# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 28 23:03:16 2022
#   Inital geometry file: a 87 line input string
#   Ligand name: O-octanoyl-D-serine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCC(=O)OC[C@@H](N)C(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
 1IC  1IC  "O-octanoyl-D-serine"  D-peptide  36  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 GRAND (side chain)
;

data_comp_1IC
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
 1IC  N    N  NH2    0  -0.809  137.6251  136.2117  164.1332
 1IC  CA   C  CH1    0  -0.271  137.7625  137.1398  165.2430
 1IC  CB   C  CH2    0  -0.143  137.8562  138.5626  164.7322
 1IC  C    C  C      0   0.421  139.0136  136.7975  166.1006
 1IC  O    O  O      0  -0.594  139.4118  135.6188  166.0538
 1IC  OG   O  O2     0  -0.466  136.6591  138.8423  163.9860
 1IC  C08  C  C      0   0.603  136.5471  140.0286  163.4053
 1IC  C09  C  CH2    0  -0.588  135.2594  140.1409  162.6300
 1IC  C10  C  CH2    0  -0.421  135.0906  141.4704  161.9096
 1IC  C11  C  CH2    0  -0.433  133.9081  141.4815  160.9449
 1IC  C12  C  CH2    0  -0.430  132.5427  141.3536  161.6127
 1IC  C13  C  CH2    0  -0.411  131.3765  141.3541  160.6264
 1IC  C14  C  CH2    0  -0.423  131.1739  142.6718  159.8868
 1IC  C15  C  CH3    0  -0.657  129.9769  142.6360  158.9461
 1IC  O16  O  O      0  -0.453  137.3831  140.8948  163.4920
 1IC  H1   H  HNH2   0   0.336  137.9199  135.2999  164.4577
 1IC  H2   H  HNH2   0   0.333  136.6560  136.1296  163.8577
 1IC  H4   H  HCH1   0   0.211  136.9049  137.0903  165.9370
 1IC  H5   H  HCH2   0   0.216  138.7262  138.6739  164.0793
 1IC  H6   H  HCH2   0   0.223  137.9466  139.2672  165.5576
 1IC  H8   H  HCH2   0   0.273  134.4333  139.9563  163.3230
 1IC  H9   H  HCH2   0   0.266  135.2242  139.3145  161.9121
 1IC  H10  H  HCH2   0   0.230  135.9994  141.6931  161.3466
 1IC  H11  H  HCH2   0   0.222  134.9751  142.2772  162.6385
 1IC  H12  H  HCH2   0   0.210  134.0313  140.6704  160.2182
 1IC  H13  H  HCH2   0   0.229  133.9487  142.4101  160.3700
 1IC  H14  H  HCH2   0   0.207  132.4117  142.1708  162.3309
 1IC  H15  H  HCH2   0   0.225  132.5029  140.4289  162.1958
 1IC  H16  H  HCH2   0   0.215  130.4554  141.1107  161.1655
 1IC  H17  H  HCH2   0   0.205  131.5209  140.5479  159.8984
 1IC  H18  H  HCH2   0   0.215  132.0699  142.9250  159.3142
 1IC  H19  H  HCH2   0   0.208  131.0437  143.4769  160.6171
 1IC  H20  H  HCH3   0   0.224  129.8461  143.5861  158.4271
 1IC  H21  H  HCH3   0   0.215  130.0972  141.8596  158.1885
 1IC  H22  H  HCH3   0   0.214  129.0532  142.4253  159.4883
 1IC  OXT  O  OC    -1  -0.599  139.4851  137.7245  166.7861

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
 1IC  C15  C14  single  1.523  0.020  1.523
 1IC  C14  C13  single  1.525  0.020  1.525
 1IC  C13  C12  single  1.527  0.020  1.527
 1IC  C11  C12  single  1.525  0.020  1.525
 1IC  C11  C10  single  1.526  0.020  1.526
 1IC  C10  C09  single  1.521  0.020  1.521
 1IC  O16  C08  double  1.207  0.020  1.207
 1IC  C09  C08  single  1.507  0.020  1.507
 1IC  C08  OG   single  1.326  0.020  1.326
 1IC  OG   CB   single  1.438  0.020  1.438
 1IC  N    CA   single  1.458  0.019  1.458
 1IC  CB   CA   single  1.521  0.033  1.521
 1IC  CA   C    single  1.525  0.021  1.525
 1IC  C    O    deloc   1.231  0.020  1.231
 1IC  N    H1   single  0.890  0.020  1.040
 1IC  N    H2   single  0.890  0.020  1.040
 1IC  CA   H4   single  0.970  0.020  1.090
 1IC  CB   H5   single  0.970  0.020  1.090
 1IC  CB   H6   single  0.970  0.020  1.090
 1IC  C09  H8   single  0.970  0.020  1.090
 1IC  C09  H9   single  0.970  0.020  1.090
 1IC  C10  H10  single  0.970  0.020  1.090
 1IC  C10  H11  single  0.970  0.020  1.090
 1IC  C11  H12  single  0.970  0.020  1.090
 1IC  C11  H13  single  0.970  0.020  1.090
 1IC  C12  H14  single  0.970  0.020  1.090
 1IC  C12  H15  single  0.970  0.020  1.090
 1IC  C13  H16  single  0.970  0.020  1.090
 1IC  C13  H17  single  0.970  0.020  1.090
 1IC  C14  H18  single  0.970  0.020  1.090
 1IC  C14  H19  single  0.970  0.020  1.090
 1IC  C15  H20  single  0.970  0.020  1.090
 1IC  C15  H21  single  0.970  0.020  1.090
 1IC  C15  H22  single  0.970  0.020  1.090
 1IC  C    OXT  deloc   1.246  0.020  1.246

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
 1IC  H2   N    H1   107.08  3.000
 1IC  H2   N    CA   110.52  3.000
 1IC  H1   N    CA   107.65  3.000
 1IC  H4   CA   C    105.56  3.000
 1IC  H4   CA   CB   107.59  3.000
 1IC  C    CA   CB   110.50  1.500
 1IC  H4   CA   N    112.20  3.000
 1IC  C    CA   N    111.00  2.800
 1IC  CB   CA   N    110.40  1.500
 1IC  H6   CB   H5   108.70  3.000
 1IC  H6   CB   OG   109.66  3.000
 1IC  H5   CB   OG   109.43  3.000
 1IC  H6   CB   CA   110.93  3.000
 1IC  H5   CB   CA   110.26  3.000
 1IC  OG   CB   CA   107.83  3.000
 1IC  OXT  C    O    127.17  3.000
 1IC  OXT  C    CA   120.80  1.700
 1IC  O    C    CA   120.80  1.700
 1IC  C08  OG   CB   118.15  3.000
 1IC  O16  C08  C09  125.12  3.000
 1IC  C09  C08  OG   111.36  3.000
 1IC  O16  C08  OG   123.52  3.000
 1IC  H9   C09  H8   105.28  3.000
 1IC  H9   C09  C10  110.21  3.000
 1IC  H8   C09  C10  111.32  3.000
 1IC  H9   C09  C08  107.96  3.000
 1IC  H8   C09  C08  107.86  3.000
 1IC  C10  C09  C08  113.80  3.000
 1IC  H11  C10  H10  106.32  3.000
 1IC  H11  C10  C11  109.52  3.000
 1IC  H10  C10  C11  108.50  3.000
 1IC  H11  C10  C09  109.93  3.000
 1IC  H10  C10  C09  109.27  3.000
 1IC  C11  C10  C09  113.06  3.000
 1IC  H13  C11  H12  106.01  3.000
 1IC  H13  C11  C12  109.56  3.000
 1IC  H12  C11  C12  109.20  3.000
 1IC  H13  C11  C10  108.05  3.000
 1IC  H12  C11  C10  109.07  3.000
 1IC  C12  C11  C10  114.60  3.000
 1IC  H15  C12  H14  106.06  3.000
 1IC  H15  C12  C13  108.46  3.000
 1IC  H14  C12  C13  109.37  3.000
 1IC  H15  C12  C11  109.68  3.000
 1IC  H14  C12  C11  109.36  3.000
 1IC  C13  C12  C11  113.63  3.000
 1IC  H17  C13  H16  105.93  3.000
 1IC  H17  C13  C14  109.33  3.000
 1IC  H16  C13  C14  108.62  3.000
 1IC  H17  C13  C12  109.15  3.000
 1IC  H16  C13  C12  108.93  3.000
 1IC  C14  C13  C12  114.52  3.000
 1IC  H19  C14  H18  106.06  3.000
 1IC  H19  C14  C15  109.62  3.000
 1IC  H18  C14  C15  109.04  3.000
 1IC  H19  C14  C13  109.14  3.000
 1IC  H18  C14  C13  110.21  3.000
 1IC  C15  C14  C13  112.57  3.000
 1IC  H22  C15  H21  107.50  3.000
 1IC  H22  C15  H20  107.64  3.000
 1IC  H21  C15  H20  107.61  3.000
 1IC  H22  C15  C14  111.28  3.000
 1IC  H21  C15  C14  111.03  3.000
 1IC  H20  C15  C14  111.58  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
 1IC  Var_01  C08  OG   CB   CA   -177.80  30.0  1
 1IC  Var_02  O16  C08  OG   CB     -1.55  30.0  2
 1IC  Var_03  C09  C08  OG   CB    178.12  30.0  2
 1IC  Var_04  C10  C09  C08  OG   -178.48  30.0  1
 1IC  Var_05  C11  C10  C09  C08   170.21  30.0  1
 1IC  Var_06  C12  C11  C10  C09    65.71  30.0  1
 1IC  Var_07  C13  C12  C11  C10  -179.46  30.0  3
 1IC  Var_08  O16  C08  C09  C10     1.18  30.0  3
 1IC  Var_09  C14  C13  C12  C11   -66.51  30.0  1
 1IC  Var_10  C15  C14  C13  C12  -178.35  30.0  1
 1IC  Var_11  H8   C09  C08  OG     57.49  30.0  1
 1IC  Var_12  H9   C09  C08  OG    -55.81  30.0  1
 1IC  Var_13  H10  C10  C09  C08    49.26  30.0  1
 1IC  Var_14  H11  C10  C09  C08   -67.06  30.0  1
 1IC  Var_15  H5   CB   OG   C08   -57.85  30.0  3
 1IC  Var_16  H6   CB   OG   C08    61.30  30.0  3
 1IC  Var_17  H12  C11  C10  C09   -57.04  30.0  1
 1IC  Var_18  H13  C11  C10  C09  -171.85  30.0  1
 1IC  Var_19  H14  C12  C11  C10    58.03  30.0  3
 1IC  Var_20  H15  C12  C11  C10   -57.89  30.0  3
 1IC  Var_21  H16  C13  C12  C11   171.66  30.0  1
 1IC  Var_22  H17  C13  C12  C11    56.42  30.0  1
 1IC  Var_23  H8   C09  C10  C11   -67.65  30.0  3
 1IC  Var_24  H9   C09  C10  C11    48.78  30.0  3
 1IC  Var_25  H18  C14  C13  C12    59.69  30.0  1
 1IC  Var_26  H19  C14  C13  C12   -56.40  30.0  1
 1IC  Var_27  H10  C10  C11  C12  -172.92  30.0  3
 1IC  Var_28  H11  C10  C11  C12   -57.25  30.0  3
 1IC  Var_29  H20  C15  C14  C13   179.91  30.0  3
 1IC  Var_30  H21  C15  C14  C13   -60.04  30.0  3
 1IC  Var_31  H22  C15  C14  C13    59.67  30.0  3
 1IC  Var_32  H12  C11  C12  C13   -56.79  30.0  1
 1IC  Var_33  H13  C11  C12  C13    58.92  30.0  1
 1IC  Var_34  H14  C12  C13  C14    55.99  30.0  3
 1IC  Var_35  H15  C12  C13  C14   171.24  30.0  3
 1IC  Var_36  H16  C13  C14  C15   -56.34  30.0  3
 1IC  Var_37  H17  C13  C14  C15    58.82  30.0  3
 1IC  Var_38  H8   C09  C08  O16  -122.85  30.0  1
 1IC  Var_39  H9   C09  C08  O16   123.85  30.0  1

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
 1IC  chir_01  CA  N  CB  C  positiv

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
 1IC  plan-1  CA   0.020
 1IC  plan-1  C    0.020
 1IC  plan-1  O    0.020
 1IC  plan-1  OXT  0.020
 1IC  plan-2  OG   0.020
 1IC  plan-2  C08  0.020
 1IC  plan-2  C09  0.020
 1IC  plan-2  O16  0.020

