# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 00:49:28 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: (2S)-2-{[(aminomethyl)(dihydroxy)silyl]methyl}-4-methylpentanal
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](C[Si](O)(O)CN)C=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
 AMM  AMM  (2S)-2-{[(aminomethyl)(dihydroxy)silyl]methyl}-4-methylpentanal  ligand  32  13  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_AMM
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
 AMM  N     N   NH2   0  -0.806  -1.5072  -0.8318  -1.1170
 AMM  CA    C   CH2   0  -0.603  -0.2417  -0.1192  -0.9366
 AMM  SI    SI  SI    0   1.167   1.1703  -1.3577  -0.9586
 AMM  O1    O   OH1   0  -0.781   2.5475  -0.4340  -0.7767
 AMM  O2    O   OH1   0  -0.779   1.1798  -2.2407  -2.3719
 AMM  CH2   C   CH2   0  -0.746   0.9923  -2.6303   0.4064
 AMM  CE    C   CH1   0  -0.351   1.0911  -2.0426   1.8266
 AMM  C     C   C1    0   0.154   2.4903  -1.5237   2.0656
 AMM  O     O   O     0  -0.387   3.4778  -2.2123   1.9719
 AMM  CB    C   CH2   0  -0.409   0.7028  -3.1024   2.8741
 AMM  CG    C   CH1   0  -0.236   0.4073  -2.6037   4.2919
 AMM  CD1   C   CH3   0  -0.659  -0.7837  -1.6496   4.3287
 AMM  CD2   C   CH3   0  -0.665   1.6154  -1.9804   4.9839
 AMM  HN1   H   HNH2  0   0.343  -1.5559  -1.2081  -2.0547
 AMM  HN2   H   HNH2  0   0.349  -2.2804  -0.1824  -1.0473
 AMM  HA1   H   HCH2  0   0.236  -0.2514   0.3645   0.0454
 AMM  HA2   H   HCH2  0   0.222  -0.0708   0.6907  -1.6617
 AMM  HO1   H   HOH1  0   0.470   3.3834  -0.9106  -0.7606
 AMM  HO2   H   HOH1  0   0.471   1.1880  -1.7291  -3.1871
 AMM  HH21  H   HCH2  0   0.257   1.7220  -3.4369   0.2892
 AMM  HH22  H   HCH2  0   0.260   0.0053  -3.0886   0.2927
 AMM  HE    H   HCH1  0   0.249   0.4050  -1.1949   1.9086
 AMM  H     H   H     0   0.204   2.5777  -0.4564   2.3350
 AMM  HB1   H   HCH2  0   0.232   1.4867  -3.8656   2.9063
 AMM  HB2   H   HCH2  0   0.235  -0.1932  -3.6064   2.5011
 AMM  HG    H   HCH1  0   0.228   0.1296  -3.4969   4.8628
 AMM  HD11  H   HCH3  0   0.226  -1.6555  -2.0740   3.8280
 AMM  HD12  H   HCH3  0   0.230  -1.0700  -1.4250   5.3573
 AMM  HD13  H   HCH3  0   0.215  -0.5529  -0.6979   3.8447
 AMM  HD21  H   HCH3  0   0.210   1.8893  -1.0221   4.5352
 AMM  HD22  H   HCH3  0   0.229   2.4895  -2.6328   4.9458
 AMM  HD23  H   HCH3  0   0.237   1.3983  -1.7815   6.0347

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
 AMM  N    CA    single  1.464  0.020  1.464
 AMM  N    HN1   single  0.890  0.020  1.040
 AMM  N    HN2   single  0.890  0.020  1.040
 AMM  CA   SI    single  1.878  0.020  1.878
 AMM  CA   HA1   single  0.970  0.020  1.090
 AMM  CA   HA2   single  0.970  0.020  1.090
 AMM  SI   O1    single  1.668  0.020  1.668
 AMM  SI   O2    single  1.667  0.020  1.667
 AMM  SI   CH2   single  1.875  0.020  1.875
 AMM  O1   HO1   single  0.850  0.020  0.980
 AMM  O2   HO2   single  0.850  0.020  0.980
 AMM  CH2  CE    single  1.540  0.020  1.540
 AMM  CH2  HH21  single  0.970  0.020  1.090
 AMM  CH2  HH22  single  0.970  0.020  1.090
 AMM  CE   C     single  1.511  0.020  1.511
 AMM  CE   CB    single  1.540  0.020  1.540
 AMM  CE   HE    single  0.970  0.020  1.090
 AMM  C    O     double  1.207  0.020  1.207
 AMM  C    H     single  0.930  0.020  1.080
 AMM  CB   CG    single  1.532  0.020  1.532
 AMM  CB   HB1   single  0.970  0.020  1.090
 AMM  CB   HB2   single  0.970  0.020  1.090
 AMM  CG   CD1   single  1.527  0.020  1.527
 AMM  CG   CD2   single  1.525  0.020  1.525
 AMM  CG   HG    single  0.970  0.020  1.090
 AMM  CD1  HD11  single  0.970  0.020  1.090
 AMM  CD1  HD12  single  0.970  0.020  1.090
 AMM  CD1  HD13  single  0.970  0.020  1.090
 AMM  CD2  HD21  single  0.970  0.020  1.090
 AMM  CD2  HD22  single  0.970  0.020  1.090
 AMM  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
 AMM  HN2   N    HN1   105.41  3.000
 AMM  HN2   N    CA    109.85  3.000
 AMM  HN1   N    CA    109.69  3.000
 AMM  HA2   CA   HA1   105.50  3.000
 AMM  HA2   CA   SI    111.15  3.000
 AMM  HA1   CA   SI    107.97  3.000
 AMM  HA2   CA   N     114.30  3.000
 AMM  HA1   CA   N     108.55  3.000
 AMM  SI    CA   N     109.12  3.000
 AMM  CH2   SI   O2    104.97  3.000
 AMM  CH2   SI   O1    112.02  3.000
 AMM  O2    SI   O1    112.40  3.000
 AMM  CH2   SI   CA    111.57  3.000
 AMM  O2    SI   CA    111.32  3.000
 AMM  O1    SI   CA    104.72  3.000
 AMM  HO1   O1   SI    116.40  3.000
 AMM  HO2   O2   SI    115.89  3.000
 AMM  HH22  CH2  HH21  106.37  3.000
 AMM  HH22  CH2  CE    108.27  3.000
 AMM  HH21  CH2  CE    109.71  3.000
 AMM  HH22  CH2  SI    107.12  3.000
 AMM  HH21  CH2  SI    111.05  3.000
 AMM  CE    CH2  SI    113.97  3.000
 AMM  HE    CE   CB    108.92  3.000
 AMM  HE    CE   C     107.63  3.000
 AMM  CB    CE   C     111.23  3.000
 AMM  HE    CE   CH2   108.95  3.000
 AMM  CB    CE   CH2   110.39  3.000
 AMM  C     CE   CH2   109.65  3.000
 AMM  H     C    O     120.36  3.000
 AMM  H     C    CE    116.34  3.000
 AMM  O     C    CE    123.30  3.000
 AMM  HB2   CB   HB1   105.99  3.000
 AMM  HB2   CB   CG    107.92  3.000
 AMM  HB1   CB   CG    109.75  3.000
 AMM  HB2   CB   CE    106.96  3.000
 AMM  HB1   CB   CE    108.62  3.000
 AMM  CG    CB   CE    117.02  3.000
 AMM  HG    CG   CD2   107.31  3.000
 AMM  HG    CG   CD1   107.41  3.000
 AMM  CD2   CG   CD1   110.58  3.000
 AMM  HG    CG   CB    105.41  3.000
 AMM  CD2   CG   CB    113.59  3.000
 AMM  CD1   CG   CB    112.10  3.000
 AMM  HD13  CD1  HD12  107.09  3.000
 AMM  HD13  CD1  HD11  107.72  3.000
 AMM  HD12  CD1  HD11  107.63  3.000
 AMM  HD13  CD1  CG    111.66  3.000
 AMM  HD12  CD1  CG    110.86  3.000
 AMM  HD11  CD1  CG    111.66  3.000
 AMM  HD23  CD2  HD22  107.57  3.000
 AMM  HD23  CD2  HD21  106.58  3.000
 AMM  HD22  CD2  HD21  108.01  3.000
 AMM  HD23  CD2  CG    110.71  3.000
 AMM  HD22  CD2  CG    111.97  3.000
 AMM  HD21  CD2  CG    111.75  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
 AMM  Var_01  O1    SI   CA  N   178.92  30.0  3
 AMM  Var_02  CE    CH2  SI  CA  -64.67  30.0  3
 AMM  Var_03  CD1   CG   CB  CE   61.96  30.0  3
 AMM  Var_04  HN1   N    CA  SI  -68.20  30.0  3
 AMM  Var_05  HD11  CD1  CG  CB   51.49  30.0  3
 AMM  Var_06  HD21  CD2  CG  CB   70.00  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
 AMM  chir_01  CE  CH2  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
 AMM  plan-1  CE  0.020
 AMM  plan-1  C   0.020
 AMM  plan-1  O   0.020
 AMM  plan-1  H   0.020

