# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 06:55:54 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: (3aR,6R,6aS)-6-[(S)-(1S)-cyclohex-2-en-1-yl(hydroxy)methyl]-6a-methyl-4-oxohexahydro-2H-furo[2,3-c]pyrrole-6-carbaldehyde
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]12OCC[C@H]1C(=O)N[C@]2(C=O)[C@@H](O)[C@H]3CCCC=C3
#
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
 SA1  SA1  (3aR,6R,6aS)-6-[(S)-(1S)-cyclohex-2-en-1-yl(hydroxy)methyl]-6a-methyl-4-oxohexahydro-2H-furo[2,3-c]pyrrole-6-carbaldehyde  ligand  41  20  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_SA1
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
 SA1  C1    C  CH2   0  -0.172   3.7595   0.9510  -0.3306
 SA1  O2    O  O2    0  -0.506   2.5544   1.0444  -1.0786
 SA1  C3    C  CT    0   0.283   1.7532  -0.1279  -0.9384
 SA1  C4    C  CH3   0  -0.687   1.5474  -0.7024  -2.3271
 SA1  C5    C  CH1   0  -0.433   2.5169  -1.0113   0.0518
 SA1  C6    C  C     0   0.538   1.9287  -0.6631   1.4072
 SA1  O7    O  O     0  -0.473   2.3746  -1.0029   2.4867
 SA1  N8    N  NH1   0  -0.628   0.8440   0.1116   1.2104
 SA1  C9    C  CT    0  -0.057   0.4460   0.2893  -0.1588
 SA1  C10   C  CH1   0   0.080  -0.7607  -0.6252  -0.5046
 SA1  C11   C  CH1   0  -0.322  -2.0572  -0.3779   0.2944
 SA1  C12   C  C1    0  -0.186  -3.1020  -1.3613  -0.1762
 SA1  C13   C  C1    0  -0.243  -4.3750  -1.0513  -0.4084
 SA1  C14   C  CH2   0  -0.473  -4.9590   0.3061  -0.1755
 SA1  C15   C  CH2   0  -0.440  -4.0311   1.1545   0.6793
 SA1  C16   C  CH2   0  -0.468  -2.5888   1.0534   0.1968
 SA1  O17   O  OH1   0  -0.651  -0.3534  -1.9656  -0.3551
 SA1  C18   C  C1    0   0.204   0.2178   1.7436  -0.5056
 SA1  O19   O  O     0  -0.366   0.3723   2.6571   0.2609
 SA1  C20   C  CH2   0  -0.488   3.9572  -0.5318  -0.0693
 SA1  H11A  H  HCH2  0   0.241   4.5687   1.3959  -0.9112
 SA1  H12A  H  HCH2  0   0.217   3.6733   1.5137   0.6063
 SA1  H41   H  HCH3  0   0.250   2.5195  -0.9191  -2.7721
 SA1  H42   H  HCH3  0   0.248   0.9741  -1.6247  -2.3199
 SA1  H43   H  HCH3  0   0.242   1.0418   0.0123  -2.9791
 SA1  H5    H  HCH1  0   0.310   2.4034  -2.0787  -0.1409
 SA1  HN8   H  HNH1  0   0.401   0.3099   0.4768   1.9859
 SA1  H10   H  HCH1  0   0.256  -0.9911  -0.4875  -1.5664
 SA1  H11   H  HCH1  0   0.244  -1.8357  -0.5922   1.3515
 SA1  H12   H  H     0   0.242  -2.7796  -2.3818  -0.3454
 SA1  H13   H  H     0   0.236  -5.0409  -1.8244  -0.7785
 SA1  H141  H  HCH2  0   0.241  -5.9384   0.2087   0.3009
 SA1  H142  H  HCH2  0   0.235  -5.1489   0.7951  -1.1379
 SA1  H151  H  HCH2  0   0.223  -4.0859   0.8191   1.7193
 SA1  H152  H  HCH2  0   0.237  -4.3500   2.1984   0.6713
 SA1  H161  H  HCH2  0   0.248  -1.9783   1.7313   0.7912
 SA1  H162  H  HCH2  0   0.226  -2.5379   1.3963  -0.8433
 SA1  HO17  H  HOH1  0   0.454  -0.3760  -2.1975   0.5802
 SA1  H18   H  H     0   0.208  -0.0981   1.9115  -1.5501
 SA1  H201  H  HCH2  0   0.261   4.4461  -1.0223  -0.9123
 SA1  H202  H  HCH2  0   0.265   4.5485  -0.7315   0.8235

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
 SA1  C1   O2    single  1.421  0.020  1.421
 SA1  C1   C20   single  1.519  0.020  1.519
 SA1  C1   H11A  single  0.970  0.020  1.090
 SA1  C1   H12A  single  0.970  0.020  1.090
 SA1  O2   C3    single  1.427  0.020  1.427
 SA1  C3   C4    single  1.517  0.020  1.517
 SA1  C3   C5    single  1.531  0.020  1.531
 SA1  C3   C9    single  1.578  0.020  1.578
 SA1  C4   H41   single  0.970  0.020  1.090
 SA1  C4   H42   single  0.970  0.020  1.090
 SA1  C4   H43   single  0.970  0.020  1.090
 SA1  C5   C6    single  1.518  0.020  1.518
 SA1  C5   C20   single  1.523  0.020  1.523
 SA1  C5   H5    single  0.970  0.020  1.090
 SA1  C6   O7    double  1.216  0.020  1.216
 SA1  C6   N8    single  1.347  0.020  1.347
 SA1  N8   C9    single  1.437  0.020  1.437
 SA1  N8   HN8   single  0.860  0.020  1.020
 SA1  C9   C10   single  1.553  0.020  1.553
 SA1  C9   C18   single  1.512  0.020  1.512
 SA1  C10  C11   single  1.543  0.020  1.543
 SA1  C10  O17   single  1.409  0.020  1.409
 SA1  C10  H10   single  0.970  0.020  1.090
 SA1  C11  C12   single  1.510  0.020  1.510
 SA1  C11  C16   single  1.530  0.020  1.530
 SA1  C11  H11   single  0.970  0.020  1.090
 SA1  C12  C13   double  1.331  0.020  1.331
 SA1  C12  H12   single  0.930  0.020  1.080
 SA1  C13  C14   single  1.496  0.020  1.496
 SA1  C13  H13   single  0.930  0.020  1.080
 SA1  C14  C15   single  1.520  0.020  1.520
 SA1  C14  H141  single  0.970  0.020  1.090
 SA1  C14  H142  single  0.970  0.020  1.090
 SA1  C15  C16   single  1.524  0.020  1.524
 SA1  C15  H151  single  0.970  0.020  1.090
 SA1  C15  H152  single  0.970  0.020  1.090
 SA1  C16  H161  single  0.970  0.020  1.090
 SA1  C16  H162  single  0.970  0.020  1.090
 SA1  O17  HO17  single  0.850  0.020  0.980
 SA1  C18  O19   double  1.202  0.020  1.202
 SA1  C18  H18   single  0.930  0.020  1.080
 SA1  C20  H201  single  0.970  0.020  1.090
 SA1  C20  H202  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
 SA1  H12A  C1   H11A  107.69  3.000
 SA1  H12A  C1   C20   111.37  3.000
 SA1  H11A  C1   C20   113.15  3.000
 SA1  H12A  C1   O2    110.45  3.000
 SA1  H11A  C1   O2    108.79  3.000
 SA1  C20   C1   O2    105.38  3.000
 SA1  C3    O2   C1    111.74  3.000
 SA1  C9    C3   C5    104.25  3.000
 SA1  C9    C3   C4    116.10  3.000
 SA1  C5    C3   C4    116.19  3.000
 SA1  C9    C3   O2    107.24  3.000
 SA1  C5    C3   O2    104.92  3.000
 SA1  C4    C3   O2    107.30  3.000
 SA1  H43   C4   H42   108.39  3.000
 SA1  H43   C4   H41   107.41  3.000
 SA1  H42   C4   H41   107.72  3.000
 SA1  H43   C4   C3    111.21  3.000
 SA1  H42   C4   C3    112.78  3.000
 SA1  H41   C4   C3    109.14  3.000
 SA1  H5    C5   C20   113.11  3.000
 SA1  H5    C5   C6    109.99  3.000
 SA1  C20   C5   C6    111.43  3.000
 SA1  H5    C5   C3    113.49  3.000
 SA1  C20   C5   C3    103.81  3.000
 SA1  C6    C5   C3    104.59  3.000
 SA1  N8    C6   O7    125.83  3.000
 SA1  N8    C6   C5    108.26  3.000
 SA1  O7    C6   C5    125.89  3.000
 SA1  HN8   N8   C9    122.71  3.000
 SA1  HN8   N8   C6    121.44  3.000
 SA1  C9    N8   C6    115.68  3.000
 SA1  C18   C9   C10   113.45  3.000
 SA1  C18   C9   N8    112.28  3.000
 SA1  C10   C9   N8    110.77  3.000
 SA1  C18   C9   C3    105.42  3.000
 SA1  C10   C9   C3    112.20  3.000
 SA1  N8    C9   C3    102.04  3.000
 SA1  H10   C10  O17   106.46  3.000
 SA1  H10   C10  C11   107.76  3.000
 SA1  O17   C10  C11   109.90  3.000
 SA1  H10   C10  C9    107.78  3.000
 SA1  O17   C10  C9    108.18  3.000
 SA1  C11   C10  C9    116.31  3.000
 SA1  H11   C11  C16   108.25  3.000
 SA1  H11   C11  C12   108.16  3.000
 SA1  C16   C11  C12   110.42  3.000
 SA1  H11   C11  C10   107.27  3.000
 SA1  C16   C11  C10   114.13  3.000
 SA1  C12   C11  C10   108.40  3.000
 SA1  H12   C12  C13   118.48  3.000
 SA1  H12   C12  C11   117.14  3.000
 SA1  C13   C12  C11   124.37  3.000
 SA1  H13   C13  C14   117.38  3.000
 SA1  H13   C13  C12   118.72  3.000
 SA1  C14   C13  C12   123.90  3.000
 SA1  H142  C14  H141  105.49  3.000
 SA1  H142  C14  C15   110.52  3.000
 SA1  H141  C14  C15   110.58  3.000
 SA1  H142  C14  C13   109.62  3.000
 SA1  H141  C14  C13   109.67  3.000
 SA1  C15   C14  C13   110.83  3.000
 SA1  H152  C15  H151  106.59  3.000
 SA1  H152  C15  C16   109.73  3.000
 SA1  H151  C15  C16   109.14  3.000
 SA1  H152  C15  C14   110.56  3.000
 SA1  H151  C15  C14   109.44  3.000
 SA1  C16   C15  C14   111.25  3.000
 SA1  H162  C16  H161  107.29  3.000
 SA1  H162  C16  C15   108.88  3.000
 SA1  H161  C16  C15   108.45  3.000
 SA1  H162  C16  C11   109.69  3.000
 SA1  H161  C16  C11   110.66  3.000
 SA1  C15   C16  C11   111.75  3.000
 SA1  HO17  O17  C10   108.97  3.000
 SA1  H18   C18  O19   121.62  3.000
 SA1  H18   C18  C9    113.97  3.000
 SA1  O19   C18  C9    124.40  3.000
 SA1  H202  C20  H201  107.92  3.000
 SA1  H202  C20  C5    112.98  3.000
 SA1  H201  C20  C5    110.11  3.000
 SA1  H202  C20  C1    113.00  3.000
 SA1  H201  C20  C1    111.37  3.000
 SA1  C5    C20  C1    101.42  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
 SA1  CONST_01  C9   N8   C6   C5     0.00   0.0  0
 SA1  CONST_02  C9   N8   C6   O7   180.00   0.0  0
 SA1  CONST_03  HN8  N8   C6   C5   180.00   0.0  0
 SA1  Var_01    C5   C20  C1   O2   -33.10  30.0  1
 SA1  Var_02    C20  C1   O2   C3    19.50  30.0  1
 SA1  Var_03    C14  C13  C12  C11   -2.83  30.0  1
 SA1  Var_04    C14  C15  C16  C11  -61.84  30.0  1
 SA1  Var_05    C15  C14  C13  C12  -14.71  30.0  1
 SA1  Var_06    C16  C15  C14  C13   45.75  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
 SA1  chir_01  C3   O2   C5   C9   negativ
 SA1  chir_02  C5   C3   C6   C20  positiv
 SA1  chir_03  C9   C3   N8   C18  negativ
 SA1  chir_04  C10  O17  C9   C11  positiv
 SA1  chir_05  C11  C16  C12  C10  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
 SA1  plan-1  C5   0.020
 SA1  plan-1  C6   0.020
 SA1  plan-1  O7   0.020
 SA1  plan-1  N8   0.020
 SA1  plan-1  C9   0.020
 SA1  plan-1  HN8  0.020
 SA1  plan-2  C9   0.020
 SA1  plan-2  C18  0.020
 SA1  plan-2  O19  0.020
 SA1  plan-2  H18  0.020

