# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 18 03:00:16 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: (2S,3S)-3-amino-2-hydroxy-N-(4-iodobenzyl)butanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](N)[C@H](O)C(=O)NCc1ccc(I)cc1
#
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
 0ML  0ML  (2S,3S)-3-amino-2-hydroxy-N-(4-iodobenzyl)butanamide  peptide  31  16  .  2022-09-22  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_0ML
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
 0ML  N    N  NH2   0  -0.802  -3.7256  -1.7709   1.1050
 0ML  C1   C  CH1   0  -0.143  -4.5260  -1.5886  -0.1047
 0ML  C2   C  CH1   0  -0.012  -5.1375  -0.1781  -0.0673
 0ML  O1   O  OH1   0  -0.675  -6.0736  -0.0285  -1.0942
 0ML  C3   C  CH3   0  -0.657  -5.5957  -2.6628  -0.2705
 0ML  C4   C  C     0   0.499  -4.1054   0.9552  -0.1884
 0ML  O2   O  O     0  -0.512  -4.3690   1.9151  -0.9087
 0ML  N2   N  NH1   0  -0.636  -2.9942   0.8253   0.5343
 0ML  C5   C  CH2   0  -0.343  -1.9335   1.8002   0.5797
 0ML  C6   C  CR6   0   0.103  -0.6150   1.2426   0.1047
 0ML  C7   C  CR16  0  -0.283  -0.5406   0.4337  -1.0254
 0ML  C8   C  CR16  0  -0.208   0.6763  -0.0565  -1.4761
 0ML  C9   C  CR6   0  -0.236   1.8351   0.2682  -0.7844
 0ML  I1   I  I     0   0.049   3.6860  -0.4758  -1.4550
 0ML  C10  C  CR16  0  -0.208   1.7882   1.0699   0.3452
 0ML  C11  C  CR16  0  -0.301   0.5596   1.5487   0.7819
 0ML  H    H  HNH2  0   0.355  -4.3335  -1.9043   1.9061
 0ML  H1   H  HCH1  0   0.243  -3.8391  -1.6444  -0.9560
 0ML  H3   H  HCH3  0   0.218  -6.3240  -2.6142   0.5425
 0ML  H4   H  HCH3  0   0.234  -6.1315  -2.5760  -1.2143
 0ML  H5   H  HCH3  0   0.233  -5.1308  -3.6496  -0.2439
 0ML  H6   H  HNH1  0   0.422  -2.9008  -0.0645   1.0365
 0ML  H7   H  HCH2  0   0.271  -2.2195   2.6511  -0.0396
 0ML  H8   H  HCH2  0   0.265  -1.8236   2.1783   1.5988
 0ML  H9   H  HCR6  0   0.261  -1.4400   0.1724  -1.5697
 0ML  H10  H  HCR6  0   0.279   0.7067  -0.6832  -2.3570
 0ML  H11  H  HCR6  0   0.279   2.6860   1.3212   0.8935
 0ML  H12  H  HCR6  0   0.264   0.5265   2.1705   1.6686
 0ML  H2   H  HNH2  0   0.370  -3.1680  -2.6120   1.0270
 0ML  H14  H  HCH1  0   0.226  -5.6208  -0.0548   0.9182
 0ML  H15  H  HOH1  0   0.445  -5.9540   0.8709  -1.4350

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
 0ML  N    C1   single    1.462  0.020  1.462
 0ML  N    H    single    0.860  0.020  0.860
 0ML  C1   C2   single    1.538  0.020  1.538
 0ML  C1   C3   single    1.525  0.020  1.525
 0ML  C1   H1   single    0.970  0.020  1.090
 0ML  C2   O1   single    1.398  0.020  1.398
 0ML  C2   C4   single    1.538  0.020  1.538
 0ML  C3   H3   single    0.970  0.020  1.090
 0ML  C3   H4   single    0.970  0.020  1.090
 0ML  C3   H5   single    0.970  0.020  1.090
 0ML  C4   O2   double    1.229  0.020  1.229
 0ML  C4   N2   single    1.332  0.020  1.332
 0ML  N2   C5   single    1.441  0.020  1.441
 0ML  N2   H6   single    0.860  0.020  1.020
 0ML  C5   C6   single    1.508  0.020  1.508
 0ML  C5   H7   single    0.970  0.020  1.090
 0ML  C5   H8   single    0.970  0.020  1.090
 0ML  C6   C7   aromatic  1.392  0.020  1.392
 0ML  C6   C11  aromatic  1.390  0.020  1.390
 0ML  C7   C8   aromatic  1.387  0.020  1.387
 0ML  C7   H9   single    0.930  0.020  1.080
 0ML  C8   C9   aromatic  1.388  0.020  1.388
 0ML  C8   H10  single    0.930  0.020  1.080
 0ML  C9   I1   single    2.105  0.020  2.105
 0ML  C9   C10  aromatic  1.386  0.020  1.386
 0ML  C10  C11  aromatic  1.389  0.020  1.389
 0ML  C10  H11  single    0.930  0.020  1.080
 0ML  C11  H12  single    0.930  0.020  1.080
 0ML  N    H2   single    0.890  0.020  1.040
 0ML  C2   H14  single    0.970  0.020  1.090
 0ML  O1   H15  single    0.850  0.020  0.980

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
 0ML  H2   N    H    106.36  3.000
 0ML  H2   N    C1   109.96  3.000
 0ML  H    N    C1   109.99  3.000
 0ML  H1   C1   C3   108.64  3.000
 0ML  H1   C1   C2   108.36  3.000
 0ML  C3   C1   C2   111.70  3.000
 0ML  H1   C1   N    107.06  3.000
 0ML  C3   C1   N    112.72  3.000
 0ML  C2   C1   N    108.17  3.000
 0ML  H14  C2   C4   106.36  3.000
 0ML  H14  C2   O1   110.52  3.000
 0ML  C4   C2   O1   108.23  3.000
 0ML  H14  C2   C1   107.34  3.000
 0ML  C4   C2   C1   114.03  3.000
 0ML  O1   C2   C1   110.28  3.000
 0ML  H15  O1   C2   105.96  3.000
 0ML  H5   C3   H4   107.63  3.000
 0ML  H5   C3   H3   107.83  3.000
 0ML  H4   C3   H3   108.27  3.000
 0ML  H5   C3   C1   109.60  3.000
 0ML  H4   C3   C1   112.53  3.000
 0ML  H3   C3   C1   110.81  3.000
 0ML  N2   C4   O2   124.98  3.000
 0ML  N2   C4   C2   116.45  3.000
 0ML  O2   C4   C2   118.55  3.000
 0ML  H6   N2   C5   120.27  3.000
 0ML  H6   N2   C4   115.22  3.000
 0ML  C5   N2   C4   124.41  3.000
 0ML  H8   C5   H7   106.62  3.000
 0ML  H8   C5   C6   109.50  3.000
 0ML  H7   C5   C6   109.81  3.000
 0ML  H8   C5   N2   109.72  3.000
 0ML  H7   C5   N2   108.47  3.000
 0ML  C6   C5   N2   112.54  3.000
 0ML  C11  C6   C7   118.58  3.000
 0ML  C11  C6   C5   120.26  3.000
 0ML  C7   C6   C5   121.15  3.000
 0ML  H9   C7   C8   118.68  3.000
 0ML  H9   C7   C6   120.25  3.000
 0ML  C8   C7   C6   121.07  3.000
 0ML  H10  C8   C9   121.20  3.000
 0ML  H10  C8   C7   119.61  3.000
 0ML  C9   C8   C7   119.20  3.000
 0ML  C10  C9   I1   119.60  3.000
 0ML  C10  C9   C8   120.88  3.000
 0ML  I1   C9   C8   119.52  3.000
 0ML  H11  C10  C11  119.65  3.000
 0ML  H11  C10  C9   121.30  3.000
 0ML  C11  C10  C9   119.05  3.000
 0ML  H12  C11  C10  118.82  3.000
 0ML  H12  C11  C6   119.95  3.000
 0ML  C10  C11  C6   121.22  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
 0ML  CONST_01  C9   C8   C7   C6     0.00   0.0  0
 0ML  CONST_02  C9   C10  C11  C6     0.00   0.0  0
 0ML  CONST_03  C10  C11  C6   C7     0.00   0.0  0
 0ML  CONST_04  C10  C9   C8   C7     0.00   0.0  0
 0ML  CONST_05  C11  C6   C7   C8     0.00   0.0  0
 0ML  CONST_06  C11  C10  C9   C8     0.00   0.0  0
 0ML  CONST_07  C8   C7   C6   C5   180.00   0.0  0
 0ML  CONST_08  C10  C11  C6   C5   180.00   0.0  0
 0ML  CONST_09  I1   C9   C8   C7   180.00   0.0  0
 0ML  CONST_10  C11  C10  C9   I1   180.00   0.0  0
 0ML  CONST_11  H10  C8   C7   C6   180.00   0.0  0
 0ML  CONST_12  H11  C10  C11  C6   180.00   0.0  0
 0ML  CONST_13  H12  C11  C6   C7   180.00   0.0  0
 0ML  CONST_14  H9   C7   C8   C9   180.00   0.0  0
 0ML  CONST_15  C5   N2   C4   C2   180.00   0.0  0
 0ML  CONST_16  C5   N2   C4   O2     0.00   0.0  0
 0ML  CONST_17  H6   N2   C4   C2     0.00   0.0  0
 0ML  Var_01    C7   C6   C5   N2    43.05  30.0  2
 0ML  Var_02    C6   C5   N2   C4  -119.72  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
 0ML  chir_01  C1  N   C2  C3  positiv
 0ML  chir_02  C2  O1  C1  C4  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
 0ML  plan-1  C5   0.020
 0ML  plan-1  C6   0.020
 0ML  plan-1  C7   0.020
 0ML  plan-1  C8   0.020
 0ML  plan-1  C9   0.020
 0ML  plan-1  I1   0.020
 0ML  plan-1  C10  0.020
 0ML  plan-1  C11  0.020
 0ML  plan-1  H9   0.020
 0ML  plan-1  H10  0.020
 0ML  plan-1  H11  0.020
 0ML  plan-1  H12  0.020
 0ML  plan-2  C2   0.020
 0ML  plan-2  C4   0.020
 0ML  plan-2  O2   0.020
 0ML  plan-2  N2   0.020
 0ML  plan-2  C5   0.020
 0ML  plan-2  H6   0.020

