# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 15:40:08 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: (2S,3S)-3-amino-N-(2,4-dimethylphenyl)-2-hydroxy-5-methylhexanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](N)[C@H](O)C(=O)Nc1ccc(C)cc1C
#
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
 3E3  3E3  (2S,3S)-3-amino-N-(2,4-dimethylphenyl)-2-hydroxy-5-methylhexanamide  ligand  43  19  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3E3
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
 3E3  N1   N  NH2   0  -0.782   3.7968  -0.4720   1.3843
 3E3  C7   C  CH1   0  -0.104   2.5215  -0.3351   0.7090
 3E3  C8   C  CH2   0  -0.427   2.6944   0.4267  -0.6037
 3E3  C9   C  CH1   0  -0.217   3.3993   1.7781  -0.4837
 3E3  C11  C  CH3   0  -0.651   3.5725   2.3960  -1.8681
 3E3  C10  C  CH3   0  -0.668   2.6521   2.7350   0.4381
 3E3  C12  C  CH1   0  -0.085   1.8236  -1.7046   0.4890
 3E3  O2   O  OH1   0  -0.664   2.5989  -2.5671  -0.2921
 3E3  C13  C  C     0   0.481   0.4491  -1.5218  -0.1422
 3E3  O1   O  O     0  -0.470   0.2488  -1.8291  -1.3060
 3E3  N2   N  NH1   0  -0.730  -0.4754  -0.9653   0.6668
 3E3  C14  C  CR6   0   0.267  -1.7704  -0.5577   0.2828
 3E3  C21  C  CR16  0  -0.259  -2.5994  -1.3926  -0.4589
 3E3  C20  C  CR16  0  -0.319  -3.8689  -0.9716  -0.8187
 3E3  C18  C  CR6   0   0.111  -4.3464   0.2781  -0.4323
 3E3  C19  C  CH3   0  -0.724  -5.7311   0.7221  -0.8050
 3E3  C17  C  CR16  0  -0.362  -3.5064   1.0917   0.3205
 3E3  C15  C  CR6   0   0.093  -2.2191   0.7044   0.6816
 3E3  C16  C  CH3   0  -0.753  -1.3363   1.6251   1.4713
 3E3  H30  H  HNH2  0   0.348   3.6775  -0.9613   2.2634
 3E3  H31  H  HCH1  0   0.220   1.8701   0.2475   1.3695
 3E3  H32  H  HCH2  0   0.223   3.2533  -0.1997  -1.3078
 3E3  H33  H  HCH2  0   0.222   1.7111   0.5939  -1.0582
 3E3  H34  H  HCH1  0   0.217   4.3932   1.6070  -0.0612
 3E3  H35  H  HCH3  0   0.211   2.6043   2.5972  -2.3339
 3E3  H36  H  HCH3  0   0.223   4.1128   3.3430  -1.8131
 3E3  H37  H  HCH3  0   0.222   4.1292   1.7343  -2.5346
 3E3  H38  H  HCH3  0   0.211   1.6326   2.9067   0.0803
 3E3  H39  H  HCH3  0   0.228   2.5905   2.3570   1.4594
 3E3  H40  H  HCH3  0   0.228   3.1503   3.7052   0.4811
 3E3  H41  H  HCH1  0   0.262   1.6947  -2.1666   1.4768
 3E3  H42  H  HOH1  0   0.446   2.2578  -2.5288  -1.1955
 3E3  H43  H  HNH1  0   0.412  -0.1910  -0.7508   1.6113
 3E3  H44  H  HCR6  0   0.262  -2.2619  -2.3770  -0.7507
 3E3  H45  H  HCR6  0   0.249  -4.4972  -1.6313  -1.4052
 3E3  H46  H  HCH3  0   0.247  -6.4860   0.1861  -0.2266
 3E3  H47  H  HCH3  0   0.244  -5.8730   1.7864  -0.6220
 3E3  H48  H  HCH3  0   0.245  -5.9389   0.5310  -1.8582
 3E3  H49  H  HCR6  0   0.244  -3.8570   2.0703   0.6299
 3E3  H50  H  HCH3  0   0.249  -0.4023   1.8352   0.9460
 3E3  H51  H  HCH3  0   0.261  -1.8320   2.5764   1.6548
 3E3  H52  H  HCH3  0   0.249  -1.0695   1.2078   2.4450
 3E3  H2   H  HNH2  0   0.339   4.4203  -1.0410   0.8238

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
 3E3  C10  C9   single    1.524  0.020  1.524
 3E3  O1   C13  double    1.220  0.020  1.220
 3E3  C8   C9   single    1.529  0.020  1.529
 3E3  C8   C7   single    1.528  0.020  1.528
 3E3  C13  C12  single    1.524  0.020  1.524
 3E3  C13  N2   single    1.349  0.020  1.349
 3E3  C12  C7   single    1.553  0.020  1.553
 3E3  C12  O2   single    1.398  0.020  1.398
 3E3  C21  C20  aromatic  1.385  0.020  1.385
 3E3  C21  C14  aromatic  1.391  0.020  1.391
 3E3  N2   C14  single    1.411  0.020  1.411
 3E3  C20  C18  aromatic  1.392  0.020  1.392
 3E3  C9   C11  single    1.526  0.020  1.526
 3E3  C14  C15  aromatic  1.398  0.020  1.398
 3E3  C7   N1   single    1.450  0.020  1.450
 3E3  C18  C19  single    1.501  0.020  1.501
 3E3  C18  C17  aromatic  1.391  0.020  1.391
 3E3  C15  C17  aromatic  1.392  0.020  1.392
 3E3  C15  C16  single    1.500  0.020  1.500
 3E3  N1   H30  single    0.890  0.020  1.040
 3E3  C7   H31  single    0.970  0.020  1.090
 3E3  C8   H32  single    0.970  0.020  1.090
 3E3  C8   H33  single    0.970  0.020  1.090
 3E3  C9   H34  single    0.970  0.020  1.090
 3E3  C11  H35  single    0.970  0.020  1.090
 3E3  C11  H36  single    0.970  0.020  1.090
 3E3  C11  H37  single    0.970  0.020  1.090
 3E3  C10  H38  single    0.970  0.020  1.090
 3E3  C10  H39  single    0.970  0.020  1.090
 3E3  C10  H40  single    0.970  0.020  1.090
 3E3  C12  H41  single    0.970  0.020  1.090
 3E3  O2   H42  single    0.850  0.020  0.980
 3E3  N2   H43  single    0.860  0.020  1.020
 3E3  C21  H44  single    0.930  0.020  1.080
 3E3  C20  H45  single    0.930  0.020  1.080
 3E3  C19  H46  single    0.970  0.020  1.090
 3E3  C19  H47  single    0.970  0.020  1.090
 3E3  C19  H48  single    0.970  0.020  1.090
 3E3  C17  H49  single    0.930  0.020  1.080
 3E3  C16  H50  single    0.970  0.020  1.090
 3E3  C16  H51  single    0.970  0.020  1.090
 3E3  C16  H52  single    0.970  0.020  1.090
 3E3  N1   H2   single    0.890  0.020  1.040

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
 3E3  H2   N1   H30  106.33  3.000
 3E3  H2   N1   C7   109.68  3.000
 3E3  H30  N1   C7   110.26  3.000
 3E3  H31  C7   C12  106.69  3.000
 3E3  H31  C7   C8   108.67  3.000
 3E3  C12  C7   C8   111.65  3.000
 3E3  H31  C7   N1   107.01  3.000
 3E3  C12  C7   N1   112.22  3.000
 3E3  C8   C7   N1   110.36  3.000
 3E3  H33  C8   H32  106.16  3.000
 3E3  H33  C8   C9   108.14  3.000
 3E3  H32  C8   C9   108.70  3.000
 3E3  H33  C8   C7   109.32  3.000
 3E3  H32  C8   C7   108.96  3.000
 3E3  C9   C8   C7   115.18  3.000
 3E3  H34  C9   C10  108.07  3.000
 3E3  H34  C9   C11  108.11  3.000
 3E3  C10  C9   C11  110.49  3.000
 3E3  H34  C9   C8   108.12  3.000
 3E3  C11  C9   C8   109.82  3.000
 3E3  C10  C9   C8   112.11  3.000
 3E3  H37  C11  H36  107.70  3.000
 3E3  H37  C11  H35  107.64  3.000
 3E3  H36  C11  H35  107.47  3.000
 3E3  H37  C11  C9   111.49  3.000
 3E3  H36  C11  C9   111.21  3.000
 3E3  H35  C11  C9   111.14  3.000
 3E3  H40  C10  H39  107.27  3.000
 3E3  H40  C10  H38  107.38  3.000
 3E3  H39  C10  H38  107.94  3.000
 3E3  H40  C10  C9   110.99  3.000
 3E3  H39  C10  C9   112.11  3.000
 3E3  H38  C10  C9   110.95  3.000
 3E3  H41  C12  C13  108.50  3.000
 3E3  H41  C12  O2   107.94  3.000
 3E3  C13  C12  O2   110.05  3.000
 3E3  H41  C12  C7   107.24  3.000
 3E3  O2   C12  C7   111.97  3.000
 3E3  C13  C12  C7   111.00  3.000
 3E3  H42  O2   C12  107.58  3.000
 3E3  N2   C13  O1   124.30  3.000
 3E3  N2   C13  C12  114.80  3.000
 3E3  O1   C13  C12  120.87  3.000
 3E3  H43  N2   C14  116.87  3.000
 3E3  H43  N2   C13  117.12  3.000
 3E3  C14  N2   C13  125.81  3.000
 3E3  C15  C14  C21  120.19  3.000
 3E3  C15  C14  N2   118.55  3.000
 3E3  C21  C14  N2   121.25  3.000
 3E3  H44  C21  C20  119.53  3.000
 3E3  H44  C21  C14  120.30  3.000
 3E3  C20  C21  C14  120.16  3.000
 3E3  H45  C20  C18  119.85  3.000
 3E3  H45  C20  C21  119.15  3.000
 3E3  C18  C20  C21  121.00  3.000
 3E3  C17  C18  C19  121.23  3.000
 3E3  C17  C18  C20  117.91  3.000
 3E3  C19  C18  C20  120.85  3.000
 3E3  H48  C19  H47  107.98  3.000
 3E3  H48  C19  H46  107.10  3.000
 3E3  H47  C19  H46  107.50  3.000
 3E3  H48  C19  C18  111.33  3.000
 3E3  H47  C19  C18  111.56  3.000
 3E3  H46  C19  C18  111.17  3.000
 3E3  H49  C17  C15  118.43  3.000
 3E3  H49  C17  C18  119.14  3.000
 3E3  C15  C17  C18  122.42  3.000
 3E3  C16  C15  C17  120.66  3.000
 3E3  C16  C15  C14  121.03  3.000
 3E3  C17  C15  C14  118.31  3.000
 3E3  H52  C16  H51  107.15  3.000
 3E3  H52  C16  H50  107.06  3.000
 3E3  H51  C16  H50  107.61  3.000
 3E3  H52  C16  C15  112.24  3.000
 3E3  H51  C16  C15  110.93  3.000
 3E3  H50  C16  C15  111.61  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
 3E3  CONST_01  C18  C20  C21  C14    0.00   0.0  0
 3E3  CONST_02  C18  C17  C15  C14    0.00   0.0  0
 3E3  CONST_03  C17  C18  C20  C21    0.00   0.0  0
 3E3  CONST_04  C17  C15  C14  C21    0.00   0.0  0
 3E3  CONST_05  C15  C14  C21  C20    0.00   0.0  0
 3E3  CONST_06  C15  C17  C18  C20    0.00   0.0  0
 3E3  CONST_07  C20  C21  C14  N2   180.00   0.0  0
 3E3  CONST_08  C17  C15  C14  N2   180.00   0.0  0
 3E3  CONST_09  C19  C18  C20  C21  180.00   0.0  0
 3E3  CONST_10  C16  C15  C14  C21  180.00   0.0  0
 3E3  CONST_11  C16  C15  C17  C18  180.00   0.0  0
 3E3  CONST_12  C15  C17  C18  C19  180.00   0.0  0
 3E3  CONST_13  H45  C20  C21  C14  180.00   0.0  0
 3E3  CONST_14  H49  C17  C15  C14  180.00   0.0  0
 3E3  CONST_15  H44  C21  C20  C18  180.00   0.0  0
 3E3  CONST_19  C14  N2   C13  C12  180.00   0.0  0
 3E3  CONST_20  C14  N2   C13  O1     0.00   0.0  0
 3E3  Var_01    H50  C16  C15  C14   57.51  30.0  2
 3E3  Var_02    H46  C19  C18  C20   72.42  30.0  2
 3E3  Var_03    C10  C9   C8   C7   -59.76  30.0  3
 3E3  Var_04    H38  C10  C9   C8   -58.57  30.0  3
 3E3  Var_05    H35  C11  C9   C8    62.78  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
 3E3  chir_01  C7   C8  C12  N1   negativ
 3E3  chir_02  C12  O2  C7   C13  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
 3E3  plan-1  N2   0.020
 3E3  plan-1  C14  0.020
 3E3  plan-1  C21  0.020
 3E3  plan-1  C20  0.020
 3E3  plan-1  C18  0.020
 3E3  plan-1  C19  0.020
 3E3  plan-1  C17  0.020
 3E3  plan-1  C15  0.020
 3E3  plan-1  C16  0.020
 3E3  plan-1  H44  0.020
 3E3  plan-1  H45  0.020
 3E3  plan-1  H49  0.020
 3E3  plan-2  C12  0.020
 3E3  plan-2  C13  0.020
 3E3  plan-2  O1   0.020
 3E3  plan-2  N2   0.020
 3E3  plan-2  C14  0.020
 3E3  plan-2  H43  0.020

