# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 08:50:06 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  42  19  .  2021-08-07  2021-08-07  
;
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  -0.591   3.2832  -2.3551   0.3703
 C3H  C11  C  C      0   0.400   4.2027  -1.7147  -0.1761
 C3H  O3   O  OC    -1  -0.609   5.2702  -2.1574  -0.6326
 C3H  C10  C  CH2    0  -0.410   4.0099  -0.1887  -0.3076
 C3H  N1   N  NH1    0  -0.625   2.7419   0.2057   0.2472
 C3H  C9   C  C      0   0.520   2.2213   1.4317   0.1866
 C3H  O1   O  O      0  -0.504   2.7999   2.3962  -0.3007
 C3H  C8   C  CH1    0  -0.215   0.7913   1.5367   0.7334
 C3H  N    N  NH2    0  -0.770   0.4304   2.8428   1.2272
 C3H  C7   C  CH2    0  -0.546  -0.1596   1.1225  -0.3873
 C3H  S    S  S2     0  -0.016  -1.8595   1.0932   0.2437
 C3H  C3   C  CT     0  -0.210  -2.6559  -0.2411  -0.7554
 C3H  C4   C  CH3    0  -0.633  -2.7793   0.2013  -2.2120
 C3H  C5   C  CH2    0  -0.446  -4.0373  -0.4568  -0.1186
 C3H  C6   C  CH2    0  -0.143  -5.0104   0.7064  -0.2226
 C3H  O    O  OH1    0  -0.675  -6.1791   0.3517   0.4886
 C3H  C2   C  CH2    0  -0.400  -1.8617  -1.5556  -0.7080
 C3H  C1   C  CH2    0  -0.428  -1.4909  -2.1043   0.6643
 C3H  C    C  CH3    0  -0.665  -0.5527  -3.3008   0.5615
 C3H  H2   H  HCH2   0   0.241   4.8369   0.3192   0.1984
 C3H  H3   H  HCH2   0   0.241   4.0761   0.0890  -1.3642
 C3H  H4   H  HNH1   0   0.384   2.2249  -0.5555   0.6676
 C3H  H5   H  HCH1   0   0.259   0.6792   0.8192   1.5523
 C3H  H6   H  HNH2   0   0.354   1.0088   3.0866   2.0214
 C3H  H7   H  HNH2   0   0.343   0.6254   3.5383   0.5161
 C3H  H9   H  HCH2   0   0.272  -0.0750   1.8155  -1.2281
 C3H  H10  H  HCH2   0   0.269   0.1102   0.1311  -0.7488
 C3H  H11  H  HCH3   0   0.239  -1.7976   0.2962  -2.6786
 C3H  H12  H  HCH3   0   0.230  -3.3455  -0.5373  -2.7861
 C3H  H13  H  HCH3   0   0.236  -3.2839   1.1619  -2.3088
 C3H  H14  H  HCH2   0   0.240  -4.4865  -1.3302  -0.6042
 C3H  H15  H  HCH2   0   0.245  -3.9133  -0.7150   0.9368
 C3H  H16  H  HCH2   0   0.195  -4.5595   1.6192   0.1859
 C3H  H17  H  HCH2   0   0.198  -5.2390   0.9112  -1.2749
 C3H  H18  H  HOH1   0   0.453  -6.8206   1.0590   0.3788
 C3H  H19  H  HCH2   0   0.236  -2.4563  -2.3035  -1.2454
 C3H  H20  H  HCH2   0   0.228  -0.9502  -1.4445  -1.3047
 C3H  H21  H  HCH2   0   0.219  -1.0125  -1.3204   1.2566
 C3H  H22  H  HCH2   0   0.222  -2.3915  -2.3939   1.2118
 C3H  H23  H  HCH3   0   0.226  -0.3383  -3.7201   1.5452
 C3H  H24  H  HCH3   0   0.215  -0.9840  -4.0969  -0.0483
 C3H  H25  H  HCH3   0   0.221   0.4017  -3.0172   0.1132

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  1.226  0.020  1.226
 C3H  S    C7   single  1.813  0.020  1.813
 C3H  S    C3   single  1.847  0.020  1.847
 C3H  O2   C11  deloc   1.247  0.020  1.247
 C3H  C7   C8   single  1.527  0.020  1.527
 C3H  C9   N1   single  1.333  0.020  1.333
 C3H  C9   C8   single  1.535  0.020  1.535
 C3H  C11  O3   deloc   1.243  0.020  1.243
 C3H  C11  C10  single  1.544  0.020  1.544
 C3H  C2   C3   single  1.537  0.020  1.537
 C3H  C2   C1   single  1.524  0.020  1.524
 C3H  C    C1   single  1.524  0.020  1.524
 C3H  N1   C10  single  1.439  0.020  1.439
 C3H  C3   C4   single  1.527  0.020  1.527
 C3H  C3   C5   single  1.536  0.020  1.536
 C3H  C8   N    single  1.442  0.020  1.442
 C3H  C5   C6   single  1.520  0.020  1.520
 C3H  C6   O    single  1.413  0.020  1.413
 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   115.35  3.000
 C3H  C10  C11  O2   116.94  3.000
 C3H  O3   C11  O2   127.71  3.000
 C3H  H3   C10  H2   106.43  3.000
 C3H  H3   C10  N1   110.85  3.000
 C3H  H2   C10  N1   111.12  3.000
 C3H  H3   C10  C11  109.00  3.000
 C3H  H2   C10  C11  108.96  3.000
 C3H  N1   C10  C11  110.37  3.000
 C3H  H4   N1   C9   120.75  3.000
 C3H  H4   N1   C10  113.85  3.000
 C3H  C9   N1   C10  125.34  3.000
 C3H  C8   C9   O1   121.85  3.000
 C3H  C8   C9   N1   114.24  3.000
 C3H  O1   C9   N1   123.87  3.000
 C3H  H5   C8   C7   107.91  3.000
 C3H  H5   C8   N    108.17  3.000
 C3H  C7   C8   N    109.95  3.000
 C3H  H5   C8   C9   108.49  3.000
 C3H  N    C8   C9   114.66  3.000
 C3H  C7   C8   C9   107.47  3.000
 C3H  H7   N    H6   105.98  3.000
 C3H  H7   N    C8   109.45  3.000
 C3H  H6   N    C8   110.11  3.000
 C3H  H10  C7   H9   107.62  3.000
 C3H  H10  C7   S    109.45  3.000
 C3H  H9   C7   S    110.52  3.000
 C3H  H10  C7   C8   109.65  3.000
 C3H  H9   C7   C8   110.14  3.000
 C3H  S    C7   C8   109.43  3.000
 C3H  C3   S    C7   103.15  3.000
 C3H  C2   C3   C5   109.38  3.000
 C3H  C5   C3   C4   111.30  3.000
 C3H  C2   C3   C4   108.61  3.000
 C3H  C5   C3   S    105.36  3.000
 C3H  C4   C3   S    109.97  3.000
 C3H  C2   C3   S    112.23  3.000
 C3H  H13  C4   H12  108.01  3.000
 C3H  H13  C4   H11  107.58  3.000
 C3H  H12  C4   H11  107.45  3.000
 C3H  H13  C4   C3   112.19  3.000
 C3H  H12  C4   C3   110.30  3.000
 C3H  H11  C4   C3   111.12  3.000
 C3H  H15  C5   H14  106.62  3.000
 C3H  H15  C5   C6   108.62  3.000
 C3H  H14  C5   C6   108.49  3.000
 C3H  H15  C5   C3   109.35  3.000
 C3H  H14  C5   C3   107.27  3.000
 C3H  C6   C5   C3   116.09  3.000
 C3H  H17  C6   H16  106.72  3.000
 C3H  H17  C6   O    110.94  3.000
 C3H  H16  C6   O    111.18  3.000
 C3H  H17  C6   C5   110.01  3.000
 C3H  H16  C6   C5   110.37  3.000
 C3H  O    C6   C5   107.63  3.000
 C3H  H18  O    C6   108.04  3.000
 C3H  H20  C2   H19  104.69  3.000
 C3H  H20  C2   C1   108.95  3.000
 C3H  H19  C2   C1   109.14  3.000
 C3H  H20  C2   C3   109.06  3.000
 C3H  H19  C2   C3   106.75  3.000
 C3H  C1   C2   C3   117.49  3.000
 C3H  H22  C1   H21  106.22  3.000
 C3H  H22  C1   C    109.46  3.000
 C3H  H21  C1   C    109.28  3.000
 C3H  H22  C1   C2   110.24  3.000
 C3H  H21  C1   C2   109.65  3.000
 C3H  C    C1   C2   111.82  3.000
 C3H  H25  C    H24  107.78  3.000
 C3H  H25  C    H23  107.36  3.000
 C3H  H24  C    H23  107.53  3.000
 C3H  H25  C    C1   111.22  3.000
 C3H  H24  C    C1   111.53  3.000
 C3H  H23  C    C1   111.23  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  Var_01    N1   C10  C11  O2     -0.35  30.0  3
 C3H  Var_02    C9   N1   C10  C11  -173.80  30.0  1
 C3H  Var_03    C    C1   C2   C3   -172.36  30.0  3
 C3H  Var_04    O    C6   C5   C3   -176.31  30.0  3
 C3H  Var_05    H9   C7   S    C3     89.72  30.0  3
 C3H  Var_06    H23  C    C1   C2   -176.82  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

