# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 12 05:15:58 2022
#   Inital geometry file: a 99 line input string
#   Ligand name: N-[(3S)-2-oxotetrahydrofuran-3-yl]decanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCC(=O)N[C@H]1CCOC1=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
 HL0  HL0  N-[(3S)-2-oxotetrahydrofuran-3-yl]decanamide  ligand  43  18  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_HL0
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
 HL0  N     N  NH1   0  -0.643    3.1593  -0.5027   0.2236
 HL0  C1    C  CH3   0  -0.663   -9.3301  -0.4178  -0.4346
 HL0  O1    O  O     0  -0.484    2.1459   1.3422   1.0348
 HL0  C2    C  CH2   0  -0.419   -8.0985   0.2175   0.1954
 HL0  O2    O  O2    0  -0.437    6.0423  -0.1793  -1.0928
 HL0  C3    C  CH2   0  -0.406   -6.7934  -0.3398  -0.3584
 HL0  O3    O  O     0  -0.421    5.0569   1.7722  -0.7432
 HL0  C4    C  CH2   0  -0.412   -5.5534   0.2863   0.2674
 HL0  C5    C  CH2   0  -0.412   -4.2523  -0.2769  -0.2889
 HL0  C6    C  CH2   0  -0.413   -3.0069   0.3379   0.3369
 HL0  C7    C  CH2   0  -0.416   -1.7142  -0.2376  -0.2260
 HL0  C8    C  CH2   0  -0.413   -0.4630   0.3559   0.4089
 HL0  C9    C  CH2   0  -0.592    0.8024  -0.2429  -0.1848
 HL0  C10   C  C     0   0.575    2.0815   0.2896   0.4226
 HL0  C11   C  CH1   0  -0.257    4.4910  -0.1619   0.6644
 HL0  C12   C  CH2   0  -0.517    5.3836  -1.3840   0.8134
 HL0  C13   C  CH2   0  -0.181    6.0063  -1.5179  -0.5716
 HL0  C14   C  C     0   0.576    5.2054   0.6229  -0.4378
 HL0  HN    H  HNH1  0   0.409    3.0374  -1.3563  -0.2997
 HL0  H1    H  HCH3  0   0.226  -10.2510  -0.0034  -0.0227
 HL0  H1A   H  HCH3  0   0.216   -9.3490  -0.2567  -1.5142
 HL0  H1B   H  HCH3  0   0.216   -9.3489  -1.4961  -0.2645
 HL0  H2    H  HCH2  0   0.210   -8.1241   1.3005   0.0393
 HL0  H2A   H  HCH2  0   0.210   -8.1236   0.0692   1.2795
 HL0  H3    H  HCH2  0   0.206   -6.7681  -1.4245  -0.2041
 HL0  H3A   H  HCH2  0   0.206   -6.7667  -0.1911  -1.4438
 HL0  H4    H  HCH2  0   0.206   -5.5767   1.3708   0.1125
 HL0  H4A   H  HCH2  0   0.206   -5.5798   0.1369   1.3526
 HL0  H5    H  HCH2  0   0.207   -4.2339  -1.3621  -0.1381
 HL0  H5A   H  HCH2  0   0.207   -4.2253  -0.1247  -1.3737
 HL0  H6    H  HCH2  0   0.209   -3.0202   1.4228   0.1851
 HL0  H6A   H  HCH2  0   0.208   -3.0315   0.1843   1.4214
 HL0  H7    H  HCH2  0   0.211   -1.7116  -1.3243  -0.0869
 HL0  H7A   H  HCH2  0   0.211   -1.6851  -0.0738  -1.3089
 HL0  H8    H  HCH2  0   0.223   -0.4621   1.4402   0.2719
 HL0  H8A   H  HCH2  0   0.222   -0.4858   0.1812   1.4884
 HL0  H9    H  HCH2  0   0.257    0.7811  -1.3328  -0.0938
 HL0  H9A   H  HCH2  0   0.273    0.8401  -0.0388  -1.2609
 HL0  H11   H  HCH1  0   0.308    4.4278   0.4370   1.5717
 HL0  H12   H  HCH2  0   0.284    6.1544  -1.1823   1.5571
 HL0  H12A  H  HCH2  0   0.284    4.8445  -2.2781   1.1222
 HL0  H13   H  HCH2  0   0.253    5.4092  -2.1373  -1.2435
 HL0  H13A  H  HCH2  0   0.267    7.0234  -1.9029  -0.5542

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
 HL0  N    C10   single  1.352  0.020  1.352
 HL0  N    C11   single  1.444  0.020  1.444
 HL0  C1   C2    single  1.522  0.020  1.522
 HL0  O1   C10   double  1.219  0.020  1.219
 HL0  C2   C3    single  1.523  0.020  1.523
 HL0  O2   C13   single  1.437  0.020  1.437
 HL0  O2   C14   single  1.332  0.020  1.332
 HL0  C3   C4    single  1.524  0.020  1.524
 HL0  O3   C14   double  1.198  0.020  1.198
 HL0  C4   C5    single  1.523  0.020  1.523
 HL0  C5   C6    single  1.523  0.020  1.523
 HL0  C6   C7    single  1.523  0.020  1.523
 HL0  C7   C8    single  1.524  0.020  1.524
 HL0  C8   C9    single  1.521  0.020  1.521
 HL0  C9   C10   single  1.513  0.020  1.513
 HL0  C11  C12   single  1.521  0.020  1.521
 HL0  C11  C14   single  1.530  0.020  1.530
 HL0  C12  C13   single  1.524  0.020  1.524
 HL0  N    HN    single  0.860  0.020  1.020
 HL0  C1   H1    single  0.970  0.020  1.090
 HL0  C1   H1A   single  0.970  0.020  1.090
 HL0  C1   H1B   single  0.970  0.020  1.090
 HL0  C2   H2    single  0.970  0.020  1.090
 HL0  C2   H2A   single  0.970  0.020  1.090
 HL0  C3   H3    single  0.970  0.020  1.090
 HL0  C3   H3A   single  0.970  0.020  1.090
 HL0  C4   H4    single  0.970  0.020  1.090
 HL0  C4   H4A   single  0.970  0.020  1.090
 HL0  C5   H5    single  0.970  0.020  1.090
 HL0  C5   H5A   single  0.970  0.020  1.090
 HL0  C6   H6    single  0.970  0.020  1.090
 HL0  C6   H6A   single  0.970  0.020  1.090
 HL0  C7   H7    single  0.970  0.020  1.090
 HL0  C7   H7A   single  0.970  0.020  1.090
 HL0  C8   H8    single  0.970  0.020  1.090
 HL0  C8   H8A   single  0.970  0.020  1.090
 HL0  C9   H9    single  0.970  0.020  1.090
 HL0  C9   H9A   single  0.970  0.020  1.090
 HL0  C11  H11   single  0.970  0.020  1.090
 HL0  C12  H12   single  0.970  0.020  1.090
 HL0  C12  H12A  single  0.970  0.020  1.090
 HL0  C13  H13   single  0.970  0.020  1.090
 HL0  C13  H13A  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
 HL0  HN    N    C11  118.02  3.000
 HL0  HN    N    C10  118.41  3.000
 HL0  C11   N    C10  123.50  3.000
 HL0  H1B   C1   H1A  107.43  3.000
 HL0  H1B   C1   H1   107.57  3.000
 HL0  H1A   C1   H1   107.62  3.000
 HL0  H1B   C1   C2   111.20  3.000
 HL0  H1A   C1   C2   111.20  3.000
 HL0  H1    C1   C2   111.61  3.000
 HL0  H2A   C2   H2   105.95  3.000
 HL0  H2A   C2   C3   109.28  3.000
 HL0  H2    C2   C3   109.28  3.000
 HL0  H2A   C2   C1   109.56  3.000
 HL0  H2    C2   C1   109.58  3.000
 HL0  C3    C2   C1   112.96  3.000
 HL0  C14   O2   C13  111.53  3.000
 HL0  H3A   C3   H3   105.86  3.000
 HL0  H3A   C3   C4   109.34  3.000
 HL0  H3    C3   C4   109.28  3.000
 HL0  H3A   C3   C2   109.35  3.000
 HL0  H3    C3   C2   109.31  3.000
 HL0  C4    C3   C2   113.43  3.000
 HL0  H4A   C4   H4   105.92  3.000
 HL0  H4A   C4   C5   109.38  3.000
 HL0  H4    C4   C5   109.42  3.000
 HL0  H4A   C4   C3   109.34  3.000
 HL0  H4    C4   C3   109.35  3.000
 HL0  C5    C4   C3   113.16  3.000
 HL0  H5A   C5   H5   105.87  3.000
 HL0  H5A   C5   C6   109.30  3.000
 HL0  H5    C5   C6   109.23  3.000
 HL0  H5A   C5   C4   109.35  3.000
 HL0  H5    C5   C4   109.28  3.000
 HL0  C6    C5   C4   113.52  3.000
 HL0  H6A   C6   H6   106.00  3.000
 HL0  H6A   C6   C7   109.39  3.000
 HL0  H6    C6   C7   109.47  3.000
 HL0  H6A   C6   C5   109.37  3.000
 HL0  H6    C6   C5   109.44  3.000
 HL0  C7    C6   C5   112.93  3.000
 HL0  H7A   C7   H7   105.89  3.000
 HL0  H7A   C7   C8   109.38  3.000
 HL0  H7    C7   C8   109.36  3.000
 HL0  H7A   C7   C6   109.35  3.000
 HL0  H7    C7   C6   109.27  3.000
 HL0  C8    C7   C6   113.32  3.000
 HL0  H8A   C8   H8   106.39  3.000
 HL0  H8A   C8   C9   109.86  3.000
 HL0  H8    C8   C9   109.95  3.000
 HL0  H8A   C8   C7   109.38  3.000
 HL0  H8    C8   C7   109.57  3.000
 HL0  C9    C8   C7   111.55  3.000
 HL0  H9A   C9   H9   105.54  3.000
 HL0  H9A   C9   C10  107.44  3.000
 HL0  H9    C9   C10  109.50  3.000
 HL0  H9A   C9   C8   109.79  3.000
 HL0  H9    C9   C8   110.10  3.000
 HL0  C10   C9   C8   114.09  3.000
 HL0  C9    C10  O1   123.37  3.000
 HL0  C9    C10  N    114.11  3.000
 HL0  O1    C10  N    122.51  3.000
 HL0  H11   C11  C14  110.20  3.000
 HL0  H11   C11  C12  113.23  3.000
 HL0  C14   C11  C12  102.05  3.000
 HL0  H11   C11  N    109.31  3.000
 HL0  C14   C11  N    109.38  3.000
 HL0  C12   C11  N    112.44  3.000
 HL0  H12A  C12  H12  107.98  3.000
 HL0  H12A  C12  C13  112.82  3.000
 HL0  H12   C12  C13  110.32  3.000
 HL0  H12A  C12  C11  113.40  3.000
 HL0  H12   C12  C11  109.46  3.000
 HL0  C13   C12  C11  102.79  3.000
 HL0  H13A  C13  H13  108.69  3.000
 HL0  H13A  C13  C12  113.49  3.000
 HL0  H13   C13  C12  112.68  3.000
 HL0  H13A  C13  O2   108.19  3.000
 HL0  H13   C13  O2   108.60  3.000
 HL0  C12   C13  O2   104.95  3.000
 HL0  C11   C14  O3   128.14  3.000
 HL0  C11   C14  O2   109.80  3.000
 HL0  O3    C14  O2   122.03  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
 HL0  CONST_01  C11  N    C10  O1     0.00   0.0  0
 HL0  CONST_02  C11  N    C10  C9   180.00   0.0  0
 HL0  CONST_03  HN   N    C10  O1   180.00   0.0  0
 HL0  Var_01    C11  C12  C13  O2    28.68  30.0  1
 HL0  Var_02    C8   C9   C10  N    160.33  30.0  1
 HL0  Var_03    C4   C3   C2   C1  -179.85  30.0  3
 HL0  Var_04    C5   C4   C3   C2   179.90  30.0  3
 HL0  Var_05    C6   C5   C4   C3  -179.67  30.0  3
 HL0  Var_06    C7   C6   C5   C4   179.83  30.0  3
 HL0  Var_07    C8   C7   C6   C5  -179.12  30.0  3
 HL0  Var_08    C9   C8   C7   C6  -179.82  30.0  3
 HL0  Var_09    C10  C9   C8   C7  -178.99  30.0  3
 HL0  Var_10    H1   C1   C2   C3   180.00  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
 HL0  chir_01  C11  N  C12  C14  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
 HL0  plan-1  N    0.020
 HL0  plan-1  O1   0.020
 HL0  plan-1  C9   0.020
 HL0  plan-1  C10  0.020
 HL0  plan-1  C11  0.020
 HL0  plan-1  HN   0.020
 HL0  plan-2  O2   0.020
 HL0  plan-2  O3   0.020
 HL0  plan-2  C11  0.020
 HL0  plan-2  C14  0.020

