107.96  3.000
 66D  H17  CB2  CA   109.97  3.000
 66D  H16  CB2  CA   110.93  3.000
 66D  H15  CB2  CA   112.01  3.000
 66D  OXT  C    O    122.46  3.000
 66D  OXT  C    CA   113.71  3.000
 66D  O    C    CA   120.80  1.700
 66D  HXT  OXT  C    109.56  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
 66D  CONST_01  HXT  OXT  C   CA  180.00   0.0  0
 66D  Var_01    H12  CE   CD  CC  -66.38  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
 66D  chir_01  CA  C   CB   N   positiv
 66D  chir_02  CC  CD  CD2  CB  negativ

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
 66D  plan-1  CA   0.020
 66D  plan-1  C    0.020
 66D  plan-1  O    0.020
 66D  plan-1  OXT  0.020
 66D  plan-1  HXT  0.020

