# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 13:04:13 2020
#   Inital geometry file: a 51 line input string
#   Ligand name: (3S)-3-methyl-L-aspartic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]([C@H](N)C(O)=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
 3MD  3MD  '(3S)-3-methyl-L-aspartic acid'  L-peptide  17  10  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3MD
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
 3MD  N     N  NH2    0  -0.809   1.5675   0.9852  -0.3812
 3MD  CB    C  CH1    0  -0.389  -0.4830  -0.1746   0.5287
 3MD  CG    C  C      0   0.425   0.0026  -0.3637   1.9860
 3MD  OD1   O  O      0  -0.608   1.2174  -0.5821   2.1846
 3MD  OD2   O  OC    -1  -0.620  -0.8753  -0.3082   2.8729
 3MD  CA    C  CH1    0  -0.183   0.6550  -0.1411  -0.5077
 3MD  CB1   C  CH3    0  -0.663  -1.4034   1.0401   0.4185
 3MD  C     C  C      0   0.402   0.0575  -0.2123  -1.9278
 3MD  O     O  O      0  -0.614   0.1430   0.8010  -2.6517
 3MD  OXT   O  OC    -1  -0.626  -0.4951  -1.2901  -2.2368
 3MD  H     H  HNH2   0   0.320   1.1100   1.8235  -0.7141
 3MD  H2    H  HNH2   0   0.325   1.7809   1.1188   0.5988
 3MD  HB    H  HCH1   0   0.213  -1.0894  -1.0606   0.3010
 3MD  HA    H  HCH1   0   0.193   1.2412  -1.0556  -0.3638
 3MD  HB11  H  HCH3   0   0.200  -0.8633   1.9706   0.6097
 3MD  HB12  H  HCH3   0   0.214  -1.8525   1.1225  -0.5726
 3MD  HB13  H  HCH3   0   0.220  -2.2133   0.9786   1.1427

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
 3MD  N    CA    single  1.458  0.019  1.458
 3MD  N    H     single  0.860  0.020  0.860
 3MD  N    H2    single  0.890  0.020  1.040
 3MD  CB   CG    single  1.548  0.020  1.548
 3MD  CB   CA    single  1.530  0.020  1.530
 3MD  CB   CB1   single  1.528  0.020  1.528
 3MD  CB   HB    single  0.970  0.020  1.090
 3MD  CG   OD1   deloc   1.250  0.020  1.250
 3MD  CG   OD2   deloc   1.249  0.020  1.249
 3MD  CA   C     single  1.525  0.021  1.525
 3MD  CA   HA    single  0.970  0.020  0.970
 3MD  CB1  HB11  single  0.970  0.020  1.090
 3MD  CB1  HB12  single  0.970  0.020  1.090
 3MD  CB1  HB13  single  0.970  0.020  1.090
 3MD  C    O     deloc   1.231  0.020  1.231
 3MD  C    OXT   deloc   1.250  0.020  1.250

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
 3MD  H2    N    H     107.74  3.000
 3MD  H2    N    CA    108.58  3.000
 3MD  H     N    CA    114.00  3.000
 3MD  HB    CB   CB1   107.10  3.000
 3MD  HB    CB   CA    106.64  3.000
 3MD  CB1   CB   CA    112.29  3.000
 3MD  HB    CB   CG    105.67  3.000
 3MD  CB1   CB   CG    110.73  3.000
 3MD  CA    CB   CG    113.86  3.000
 3MD  OD2   CG   OD1   125.30  3.000
 3MD  OD2   CG   CB    116.27  3.000
 3MD  OD1   CG   CB    118.41  3.000
 3MD  HA    CA   C     109.00  3.000
 3MD  HA    CA   CB    109.00  3.000
 3MD  C     CA   CB    110.10  1.900
 3MD  HA    CA   N     110.00  3.000
 3MD  C     CA   N     111.00  2.800
 3MD  CB    CA   N     110.50  1.700
 3MD  HB13  CB1  HB12  107.60  3.000
 3MD  HB13  CB1  HB11  107.44  3.000
 3MD  HB12  CB1  HB11  107.34  3.000
 3MD  HB13  CB1  CB    110.81  3.000
 3MD  HB12  CB1  CB    111.92  3.000
 3MD  HB11  CB1  CB    111.51  3.000
 3MD  OXT   C    O     125.93  3.000
 3MD  OXT   C    CA    116.02  3.000
 3MD  O     C    CA    120.80  1.700

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
 3MD  chir_01  CB  CG  CA  CB1  positiv
 3MD  chir_02  CA  N   CB  C    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
 3MD  plan-1  CB   0.020
 3MD  plan-1  CG   0.020
 3MD  plan-1  OD1  0.020
 3MD  plan-1  OD2  0.020
 3MD  plan-2  CA   0.020
 3MD  plan-2  C    0.020
 3MD  plan-2  O    0.020
 3MD  plan-2  OXT  0.020

