# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 10:56:38 2022
#   Inital geometry file: a 60 line input string
#   Ligand name: 3-methyl-L-alloisoleucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(C)(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
 I2M  I2M  3-methyl-L-alloisoleucine  L-peptide  24  10  .  2012-08-28  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT (side chain)
;

data_comp_I2M
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
 I2M  N     N  NH2    0  -0.811  18.5187  4.0144   0.1463
 I2M  CA    C  CH1    0  -0.161  17.6446  4.0913  -1.0167
 I2M  CB    C  CT     0  -0.092  17.7855  5.3882  -1.8729
 I2M  CG3   C  CH3    0  -0.641  19.1640  5.4845  -2.5316
 I2M  CG2   C  CH3    0  -0.639  16.7184  5.4143  -2.9704
 I2M  CG1   C  CH2    0  -0.416  17.6165  6.6396  -0.9862
 I2M  CD1   C  CH3    0  -0.673  16.3328  6.7353  -0.1705
 I2M  C     C  C      0   0.411  17.8464  2.8091  -1.8636
 I2M  O     O  O      0  -0.606  19.0098  2.3579  -1.9276
 I2M  OXT   O  OC    -1  -0.606  16.8383  2.3280  -2.4184
 I2M  H     H  HNH2   0   0.328  19.4566  3.8016  -0.1680
 I2M  H2    H  HNH2   0   0.333  18.5623  4.8997   0.6345
 I2M  HA    H  HCH1   0   0.195  16.6104  4.0750  -0.6543
 I2M  HG31  H  HCH3   0   0.221  19.3241  4.6941  -3.2647
 I2M  HG32  H  HCH3   0   0.210  19.2679  6.4401  -3.0511
 I2M  HG33  H  HCH3   0   0.210  19.9687  5.4257  -1.7961
 I2M  HG21  H  HCH3   0   0.214  15.7134  5.2694  -2.5702
 I2M  HG22  H  HCH3   0   0.206  16.7313  6.3747  -3.4917
 I2M  HG23  H  HCH3   0   0.223  16.8858  4.6348  -3.7123
 I2M  HG12  H  HCH2   0   0.210  18.4738  6.7302  -0.3105
 I2M  HG13  H  HCH2   0   0.218  17.6809  7.5158  -1.6396
 I2M  HD11  H  HCH3   0   0.219  16.2611  5.9556   0.5894
 I2M  HD12  H  HCH3   0   0.226  16.2857  7.6931   0.3498
 I2M  HD13  H  HCH3   0   0.220  15.4427  6.6644  -0.7967

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
 I2M  N    CA    single  1.458  0.019  1.458
 I2M  CA   CB    single  1.540  0.027  1.540
 I2M  CA   C     single  1.525  0.021  1.525
 I2M  CB   CG3   single  1.531  0.020  1.531
 I2M  CB   CG2   single  1.531  0.020  1.531
 I2M  CB   CG1   single  1.543  0.020  1.543
 I2M  CG1  CD1   single  1.524  0.020  1.524
 I2M  C    O     deloc   1.231  0.020  1.231
 I2M  C    OXT   deloc   1.247  0.020  1.247
 I2M  N    H     single  0.860  0.020  0.860
 I2M  N    H2    single  0.890  0.020  1.040
 I2M  CA   HA    single  0.970  0.020  0.970
 I2M  CG3  HG31  single  0.970  0.020  1.090
 I2M  CG3  HG32  single  0.970  0.020  1.090
 I2M  CG3  HG33  single  0.970  0.020  1.090
 I2M  CG2  HG21  single  0.970  0.020  1.090
 I2M  CG2  HG22  single  0.970  0.020  1.090
 I2M  CG2  HG23  single  0.970  0.020  1.090
 I2M  CG1  HG12  single  0.970  0.020  1.090
 I2M  CG1  HG13  single  0.970  0.020  1.090
 I2M  CD1  HD11  single  0.970  0.020  1.090
 I2M  CD1  HD12  single  0.970  0.020  1.090
 I2M  CD1  HD13  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
 I2M  H2    N    H     107.10  3.000
 I2M  H2    N    CA    111.39  3.000
 I2M  H     N    CA    114.00  3.000
 I2M  HA    CA   C     109.00  3.000
 I2M  HA    CA   CB    109.00  3.000
 I2M  C     CA   CB    111.60  2.000
 I2M  HA    CA   N     110.00  3.000
 I2M  C     CA   N     111.00  2.800
 I2M  CB    CA   N     111.50  1.700
 I2M  CG1   CB   CG2   108.77  3.000
 I2M  CG1   CB   CG3   107.15  3.000
 I2M  CG2   CB   CG3   108.54  3.000
 I2M  CG1   CB   CA    110.42  3.000
 I2M  CG2   CB   CA    110.16  3.000
 I2M  CG3   CB   CA    111.70  3.000
 I2M  HG33  CG3  HG32  107.30  3.000
 I2M  HG33  CG3  HG31  107.81  3.000
 I2M  HG32  CG3  HG31  107.49  3.000
 I2M  HG33  CG3  CB    111.74  3.000
 I2M  HG32  CG3  CB    110.20  3.000
 I2M  HG31  CG3  CB    112.09  3.000
 I2M  HG23  CG2  HG22  107.60  3.000
 I2M  HG23  CG2  HG21  107.23  3.000
 I2M  HG22  CG2  HG21  107.60  3.000
 I2M  HG23  CG2  CB    111.66  3.000
 I2M  HG22  CG2  CB    110.41  3.000
 I2M  HG21  CG2  CB    112.13  3.000
 I2M  HG13  CG1  HG12  104.83  3.000
 I2M  HG13  CG1  CD1   108.58  3.000
 I2M  HG12  CG1  CD1   108.90  3.000
 I2M  HG13  CG1  CB    107.44  3.000
 I2M  HG12  CG1  CB    109.63  3.000
 I2M  CD1   CG1  CB    116.79  3.000
 I2M  HD13  CD1  HD12  107.20  3.000
 I2M  HD13  CD1  HD11  107.45  3.000
 I2M  HD12  CD1  HD11  107.00  3.000
 I2M  HD13  CD1  CG1   112.09  3.000
 I2M  HD12  CD1  CG1   110.29  3.000
 I2M  HD11  CD1  CG1   112.53  3.000
 I2M  OXT   C    O     126.20  3.000
 I2M  OXT   C    CA    117.19  3.000
 I2M  O     C    CA    120.80  1.700

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
 I2M  Var_01  CD1   CG1  CB   CA  -55.42  30.0  3
 I2M  Var_02  HG31  CG3  CB   CA   65.32  30.0  3
 I2M  Var_03  HG21  CG2  CB   CA   52.90  30.0  3
 I2M  Var_04  HD11  CD1  CG1  CB   65.28  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
 I2M  chir_01  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
 I2M  plan-1  CA   0.020
 I2M  plan-1  C    0.020
 I2M  plan-1  O    0.020
 I2M  plan-1  OXT  0.020

