# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 21:20:56 2022
#   Inital geometry file: a 66 line input string
#   Ligand name: (4R)-N,4-dimethyl-L-norleucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@@H](C)C[C@H](NC)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
 MNL  MNL  (4R)-N,4-dimethyl-L-norleucine  L-peptide  27  11  .  2012-08-28  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MNL
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
 MNL  N     N  NH1    0  -0.583   9.0518  39.2430  15.0854
 MNL  CA    C  CH1    0  -0.246   7.6233  39.2250  14.7949
 MNL  C     C  C      0   0.409   6.8018  38.2757  15.7202
 MNL  O     O  O      0  -0.603   5.6808  37.9067  15.3143
 MNL  OXT   O  OC    -1  -0.609   7.3116  38.0107  16.8288
 MNL  CB    C  CH2    0  -0.415   7.3457  38.9986  13.3103
 MNL  CG    C  CH1    0  -0.205   8.0848  39.9204  12.3360
 MNL  CD    C  CH2    0  -0.404   7.7070  39.5418  10.9002
 MNL  CE    C  CH3    0  -0.666   8.5399  40.2221   9.8216
 MNL  CM1   C  CH3    0  -0.527   9.7407  38.0106  14.7509
 MNL  CM4   C  CH3    0  -0.668   7.7995  41.3915  12.6209
 MNL  H     H  HNH1   0   0.330   9.1388  39.3750  16.0847
 MNL  HA    H  HCH1   0   0.220   7.2565  40.2324  15.0406
 MNL  HB2   H  HCH2   0   0.207   7.5669  37.9589  13.0437
 MNL  HB3   H  HCH2   0   0.210   6.2716  39.1164  13.1491
 MNL  HG    H  HCH1   0   0.203   9.1634  39.7580  12.4467
 MNL  HD2   H  HCH2   0   0.211   7.8080  38.4575  10.7890
 MNL  HD3   H  HCH2   0   0.201   6.6456  39.7630  10.7414
 MNL  HE1   H  HCH3   0   0.224   8.2610  39.8681   8.8283
 MNL  HE2   H  HCH3   0   0.217   8.4145  41.3053   9.8251
 MNL  HE3   H  HCH3   0   0.213   9.6031  40.0139   9.9575
 MNL  HM11  H  HCH3   0   0.220  10.7428  38.0332  15.1813
 MNL  HM12  H  HCH3   0   0.189   9.2498  37.0968  15.1100
 MNL  HM13  H  HCH3   0   0.213   9.8641  37.9144  13.6705
 MNL  HM41  H  HCH3   0   0.224   8.2916  42.0484  11.9024
 MNL  HM42  H  HCH3   0   0.206   6.7263  41.5959  12.5733
 MNL  HM43  H  HCH3   0   0.226   8.1507  41.6833  13.6107

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
 MNL  N    CA    single  1.458  0.019  1.458
 MNL  N    CM1   single  1.451  0.020  1.451
 MNL  N    H     single  0.860  0.020  0.860
 MNL  CA   C     single  1.525  0.021  1.525
 MNL  CA   CB    single  1.530  0.020  1.530
 MNL  CA   HA    single  0.970  0.020  0.970
 MNL  C    O     deloc   1.231  0.020  1.231
 MNL  C    OXT   deloc   1.249  0.020  1.249
 MNL  CB   CG    single  1.531  0.020  1.531
 MNL  CB   HB2   single  0.970  0.020  1.090
 MNL  CB   HB3   single  0.970  0.020  1.090
 MNL  CG   CD    single  1.532  0.020  1.532
 MNL  CG   CM4   single  1.525  0.020  1.525
 MNL  CG   HG    single  0.970  0.020  1.090
 MNL  CD   CE    single  1.523  0.020  1.523
 MNL  CD   HD2   single  0.970  0.020  1.090
 MNL  CD   HD3   single  0.970  0.020  1.090
 MNL  CE   HE1   single  0.970  0.020  1.090
 MNL  CE   HE2   single  0.970  0.020  1.090
 MNL  CE   HE3   single  0.970  0.020  1.090
 MNL  CM1  HM11  single  0.970  0.020  1.090
 MNL  CM1  HM12  single  0.970  0.020  1.090
 MNL  CM1  HM13  single  0.970  0.020  1.090
 MNL  CM4  HM41  single  0.970  0.020  1.090
 MNL  CM4  HM42  single  0.970  0.020  1.090
 MNL  CM4  HM43  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
 MNL  H     N    CM1   107.32  3.000
 MNL  H     N    CA    114.00  3.000
 MNL  CM1   N    CA    114.13  3.000
 MNL  HA    CA   CB    109.00  3.000
 MNL  HA    CA   C     109.00  3.000
 MNL  CB    CA   C     110.10  1.900
 MNL  HA    CA   N     110.00  3.000
 MNL  CB    CA   N     110.50  1.700
 MNL  C     CA   N     111.00  2.800
 MNL  OXT   C    O     126.35  3.000
 MNL  OXT   C    CA    116.16  3.000
 MNL  O     C    CA    120.80  1.700
 MNL  HB3   CB   HB2   105.36  3.000
 MNL  HB3   CB   CG    108.40  3.000
 MNL  HB2   CB   CG    108.59  3.000
 MNL  HB3   CB   CA    107.83  3.000
 MNL  HB2   CB   CA    109.91  3.000
 MNL  CG    CB   CA    116.20  3.000
 MNL  HG    CG   CM4   107.94  3.000
 MNL  HG    CG   CD    107.49  3.000
 MNL  CM4   CG   CD    111.54  3.000
 MNL  HG    CG   CB    108.75  3.000
 MNL  CM4   CG   CB    111.80  3.000
 MNL  CD    CG   CB    109.18  3.000
 MNL  HD3   CD   HD2   105.94  3.000
 MNL  HD3   CD   CE    109.69  3.000
 MNL  HD2   CD   CE    108.66  3.000
 MNL  HD3   CD   CG    108.95  3.000
 MNL  HD2   CD   CG    108.50  3.000
 MNL  CE    CD   CG    114.73  3.000
 MNL  HE3   CE   HE2   107.52  3.000
 MNL  HE3   CE   HE1   107.49  3.000
 MNL  HE2   CE   HE1   107.21  3.000
 MNL  HE3   CE   CD    111.05  3.000
 MNL  HE2   CE   CD    112.24  3.000
 MNL  HE1   CE   CD    111.10  3.000
 MNL  HM13  CM1  HM12  107.52  3.000
 MNL  HM13  CM1  HM11  106.76  3.000
 MNL  HM12  CM1  HM11  107.39  3.000
 MNL  HM13  CM1  N     110.90  3.000
 MNL  HM12  CM1  N     114.79  3.000
 MNL  HM11  CM1  N     109.13  3.000
 MNL  HM43  CM4  HM42  107.80  3.000
 MNL  HM43  CM4  HM41  106.95  3.000
 MNL  HM42  CM4  HM41  107.55  3.000
 MNL  HM43  CM4  CG    111.56  3.000
 MNL  HM42  CM4  CG    110.83  3.000
 MNL  HM41  CM4  CG    111.92  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
 MNL  Var_01  HM11  CM1  N   CA  -168.55  30.0  3
 MNL  Var_02  HE1   CE   CD  CG   176.72  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
 MNL  chir_01  CA  N   C   CB   positiv
 MNL  chir_02  CG  CB  CD  CM4  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
 MNL  plan-1  CA   0.020
 MNL  plan-1  C    0.020
 MNL  plan-1  O    0.020
 MNL  plan-1  OXT  0.020

