# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 11:11:42 2022
#   Inital geometry file: a 60 line input string
#   Ligand name: 5-methyl-L-norleucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)CC[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
 HLX  HLX  '5-methyl-L-norleucine    '  L-peptide  24  10  .  2019-03-22  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_HLX
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
 HLX  N    N  NH2    0  -0.807  56.5741  79.8966  150.0227
 HLX  CA   C  CH1    0  -0.218  56.2318  80.3055  148.6670
 HLX  C    C  C      0   0.407  57.5056  80.5644  147.8224
 HLX  O    O  O      0  -0.604  58.5793  80.0975  148.2544
 HLX  CB   C  CH2    0  -0.402  55.2797  81.5027  148.6962
 HLX  CG   C  CH2    0  -0.392  55.8747  82.7749  149.2859
 HLX  C7   C  CH1    0  -0.226  54.9338  83.9822  149.2692
 HLX  C8   C  CH3    0  -0.648  55.6851  85.2444  149.6828
 HLX  C9   C  CH3    0  -0.654  53.7089  83.7773  150.1556
 HLX  O1   O  OC    -1  -0.610  57.3412  81.1778  146.7489
 HLX  H1   H  HNH2   0   0.325  55.8090  79.3707  150.4247
 HLX  H2   H  HNH2   0   0.329  57.3710  79.2762  149.9770
 HLX  H4   H  HCH1   0   0.196  55.6967  79.5023  148.1280
 HLX  H5   H  HCH2   0   0.197  54.9411  81.7021  147.6766
 HLX  H6   H  HCH2   0   0.203  54.3849  81.2129  149.2571
 HLX  H7   H  HCH2   0   0.194  56.2003  82.5916  150.3150
 HLX  H8   H  HCH2   0   0.208  56.7742  83.0376  148.7206
 HLX  H9   H  HCH1   0   0.201  54.5853  84.1226  148.2383
 HLX  H10  H  HCH3   0   0.219  55.0412  86.1251  149.6421
 HLX  H11  H  HCH3   0   0.208  56.0605  85.1576  150.7057
 HLX  H12  H  HCH3   0   0.220  56.5415  85.4287  149.0317
 HLX  H13  H  HCH3   0   0.220  53.0665  84.6598  150.1463
 HLX  H14  H  HCH3   0   0.225  53.1040  82.9300  149.8320
 HLX  H15  H  HCH3   0   0.208  54.0074  83.5955  151.1914

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
 HLX  C   O    deloc   1.231  0.020  1.231
 HLX  C   CA   single  1.525  0.021  1.525
 HLX  CA  CB   single  1.521  0.033  1.521
 HLX  CA  N    single  1.458  0.019  1.458
 HLX  CB  CG   single  1.523  0.020  1.523
 HLX  CG  C7   single  1.531  0.020  1.531
 HLX  C7  C9   single  1.526  0.020  1.526
 HLX  C7  C8   single  1.526  0.020  1.526
 HLX  C   O1   deloc   1.247  0.020  1.247
 HLX  N   H1   single  0.890  0.020  1.040
 HLX  N   H2   single  0.890  0.020  1.040
 HLX  CA  H4   single  0.970  0.020  1.090
 HLX  CB  H5   single  0.970  0.020  1.090
 HLX  CB  H6   single  0.970  0.020  1.090
 HLX  CG  H7   single  0.970  0.020  1.090
 HLX  CG  H8   single  0.970  0.020  1.090
 HLX  C7  H9   single  0.970  0.020  1.090
 HLX  C8  H10  single  0.970  0.020  1.090
 HLX  C8  H11  single  0.970  0.020  1.090
 HLX  C8  H12  single  0.970  0.020  1.090
 HLX  C9  H13  single  0.970  0.020  1.090
 HLX  C9  H14  single  0.970  0.020  1.090
 HLX  C9  H15  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
 HLX  H2   N   H1   107.16  3.000
 HLX  H2   N   CA   108.39  3.000
 HLX  H1   N   CA   109.76  3.000
 HLX  H4   CA  CB   106.05  3.000
 HLX  H4   CA  C    104.68  3.000
 HLX  CB   CA  C    110.50  1.500
 HLX  H4   CA  N    111.32  3.000
 HLX  CB   CA  N    110.40  1.500
 HLX  C    CA  N    111.00  2.800
 HLX  O1   C   O    126.54  3.000
 HLX  O1   C   CA   116.28  3.000
 HLX  O    C   CA   120.80  1.700
 HLX  H6   CB  H5   105.84  3.000
 HLX  H6   CB  CG   109.99  3.000
 HLX  H5   CB  CG   109.26  3.000
 HLX  H6   CB  CA   108.13  3.000
 HLX  H5   CB  CA   108.54  3.000
 HLX  CG   CB  CA   114.70  3.000
 HLX  H8   CG  H7   106.33  3.000
 HLX  H8   CG  C7   108.08  3.000
 HLX  H7   CG  C7   108.97  3.000
 HLX  H8   CG  CB   108.76  3.000
 HLX  H7   CG  CB   109.89  3.000
 HLX  C7   CG  CB   114.49  3.000
 HLX  H9   C7  C9   107.94  3.000
 HLX  H9   C7  C8   107.77  3.000
 HLX  C9   C7  C8   110.42  3.000
 HLX  H9   C7  CG   107.84  3.000
 HLX  C8   C7  CG   110.29  3.000
 HLX  C9   C7  CG   112.41  3.000
 HLX  H12  C8  H11  107.59  3.000
 HLX  H12  C8  H10  107.71  3.000
 HLX  H11  C8  H10  107.54  3.000
 HLX  H12  C8  C7   111.36  3.000
 HLX  H11  C8  C7   110.92  3.000
 HLX  H10  C8  C7   111.52  3.000
 HLX  H15  C9  H14  107.67  3.000
 HLX  H15  C9  H13  107.65  3.000
 HLX  H14  C9  H13  107.42  3.000
 HLX  H15  C9  C7   110.71  3.000
 HLX  H14  C9  C7   112.17  3.000
 HLX  H13  C9  C7   111.03  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
 HLX  Var_01  C7   CG  CB  CA  178.03  30.0  3
 HLX  Var_02  C9   C7  CG  CB   64.76  30.0  3
 HLX  Var_03  H13  C9  C7  CG  178.61  30.0  3
 HLX  Var_04  H10  C8  C7  CG  177.89  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
 HLX  chir_01  CA  C  CB  N  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
 HLX  plan-1  CA  0.020
 HLX  plan-1  C   0.020
 HLX  plan-1  O   0.020
 HLX  plan-1  O1  0.020

