# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 19:17:01 2022
#   Inital geometry file: a 60 line input string
#   Ligand name: N-methyl-D-leucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN[C@H](CC(C)C)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
 MLU  MLU  'N-methyl-D-leucine       '  D-peptide  24  10  .  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
;

data_comp_MLU
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
 MLU  N     N  NH1    0  -0.585  20.6775  25.4196  26.3488
 MLU  CN    C  CH3    0  -0.519  20.5187  25.7145  24.9390
 MLU  CA    C  CH1    0  -0.180  19.5052  25.7641  27.1432
 MLU  C     C  C      0   0.389  18.2506  24.9283  26.7870
 MLU  O     O  O      0  -0.612  18.4310  23.6960  26.6813
 MLU  CB    C  CH2    0  -0.402  19.8640  25.5840  28.6207
 MLU  CG    C  CH1    0  -0.236  18.7663  25.8962  29.6393
 MLU  CD1   C  CH3    0  -0.647  19.2905  25.6462  31.0509
 MLU  CD2   C  CH3    0  -0.657  18.2407  27.3225  29.5138
 MLU  OXT   O  OC    -1  -0.607  17.1691  25.5364  26.6525
 MLU  H     H  HNH1   0   0.323  20.8234  24.4212  26.4493
 MLU  HCN1  H  HCH3   0   0.222  21.4103  25.4011  24.3941
 MLU  HCN2  H  HCH3   0   0.188  19.6549  25.2339  24.4589
 MLU  HCN3  H  HCH3   0   0.213  20.4129  26.7919  24.7953
 MLU  HA    H  HCH1   0   0.196  19.2900  26.8221  26.9570
 MLU  HB2   H  HCH2   0   0.203  20.1897  24.5476  28.7705
 MLU  HB3   H  HCH2   0   0.203  20.7354  26.2115  28.8411
 MLU  HG    H  HCH1   0   0.211  17.9289  25.2103  29.4713
 MLU  HD11  H  HCH3   0   0.220  18.5128  25.8116  31.7989
 MLU  HD12  H  HCH3   0   0.219  19.6527  24.6230  31.1691
 MLU  HD13  H  HCH3   0   0.209  20.1197  26.3189  31.2837
 MLU  HD21  H  HCH3   0   0.218  17.5104  27.5390  30.2961
 MLU  HD22  H  HCH3   0   0.206  19.0521  28.0485  29.6114
 MLU  HD23  H  HCH3   0   0.226  17.7528  27.4867  28.5539

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
 MLU  N    CN    single  1.449  0.020  1.449
 MLU  N    CA    single  1.458  0.019  1.458
 MLU  CA   C     single  1.525  0.021  1.525
 MLU  CA   CB    single  1.521  0.033  1.521
 MLU  C    O     deloc   1.231  0.020  1.231
 MLU  C    OXT   deloc   1.248  0.020  1.248
 MLU  CB   CG    single  1.530  0.020  1.530
 MLU  CG   CD1   single  1.526  0.020  1.526
 MLU  CG   CD2   single  1.525  0.020  1.525
 MLU  N    H     single  0.860  0.020  0.860
 MLU  CN   HCN1  single  0.970  0.020  1.090
 MLU  CN   HCN2  single  0.970  0.020  1.090
 MLU  CN   HCN3  single  0.970  0.020  1.090
 MLU  CA   HA    single  0.970  0.020  0.970
 MLU  CB   HB2   single  0.970  0.020  1.090
 MLU  CB   HB3   single  0.970  0.020  1.090
 MLU  CG   HG    single  0.970  0.020  1.090
 MLU  CD1  HD11  single  0.970  0.020  1.090
 MLU  CD1  HD12  single  0.970  0.020  1.090
 MLU  CD1  HD13  single  0.970  0.020  1.090
 MLU  CD2  HD21  single  0.970  0.020  1.090
 MLU  CD2  HD22  single  0.970  0.020  1.090
 MLU  CD2  HD23  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
 MLU  H     N    CA    114.00  3.000
 MLU  H     N    CN    108.22  3.000
 MLU  CA    N    CN    113.20  3.000
 MLU  HCN3  CN   HCN2  107.33  3.000
 MLU  HCN3  CN   HCN1  107.27  3.000
 MLU  HCN2  CN   HCN1  107.37  3.000
 MLU  HCN3  CN   N     109.85  3.000
 MLU  HCN2  CN   N     114.98  3.000
 MLU  HCN1  CN   N     109.75  3.000
 MLU  HA    CA   CB    109.00  3.000
 MLU  HA    CA   C     110.00  3.000
 MLU  CB    CA   C     110.50  1.500
 MLU  HA    CA   N     110.00  3.000
 MLU  CB    CA   N     110.40  1.500
 MLU  C     CA   N     111.00  2.800
 MLU  OXT   C    O     126.61  3.000
 MLU  OXT   C    CA    120.80  1.700
 MLU  O     C    CA    120.80  1.700
 MLU  HB3   CB   HB2   106.11  3.000
 MLU  HB3   CB   CG    108.65  3.000
 MLU  HB2   CB   CG    108.37  3.000
 MLU  HB3   CB   CA    108.24  3.000
 MLU  HB2   CB   CA    108.21  3.000
 MLU  CG    CB   CA    116.77  3.000
 MLU  HG    CG   CD2   108.03  3.000
 MLU  HG    CG   CD1   107.56  3.000
 MLU  CD2   CG   CD1   110.34  3.000
 MLU  HG    CG   CB    108.58  3.000
 MLU  CD2   CG   CB    112.54  3.000
 MLU  CD1   CG   CB    109.63  3.000
 MLU  HD13  CD1  HD12  107.59  3.000
 MLU  HD13  CD1  HD11  107.54  3.000
 MLU  HD12  CD1  HD11  107.71  3.000
 MLU  HD13  CD1  CG    110.89  3.000
 MLU  HD12  CD1  CG    111.56  3.000
 MLU  HD11  CD1  CG    111.36  3.000
 MLU  HD23  CD2  HD22  108.13  3.000
 MLU  HD23  CD2  HD21  107.56  3.000
 MLU  HD22  CD2  HD21  107.51  3.000
 MLU  HD23  CD2  CG    111.58  3.000
 MLU  HD22  CD2  CG    110.97  3.000
 MLU  HD21  CD2  CG    110.92  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
 MLU  Var_01  CD1   CG   CB  CA   179.28  30.0  3
 MLU  Var_02  HCN1  CN   N   CA  -177.87  30.0  3
 MLU  Var_03  HD11  CD1  CG  CB  -177.10  30.0  3
 MLU  Var_04  HD21  CD2  CG  CB  -176.02  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
 MLU  chir_01  CA  N  C  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
 MLU  plan-1  CA   0.020
 MLU  plan-1  C    0.020
 MLU  plan-1  O    0.020
 MLU  plan-1  OXT  0.020

