# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jun 25 04:24:45 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: 4-[(3aS,4R,7R,8aS,8bR)-2-(1,3-benzodioxol-5-ylmethyl)-7-hydroxy-1,3-dioxodecahydropyrrolo[3,4-a]pyrrolizin-4-yl]benzenecarboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc(cc1)[C@H]2[C@@H]3[C@H]([C@@H]4C[C@@H](O)CN24)C(=O)N(Cc5ccc6OCOc6c5)C3=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
 SHY  SHY  4-[(3aS,4R,7R,8aS,8bR)-2-(1,3-benzodioxol-5-ylmethyl)-7-hydroxy-1,3-dioxodecahydropyrrolo[3,4-a]pyrrolizin-4-yl]benzenecarboximidamide  ligand  57  33  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SHY
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
 SHY  N1    N  N     0  -0.642   4.6135   0.1787   5.2965
 SHY  C3    C  C     0   0.329   4.1121  -0.4018   4.2738
 SHY  N2    N  NH2   0  -0.804   4.8060  -1.3808   3.6266
 SHY  C4    C  CR6   0  -0.005   2.7557  -0.1260   3.7234
 SHY  C9    C  CR16  0  -0.279   2.2289   1.1626   3.7823
 SHY  C8    C  CR16  0  -0.290   0.9630   1.4270   3.2888
 SHY  C7    C  CR6   0   0.113   0.1891   0.4159   2.7293
 SHY  C6    C  CR16  0  -0.280   0.7101  -0.8720   2.6773
 SHY  C5    C  CR16  0  -0.265   1.9809  -1.1392   3.1629
 SHY  C10   C  CH1   0  -0.100  -1.1661   0.7411   2.1598
 SHY  N11   N  NR5   0  -0.415  -2.0757  -0.3997   2.2137
 SHY  C12   C  CH2   0  -0.371  -2.7873  -0.5134   3.4744
 SHY  C13   C  CR15  0   0.047  -3.9789   0.4796   3.4085
 SHY  C14   C  CH2   0  -0.492  -4.1330   0.7733   1.9065
 SHY  C15   C  CR15  0  -0.113  -3.1193  -0.1601   1.2242
 SHY  C16   C  CR15  0  -0.397  -2.3575   0.4232   0.0481
 SHY  C17   C  CR5   0   0.604  -1.7294  -0.6568  -0.8054
 SHY  N19   N  NR5   0  -0.517  -0.3713  -0.4434  -0.8546
 SHY  C20   C  CR5   0   0.609   0.0297   0.6466  -0.1114
 SHY  O21   O  O     0  -0.413   1.1535   1.0798  -0.0947
 SHY  C22   C  CR15  0  -0.431  -1.1625   1.1587   0.6577
 SHY  C23   C  CH2   0  -0.434   0.5497  -1.2402  -1.6494
 SHY  C24   C  CR6   0   0.119   0.7933  -0.6524  -3.0144
 SHY  C32   C  CR16  0  -0.310   1.9386   0.0895  -3.2643
 SHY  C31   C  CR16  0  -0.333   2.1911   0.6619  -4.5176
 SHY  C30   C  CR56  0   0.294   1.2468   0.4599  -5.4918
 SHY  O29   O  O     0  -0.484   1.2506   0.8741  -6.7814
 SHY  C28   C  CH2   0   0.068  -0.0334   0.5536  -7.3021
 SHY  O20   O  OH1   0  -0.674  -5.1728  -0.0582   3.9309
 SHY  O27   O  O     0  -0.486  -0.6358  -0.3515  -6.3868
 SHY  C26   C  CR56  0   0.314   0.0995  -0.2823  -5.2504
 SHY  C25   C  CR16  0  -0.381  -0.1566  -0.8530  -4.0308
 SHY  O24   O  O     0  -0.433  -2.3018  -1.5590  -1.3671
 SHY  H1N   H  H     0   0.331   3.9381   0.8012   5.7240
 SHY  H2N1  H  HNH2  0   0.384   5.7710  -1.4925   3.8946
 SHY  H2N2  H  HNH2  0   0.391   4.6323  -1.5195   2.6452
 SHY  H9    H  HCR6  0   0.260   2.8144   1.9720   4.2012
 SHY  H8    H  HCR6  0   0.252   0.5736   2.4373   3.3363
 SHY  H6    H  HCR6  0   0.254   0.1158  -1.6747   2.2609
 SHY  H5    H  HCR6  0   0.260   2.3578  -2.1533   3.1217
 SHY  H10   H  HCH1  0   0.262  -1.5571   1.6067   2.7148
 SHY  H121  H  HCH2  0   0.253  -2.1194  -0.3398   4.3195
 SHY  H122  H  HCH2  0   0.248  -3.1837  -1.5283   3.5717
 SHY  H13   H  HCR5  0   0.218  -3.7195   1.4029   3.9387
 SHY  H141  H  HCH2  0   0.253  -3.9080   1.8208   1.6952
 SHY  H142  H  HCH2  0   0.260  -5.1522   0.5899   1.5648
 SHY  H15   H  HCR5  0   0.272  -3.6048  -1.1036   0.9613
 SHY  H16   H  HCR5  0   0.329  -2.9793   1.0534  -0.5914
 SHY  H22   H  HCR5  0   0.320  -1.2104   2.2429   0.5692
 SHY  H231  H  HCH2  0   0.288   1.4831  -1.3215  -1.0943
 SHY  H232  H  HCH2  0   0.290   0.1311  -2.2430  -1.7265
 SHY  H32   H  HCR6  0   0.257   2.6610   0.2365  -2.4724
 SHY  H31   H  HCR6  0   0.274   3.0907   1.2327  -4.7037
 SHY  H281  H  HCH2  0   0.234  -0.6395   1.4626  -7.3800
 SHY  H282  H  HCH2  0   0.247   0.0719   0.0784  -8.2770
 SHY  H20   H  HOH1  0   0.450  -5.0666  -0.1577   4.8819
 SHY  H25   H  HCR6  0   0.269  -1.0479  -1.4424  -3.8598

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
 SHY  N1   C3    double    1.278  0.020  1.278
 SHY  N1   H1N   single    0.890  0.020  1.040
 SHY  C3   N2    single    1.363  0.020  1.363
 SHY  C3   C4    single    1.490  0.020  1.490
 SHY  N2   H2N1  single    0.890  0.020  1.040
 SHY  N2   H2N2  single    0.890  0.020  1.040
 SHY  C4   C9    aromatic  1.393  0.020  1.393
 SHY  C4   C5    aromatic  1.393  0.020  1.393
 SHY  C9   C8    aromatic  1.384  0.020  1.384
 SHY  C9   H9    single    0.930  0.020  1.080
 SHY  C8   C7    aromatic  1.391  0.020  1.391
 SHY  C8   H8    single    0.930  0.020  1.080
 SHY  C7   C6    aromatic  1.390  0.020  1.390
 SHY  C7   C10   single    1.506  0.020  1.506
 SHY  C6   C5    aromatic  1.386  0.020  1.386
 SHY  C6   H6    single    0.930  0.020  1.080
 SHY  C5   H5    single    0.930  0.020  1.080
 SHY  C10  N11   single    1.460  0.020  1.460
 SHY  C10  C22   single    1.559  0.020  1.559
 SHY  C10  H10   single    0.970  0.020  1.090
 SHY  N11  C12   single    1.452  0.020  1.452
 SHY  N11  C15   single    1.458  0.020  1.458
 SHY  C12  C13   single    1.552  0.020  1.552
 SHY  C12  H121  single    0.970  0.020  1.090
 SHY  C12  H122  single    0.970  0.020  1.090
 SHY  C13  C14   single    1.538  0.020  1.538
 SHY  C13  O20   single    1.410  0.020  1.410
 SHY  C13  H13   single    0.970  0.020  1.090
 SHY  C14  C15   single    1.538  0.020  1.538
 SHY  C14  H141  single    0.970  0.020  1.090
 SHY  C14  H142  single    0.970  0.020  1.090
 SHY  C15  C16   single    1.518  0.020  1.518
 SHY  C15  H15   single    0.970  0.020  1.090
 SHY  C16  C17   single    1.513  0.020  1.513
 SHY  C16  C22   single    1.530  0.020  1.530
 SHY  C16  H16   single    0.970  0.020  1.090
 SHY  C17  N19   single    1.376  0.020  1.376
 SHY  C17  O24   double    1.207  0.020  1.207
 SHY  N19  C20   single    1.379  0.020  1.379
 SHY  N19  C23   single    1.454  0.020  1.454
 SHY  C20  O21   double    1.205  0.020  1.205
 SHY  C20  C22   single    1.508  0.020  1.508
 SHY  C22  H22   single    0.970  0.020  1.090
 SHY  C23  C24   single    1.506  0.020  1.506
 SHY  C23  H231  single    0.970  0.020  1.090
 SHY  C23  H232  single    0.970  0.020  1.090
 SHY  C24  C32   aromatic  1.387  0.020  1.387
 SHY  C24  C25   aromatic  1.406  0.020  1.406
 SHY  C32  C31   aromatic  1.401  0.020  1.401
 SHY  C32  H32   single    0.930  0.020  1.080
 SHY  C31  C30   aromatic  1.372  0.020  1.372
 SHY  C31  H31   single    0.930  0.020  1.080
 SHY  C30  O29   single    1.354  0.020  1.354
 SHY  C30  C26   aromatic  1.388  0.020  1.388
 SHY  O29  C28   single    1.422  0.020  1.422
 SHY  C28  O27   single    1.421  0.020  1.421
 SHY  C28  H281  single    0.970  0.020  1.090
 SHY  C28  H282  single    0.970  0.020  1.090
 SHY  O20  H20   single    0.850  0.020  0.980
 SHY  O27  C26   single    1.355  0.020  1.355
 SHY  C26  C25   aromatic  1.371  0.020  1.371
 SHY  C25  H25   single    0.930  0.020  1.080

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
 SHY  H1N   N1   C3    110.80  3.000
 SHY  C4    C3   N2    114.90  3.000
 SHY  C4    C3   N1    124.66  3.000
 SHY  N2    C3   N1    120.41  3.000
 SHY  H2N2  N2   H2N1  114.17  3.000
 SHY  H2N2  N2   C3    118.31  3.000
 SHY  H2N1  N2   C3    116.15  3.000
 SHY  C5    C4   C9    118.64  3.000
 SHY  C5    C4   C3    121.36  3.000
 SHY  C9    C4   C3    119.99  3.000
 SHY  H9    C9   C8    119.31  3.000
 SHY  H9    C9   C4    120.20  3.000
 SHY  C8    C9   C4    120.49  3.000
 SHY  H8    C8   C7    119.70  3.000
 SHY  H8    C8   C9    119.41  3.000
 SHY  C7    C8   C9    120.89  3.000
 SHY  C10   C7   C6    121.55  3.000
 SHY  C10   C7   C8    119.74  3.000
 SHY  C6    C7   C8    118.69  3.000
 SHY  H6    C6   C5    119.69  3.000
 SHY  H6    C6   C7    119.72  3.000
 SHY  C5    C6   C7    120.59  3.000
 SHY  H5    C5   C6    119.09  3.000
 SHY  H5    C5   C4    120.19  3.000
 SHY  C6    C5   C4    120.70  3.000
 SHY  H10   C10  C22   106.03  3.000
 SHY  H10   C10  N11   112.01  3.000
 SHY  C22   C10  N11   104.26  3.000
 SHY  H10   C10  C7    107.40  3.000
 SHY  C22   C10  C7    114.85  3.000
 SHY  N11   C10  C7    112.22  3.000
 SHY  C15   N11  C12   104.56  3.000
 SHY  C15   N11  C10   107.00  3.000
 SHY  C12   N11  C10   113.49  3.000
 SHY  H122  C12  H121  107.49  3.000
 SHY  H122  C12  C13   108.61  3.000
 SHY  H121  C12  C13   113.64  3.000
 SHY  H122  C12  N11   109.11  3.000
 SHY  H121  C12  N11   111.10  3.000
 SHY  C13   C12  N11   106.81  3.000
 SHY  H13   C13  O20   110.03  3.000
 SHY  H13   C13  C14   109.59  3.000
 SHY  O20   C13  C14   110.48  3.000
 SHY  H13   C13  C12   109.68  3.000
 SHY  O20   C13  C12   112.97  3.000
 SHY  C14   C13  C12   103.92  3.000
 SHY  H142  C14  H141  107.05  3.000
 SHY  H142  C14  C15   112.02  3.000
 SHY  H141  C14  C15   111.14  3.000
 SHY  H142  C14  C13   111.56  3.000
 SHY  H141  C14  C13   110.58  3.000
 SHY  C15   C14  C13   104.56  3.000
 SHY  H15   C15  C16   111.61  3.000
 SHY  H15   C15  C14   109.75  3.000
 SHY  C16   C15  C14   116.20  3.000
 SHY  H15   C15  N11   109.83  3.000
 SHY  C16   C15  N11   103.28  3.000
 SHY  C14   C15  N11   105.69  3.000
 SHY  H16   C16  C22   113.62  3.000
 SHY  H16   C16  C17   108.54  3.000
 SHY  C22   C16  C17   104.10  3.000
 SHY  H16   C16  C15   112.94  3.000
 SHY  C22   C16  C15   105.55  3.000
 SHY  C17   C16  C15   111.78  3.000
 SHY  O24   C17  N19   124.58  3.000
 SHY  O24   C17  C16   126.81  3.000
 SHY  N19   C17  C16   108.62  3.000
 SHY  C23   N19  C20   122.92  3.000
 SHY  C23   N19  C17   124.04  3.000
 SHY  C20   N19  C17   112.99  3.000
 SHY  C22   C20  O21   127.47  3.000
 SHY  C22   C20  N19   108.26  3.000
 SHY  O21   C20  N19   124.27  3.000
 SHY  H22   C22  C20   109.35  3.000
 SHY  H22   C22  C16   114.32  3.000
 SHY  C20   C22  C16   104.54  3.000
 SHY  H22   C22  C10   110.17  3.000
 SHY  C20   C22  C10   113.71  3.000
 SHY  C16   C22  C10   104.67  3.000
 SHY  H232  C23  H231  107.26  3.000
 SHY  H232  C23  C24   110.93  3.000
 SHY  H231  C23  C24   110.64  3.000
 SHY  H232  C23  N19   107.45  3.000
 SHY  H231  C23  N19   107.77  3.000
 SHY  C24   C23  N19   112.58  3.000
 SHY  C25   C24  C32   120.27  3.000
 SHY  C25   C24  C23   119.37  3.000
 SHY  C32   C24  C23   120.36  3.000
 SHY  H32   C32  C31   118.62  3.000
 SHY  H32   C32  C24   119.48  3.000
 SHY  C31   C32  C24   121.90  3.000
 SHY  H31   C31  C30   121.88  3.000
 SHY  H31   C31  C32   121.30  3.000
 SHY  C30   C31  C32   116.82  3.000
 SHY  C26   C30  O29   109.36  3.000
 SHY  C26   C30  C31   121.62  3.000
 SHY  O29   C30  C31   128.99  3.000
 SHY  C28   O29  C30   106.09  3.000
 SHY  H282  C28  H281  110.59  3.000
 SHY  H282  C28  O27   109.84  3.000
 SHY  H281  C28  O27   109.86  3.000
 SHY  H282  C28  O29   109.80  3.000
 SHY  H281  C28  O29   109.79  3.000
 SHY  O27   C28  O29   106.88  3.000
 SHY  H20   O20  C13   108.19  3.000
 SHY  C26   O27  C28   106.11  3.000
 SHY  C25   C26  O27   128.57  3.000
 SHY  C25   C26  C30   122.14  3.000
 SHY  O27   C26  C30   109.27  3.000
 SHY  H25   C25  C26   121.42  3.000
 SHY  H25   C25  C24   121.34  3.000
 SHY  C26   C25  C24   117.24  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
 SHY  CONST_01  C7    C8   C9   C4     0.00   0.0  0
 SHY  CONST_02  C7    C6   C5   C4     0.00   0.0  0
 SHY  CONST_03  C6    C5   C4   C9     0.00   0.0  0
 SHY  CONST_04  C6    C7   C8   C9     0.00   0.0  0
 SHY  CONST_05  C5    C4   C9   C8     0.00   0.0  0
 SHY  CONST_06  C5    C6   C7   C8     0.00   0.0  0
 SHY  CONST_07  C30   C31  C32  C24    0.00   0.0  0
 SHY  CONST_08  C30   C26  C25  C24    0.00   0.0  0
 SHY  CONST_09  C26   C25  C24  C32    0.00   0.0  0
 SHY  CONST_10  C26   C30  C31  C32    0.00   0.0  0
 SHY  CONST_11  C25   C24  C32  C31    0.00   0.0  0
 SHY  CONST_12  C25   C26  C30  C31    0.00   0.0  0
 SHY  CONST_13  C10   C7   C8   C9   180.00   0.0  0
 SHY  CONST_14  C10   C7   C6   C5   180.00   0.0  0
 SHY  CONST_15  C20   N19  C17  C16    0.00   0.0  0
 SHY  CONST_16  C8    C9   C4   C3   180.00   0.0  0
 SHY  CONST_17  C6    C5   C4   C3   180.00   0.0  0
 SHY  CONST_18  C31   C32  C24  C23  180.00   0.0  0
 SHY  CONST_19  C26   C25  C24  C23  180.00   0.0  0
 SHY  CONST_20  C23   N19  C17  C16  180.00   0.0  0
 SHY  CONST_21  O24   C17  N19  C20  180.00   0.0  0
 SHY  CONST_22  H8    C8   C9   C4   180.00   0.0  0
 SHY  CONST_23  H6    C6   C5   C4   180.00   0.0  0
 SHY  CONST_24  H5    C5   C4   C9   180.00   0.0  0
 SHY  CONST_25  H9    C9   C8   C7   180.00   0.0  0
 SHY  CONST_26  H31   C31  C32  C24  180.00   0.0  0
 SHY  CONST_27  H25   C25  C24  C32  180.00   0.0  0
 SHY  CONST_28  H32   C32  C31  C30  180.00   0.0  0
 SHY  CONST_29  O24   C17  N19  C23    0.00   0.0  0
 SHY  CONST_30  H1N   N1   C3   C4     0.00   0.0  0
 SHY  CONST_31  H2N1  N2   C3   C4   180.00   0.0  0
 SHY  Var_01    C13   C12  N11  C10   80.93  30.0  1
 SHY  Var_02    C22   C20  N19  C17    6.71  30.0  1
 SHY  Var_03    O27   C28  O29  C30  -14.63  30.0  1
 SHY  Var_04    C26   C30  O29  C28    9.04  30.0  1
 SHY  Var_05    C25   C26  O27  C28  172.30  30.0  1
 SHY  Var_06    C24   C23  N19  C17   92.83  30.0  3
 SHY  Var_07    C32   C24  C23  N19   99.69  30.0  2
 SHY  Var_08    C9    C4   C3   N1    34.12  30.0  2

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
 SHY  chir_01  C10  C7   N11  C22  positiv
 SHY  chir_02  C13  O20  C12  C14  negativ
 SHY  chir_03  C15  N11  C16  C14  positiv
 SHY  chir_04  C16  C15  C17  C22  positiv
 SHY  chir_05  C22  C10  C16  C20  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
 SHY  plan-1  C3    0.020
 SHY  plan-1  C4    0.020
 SHY  plan-1  C9    0.020
 SHY  plan-1  C8    0.020
 SHY  plan-1  C7    0.020
 SHY  plan-1  C6    0.020
 SHY  plan-1  C5    0.020
 SHY  plan-1  C10   0.020
 SHY  plan-1  H9    0.020
 SHY  plan-1  H8    0.020
 SHY  plan-1  H6    0.020
 SHY  plan-1  H5    0.020
 SHY  plan-2  C23   0.020
 SHY  plan-2  C24   0.020
 SHY  plan-2  C32   0.020
 SHY  plan-2  C31   0.020
 SHY  plan-2  C30   0.020
 SHY  plan-2  O29   0.020
 SHY  plan-2  O27   0.020
 SHY  plan-2  C26   0.020
 SHY  plan-2  C25   0.020
 SHY  plan-2  H32   0.020
 SHY  plan-2  H31   0.020
 SHY  plan-2  H25   0.020
 SHY  plan-3  N19   0.020
 SHY  plan-3  C20   0.020
 SHY  plan-3  O21   0.020
 SHY  plan-3  C22   0.020
 SHY  plan-4  N1    0.020
 SHY  plan-4  C3    0.020
 SHY  plan-4  N2    0.020
 SHY  plan-4  C4    0.020
 SHY  plan-4  H1N   0.020
 SHY  plan-4  H2N1  0.020
 SHY  plan-4  H2N2  0.020
 SHY  plan-5  C16   0.020
 SHY  plan-5  C17   0.020
 SHY  plan-5  N19   0.020
 SHY  plan-5  C20   0.020
 SHY  plan-5  C23   0.020
 SHY  plan-5  O24   0.020

