# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 06:16:55 2022
#   Inital geometry file: a 58 line input string
#   Ligand name: (4R)-5-amino-L-leucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](CN)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
 Y1V  Y1V  '(4R)-5-amino-L-leucine   '  L-peptide  23  10  .  2022-08-11  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_Y1V
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
 Y1V  C     C  C      0   0.385  6.2444  17.0132  -4.9697
 Y1V  O     O  O      0  -0.604  6.9772  17.7204  -5.6904
 Y1V  CB    C  CH2    0  -0.391  5.4637  14.7118  -5.5960
 Y1V  CG    C  CH1    0  -0.223  4.4482  13.7599  -6.2300
 Y1V  CD    C  CH2    0  -0.290  3.0360  13.9118  -5.6664
 Y1V  NE    N  NH2    0  -0.801  2.9785  13.6930  -4.2270
 Y1V  CM    C  CH3    0  -0.663  4.9412  12.3180  -6.1193
 Y1V  CQ    C  CH1    0  -0.221  5.1215  16.2031  -5.6690
 Y1V  NA    N  NH2    0  -0.786  4.8403  16.5903  -7.0441
 Y1V  O1    O  OC    -1  -0.619  6.3299  16.8720  -3.7311
 Y1V  HB3   H  HCH2   0   0.206  5.6067  14.4412  -4.5481
 Y1V  HB2   H  HCH2   0   0.200  6.4337  14.5489  -6.0840
 Y1V  HG2   H  HCH1   0   0.208  4.3743  14.0043  -7.2940
 Y1V  HD2   H  HCH2   0   0.219  2.6795  14.9250  -5.8667
 Y1V  HD3   H  HCH2   0   0.193  2.3710  13.2414  -6.2321
 Y1V  H     H  HNH2   0   0.343  2.0410  13.8816  -3.8967
 Y1V  H1    H  HNH2   0   0.338  3.1432  12.7154  -4.0237
 Y1V  HM11  H  HCH3   0   0.219  4.2430  11.6199  -6.5860
 Y1V  HM1   H  HCH3   0   0.224  5.9073  12.1955  -6.6123
 Y1V  HM2   H  HCH3   0   0.210  5.0734  12.0114  -5.0789
 Y1V  HA    H  HCH1   0   0.205  4.2040  16.3629  -5.0913
 Y1V  HN1   H  HNH2   0   0.329  4.5301  17.5546  -7.0513
 Y1V  HN3   H  HNH2   0   0.319  5.7201  16.6083  -7.5483

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
 Y1V  NA  CQ    single  1.456  0.020  1.456
 Y1V  CM  CG    single  1.528  0.020  1.528
 Y1V  CG  CB    single  1.530  0.020  1.530
 Y1V  CG  CD    single  1.528  0.020  1.528
 Y1V  CQ  CB    single  1.532  0.020  1.532
 Y1V  CQ  C     single  1.551  0.020  1.551
 Y1V  CD  NE    single  1.457  0.020  1.457
 Y1V  O   C     deloc   1.231  0.020  1.231
 Y1V  C   O1    deloc   1.249  0.020  1.249
 Y1V  CB  HB3   single  0.970  0.020  1.090
 Y1V  CB  HB2   single  0.970  0.020  1.090
 Y1V  CG  HG2   single  0.970  0.020  1.090
 Y1V  CD  HD2   single  0.970  0.020  1.090
 Y1V  CD  HD3   single  0.970  0.020  1.090
 Y1V  NE  H     single  0.890  0.020  1.040
 Y1V  NE  H1    single  0.890  0.020  1.040
 Y1V  CM  HM11  single  0.970  0.020  1.090
 Y1V  CM  HM1   single  0.970  0.020  1.090
 Y1V  CM  HM2   single  0.970  0.020  1.090
 Y1V  CQ  HA    single  0.970  0.020  1.090
 Y1V  NA  HN1   single  0.890  0.020  1.040
 Y1V  NA  HN3   single  0.890  0.020  1.040

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
 Y1V  O1    C   CQ    115.94  3.000
 Y1V  O1    C   O     126.62  3.000
 Y1V  CQ    C   O     117.43  3.000
 Y1V  HB2   CB  HB3   105.92  3.000
 Y1V  HB2   CB  CQ    108.70  3.000
 Y1V  HB3   CB  CQ    108.44  3.000
 Y1V  HB2   CB  CG    108.06  3.000
 Y1V  HB3   CB  CG    109.30  3.000
 Y1V  CQ    CB  CG    115.96  3.000
 Y1V  HG2   CG  CM    107.63  3.000
 Y1V  HG2   CG  CD    105.91  3.000
 Y1V  CM    CG  CD    111.43  3.000
 Y1V  HG2   CG  CB    108.00  3.000
 Y1V  CD    CG  CB    113.51  3.000
 Y1V  CM    CG  CB    110.06  3.000
 Y1V  HD3   CD  HD2   105.87  3.000
 Y1V  HD3   CD  NE    113.10  3.000
 Y1V  HD2   CD  NE    107.91  3.000
 Y1V  HD3   CD  CG    107.95  3.000
 Y1V  HD2   CD  CG    109.03  3.000
 Y1V  NE    CD  CG    112.70  3.000
 Y1V  H1    NE  H     105.38  3.000
 Y1V  H1    NE  CD    109.70  3.000
 Y1V  H     NE  CD    109.33  3.000
 Y1V  HM2   CM  HM1   106.94  3.000
 Y1V  HM2   CM  HM11  107.75  3.000
 Y1V  HM1   CM  HM11  107.53  3.000
 Y1V  HM2   CM  CG    111.89  3.000
 Y1V  HM1   CM  CG    111.03  3.000
 Y1V  HM11  CM  CG    111.47  3.000
 Y1V  HA    CQ  NA    107.30  3.000
 Y1V  HA    CQ  CB    107.69  3.000
 Y1V  NA    CQ  CB    110.31  3.000
 Y1V  HA    CQ  C     106.99  3.000
 Y1V  CB    CQ  C     108.98  3.000
 Y1V  NA    CQ  C     115.26  3.000
 Y1V  HN3   NA  HN1   104.19  3.000
 Y1V  HN3   NA  CQ    107.86  3.000
 Y1V  HN1   NA  CQ    108.60  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
 Y1V  Var_01  H  NE  CD  CG  175.27  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
 Y1V  chir_01  CG  CM  CB  CD  positiv
 Y1V  chir_02  CQ  NA  C   CB  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
 Y1V  plan-1  C   0.020
 Y1V  plan-1  O   0.020
 Y1V  plan-1  CQ  0.020
 Y1V  plan-1  O1  0.020

