# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 16:52:59 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: 2-[[(2~{R})-2-azanyl-3-[(3~{S})-3-methyl-1-oxidanyl-hexan-3-yl]sulfanyl-propanoyl]amino]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC[C@@](C)(CCO)SC[C@H](N)C(=O)NCC(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
 C3H  C3H  '2-[[(2~{R})-2-azanyl-3-[(3~{S})-3-methyl-1-oxidanyl-hexan-3-yl]sulfanyl-propanoyl]amino]ethanoic acid'  ligand  43  19  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C3H
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
 C3H  O2   O  O     0  -0.434   4.3109  -1.9109  -0.1976
 C3H  C11  C  C     0   0.521   4.8501  -0.9293  -0.6409
 C3H  O3   O  OH1   0  -0.585   6.0207  -0.9324  -1.2540
 C3H  C10  C  CH2   0  -0.368   4.2829   0.4646  -0.5669
 C3H  N1   N  NH1   0  -0.642   3.0051   0.4486   0.0887
 C3H  C9   C  C     0   0.538   2.2605   1.5552   0.2244
 C3H  O1   O  O     0  -0.487   2.6203   2.6487  -0.1851
 C3H  C8   C  CH1   0  -0.215   0.8976   1.3437   0.8953
 C3H  N    N  NH2   0  -0.766   0.3901   2.5151   1.5647
 C3H  C7   C  CH2   0  -0.551  -0.0841   0.8867  -0.1832
 C3H  S    S  S2    0   0.005  -1.7368   0.7350   0.5478
 C3H  C3   C  CT    0  -0.213  -2.5848  -0.4228  -0.6127
 C3H  C4   C  CH3   0  -0.648  -2.3859   0.0287  -2.0572
 C3H  C5   C  CH2   0  -0.454  -4.0689  -0.3838  -0.2211
 C3H  C6   C  CH2   0  -0.139  -4.8076   0.8996  -0.5619
 C3H  O    O  OH1   0  -0.676  -6.1103   0.8039  -0.0210
 C3H  C2   C  CH2   0  -0.372  -2.0391  -1.8494  -0.4625
 C3H  C1   C  CH2   0  -0.428  -2.2140  -2.5160   0.8951
 C3H  C    C  CH3   0  -0.659  -1.5271  -3.8744   0.9491
 C3H  H1   H  HOH1  0   0.490   6.3765  -1.8327  -1.2975
 C3H  H2   H  HCH2  0   0.291   4.9987   1.1033  -0.0396
 C3H  H3   H  HCH2  0   0.292   4.2015   0.8633  -1.5823
 C3H  H4   H  HNH1  0   0.404   2.6846  -0.4260   0.4756
 C3H  H5   H  HCH1  0   0.265   0.9884   0.5423   1.6351
 C3H  H6   H  HNH2  0   0.357   1.0058   2.7802   2.3229
 C3H  H7   H  HNH2  0   0.346   0.3709   3.3002   0.9245
 C3H  H9   H  HCH2  0   0.270  -0.1011   1.6054  -1.0058
 C3H  H10  H  HCH2  0   0.269   0.2308  -0.0747  -0.5913
 C3H  H11  H  HCH3  0   0.240  -1.3524  -0.1103  -2.3773
 C3H  H12  H  HCH3  0   0.239  -3.0146  -0.5660  -2.7246
 C3H  H13  H  HCH3  0   0.240  -2.6389   1.0783  -2.2022
 C3H  H14  H  HCH2  0   0.242  -4.5628  -1.2208  -0.7274
 C3H  H15  H  HCH2  0   0.243  -4.1709  -0.5690   0.8526
 C3H  H16  H  HCH2  0   0.193  -4.2681   1.7627  -0.1533
 C3H  H17  H  HCH2  0   0.198  -4.8449   1.0341  -1.6491
 C3H  H18  H  HOH1  0   0.453  -6.6094   1.5715  -0.3132
 C3H  H19  H  HCH2  0   0.225  -2.5276  -2.4648  -1.2282
 C3H  H20  H  HCH2  0   0.222  -0.9755  -1.8518  -0.7250
 C3H  H21  H  HCH2  0   0.216  -1.8025  -1.8677   1.6727
 C3H  H22  H  HCH2  0   0.220  -3.2760  -2.6405   1.1220
 C3H  H23  H  HCH3  0   0.227  -1.6470  -4.3412   1.9274
 C3H  H24  H  HCH3  0   0.216  -1.9376  -4.5592   0.2046
 C3H  H25  H  HCH3  0   0.216  -0.4569  -3.7812   0.7544

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
 C3H  O1   C9   double  1.222  0.020  1.222
 C3H  S    C7   single  1.814  0.020  1.814
 C3H  S    C3   single  1.846  0.020  1.846
 C3H  O2   C11  double  1.205  0.020  1.205
 C3H  C7   C8   single  1.528  0.020  1.528
 C3H  C9   N1   single  1.341  0.020  1.341
 C3H  C9   C8   single  1.534  0.020  1.534
 C3H  C11  O3   single  1.321  0.020  1.321
 C3H  C11  C10  single  1.507  0.020  1.507
 C3H  C2   C3   single  1.535  0.020  1.535
 C3H  C2   C1   single  1.523  0.020  1.523
 C3H  C    C1   single  1.523  0.020  1.523
 C3H  N1   C10  single  1.436  0.020  1.436
 C3H  C3   C4   single  1.526  0.020  1.526
 C3H  C3   C5   single  1.535  0.020  1.535
 C3H  C8   N    single  1.441  0.020  1.441
 C3H  C5   C6   single  1.519  0.020  1.519
 C3H  C6   O    single  1.414  0.020  1.414
 C3H  O3   H1   single  0.850  0.020  0.980
 C3H  C10  H2   single  0.970  0.020  1.090
 C3H  C10  H3   single  0.970  0.020  1.090
 C3H  N1   H4   single  0.860  0.020  1.020
 C3H  C8   H5   single  0.970  0.020  1.090
 C3H  N    H6   single  0.890  0.020  1.040
 C3H  N    H7   single  0.890  0.020  1.040
 C3H  C7   H9   single  0.970  0.020  1.090
 C3H  C7   H10  single  0.970  0.020  1.090
 C3H  C4   H11  single  0.970  0.020  1.090
 C3H  C4   H12  single  0.970  0.020  1.090
 C3H  C4   H13  single  0.970  0.020  1.090
 C3H  C5   H14  single  0.970  0.020  1.090
 C3H  C5   H15  single  0.970  0.020  1.090
 C3H  C6   H16  single  0.970  0.020  1.090
 C3H  C6   H17  single  0.970  0.020  1.090
 C3H  O    H18  single  0.850  0.020  0.980
 C3H  C2   H19  single  0.970  0.020  1.090
 C3H  C2   H20  single  0.970  0.020  1.090
 C3H  C1   H21  single  0.970  0.020  1.090
 C3H  C1   H22  single  0.970  0.020  1.090
 C3H  C    H23  single  0.970  0.020  1.090
 C3H  C    H24  single  0.970  0.020  1.090
 C3H  C    H25  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
 C3H  C10  C11  O3   111.00  3.000
 C3H  C10  C11  O2   124.56  3.000
 C3H  O3   C11  O2   124.43  3.000
 C3H  H1   O3   C11  110.38  3.000
 C3H  H3   C10  H2   106.45  3.000
 C3H  H3   C10  N1   111.20  3.000
 C3H  H2   C10  N1   111.61  3.000
 C3H  H3   C10  C11  108.64  3.000
 C3H  H2   C10  C11  108.50  3.000
 C3H  N1   C10  C11  110.30  3.000
 C3H  H4   N1   C9   120.03  3.000
 C3H  H4   N1   C10  117.87  3.000
 C3H  C9   N1   C10  122.08  3.000
 C3H  C8   C9   O1   122.12  3.000
 C3H  C8   C9   N1   115.09  3.000
 C3H  O1   C9   N1   122.77  3.000
 C3H  H5   C8   C7   108.14  3.000
 C3H  H5   C8   N    108.08  3.000
 C3H  C7   C8   N    110.15  3.000
 C3H  H5   C8   C9   108.84  3.000
 C3H  N    C8   C9   113.83  3.000
 C3H  C7   C8   C9   107.66  3.000
 C3H  H7   N    H6   106.38  3.000
 C3H  H7   N    C8   110.06  3.000
 C3H  H6   N    C8   110.27  3.000
 C3H  H10  C7   H9   107.61  3.000
 C3H  H10  C7   S    109.89  3.000
 C3H  H9   C7   S    110.14  3.000
 C3H  H10  C7   C8   110.00  3.000
 C3H  H9   C7   C8   110.16  3.000
 C3H  S    C7   C8   109.02  3.000
 C3H  C3   S    C7   102.58  3.000
 C3H  C2   C3   C5   110.02  3.000
 C3H  C5   C3   C4   111.09  3.000
 C3H  C2   C3   C4   108.74  3.000
 C3H  C5   C3   S    105.53  3.000
 C3H  C4   C3   S    110.46  3.000
 C3H  C2   C3   S    110.99  3.000
 C3H  H13  C4   H12  108.02  3.000
 C3H  H13  C4   H11  107.68  3.000
 C3H  H12  C4   H11  107.24  3.000
 C3H  H13  C4   C3   112.38  3.000
 C3H  H12  C4   C3   110.00  3.000
 C3H  H11  C4   C3   111.32  3.000
 C3H  H15  C5   H14  106.38  3.000
 C3H  H15  C5   C6   108.52  3.000
 C3H  H14  C5   C6   108.81  3.000
 C3H  H15  C5   C3   109.64  3.000
 C3H  H14  C5   C3   107.36  3.000
 C3H  C6   C5   C3   115.74  3.000
 C3H  H17  C6   H16  106.83  3.000
 C3H  H17  C6   O    110.89  3.000
 C3H  H16  C6   O    111.34  3.000
 C3H  H17  C6   C5   110.04  3.000
 C3H  H16  C6   C5   110.00  3.000
 C3H  O    C6   C5   107.76  3.000
 C3H  H18  O    C6   107.95  3.000
 C3H  H20  C2   H19  105.30  3.000
 C3H  H20  C2   C1   108.92  3.000
 C3H  H19  C2   C1   109.00  3.000
 C3H  H20  C2   C3   108.89  3.000
 C3H  H19  C2   C3   107.14  3.000
 C3H  C1   C2   C3   116.96  3.000
 C3H  H22  C1   H21  106.61  3.000
 C3H  H22  C1   C    109.22  3.000
 C3H  H21  C1   C    109.51  3.000
 C3H  H22  C1   C2   110.28  3.000
 C3H  H21  C1   C2   109.36  3.000
 C3H  C    C1   C2   111.73  3.000
 C3H  H25  C    H24  107.49  3.000
 C3H  H25  C    H23  107.71  3.000
 C3H  H24  C    H23  107.58  3.000
 C3H  H25  C    C1   111.07  3.000
 C3H  H24  C    C1   111.45  3.000
 C3H  H23  C    C1   111.34  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
 C3H  CONST_01  O1   C9   N1   C10     0.00   0.0  0
 C3H  CONST_02  C8   C9   N1   C10   180.00   0.0  0
 C3H  CONST_03  H4   N1   C9   O1    180.00   0.0  0
 C3H  CONST_04  H1   O3   C11  O2      0.00   0.0  0
 C3H  Var_01    N1   C10  C11  O2     -0.80  30.0  3
 C3H  Var_02    C9   N1   C10  C11  -176.73  30.0  1
 C3H  Var_03    C    C1   C2   C3   -175.09  30.0  3
 C3H  Var_04    O    C6   C5   C3   -174.59  30.0  3
 C3H  Var_05    H9   C7   S    C3     81.03  30.0  3
 C3H  Var_06    H23  C    C1   C2    179.37  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
 C3H  chir_01  C8  C7  C9  N   negativ
 C3H  chir_02  C3  C2  C4  C5  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
 C3H  plan-1  C10  0.020
 C3H  plan-1  N1   0.020
 C3H  plan-1  C9   0.020
 C3H  plan-1  O1   0.020
 C3H  plan-1  C8   0.020
 C3H  plan-1  H4   0.020
 C3H  plan-2  O2   0.020
 C3H  plan-2  C11  0.020
 C3H  plan-2  O3   0.020
 C3H  plan-2  C10  0.020
 C3H  plan-2  H1   0.020

