# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 03:09:35 2022
#   Inital geometry file: a 124 line input string
#   Ligand name: [(3~{a}~{S},5~{R},5~{a}~{S},6~{S},8~{S},8~{a}~{S},9~{S},9~{a}~{R})-9-acetyloxy-5,8~{a}-dimethyl-1-methylidene-8-oxidanyl-2-oxidanylidene-4,5,5~{a},6,7,8,9,9~{a}-octahydro-3~{a}~{H}-azuleno[6,5-b]furan-6-yl] ethanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1C[C@@H]2OC(=O)C(=C)[C@H]2[C@H](OC(C)=O)[C@]3(C)[C@@H](O)C[C@H](OC(C)=O)[C@@H]13
#
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
 XXT  XXT  '[(3~{a}~{S},5~{R},5~{a}~{S},6~{S},8~{S},8~{a}~{S},9~{S},9~{a}~{R})-9-acetyloxy-5,8~{a}-dimethyl-1-methylidene-8-oxidanyl-2-oxidanylidene-4,5,5~{a},6,7,8,9,9~{a}-octahydro-3~{a}~{H}-azuleno[6,5-b]furan-6-yl] ethanoate'  ligand  52  26  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XXT
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
 XXT  C2   C  CH2   0  -0.508   2.1598   2.0416   0.2497
 XXT  C1   C  CH1   0   0.056   2.5376   0.5661   0.3922
 XXT  O7   O  O     0  -0.429  -3.0543   2.5738   0.5658
 XXT  C6   C  CH1   0   0.104  -1.3439   0.4618   0.2995
 XXT  C5   C  CH1   0  -0.239   1.2257  -0.2469   0.3332
 XXT  C3   C  CH1   0   0.117   0.6707   2.0241  -0.0573
 XXT  C4   C  CT    0  -0.158   0.1303   0.8003   0.7143
 XXT  C19  C  CH3   0  -0.742  -2.7294   3.2032  -1.7288
 XXT  O6   O  O2    0  -0.478  -1.7718   1.3006  -0.7693
 XXT  C15  C  CH3   0  -0.675   0.1391   1.0868   2.2202
 XXT  O2   O  OH1   0  -0.648  -0.0043   3.2020   0.2987
 XXT  C7   C  CH1   0  -0.398  -1.5772  -0.9744  -0.1427
 XXT  C11  C  C     0   0.018  -3.0007  -1.3562  -0.4337
 XXT  C14  C  C2    0  -0.521  -3.9306  -0.7968  -1.1972
 XXT  C12  C  C     0   0.523  -3.2620  -2.6505   0.2483
 XXT  O3   O  O     0  -0.377  -4.2442  -3.3313   0.2086
 XXT  O1   O  O2    0  -0.447  -2.1774  -2.9982   0.9494
 XXT  C8   C  CH1   0   0.104  -1.2045  -1.9503   0.9850
 XXT  C9   C  CH2   0  -0.451   0.1779  -2.5395   0.8624
 XXT  C10  C  CH1   0  -0.253   1.3087  -1.5502   1.1529
 XXT  C13  C  CH3   0  -0.640   2.6263  -2.3015   0.9446
 XXT  O4   O  O2    0  -0.465   3.3766   0.1055  -0.6703
 XXT  C16  C  C     0   0.554   4.6723   0.4231  -0.6168
 XXT  O5   O  O     0  -0.403   5.1576   1.0982   0.2493
 XXT  C17  C  CH3   0  -0.753   5.4342  -0.2027  -1.7501
 XXT  H1   H  HCH2  0   0.248   2.3580   2.5779   1.1787
 XXT  H2   H  HCH2  0   0.257   2.7284   2.5455  -0.5324
 XXT  H3   H  HCH1  0   0.246   3.0502   0.4046   1.3435
 XXT  H4   H  HCH1  0   0.261  -1.9899   0.6464   1.1612
 XXT  H5   H  HCH1  0   0.239   1.0818  -0.5128  -0.7223
 XXT  H6   H  HCH1  0   0.213   0.5554   1.8249  -1.1318
 XXT  H7   H  HCH3  0   0.255  -3.3273   4.0800  -1.5005
 XXT  H8   H  HCH3  0   0.253  -1.7649   3.5199  -2.1226
 XXT  H9   H  HCH3  0   0.254  -3.2267   2.6387  -2.5182
 XXT  H10  H  HCH3  0   0.233   1.1365   1.2942   2.6095
 XXT  H11  H  HCH3  0   0.262  -0.4912   1.9427   2.4563
 XXT  H12  H  HCH3  0   0.228  -0.2481   0.2459   2.7943
 XXT  H13  H  HOH1  0   0.434   0.4309   3.9431  -0.1303
 XXT  H14  H  HCH1  0   0.275  -0.9754  -1.1989  -1.0310
 XXT  H16  H  H     0   0.244  -3.7721   0.1098  -1.7593
 XXT  H17  H  H     0   0.266  -4.9047  -1.2599  -1.2867
 XXT  H19  H  HCH1  0   0.230  -1.3127  -1.4597   1.9602
 XXT  H20  H  HCH2  0   0.247   0.2665  -3.3759   1.5607
 XXT  H21  H  HCH2  0   0.222   0.3040  -2.9558  -0.1433
 XXT  H22  H  HCH1  0   0.229   1.2569  -1.2841   2.2148
 XXT  H23  H  HCH3  0   0.230   3.4932  -1.7460   1.2991
 XXT  H24  H  HCH3  0   0.226   2.6067  -3.2384   1.5031
 XXT  H25  H  HCH3  0   0.220   2.7889  -2.5469  -0.1059
 XXT  H26  H  HCH3  0   0.247   4.8398  -0.2658  -2.6591
 XXT  H27  H  HCH3  0   0.258   6.3448   0.3575  -1.9436
 XXT  H28  H  HCH3  0   0.257   5.7197  -1.2192  -1.4725
 XXT  C18  C  C     0   0.575  -2.5476   2.3610  -0.5024

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
 XXT  C17  C16  single  1.502  0.020  1.502
 XXT  O5   C16  double  1.201  0.020  1.201
 XXT  C16  O4   single  1.335  0.020  1.335
 XXT  O4   C1   single  1.430  0.020  1.430
 XXT  C13  C10  single  1.531  0.020  1.531
 XXT  C1   C2   single  1.530  0.020  1.530
 XXT  C1   C5   single  1.544  0.020  1.544
 XXT  C10  C5   single  1.542  0.020  1.542
 XXT  C10  C9   single  1.530  0.020  1.530
 XXT  C2   C3   single  1.521  0.020  1.521
 XXT  C5   C4   single  1.563  0.020  1.563
 XXT  O7   C18  double  1.201  0.020  1.201
 XXT  C9   C8   single  1.508  0.020  1.508
 XXT  C3   C4   single  1.544  0.020  1.544
 XXT  C3   O2   single  1.404  0.020  1.404
 XXT  C18  C19  single  1.499  0.020  1.499
 XXT  C18  O6   single  1.341  0.020  1.341
 XXT  C4   C15  single  1.533  0.020  1.533
 XXT  C4   C6   single  1.568  0.020  1.568
 XXT  C8   O1   single  1.430  0.020  1.430
 XXT  C8   C7   single  1.537  0.020  1.537
 XXT  O1   C12  single  1.337  0.020  1.337
 XXT  C7   C6   single  1.521  0.020  1.521
 XXT  C7   C11  single  1.502  0.020  1.502
 XXT  O6   C6   single  1.424  0.020  1.424
 XXT  C12  C11  single  1.486  0.020  1.486
 XXT  C12  O3   double  1.196  0.020  1.196
 XXT  C11  C14  double  1.327  0.020  1.327
 XXT  C2   H1   single  0.970  0.020  1.090
 XXT  C2   H2   single  0.970  0.020  1.090
 XXT  C1   H3   single  0.970  0.020  1.090
 XXT  C6   H4   single  0.970  0.020  1.090
 XXT  C5   H5   single  0.970  0.020  1.090
 XXT  C3   H6   single  0.970  0.020  1.090
 XXT  C19  H7   single  0.970  0.020  1.090
 XXT  C19  H8   single  0.970  0.020  1.090
 XXT  C19  H9   single  0.970  0.020  1.090
 XXT  C15  H10  single  0.970  0.020  1.090
 XXT  C15  H11  single  0.970  0.020  1.090
 XXT  C15  H12  single  0.970  0.020  1.090
 XXT  O2   H13  single  0.850  0.020  0.980
 XXT  C7   H14  single  0.970  0.020  1.090
 XXT  C14  H16  single  0.930  0.020  1.080
 XXT  C14  H17  single  0.930  0.020  1.080
 XXT  C8   H19  single  0.970  0.020  1.090
 XXT  C9   H20  single  0.970  0.020  1.090
 XXT  C9   H21  single  0.970  0.020  1.090
 XXT  C10  H22  single  0.970  0.020  1.090
 XXT  C13  H23  single  0.970  0.020  1.090
 XXT  C13  H24  single  0.970  0.020  1.090
 XXT  C13  H25  single  0.970  0.020  1.090
 XXT  C17  H26  single  0.970  0.020  1.090
 XXT  C17  H27  single  0.970  0.020  1.090
 XXT  C17  H28  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
 XXT  H2   C2   H1   106.80  3.000
 XXT  H2   C2   C3   111.79  3.000
 XXT  H1   C2   C3   110.82  3.000
 XXT  H2   C2   C1   112.57  3.000
 XXT  H1   C2   C1   110.49  3.000
 XXT  C3   C2   C1   104.45  3.000
 XXT  H3   C1   O4   108.91  3.000
 XXT  H3   C1   C5   110.73  3.000
 XXT  O4   C1   C5   107.48  3.000
 XXT  H3   C1   C2   109.85  3.000
 XXT  C5   C1   C2   107.12  3.000
 XXT  O4   C1   C2   112.73  3.000
 XXT  H4   C6   C7   107.34  3.000
 XXT  H4   C6   O6   108.33  3.000
 XXT  C7   C6   O6   106.97  3.000
 XXT  H4   C6   C4   108.11  3.000
 XXT  O6   C6   C4   110.72  3.000
 XXT  C7   C6   C4   115.14  3.000
 XXT  H5   C5   C10  108.27  3.000
 XXT  H5   C5   C4   107.75  3.000
 XXT  C10  C5   C4   118.33  3.000
 XXT  H5   C5   C1   105.99  3.000
 XXT  C4   C5   C1   103.49  3.000
 XXT  C10  C5   C1   112.27  3.000
 XXT  H6   C3   O2   110.47  3.000
 XXT  H6   C3   C4   107.94  3.000
 XXT  O2   C3   C4   111.72  3.000
 XXT  H6   C3   C2   107.59  3.000
 XXT  O2   C3   C2   114.21  3.000
 XXT  C4   C3   C2   104.53  3.000
 XXT  C15  C4   C3   109.92  3.000
 XXT  C15  C4   C5   111.15  3.000
 XXT  C3   C4   C5    99.44  3.000
 XXT  C15  C4   C6   107.79  3.000
 XXT  C3   C4   C6   111.58  3.000
 XXT  C5   C4   C6   116.73  3.000
 XXT  H9   C19  H8   107.02  3.000
 XXT  H9   C19  H7   108.62  3.000
 XXT  H8   C19  H7   109.21  3.000
 XXT  H9   C19  C18  110.90  3.000
 XXT  H8   C19  C18  110.61  3.000
 XXT  H7   C19  C18  110.40  3.000
 XXT  C18  O6   C6   119.35  3.000
 XXT  H12  C15  H11  106.67  3.000
 XXT  H12  C15  H10  106.49  3.000
 XXT  H11  C15  H10  107.61  3.000
 XXT  H12  C15  C4   111.80  3.000
 XXT  H11  C15  C4   110.89  3.000
 XXT  H10  C15  C4   113.05  3.000
 XXT  H13  O2   C3   108.44  3.000
 XXT  H14  C7   C8   109.35  3.000
 XXT  H14  C7   C11  108.13  3.000
 XXT  C8   C7   C11  102.16  3.000
 XXT  H14  C7   C6   110.17  3.000
 XXT  C11  C7   C6   116.21  3.000
 XXT  C8   C7   C6   110.43  3.000
 XXT  C12  C11  C14  120.53  3.000
 XXT  C14  C11  C7   131.95  3.000
 XXT  C12  C11  C7   107.40  3.000
 XXT  H17  C14  H16  116.68  3.000
 XXT  H17  C14  C11  119.87  3.000
 XXT  H16  C14  C11  123.45  3.000
 XXT  O1   C12  O3   122.38  3.000
 XXT  O3   C12  C11  128.69  3.000
 XXT  O1   C12  C11  108.93  3.000
 XXT  C8   O1   C12  111.97  3.000
 XXT  H19  C8   C9   109.72  3.000
 XXT  H19  C8   O1   106.42  3.000
 XXT  C9   C8   O1   109.59  3.000
 XXT  H19  C8   C7   110.14  3.000
 XXT  O1   C8   C7   106.38  3.000
 XXT  C9   C8   C7   114.26  3.000
 XXT  H21  C9   H20  106.63  3.000
 XXT  H21  C9   C10  109.56  3.000
 XXT  H20  C9   C10  108.27  3.000
 XXT  H21  C9   C8   109.18  3.000
 XXT  H20  C9   C8   108.75  3.000
 XXT  C10  C9   C8   114.17  3.000
 XXT  H22  C10  C13  106.96  3.000
 XXT  H22  C10  C9   107.82  3.000
 XXT  C13  C10  C9   107.03  3.000
 XXT  H22  C10  C5   107.90  3.000
 XXT  C9   C10  C5   113.94  3.000
 XXT  C13  C10  C5   112.88  3.000
 XXT  H25  C13  H24  107.61  3.000
 XXT  H25  C13  H23  108.03  3.000
 XXT  H24  C13  H23  106.60  3.000
 XXT  H25  C13  C10  111.70  3.000
 XXT  H24  C13  C10  109.65  3.000
 XXT  H23  C13  C10  112.99  3.000
 XXT  C16  O4   C1   117.58  3.000
 XXT  C17  C16  O5   125.00  3.000
 XXT  O5   C16  O4   123.70  3.000
 XXT  C17  C16  O4   111.28  3.000
 XXT  H28  C17  H27  107.83  3.000
 XXT  H28  C17  H26  107.54  3.000
 XXT  H27  C17  H26  109.82  3.000
 XXT  H28  C17  C16  109.19  3.000
 XXT  H27  C17  C16  110.16  3.000
 XXT  H26  C17  C16  112.17  3.000
 XXT  O6   C18  C19  110.59  3.000
 XXT  O6   C18  O7   124.14  3.000
 XXT  C19  C18  O7   125.23  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
 XXT  Var_01  O1   C12  C11  C7    3.55  30.0  1
 XXT  Var_02  H16  C14  C11  C7   -0.90  30.0  2
 XXT  Var_03  C17  C16  O4   C1  176.38  30.0  1
 XXT  Var_04  C19  C18  O6   C6  172.46  30.0  2
 XXT  Var_05  H7   C19  C18  O7    4.21  30.0  3
 XXT  Var_06  H26  C17  C16  O4   34.11  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
 XXT  chir_01  C1   O4   C2   C5  negativ
 XXT  chir_02  C6   O6   C4   C7  positiv
 XXT  chir_03  C5   C4   C10  C1  positiv
 XXT  chir_04  C3   O2   C2   C4  negativ
 XXT  chir_05  C4   C3   C5   C6  positiv
 XXT  chir_06  C7   C11  C6   C8  negativ
 XXT  chir_07  C8   O1   C9   C7  negativ
 XXT  chir_08  C10  C13  C5   C9  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
 XXT  plan-1  C11  0.020
 XXT  plan-1  C12  0.020
 XXT  plan-1  O3   0.020
 XXT  plan-1  O1   0.020
 XXT  plan-2  O4   0.020
 XXT  plan-2  C16  0.020
 XXT  plan-2  O5   0.020
 XXT  plan-2  C17  0.020
 XXT  plan-3  O7   0.020
 XXT  plan-3  C19  0.020
 XXT  plan-3  O6   0.020
 XXT  plan-3  C18  0.020

