# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue May 26 03:36:55 2020
#   Inital geometry file: a 160 line input string
#   Ligand name: 4-[(1R,3aS,4R,8aS,8bR)-2-(4-methoxybenzyl)-1-(1-methylethyl)-3-oxodecahydropyrrolo[3,4-a]pyrrolizin-4-yl]benzenecarboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(CN2[C@H](C(C)C)[C@H]3[C@@H]4CCCN4[C@H]([C@H]3C2=O)c5ccc(cc5)C(N)=N)cc1
#
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
 348  348  4-[(1R,3aS,4R,8aS,8bR)-2-(4-methoxybenzyl)-1-(1-methylethyl)-3-oxodecahydropyrrolo[3,4-a]pyrrolizin-4-yl]benzenecarboximidamide  ligand  67  33  .  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_348
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
 348  N1    N  NH2   0  -0.823  -6.0990   2.8372   0.6266
 348  C3    C  C     0   0.330  -5.0800   3.3895   1.3500
 348  N2    N  N     0  -0.655  -5.2108   4.1261   2.3871
 348  C4    C  CR6   0   0.031  -3.7100   3.0310   0.8946
 348  C9    C  CR16  0  -0.265  -2.6393   3.8667   1.2080
 348  C8    C  CR16  0  -0.304  -1.3566   3.5497   0.7983
 348  C7    C  CR6   0   0.153  -1.0978   2.3795   0.0891
 348  C6    C  CR16  0  -0.280  -2.1630   1.5465  -0.2227
 348  C5    C  CR16  0  -0.282  -3.4534   1.8680   0.1708
 348  C10   C  CH1   0  -0.083   0.3140   2.0590  -0.3327
 348  N11   N  NT    0  -0.445   0.3976   1.0514  -1.3617
 348  C12   C  CH2   0  -0.262   0.1992   1.5075  -2.7313
 348  C13   C  CH2   0  -0.474   1.2047   0.7023  -3.5523
 348  C14   C  CH2   0  -0.459   2.3818   0.5760  -2.5898
 348  C15   C  CH1   0  -0.014   1.6726   0.3251  -1.2635
 348  C16   C  CR15  0  -0.312   2.3607   0.8262   0.0133
 348  C17   C  CR15  0  -0.046   2.7963  -0.3066   0.9459
 348  N19   N  NR5   0  -0.451   1.5558  -0.6006   1.6522
 348  C20   C  CR5   0   0.588   0.6519   0.4064   1.6162
 348  O21   O  O     0  -0.481  -0.4336   0.4018   2.1680
 348  C22   C  CR15  0  -0.407   1.2329   1.5280   0.7735
 348  C23   C  CH2   0  -0.418   1.1985  -1.9436   2.0680
 348  C24   C  CR6   0   0.100   0.8929  -2.8157   0.8771
 348  C32   C  CR16  0  -0.287   1.7660  -3.8253   0.4819
 348  C31   C  CR16  0  -0.334   1.5206  -4.5906  -0.6456
 348  C30   C  CR6   0   0.371   0.3811  -4.3557  -1.4143
 348  O29   O  O2    0  -0.472   0.2167  -5.1367  -2.5003
 348  C28   C  CH3   0  -0.436  -0.9122  -4.9173  -3.3216
 348  C26   C  CR16  0  -0.366  -0.5058  -3.3512  -1.0291
 348  C25   C  CR16  0  -0.267  -0.2414  -2.5956   0.1043
 348  C18   C  CH1   0  -0.227   3.9570   0.1030   1.8669
 348  C41   C  CH3   0  -0.671   4.1341  -0.8244   3.0641
 348  C42   C  CH3   0  -0.662   5.2531   0.1645   1.0627
 348  H1N1  H  HNH2  0   0.393  -5.9376   2.6266  -0.3446
 348  H1N2  H  HNH2  0   0.389  -7.0323   3.1661   0.8169
 348  H2N   H  H     0   0.321  -6.1905   4.3188   2.5787
 348  H9    H  HCR6  0   0.247  -2.8221   4.7759   1.7649
 348  H8    H  HCR6  0   0.241  -0.5421   4.2260   1.0348
 348  H6    H  HCR6  0   0.248  -1.9754   0.6316  -0.7688
 348  H5    H  HCR6  0   0.248  -4.2579   1.1857  -0.0744
 348  H10   H  HCH1  0   0.227   0.7637   3.0101  -0.6724
 348  H121  H  HCH2  0   0.199   0.4176   2.5818  -2.8247
 348  H122  H  HCH2  0   0.224  -0.8304   1.3599  -3.0677
 348  H131  H  HCH2  0   0.242   1.4594   1.1900  -4.4933
 348  H132  H  HCH2  0   0.229   0.8005  -0.2852  -3.7890
 348  H141  H  HCH2  0   0.224   2.9440   1.5145  -2.5579
 348  H142  H  HCH2  0   0.240   3.0797  -0.2196  -2.8531
 348  H15   H  HCH1  0   0.241   1.4676  -0.7499  -1.1735
 348  H16   H  HCR5  0   0.264   3.1790   1.5078  -0.2214
 348  H17   H  HCR5  0   0.247   3.1005  -1.1910   0.3732
 348  H22   H  HCR5  0   0.294   1.5683   2.3427   1.4203
 348  H231  H  HCH2  0   0.271   0.3359  -1.8700   2.7301
 348  H232  H  HCH2  0   0.268   2.0071  -2.3821   2.6516
 348  H32   H  HCR6  0   0.251   2.6610  -4.0166   1.0634
 348  H31   H  HCR6  0   0.260   2.2142  -5.3687  -0.9394
 348  H281  H  HCH3  0   0.226  -0.9249  -3.9063  -3.7376
 348  H282  H  HCH3  0   0.259  -0.8432  -5.6302  -4.1394
 348  H283  H  HCH3  0   0.228  -1.8493  -5.0878  -2.7849
 348  H26   H  HCR6  0   0.276  -1.4035  -3.1436  -1.5962
 348  H25   H  HCR6  0   0.253  -0.9436  -1.8182   0.3804
 348  H18   H  HCH1  0   0.224   3.7379   1.1069   2.2511
 348  H411  H  HCH3  0   0.216   4.3356  -1.8514   2.7488
 348  H412  H  HCH3  0   0.237   4.9811  -0.4981   3.6691
 348  H413  H  HCH3  0   0.236   3.2568  -0.8308   3.7103
 348  H421  H  HCH3  0   0.234   6.0779   0.5127   1.6854
 348  H422  H  HCH3  0   0.220   5.5197  -0.8251   0.6838
 348  H423  H  HCH3  0   0.232   5.1870   0.8387   0.2079

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
 348  N1   C3    single    1.366  0.020  1.366
 348  N1   H1N1  single    0.890  0.020  1.040
 348  N1   H1N2  single    0.890  0.020  1.040
 348  C3   N2    double    1.279  0.020  1.279
 348  C3   C4    single    1.488  0.020  1.488
 348  N2   H2N   single    0.890  0.020  1.040
 348  C4   C9    aromatic  1.394  0.020  1.394
 348  C4   C5    aromatic  1.394  0.020  1.394
 348  C9   C8    aromatic  1.383  0.020  1.383
 348  C9   H9    single    0.930  0.020  1.080
 348  C8   C7    aromatic  1.393  0.020  1.393
 348  C8   H8    single    0.930  0.020  1.080
 348  C7   C6    aromatic  1.388  0.020  1.388
 348  C7   C10   single    1.508  0.020  1.508
 348  C6   C5    aromatic  1.387  0.020  1.387
 348  C6   H6    single    0.930  0.020  1.080
 348  C5   H5    single    0.930  0.020  1.080
 348  C10  N11   single    1.443  0.020  1.443
 348  C10  C22   single    1.533  0.020  1.533
 348  C10  H10   single    0.970  0.020  1.090
 348  N11  C12   single    1.457  0.020  1.457
 348  N11  C15   single    1.471  0.020  1.471
 348  C12  C13   single    1.528  0.020  1.528
 348  C12  H121  single    0.970  0.020  1.090
 348  C12  H122  single    0.970  0.020  1.090
 348  C13  C14   single    1.526  0.020  1.526
 348  C13  H131  single    0.970  0.020  1.090
 348  C13  H132  single    0.970  0.020  1.090
 348  C14  C15   single    1.525  0.020  1.525
 348  C14  H141  single    0.970  0.020  1.090
 348  C14  H142  single    0.970  0.020  1.090
 348  C15  C16   single    1.535  0.020  1.535
 348  C15  H15   single    0.970  0.020  1.090
 348  C16  C17   single    1.531  0.020  1.531
 348  C16  C22   single    1.531  0.020  1.531
 348  C16  H16   single    0.970  0.020  1.090
 348  C17  N19   single    1.457  0.020  1.457
 348  C17  C18   single    1.537  0.020  1.537
 348  C17  H17   single    0.970  0.020  1.090
 348  N19  C20   single    1.354  0.020  1.354
 348  N19  C23   single    1.451  0.020  1.451
 348  C20  O21   double    1.218  0.020  1.218
 348  C20  C22   single    1.518  0.020  1.518
 348  C22  H22   single    0.970  0.020  1.090
 348  C23  C24   single    1.507  0.020  1.507
 348  C23  H231  single    0.970  0.020  1.090
 348  C23  H232  single    0.970  0.020  1.090
 348  C24  C32   aromatic  1.392  0.020  1.392
 348  C24  C25   aromatic  1.390  0.020  1.390
 348  C32  C31   aromatic  1.385  0.020  1.385
 348  C32  H32   single    0.930  0.020  1.080
 348  C31  C30   aromatic  1.395  0.020  1.395
 348  C31  H31   single    0.930  0.020  1.080
 348  C30  O29   single    1.348  0.020  1.348
 348  C30  C26   aromatic  1.394  0.020  1.394
 348  O29  C28   single    1.413  0.020  1.413
 348  C28  H281  single    0.970  0.020  1.090
 348  C28  H282  single    0.970  0.020  1.090
 348  C28  H283  single    0.970  0.020  1.090
 348  C26  C25   aromatic  1.388  0.020  1.388
 348  C26  H26   single    0.930  0.020  1.080
 348  C25  H25   single    0.930  0.020  1.080
 348  C18  C41   single    1.525  0.020  1.525
 348  C18  C42   single    1.527  0.020  1.527
 348  C18  H18   single    0.970  0.020  1.090
 348  C41  H411  single    0.970  0.020  1.090
 348  C41  H412  single    0.970  0.020  1.090
 348  C41  H413  single    0.970  0.020  1.090
 348  C42  H421  single    0.970  0.020  1.090
 348  C42  H422  single    0.970  0.020  1.090
 348  C42  H423  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
 348  H1N2  N1   H1N1  113.52  3.000
 348  H1N2  N1   C3    117.30  3.000
 348  H1N1  N1   C3    118.40  3.000
 348  C4    C3   N2    118.77  3.000
 348  C4    C3   N1    115.30  3.000
 348  N2    C3   N1    125.87  3.000
 348  H2N   N2   C3    111.14  3.000
 348  C5    C4   C9    118.40  3.000
 348  C5    C4   C3    121.98  3.000
 348  C9    C4   C3    119.61  3.000
 348  H9    C9   C8    120.12  3.000
 348  H9    C9   C4    119.33  3.000
 348  C8    C9   C4    120.55  3.000
 348  H8    C8   C7    119.70  3.000
 348  H8    C8   C9    119.26  3.000
 348  C7    C8   C9    121.04  3.000
 348  C10   C7   C6    121.89  3.000
 348  C10   C7   C8    119.67  3.000
 348  C6    C7   C8    118.43  3.000
 348  H6    C6   C5    120.04  3.000
 348  H6    C6   C7    119.20  3.000
 348  C5    C6   C7    120.76  3.000
 348  H5    C5   C6    118.75  3.000
 348  H5    C5   C4    120.44  3.000
 348  C6    C5   C4    120.80  3.000
 348  H10   C10  C22   106.01  3.000
 348  H10   C10  N11   110.99  3.000
 348  C22   C10  N11   103.77  3.000
 348  H10   C10  C7    106.49  3.000
 348  C22   C10  C7    115.66  3.000
 348  N11   C10  C7    113.72  3.000
 348  C15   N11  C12   109.60  3.000
 348  C15   N11  C10   110.34  3.000
 348  C12   N11  C10   116.35  3.000
 348  H122  C12  H121  107.02  3.000
 348  H122  C12  C13   112.55  3.000
 348  H121  C12  C13   109.78  3.000
 348  H122  C12  N11   112.04  3.000
 348  H121  C12  N11   111.00  3.000
 348  C13   C12  N11   104.51  3.000
 348  H132  C13  H131  107.68  3.000
 348  H132  C13  C14   110.31  3.000
 348  H131  C13  C14   113.66  3.000
 348  H132  C13  C12   110.44  3.000
 348  H131  C13  C12   112.45  3.000
 348  C14   C13  C12   102.27  3.000
 348  H142  C14  H141  107.69  3.000
 348  H142  C14  C15   112.81  3.000
 348  H141  C14  C15   110.77  3.000
 348  H142  C14  C13   113.69  3.000
 348  H141  C14  C13   110.10  3.000
 348  C15   C14  C13   101.74  3.000
 348  H15   C15  C16   109.58  3.000
 348  H15   C15  C14   108.62  3.000
 348  C16   C15  C14   117.48  3.000
 348  H15   C15  N11   109.10  3.000
 348  C16   C15  N11   106.44  3.000
 348  C14   C15  N11   105.30  3.000
 348  H16   C16  C22   111.91  3.000
 348  H16   C16  C17   112.34  3.000
 348  C22   C16  C17   104.27  3.000
 348  H16   C16  C15   111.19  3.000
 348  C22   C16  C15   103.45  3.000
 348  C17   C16  C15   113.14  3.000
 348  H17   C17  C18   108.56  3.000
 348  H17   C17  N19   109.06  3.000
 348  C18   C17  N19   113.96  3.000
 348  H17   C17  C16   110.95  3.000
 348  C18   C17  C16   112.51  3.000
 348  N19   C17  C16   101.67  3.000
 348  C23   N19  C20   122.14  3.000
 348  C23   N19  C17   122.36  3.000
 348  C20   N19  C17   113.91  3.000
 348  C22   C20  O21   126.53  3.000
 348  C22   C20  N19   107.99  3.000
 348  O21   C20  N19   125.48  3.000
 348  H22   C22  C20   109.85  3.000
 348  H22   C22  C16   114.18  3.000
 348  C20   C22  C16   102.64  3.000
 348  H22   C22  C10   110.66  3.000
 348  C20   C22  C10   115.28  3.000
 348  C16   C22  C10   104.01  3.000
 348  H232  C23  H231  106.81  3.000
 348  H232  C23  C24   109.93  3.000
 348  H231  C23  C24   111.01  3.000
 348  H232  C23  N19   110.08  3.000
 348  H231  C23  N19   107.85  3.000
 348  C24   C23  N19   111.05  3.000
 348  C25   C24  C32   117.96  3.000
 348  C25   C24  C23   120.87  3.000
 348  C32   C24  C23   121.11  3.000
 348  H32   C32  C31   119.04  3.000
 348  H32   C32  C24   119.56  3.000
 348  C31   C32  C24   121.39  3.000
 348  H31   C31  C30   119.66  3.000
 348  H31   C31  C32   120.30  3.000
 348  C30   C31  C32   120.04  3.000
 348  C26   C30  O29   124.23  3.000
 348  C26   C30  C31   119.26  3.000
 348  O29   C30  C31   116.50  3.000
 348  C28   O29  C30   118.41  3.000
 348  H283  C28  H282  108.76  3.000
 348  H283  C28  H281  108.72  3.000
 348  H282  C28  H281  108.72  3.000
 348  H283  C28  O29   112.04  3.000
 348  H282  C28  O29   106.54  3.000
 348  H281  C28  O29   111.96  3.000
 348  H26   C26  C25   118.80  3.000
 348  H26   C26  C30   121.41  3.000
 348  C25   C26  C30   119.79  3.000
 348  H25   C25  C26   118.39  3.000
 348  H25   C25  C24   120.06  3.000
 348  C26   C25  C24   121.56  3.000
 348  H18   C18  C42   108.49  3.000
 348  H18   C18  C41   107.75  3.000
 348  C42   C18  C41   109.85  3.000
 348  H18   C18  C17   107.63  3.000
 348  C42   C18  C17   109.64  3.000
 348  C41   C18  C17   113.33  3.000
 348  H413  C41  H412  107.33  3.000
 348  H413  C41  H411  108.29  3.000
 348  H412  C41  H411  107.34  3.000
 348  H413  C41  C18   112.07  3.000
 348  H412  C41  C18   110.11  3.000
 348  H411  C41  C18   111.50  3.000
 348  H423  C42  H422  107.63  3.000
 348  H423  C42  H421  107.21  3.000
 348  H422  C42  H421  107.62  3.000
 348  H423  C42  C18   112.73  3.000
 348  H422  C42  C18   110.69  3.000
 348  H421  C42  C18   110.74  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
 348  CONST_01  C7    C8   C9   C4     0.00   0.0  0
 348  CONST_02  C7    C6   C5   C4     0.00   0.0  0
 348  CONST_03  C6    C5   C4   C9     0.00   0.0  0
 348  CONST_04  C6    C7   C8   C9     0.00   0.0  0
 348  CONST_05  C5    C4   C9   C8     0.00   0.0  0
 348  CONST_06  C5    C6   C7   C8     0.00   0.0  0
 348  CONST_07  C30   C31  C32  C24    0.00   0.0  0
 348  CONST_08  C30   C26  C25  C24    0.00   0.0  0
 348  CONST_09  C26   C25  C24  C32    0.00   0.0  0
 348  CONST_10  C26   C30  C31  C32    0.00   0.0  0
 348  CONST_11  C25   C24  C32  C31    0.00   0.0  0
 348  CONST_12  C25   C26  C30  C31    0.00   0.0  0
 348  CONST_13  C10   C7   C8   C9   180.00   0.0  0
 348  CONST_14  C10   C7   C6   C5   180.00   0.0  0
 348  CONST_15  C22   C20  N19  C17    0.00   0.0  0
 348  CONST_16  C8    C9   C4   C3   180.00   0.0  0
 348  CONST_17  C6    C5   C4   C3   180.00   0.0  0
 348  CONST_18  C31   C32  C24  C23  180.00   0.0  0
 348  CONST_19  C26   C25  C24  C23  180.00   0.0  0
 348  CONST_20  O29   C30  C31  C32  180.00   0.0  0
 348  CONST_21  C25   C26  C30  O29  180.00   0.0  0
 348  CONST_22  O21   C20  N19  C17  180.00   0.0  0
 348  CONST_24  H8    C8   C9   C4   180.00   0.0  0
 348  CONST_25  H6    C6   C5   C4   180.00   0.0  0
 348  CONST_26  H5    C5   C4   C9   180.00   0.0  0
 348  CONST_27  H9    C9   C8   C7   180.00   0.0  0
 348  CONST_28  H31   C31  C32  C24  180.00   0.0  0
 348  CONST_29  H26   C26  C25  C24  180.00   0.0  0
 348  CONST_30  H25   C25  C24  C32  180.00   0.0  0
 348  CONST_31  H32   C32  C31  C30  180.00   0.0  0
 348  CONST_34  H1N2  N1   C3   C4   180.00   0.0  0
 348  CONST_35  H2N   N2   C3   C4   180.00   0.0  0
 348  Var_01    C13   C12  N11  C10  141.45  30.0  1
 348  Var_02    C14   C13  C12  N11  -34.77  30.0  1
 348  Var_03    C15   C14  C13  C12   40.26  30.0  1
 348  Var_04    C24   C23  N19  C17  -68.74  30.0  3
 348  Var_05    C32   C24  C23  N19  108.24  30.0  2
 348  Var_06    C9    C4   C3   N1   156.92  30.0  2
 348  Var_07    C26   C30  O29  C28    1.13  30.0  1
 348  Var_08    H411  C41  C18  C17   59.85  30.0  3
 348  Var_09    H421  C42  C18  C17  176.53  30.0  3
 348  Var_10    H281  C28  O29  C30   60.17  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
 348  chir_01  C10  C7   N11  C22  positiv
 348  chir_02  C15  N11  C14  C16  negativ
 348  chir_03  C16  C15  C17  C22  positiv
 348  chir_04  C17  N19  C16  C18  negativ
 348  chir_05  C22  C20  C16  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
 348  plan-1  C3    0.020
 348  plan-1  C4    0.020
 348  plan-1  C9    0.020
 348  plan-1  C8    0.020
 348  plan-1  C7    0.020
 348  plan-1  C6    0.020
 348  plan-1  C5    0.020
 348  plan-1  C10   0.020
 348  plan-1  H9    0.020
 348  plan-1  H8    0.020
 348  plan-1  H6    0.020
 348  plan-1  H5    0.020
 348  plan-2  C23   0.020
 348  plan-2  C24   0.020
 348  plan-2  C32   0.020
 348  plan-2  C31   0.020
 348  plan-2  C30   0.020
 348  plan-2  O29   0.020
 348  plan-2  C26   0.020
 348  plan-2  C25   0.020
 348  plan-2  H32   0.020
 348  plan-2  H31   0.020
 348  plan-2  H26   0.020
 348  plan-2  H25   0.020
 348  plan-3  N1    0.020
 348  plan-3  C3    0.020
 348  plan-3  N2    0.020
 348  plan-3  C4    0.020
 348  plan-3  H1N1  0.020
 348  plan-3  H1N2  0.020
 348  plan-3  H2N   0.020
 348  plan-4  C17   0.020
 348  plan-4  N19   0.020
 348  plan-4  C20   0.020
 348  plan-4  O21   0.020
 348  plan-4  C22   0.020
 348  plan-4  C23   0.020

