# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 16:52:17 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: N-decanoyl-L-homoserine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCC(=O)N[C@@H](CCO)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
 1K4  1K4  'N-decanoyl-L-homoserine  '  ligand  45  19  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1K4
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
 1K4  OXT  O  OC     0  -0.617  -5.4126  -2.1563   0.3694
 1K4  C    C  C      0   0.417  -4.3256  -1.6960  -0.0340
 1K4  O    O  O     -1  -0.593  -3.4185  -2.3083  -0.6201
 1K4  CA   C  CH1    0  -0.214  -4.1127  -0.1821   0.2441
 1K4  CB   C  CH2    0  -0.483  -5.2053   0.6576  -0.4137
 1K4  CAG  C  CH2    0  -0.131  -5.1388   2.1214  -0.0203
 1K4  OAD  O  OH1    0  -0.676  -6.2251   2.7984  -0.6196
 1K4  N    N  NH1    0  -0.619  -2.8118   0.2843  -0.1722
 1K4  CAQ  C  C      0   0.564  -1.7023   0.1393   0.5668
 1K4  OAB  O  O      0  -0.516  -1.7178  -0.2758   1.7199
 1K4  CAN  C  CH2    0  -0.584  -0.4239   0.6030  -0.1036
 1K4  CAM  C  CH2    0  -0.412   0.8254  -0.0901   0.4197
 1K4  CAL  C  CH2    0  -0.415   2.0967   0.4564  -0.2169
 1K4  CAK  C  CH2    0  -0.412   3.3613  -0.1977   0.3242
 1K4  CAJ  C  CH2    0  -0.412   4.6389   0.3659  -0.2845
 1K4  CAI  C  CH2    0  -0.412   5.9042  -0.2660   0.2813
 1K4  CAH  C  CH2    0  -0.407   7.1842   0.3101  -0.3099
 1K4  CAF  C  CH2    0  -0.419   8.4486  -0.3161   0.2652
 1K4  CAA  C  CH3    0  -0.662   9.7241   0.2726  -0.3208
 1K4  H2   H  HCH1   0   0.238  -4.1808  -0.0392   1.3266
 1K4  H3   H  HCH2   0   0.224  -5.1429   0.5634  -1.5043
 1K4  H4   H  HCH2   0   0.239  -6.1708   0.2479  -0.1144
 1K4  H5   H  HCH2   0   0.186  -5.1748   2.1985   1.0755
 1K4  H6   H  HCH2   0   0.192  -4.1810   2.5534  -0.3351
 1K4  H7   H  HOH1   0   0.451  -6.1503   3.7321  -0.4043
 1K4  H8   H  HNH1   0   0.383  -2.6935   0.4940  -1.1507
 1K4  H9   H  HCH2   0   0.244  -0.4980   0.4793  -1.1876
 1K4  H10  H  HCH2   0   0.262  -0.3381   1.6824   0.0671
 1K4  H11  H  HCH2   0   0.219   0.8839   0.0311   1.5039
 1K4  H12  H  HCH2   0   0.219   0.7576  -1.1663   0.2340
 1K4  H13  H  HCH2   0   0.210   2.0523   0.3229  -1.3033
 1K4  H14  H  HCH2   0   0.209   2.1496   1.5380  -0.0485
 1K4  H15  H  HCH2   0   0.207   3.3943  -0.0731   1.4124
 1K4  H16  H  HCH2   0   0.208   3.3179  -1.2778   0.1462
 1K4  H17  H  HCH2   0   0.207   4.6165   0.2278  -1.3712
 1K4  H18  H  HCH2   0   0.206   4.6707   1.4488  -0.1199
 1K4  H19  H  HCH2   0   0.206   5.9176  -0.1346   1.3692
 1K4  H20  H  HCH2   0   0.207   5.8788  -1.3479   0.1098
 1K4  H21  H  HCH2   0   0.206   7.1757   0.1775  -1.3976
 1K4  H22  H  HCH2   0   0.205   7.2075   1.3925  -0.1399
 1K4  H23  H  HCH2   0   0.210   8.4519  -0.1875   1.3522
 1K4  H24  H  HCH2   0   0.210   8.4288  -1.3963   0.0902
 1K4  H25  H  HCH3   0   0.215   9.7667   0.1267  -1.4019
 1K4  H26  H  HCH3   0   0.215   9.7853   1.3465  -0.1337
 1K4  H27  H  HCH3   0   0.225  10.6137  -0.1886   0.1095

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
 1K4  CAG  CB   single  1.517  0.020  1.517
 1K4  CAG  OAD  single  1.413  0.020  1.413
 1K4  CB   CA   single  1.527  0.020  1.527
 1K4  O    C    deloc   1.241  0.020  1.241
 1K4  C    CA   single  1.554  0.020  1.554
 1K4  C    OXT  deloc   1.247  0.020  1.247
 1K4  CA   N    single  1.443  0.020  1.443
 1K4  N    CAQ  single  1.341  0.020  1.341
 1K4  CAQ  OAB  double  1.226  0.020  1.226
 1K4  CAQ  CAN  single  1.516  0.020  1.516
 1K4  CAN  CAM  single  1.521  0.020  1.521
 1K4  CAL  CAM  single  1.523  0.020  1.523
 1K4  CAL  CAK  single  1.523  0.020  1.523
 1K4  CAK  CAJ  single  1.523  0.020  1.523
 1K4  CAJ  CAI  single  1.523  0.020  1.523
 1K4  CAI  CAH  single  1.523  0.020  1.523
 1K4  CAH  CAF  single  1.524  0.020  1.524
 1K4  CAF  CAA  single  1.522  0.020  1.522
 1K4  CA   H2   single  0.970  0.020  1.090
 1K4  CB   H3   single  0.970  0.020  1.090
 1K4  CB   H4   single  0.970  0.020  1.090
 1K4  CAG  H5   single  0.970  0.020  1.090
 1K4  CAG  H6   single  0.970  0.020  1.090
 1K4  OAD  H7   single  0.850  0.020  0.980
 1K4  N    H8   single  0.860  0.020  1.020
 1K4  CAN  H9   single  0.970  0.020  1.090
 1K4  CAN  H10  single  0.970  0.020  1.090
 1K4  CAM  H11  single  0.970  0.020  1.090
 1K4  CAM  H12  single  0.970  0.020  1.090
 1K4  CAL  H13  single  0.970  0.020  1.090
 1K4  CAL  H14  single  0.970  0.020  1.090
 1K4  CAK  H15  single  0.970  0.020  1.090
 1K4  CAK  H16  single  0.970  0.020  1.090
 1K4  CAJ  H17  single  0.970  0.020  1.090
 1K4  CAJ  H18  single  0.970  0.020  1.090
 1K4  CAI  H19  single  0.970  0.020  1.090
 1K4  CAI  H20  single  0.970  0.020  1.090
 1K4  CAH  H21  single  0.970  0.020  1.090
 1K4  CAH  H22  single  0.970  0.020  1.090
 1K4  CAF  H23  single  0.970  0.020  1.090
 1K4  CAF  H24  single  0.970  0.020  1.090
 1K4  CAA  H25  single  0.970  0.020  1.090
 1K4  CAA  H26  single  0.970  0.020  1.090
 1K4  CAA  H27  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
 1K4  CA   C    O    117.70  3.000
 1K4  CA   C    OXT  114.90  3.000
 1K4  O    C    OXT  127.40  3.000
 1K4  H2   CA   N    107.41  3.000
 1K4  H2   CA   CB   108.06  3.000
 1K4  N    CA   CB   110.06  3.000
 1K4  H2   CA   C    107.21  3.000
 1K4  N    CA   C    112.75  3.000
 1K4  CB   CA   C    111.14  3.000
 1K4  H4   CB   H3   106.93  3.000
 1K4  H4   CB   CAG  109.27  3.000
 1K4  H3   CB   CAG  109.77  3.000
 1K4  H4   CB   CA   107.98  3.000
 1K4  H3   CB   CA   109.91  3.000
 1K4  CAG  CB   CA   112.80  3.000
 1K4  H6   CAG  H5   106.68  3.000
 1K4  H6   CAG  OAD  111.15  3.000
 1K4  H5   CAG  OAD  111.35  3.000
 1K4  H6   CAG  CB   110.11  3.000
 1K4  H5   CAG  CB   108.95  3.000
 1K4  OAD  CAG  CB   108.57  3.000
 1K4  H7   OAD  CAG  108.09  3.000
 1K4  H8   N    CAQ  117.41  3.000
 1K4  H8   N    CA   116.95  3.000
 1K4  CAQ  N    CA   123.50  3.000
 1K4  CAN  CAQ  OAB  122.02  3.000
 1K4  CAN  CAQ  N    114.90  3.000
 1K4  OAB  CAQ  N    123.00  3.000
 1K4  H10  CAN  H9   105.72  3.000
 1K4  H10  CAN  CAM  109.31  3.000
 1K4  H9   CAN  CAM  110.19  3.000
 1K4  H10  CAN  CAQ  107.36  3.000
 1K4  H9   CAN  CAQ  110.28  3.000
 1K4  CAM  CAN  CAQ  113.64  3.000
 1K4  H12  CAM  H11  106.31  3.000
 1K4  H12  CAM  CAL  109.49  3.000
 1K4  H11  CAM  CAL  109.29  3.000
 1K4  H12  CAM  CAN  109.80  3.000
 1K4  H11  CAM  CAN  109.56  3.000
 1K4  CAL  CAM  CAN  112.22  3.000
 1K4  H14  CAL  H13  105.94  3.000
 1K4  H14  CAL  CAK  109.22  3.000
 1K4  H13  CAL  CAK  109.49  3.000
 1K4  H14  CAL  CAM  109.28  3.000
 1K4  H13  CAL  CAM  109.69  3.000
 1K4  CAK  CAL  CAM  112.98  3.000
 1K4  H16  CAK  H15  105.94  3.000
 1K4  H16  CAK  CAJ  109.46  3.000
 1K4  H15  CAK  CAJ  109.24  3.000
 1K4  H16  CAK  CAL  109.44  3.000
 1K4  H15  CAK  CAL  109.20  3.000
 1K4  CAJ  CAK  CAL  113.30  3.000
 1K4  H18  CAJ  H17  105.91  3.000
 1K4  H18  CAJ  CAI  109.27  3.000
 1K4  H17  CAJ  CAI  109.45  3.000
 1K4  H18  CAJ  CAK  109.27  3.000
 1K4  H17  CAJ  CAK  109.43  3.000
 1K4  CAI  CAJ  CAK  113.25  3.000
 1K4  H20  CAI  H19  105.90  3.000
 1K4  H20  CAI  CAH  109.40  3.000
 1K4  H19  CAI  CAH  109.25  3.000
 1K4  H20  CAI  CAJ  109.41  3.000
 1K4  H19  CAI  CAJ  109.22  3.000
 1K4  CAH  CAI  CAJ  113.39  3.000
 1K4  H22  CAH  H21  105.88  3.000
 1K4  H22  CAH  CAF  109.25  3.000
 1K4  H21  CAH  CAF  109.36  3.000
 1K4  H22  CAH  CAI  109.34  3.000
 1K4  H21  CAH  CAI  109.45  3.000
 1K4  CAF  CAH  CAI  113.29  3.000
 1K4  H24  CAF  H23  105.95  3.000
 1K4  H24  CAF  CAA  109.59  3.000
 1K4  H23  CAF  CAA  109.54  3.000
 1K4  H24  CAF  CAH  109.28  3.000
 1K4  H23  CAF  CAH  109.21  3.000
 1K4  CAA  CAF  CAH  113.02  3.000
 1K4  H27  CAA  H26  107.62  3.000
 1K4  H27  CAA  H25  107.60  3.000
 1K4  H26  CAA  H25  107.40  3.000
 1K4  H27  CAA  CAF  111.60  3.000
 1K4  H26  CAA  CAF  111.19  3.000
 1K4  H25  CAA  CAF  111.24  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
 1K4  CONST_01  OAB  CAQ  N    CA      0.00   0.0  0
 1K4  CONST_02  CAN  CAQ  N    CA    180.00   0.0  0
 1K4  CONST_03  H8   N    CAQ  OAB   180.00   0.0  0
 1K4  Var_01    OAD  CAG  CB   CA   -176.96  30.0  1
 1K4  Var_02    CAM  CAN  CAQ  N    -154.40  30.0  3
 1K4  Var_03    CAL  CAM  CAN  CAQ  -176.68  30.0  3
 1K4  Var_04    CAK  CAL  CAM  CAN   178.34  30.0  2
 1K4  Var_05    CAJ  CAK  CAL  CAM  -178.68  30.0  3
 1K4  Var_06    CAI  CAJ  CAK  CAL   178.64  30.0  3
 1K4  Var_07    CAH  CAI  CAJ  CAK  -179.13  30.0  3
 1K4  Var_08    CAF  CAH  CAI  CAJ   179.56  30.0  3
 1K4  Var_09    CAA  CAF  CAH  CAI  -179.49  30.0  3
 1K4  Var_10    H25  CAA  CAF  CAH   -60.06  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
 1K4  chir_01  CA  CB  C  N  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
 1K4  plan-1  CA   0.020
 1K4  plan-1  N    0.020
 1K4  plan-1  CAQ  0.020
 1K4  plan-1  OAB  0.020
 1K4  plan-1  CAN  0.020
 1K4  plan-1  H8   0.020
 1K4  plan-2  OXT  0.020
 1K4  plan-2  C    0.020
 1K4  plan-2  O    0.020
 1K4  plan-2  CA   0.020

