# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 08:29:40 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: (3S,4E)-5-[(1R,5R,8S)-8-hydroxy-1,5-dimethyl-3-oxo-6-oxabicyclo[3.2.1]octan-8-yl]-3-methylpent-4-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](CC(O)=O)\C=C\[C@]1(O)[C@@]2(C)CO[C@]1(C)CC(=O)C2
#
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
 6LM  6LM  '(3S,4E)-5-[(1R,5R,8S)-8-hydroxy-1,5-dimethyl-3-oxo-6-oxabicyclo[3.2.1]octan-8-yl]-3-methylpent-4-enoic acid'  ligand  42  20  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6LM
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
 6LM  C10  C  CT    0  -0.158  -1.8549  -0.7117   1.0565
 6LM  C15  C  CT    0   0.241  -2.3826   0.9339  -0.5323
 6LM  C17  C  CH2   0  -0.123  -3.2943  -0.2385   1.2720
 6LM  C01  C  CH3   0  -0.653   3.2359   1.9790  -0.6200
 6LM  C02  C  CH1   0  -0.317   2.5885   0.6259  -0.3206
 6LM  C03  C  CH2   0  -0.564   3.4614  -0.2239   0.6036
 6LM  C04  C  C     0   0.547   4.7471  -0.6938  -0.0222
 6LM  O05  O  OH1   0  -0.594   5.6270  -1.0868   0.8932
 6LM  O06  O  O     0  -0.444   4.9640  -0.7524  -1.2073
 6LM  C07  C  C1    0  -0.173   1.2507   0.8329   0.3248
 6LM  C09  C  CT    0   0.206  -1.2421   0.5761   0.4579
 6LM  C11  C  CH2   0  -0.572  -1.8395  -1.8277   0.0043
 6LM  C12  C  C     0   0.435  -2.4731  -1.4640  -1.3180
 6LM  O13  O  O     0  -0.403  -2.9815  -2.3023  -2.0282
 6LM  C14  C  CH2   0  -0.593  -2.3998  -0.0142  -1.7324
 6LM  O16  O  O2    0  -0.511  -3.5667   0.6831   0.2238
 6LM  C18  C  CH3   0  -0.692  -2.3739   2.3767  -0.9955
 6LM  C19  C  CH3   0  -0.651  -1.1860  -1.2015   2.3281
 6LM  O20  O  OH1   0  -0.672  -1.1950   1.5157   1.5006
 6LM  H1   H  HCH2  0   0.225  -4.0050  -1.0700   1.2307
 6LM  H2   H  HCH2  0   0.222  -3.4126   0.2495   2.2446
 6LM  H4   H  HCH3  0   0.236   4.2066   1.8645  -1.1027
 6LM  H5   H  HCH3  0   0.236   2.6035   2.5714  -1.2815
 6LM  H6   H  HCH1  0   0.247   2.4437   0.0844  -1.2596
 6LM  H7   H  HCH2  0   0.270   3.6807   0.3132   1.5301
 6LM  H8   H  HCH2  0   0.296   2.9167  -1.1263   0.9045
 6LM  H9   H  HOH1  0   0.479   6.4230  -1.4307   0.4606
 6LM  H10  H  H     0   0.244   1.2615   1.3882   1.2599
 6LM  H12  H  HCH2  0   0.286  -0.8053  -2.1254  -0.2081
 6LM  H13  H  HCH2  0   0.283  -2.3340  -2.7191   0.3979
 6LM  H14  H  HCH2  0   0.285  -3.2558   0.2137  -2.3722
 6LM  H15  H  HCH2  0   0.279  -1.5146   0.1147  -2.3639
 6LM  H16  H  HCH3  0   0.237  -1.4280   2.6152  -1.4849
 6LM  H17  H  HCH3  0   0.248  -3.1707   2.5553  -1.7188
 6LM  H18  H  HCH3  0   0.243  -2.5191   3.0722  -0.1690
 6LM  H19  H  HCH3  0   0.234  -1.6868  -2.1000   2.6939
 6LM  H20  H  HCH3  0   0.234  -0.1413  -1.4585   2.1437
 6LM  H21  H  HCH3  0   0.241  -1.2172  -0.4558   3.1204
 6LM  H22  H  HOH1  0   0.453  -0.8201   2.3376   1.1649
 6LM  C08  C  C1    0  -0.257   0.1045   0.3834  -0.1759
 6LM  H3   H  HCH3  0   0.221   3.3848   2.5499   0.2990
 6LM  H11  H  H     0   0.248   0.1431  -0.1824  -1.1006

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
 6LM  O06  C04  double  1.206  0.020  1.206
 6LM  O05  C04  single  1.329  0.020  1.329
 6LM  C04  C03  single  1.505  0.020  1.505
 6LM  C19  C10  single  1.518  0.020  1.518
 6LM  C11  C10  single  1.534  0.020  1.534
 6LM  C11  C12  single  1.511  0.020  1.511
 6LM  C03  C02  single  1.529  0.020  1.529
 6LM  C10  C17  single  1.530  0.020  1.530
 6LM  C10  C09  single  1.547  0.020  1.547
 6LM  C07  C02  single  1.500  0.020  1.500
 6LM  C07  C08  double  1.329  0.020  1.329
 6LM  O13  C12  double  1.211  0.020  1.211
 6LM  C02  C01  single  1.530  0.020  1.530
 6LM  C17  O16  single  1.422  0.020  1.422
 6LM  C12  C14  single  1.510  0.020  1.510
 6LM  C09  C08  single  1.501  0.020  1.501
 6LM  C09  O20  single  1.404  0.020  1.404
 6LM  C09  C15  single  1.552  0.020  1.552
 6LM  C14  C15  single  1.529  0.020  1.529
 6LM  O16  C15  single  1.427  0.020  1.427
 6LM  C15  C18  single  1.515  0.020  1.515
 6LM  C17  H1   single  0.970  0.020  1.090
 6LM  C17  H2   single  0.970  0.020  1.090
 6LM  C01  H3   single  0.970  0.020  1.090
 6LM  C01  H4   single  0.970  0.020  1.090
 6LM  C01  H5   single  0.970  0.020  1.090
 6LM  C02  H6   single  0.970  0.020  1.090
 6LM  C03  H7   single  0.970  0.020  1.090
 6LM  C03  H8   single  0.970  0.020  1.090
 6LM  O05  H9   single  0.850  0.020  0.980
 6LM  C07  H10  single  0.930  0.020  1.080
 6LM  C08  H11  single  0.930  0.020  1.080
 6LM  C11  H12  single  0.970  0.020  1.090
 6LM  C11  H13  single  0.970  0.020  1.090
 6LM  C14  H14  single  0.970  0.020  1.090
 6LM  C14  H15  single  0.970  0.020  1.090
 6LM  C18  H16  single  0.970  0.020  1.090
 6LM  C18  H17  single  0.970  0.020  1.090
 6LM  C18  H18  single  0.970  0.020  1.090
 6LM  C19  H19  single  0.970  0.020  1.090
 6LM  C19  H20  single  0.970  0.020  1.090
 6LM  C19  H21  single  0.970  0.020  1.090
 6LM  O20  H22  single  0.850  0.020  0.980

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
 6LM  C19  C10  C11  109.60  3.000
 6LM  C11  C10  C09  109.65  3.000
 6LM  C19  C10  C09  114.73  3.000
 6LM  C09  C10  C17   99.77  3.000
 6LM  C11  C10  C17  109.33  3.000
 6LM  C19  C10  C17  113.35  3.000
 6LM  C18  C15  O16  109.51  3.000
 6LM  C18  C15  C14  110.51  3.000
 6LM  O16  C15  C14  107.31  3.000
 6LM  C18  C15  C09  114.22  3.000
 6LM  O16  C15  C09  103.36  3.000
 6LM  C14  C15  C09  111.47  3.000
 6LM  H2   C17  H1   107.58  3.000
 6LM  H2   C17  O16  110.20  3.000
 6LM  H1   C17  O16  109.88  3.000
 6LM  H2   C17  C10  111.39  3.000
 6LM  H1   C17  C10  111.74  3.000
 6LM  O16  C17  C10  106.07  3.000
 6LM  H5   C01  H4   107.75  3.000
 6LM  H5   C01  H3   107.80  3.000
 6LM  H4   C01  H3   107.82  3.000
 6LM  H5   C01  C02  110.73  3.000
 6LM  H4   C01  C02  111.75  3.000
 6LM  H3   C01  C02  110.82  3.000
 6LM  H6   C02  C07  108.65  3.000
 6LM  H6   C02  C03  108.63  3.000
 6LM  C07  C02  C03  109.01  3.000
 6LM  H6   C02  C01  109.03  3.000
 6LM  C07  C02  C01  109.86  3.000
 6LM  C03  C02  C01  111.61  3.000
 6LM  H8   C03  H7   105.75  3.000
 6LM  H8   C03  C04  106.36  3.000
 6LM  H7   C03  C04  109.53  3.000
 6LM  H8   C03  C02  109.86  3.000
 6LM  H7   C03  C02  110.72  3.000
 6LM  C04  C03  C02  114.19  3.000
 6LM  O06  C04  O05  122.90  3.000
 6LM  O05  C04  C03  111.80  3.000
 6LM  O06  C04  C03  125.26  3.000
 6LM  H9   O05  C04  109.96  3.000
 6LM  H10  C07  C08  120.34  3.000
 6LM  H10  C07  C02  115.57  3.000
 6LM  C08  C07  C02  124.09  3.000
 6LM  O20  C09  C08  111.68  3.000
 6LM  O20  C09  C15  110.13  3.000
 6LM  C08  C09  C15  114.80  3.000
 6LM  C15  C09  C10   98.49  3.000
 6LM  O20  C09  C10  106.44  3.000
 6LM  C08  C09  C10  114.33  3.000
 6LM  H13  C11  H12  105.97  3.000
 6LM  H13  C11  C12  108.77  3.000
 6LM  H12  C11  C12  106.93  3.000
 6LM  H13  C11  C10  109.99  3.000
 6LM  H12  C11  C10  109.86  3.000
 6LM  C12  C11  C10  114.90  3.000
 6LM  C14  C12  O13  121.63  3.000
 6LM  C14  C12  C11  116.81  3.000
 6LM  O13  C12  C11  121.53  3.000
 6LM  H15  C14  H14  105.72  3.000
 6LM  H15  C14  C12  108.09  3.000
 6LM  H14  C14  C12  108.84  3.000
 6LM  H15  C14  C15  111.75  3.000
 6LM  H14  C14  C15  109.81  3.000
 6LM  C12  C14  C15  112.37  3.000
 6LM  C17  O16  C15  110.21  3.000
 6LM  H18  C18  H17  107.52  3.000
 6LM  H18  C18  H16  108.43  3.000
 6LM  H17  C18  H16  107.46  3.000
 6LM  H18  C18  C15  112.02  3.000
 6LM  H17  C18  C15  110.75  3.000
 6LM  H16  C18  C15  110.49  3.000
 6LM  H21  C19  H20  108.16  3.000
 6LM  H21  C19  H19  107.86  3.000
 6LM  H20  C19  H19  107.57  3.000
 6LM  H21  C19  C10  112.09  3.000
 6LM  H20  C19  C10  110.87  3.000
 6LM  H19  C19  C10  110.13  3.000
 6LM  H22  O20  C09  108.97  3.000
 6LM  H11  C08  C09  117.32  3.000
 6LM  H11  C08  C07  117.83  3.000
 6LM  C09  C08  C07  124.84  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
 6LM  CONST_01  H9   O05  C04  C03  180.00   0.0  0
 6LM  Var_01    C14  C12  C11  C10   30.17  30.0  1
 6LM  Var_02    C11  C12  C14  C15  -30.12  30.0  1
 6LM  Var_03    C09  C08  C07  C02  179.75   0.0  2
 6LM  Var_04    O06  C04  C03  C02  -19.82  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
 6LM  chir_01  C10  C11  C17  C09  positiv
 6LM  chir_02  C15  C18  C14  C09  negativ
 6LM  chir_03  C02  C03  C07  C01  negativ
 6LM  chir_04  C09  C15  C08  C10  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
 6LM  plan-1  C11  0.020
 6LM  plan-1  C12  0.020
 6LM  plan-1  O13  0.020
 6LM  plan-1  C14  0.020
 6LM  plan-2  C03  0.020
 6LM  plan-2  C04  0.020
 6LM  plan-2  O05  0.020
 6LM  plan-2  O06  0.020
 6LM  plan-2  H9   0.020
 6LM  plan-3  C02  0.020
 6LM  plan-3  C07  0.020
 6LM  plan-3  C09  0.020
 6LM  plan-3  H10  0.020
 6LM  plan-3  C08  0.020
 6LM  plan-3  H11  0.020

