# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue Jul  7 21:47:27 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: 3-[(3aS,4R,5S,8aS,8bR)-4-[2-(5-chlorothiophen-2-yl)-1,3-oxazol-4-yl]-1,3-dioxo-4,6,7,8,8a,8b-hexahydro-3aH-pyrrolo[3,4-a]pyrrolizin-2-yl]propyl-trimethyl-azanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[N+](C)(C)CCCN1C(=O)[C@H]2[C@@H]3CCCN3[C@H]([C@H]2C1=O)c4coc(n4)c5sc(Cl)cc5
#
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
 Y5H  Y5H  3-[(3aS,4R,5S,8aS,8bR)-4-[2-(5-chlorothiophen-2-yl)-1,3-oxazol-4-yl]-1,3-dioxo-4,6,7,8,8a,8b-hexahydro-3aH-pyrrolo[3,4-a]pyrrolizin-2-yl]propyl-trimethyl-azanium  ligand  59  31  .  2021-08-25  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_Y5H
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
 Y5H  CL1   CL  CL    0  -0.066  -5.2931   1.2853  -1.5520
 Y5H  C25   C   CR5   0  -0.252  -4.0406   1.9759  -0.6260
 Y5H  C24   C   CR15  0  -0.114  -4.1506   2.9988   0.2642
 Y5H  C22   C   CR15  0  -0.212  -2.9024   3.3138   0.8543
 Y5H  S1    S   S2    0   0.323  -2.4358   1.3786  -0.7693
 Y5H  C20   C   CR5   0  -0.295  -1.8853   2.5257   0.3953
 Y5H  C17   C   CR5   0   0.535  -0.4924   2.5255   0.7507
 Y5H  N16   N   N     0  -0.440   0.4295   1.7735   0.2545
 Y5H  O10   O   O     0  -0.409  -0.0570   3.3629   1.6983
 Y5H  C9    C   CR15  0  -0.059   1.2711   3.1017   1.8127
 Y5H  C4    C   CR5   0   0.188   1.5750   2.1249   0.9331
 Y5H  C1    C   CH1   0  -0.170   2.8796   1.4606   0.6735
 Y5H  N3    N   NT    0  -0.404   3.2068   1.5301  -0.7525
 Y5H  C7    C   CH1   0  -0.118   4.1256   0.4340  -1.0289
 Y5H  C14   C   CH2   0  -0.458   5.5168   0.9335  -0.5997
 Y5H  C15   C   CH2   0  -0.475   5.4280   2.4621  -0.7662
 Y5H  C8    C   CH2   0  -0.335   3.9431   2.7333  -1.1133
 Y5H  C5    C   CR15  0  -0.399   3.5581  -0.7114  -0.2130
 Y5H  C2    C   CR15  0  -0.436   2.9270  -0.0583   1.0173
 Y5H  C6    C   CR5   0   0.605   1.5680  -0.7027   1.1270
 Y5H  O13   O   O     0  -0.424   0.8130  -0.6726   2.0655
 Y5H  C11   C   CR5   0   0.599   2.3949  -1.3899  -0.9031
 Y5H  O18   O   O     0  -0.430   2.3918  -1.8936  -1.9994
 Y5H  N12   N   NR5   0  -0.525   1.3114  -1.3633  -0.0552
 Y5H  C19   C   CH2   0  -0.311   0.0373  -1.9759  -0.3514
 Y5H  C21   C   CH2   0  -0.489  -0.0636  -3.3878   0.2190
 Y5H  C23   C   CH2   0  -0.313  -1.3966  -3.9831  -0.1952
 Y5H  N29   N   NT    1  -0.386  -1.7497  -5.2851   0.4697
 Y5H  C32   C   CH3   0  -0.546  -3.0209  -5.7741  -0.1365
 Y5H  C31   C   CH3   0  -0.553  -0.6852  -6.3021   0.2515
 Y5H  C30   C   CH3   0  -0.551  -1.9616  -5.0944   1.9315
 Y5H  H24   H   HCR5  0   0.296  -5.0767   3.5068   0.4876
 Y5H  H22   H   HCR5  0   0.283  -2.7725   4.0955   1.5886
 Y5H  H9    H   HCR5  0   0.304   1.8352   3.6688   2.5342
 Y5H  H1    H   HCH1  0   0.268   3.6345   1.9534   1.3009
 Y5H  H7    H   HCH1  0   0.266   4.1250   0.2092  -2.0989
 Y5H  H82   H   HCH2  0   0.245   3.8321   2.9063  -2.1857
 Y5H  H81   H   HCH2  0   0.247   3.5327   3.6074  -0.6060
 Y5H  H5    H   HCR5  0   0.328   4.3075  -1.4690   0.0272
 Y5H  H2    H   HCR5  0   0.322   3.4766  -0.2152   1.9435
 Y5H  H141  H   HCH2  0   0.240   5.7177   0.6651   0.4400
 Y5H  H142  H   HCH2  0   0.251   6.3082   0.4846  -1.1994
 Y5H  H151  H   HCH2  0   0.240   5.7245   2.9739   0.1496
 Y5H  H152  H   HCH2  0   0.244   6.0821   2.8269  -1.5581
 Y5H  H191  H   HCH2  0   0.271  -0.7459  -1.3410   0.0634
 Y5H  H192  H   HCH2  0   0.281  -0.0872  -1.9843  -1.4340
 Y5H  H211  H   HCH2  0   0.273   0.7636  -3.9887  -0.1620
 Y5H  H212  H   HCH2  0   0.273   0.0332  -3.3349   1.3041
 Y5H  H231  H   HCH2  0   0.303  -2.2161  -3.2984   0.0284
 Y5H  H232  H   HCH2  0   0.309  -1.4070  -4.1721  -1.2689
 Y5H  H321  H   HCH3  0   0.296  -2.8643  -5.9546  -1.1963
 Y5H  H322  H   HCH3  0   0.296  -3.3158  -6.6969   0.3545
 Y5H  H323  H   HCH3  0   0.297  -3.7913  -5.0199   0.0001
 Y5H  H311  H   HCH3  0   0.298   0.2249  -5.9957   0.7575
 Y5H  H312  H   HCH3  0   0.300  -1.0201  -7.2504   0.6626
 Y5H  H313  H   HCH3  0   0.298  -0.5015  -6.4065  -0.8145
 Y5H  H301  H   HCH3  0   0.297  -2.7245  -4.3364   2.0866
 Y5H  H302  H   HCH3  0   0.298  -2.2858  -6.0369   2.3640
 Y5H  H303  H   HCH3  0   0.296  -1.0338  -4.7887   2.4041

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
 Y5H  C1   C2    single    1.558  0.020  1.558
 Y5H  C1   N3    single    1.465  0.020  1.465
 Y5H  C1   C4    single    1.487  0.020  1.487
 Y5H  S1   C20   aromatic  1.725  0.020  1.725
 Y5H  S1   C25   aromatic  1.718  0.020  1.718
 Y5H  CL1  C25   single    1.704  0.020  1.704
 Y5H  C2   C5    single    1.529  0.020  1.529
 Y5H  C2   C6    single    1.508  0.020  1.508
 Y5H  N3   C7    single    1.457  0.020  1.457
 Y5H  N3   C8    single    1.456  0.020  1.456
 Y5H  C4   C9    aromatic  1.349  0.020  1.349
 Y5H  C4   N16   aromatic  1.377  0.020  1.377
 Y5H  C5   C7    single    1.516  0.020  1.516
 Y5H  C5   C11   single    1.513  0.020  1.513
 Y5H  C6   N12   single    1.378  0.020  1.378
 Y5H  C6   O13   double    1.205  0.020  1.205
 Y5H  C7   C14   single    1.539  0.020  1.539
 Y5H  C8   C15   single    1.549  0.020  1.549
 Y5H  C9   O10   aromatic  1.358  0.020  1.358
 Y5H  O10  C17   aromatic  1.337  0.020  1.337
 Y5H  C11  N12   single    1.376  0.020  1.376
 Y5H  C11  O18   double    1.207  0.020  1.207
 Y5H  N12  C19   single    1.444  0.020  1.444
 Y5H  C14  C15   single    1.540  0.020  1.540
 Y5H  N16  C17   aromatic  1.289  0.020  1.289
 Y5H  C17  C20   single    1.438  0.020  1.438
 Y5H  C19  C21   single    1.526  0.020  1.526
 Y5H  C20  C22   aromatic  1.366  0.020  1.366
 Y5H  C21  C23   single    1.517  0.020  1.517
 Y5H  C22  C24   aromatic  1.416  0.020  1.416
 Y5H  C23  N29   single    1.504  0.020  1.504
 Y5H  C24  C25   aromatic  1.360  0.020  1.360
 Y5H  N29  C30   single    1.489  0.020  1.489
 Y5H  N29  C31   single    1.488  0.020  1.488
 Y5H  N29  C32   single    1.491  0.020  1.491
 Y5H  C24  H24   single    0.930  0.020  1.080
 Y5H  C22  H22   single    0.930  0.020  1.080
 Y5H  C9   H9    single    0.930  0.020  1.080
 Y5H  C1   H1    single    0.970  0.020  1.090
 Y5H  C7   H7    single    0.970  0.020  1.090
 Y5H  C8   H82   single    0.970  0.020  1.090
 Y5H  C8   H81   single    0.970  0.020  1.090
 Y5H  C5   H5    single    0.970  0.020  1.090
 Y5H  C2   H2    single    0.970  0.020  1.090
 Y5H  C14  H141  single    0.970  0.020  1.090
 Y5H  C14  H142  single    0.970  0.020  1.090
 Y5H  C15  H151  single    0.970  0.020  1.090
 Y5H  C15  H152  single    0.970  0.020  1.090
 Y5H  C19  H191  single    0.970  0.020  1.090
 Y5H  C19  H192  single    0.970  0.020  1.090
 Y5H  C21  H211  single    0.970  0.020  1.090
 Y5H  C21  H212  single    0.970  0.020  1.090
 Y5H  C23  H231  single    0.970  0.020  1.090
 Y5H  C23  H232  single    0.970  0.020  1.090
 Y5H  C32  H321  single    0.970  0.020  1.090
 Y5H  C32  H322  single    0.970  0.020  1.090
 Y5H  C32  H323  single    0.970  0.020  1.090
 Y5H  C31  H311  single    0.970  0.020  1.090
 Y5H  C31  H312  single    0.970  0.020  1.090
 Y5H  C31  H313  single    0.970  0.020  1.090
 Y5H  C30  H301  single    0.970  0.020  1.090
 Y5H  C30  H302  single    0.970  0.020  1.090
 Y5H  C30  H303  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
 Y5H  S1    C25  C24   113.05  3.000
 Y5H  C24   C25  CL1   126.94  3.000
 Y5H  S1    C25  CL1   120.02  3.000
 Y5H  H24   C24  C22   124.41  3.000
 Y5H  H24   C24  C25   123.96  3.000
 Y5H  C22   C24  C25   111.63  3.000
 Y5H  H22   C22  C20   123.80  3.000
 Y5H  H22   C22  C24   123.38  3.000
 Y5H  C20   C22  C24   112.82  3.000
 Y5H  C20   S1   C25    90.60  3.000
 Y5H  C17   C20  S1    118.43  3.000
 Y5H  C17   C20  C22   129.67  3.000
 Y5H  S1    C20  C22   111.90  3.000
 Y5H  O10   C17  N16   113.90  3.000
 Y5H  N16   C17  C20   126.72  3.000
 Y5H  O10   C17  C20   119.38  3.000
 Y5H  C4    N16  C17   104.86  3.000
 Y5H  C9    O10  C17   104.92  3.000
 Y5H  H9    C9   C4    134.42  3.000
 Y5H  H9    C9   O10   117.85  3.000
 Y5H  C4    C9   O10   107.73  3.000
 Y5H  C1    C4   C9    129.42  3.000
 Y5H  C9    C4   N16   108.58  3.000
 Y5H  C1    C4   N16   122.00  3.000
 Y5H  H1    C1   C2    106.88  3.000
 Y5H  H1    C1   N3    112.42  3.000
 Y5H  C2    C1   N3    104.73  3.000
 Y5H  H1    C1   C4    107.63  3.000
 Y5H  N3    C1   C4    110.17  3.000
 Y5H  C2    C1   C4    115.07  3.000
 Y5H  C8    N3   C7    104.82  3.000
 Y5H  C8    N3   C1    113.17  3.000
 Y5H  C7    N3   C1    106.85  3.000
 Y5H  H7    C7   C5    111.78  3.000
 Y5H  H7    C7   C14   109.88  3.000
 Y5H  C5    C7   C14   115.68  3.000
 Y5H  H7    C7   N3    109.88  3.000
 Y5H  C14   C7   N3    105.84  3.000
 Y5H  C5    C7   N3    103.31  3.000
 Y5H  H142  C14  H141  106.80  3.000
 Y5H  H142  C14  C15   113.03  3.000
 Y5H  H141  C14  C15   110.94  3.000
 Y5H  H142  C14  C7    111.67  3.000
 Y5H  H141  C14  C7    110.60  3.000
 Y5H  C15   C14  C7    103.87  3.000
 Y5H  H152  C15  H151  106.86  3.000
 Y5H  H152  C15  C8    110.73  3.000
 Y5H  H151  C15  C8    111.52  3.000
 Y5H  H152  C15  C14   112.09  3.000
 Y5H  H151  C15  C14   111.06  3.000
 Y5H  C8    C15  C14   104.67  3.000
 Y5H  H81   C8   H82   106.95  3.000
 Y5H  H81   C8   C15   113.38  3.000
 Y5H  H82   C8   C15   110.20  3.000
 Y5H  H81   C8   N3    110.89  3.000
 Y5H  H82   C8   N3    108.83  3.000
 Y5H  C15   C8   N3    106.54  3.000
 Y5H  H5    C5   C11   108.46  3.000
 Y5H  H5    C5   C2    113.73  3.000
 Y5H  C11   C5   C2    103.96  3.000
 Y5H  H5    C5   C7    112.67  3.000
 Y5H  C11   C5   C7    112.40  3.000
 Y5H  C2    C5   C7    105.35  3.000
 Y5H  H2    C2   C6    109.36  3.000
 Y5H  H2    C2   C5    114.50  3.000
 Y5H  C6    C2   C5    104.36  3.000
 Y5H  H2    C2   C1    110.10  3.000
 Y5H  C6    C2   C1    113.91  3.000
 Y5H  C5    C2   C1    104.56  3.000
 Y5H  N12   C6   O13   124.30  3.000
 Y5H  O13   C6   C2    127.64  3.000
 Y5H  N12   C6   C2    108.07  3.000
 Y5H  N12   C11  O18   124.47  3.000
 Y5H  O18   C11  C5    127.13  3.000
 Y5H  N12   C11  C5    108.40  3.000
 Y5H  C19   N12  C11   124.05  3.000
 Y5H  C19   N12  C6    122.91  3.000
 Y5H  C11   N12  C6    113.03  3.000
 Y5H  H192  C19  H191  107.48  3.000
 Y5H  H192  C19  C21   110.90  3.000
 Y5H  H191  C19  C21   110.43  3.000
 Y5H  H192  C19  N12   107.93  3.000
 Y5H  H191  C19  N12   107.98  3.000
 Y5H  C21   C19  N12   111.97  3.000
 Y5H  H212  C21  H211  107.87  3.000
 Y5H  H212  C21  C23   111.62  3.000
 Y5H  H211  C21  C23   110.77  3.000
 Y5H  H212  C21  C19   108.73  3.000
 Y5H  H211  C21  C19   109.20  3.000
 Y5H  C23   C21  C19   108.60  3.000
 Y5H  H232  C23  H231  107.66  3.000
 Y5H  H232  C23  N29   106.44  3.000
 Y5H  H231  C23  N29   106.04  3.000
 Y5H  H232  C23  C21   110.19  3.000
 Y5H  H231  C23  C21   110.96  3.000
 Y5H  N29   C23  C21   115.16  3.000
 Y5H  C30   N29  C31   109.46  3.000
 Y5H  C31   N29  C32   109.03  3.000
 Y5H  C30   N29  C32   108.65  3.000
 Y5H  C32   N29  C23   107.72  3.000
 Y5H  C31   N29  C23   111.02  3.000
 Y5H  C30   N29  C23   110.88  3.000
 Y5H  H323  C32  H322  109.90  3.000
 Y5H  H323  C32  H321  109.88  3.000
 Y5H  H322  C32  H321  109.81  3.000
 Y5H  H323  C32  N29   109.01  3.000
 Y5H  H322  C32  N29   109.05  3.000
 Y5H  H321  C32  N29   109.17  3.000
 Y5H  H313  C31  H312  109.84  3.000
 Y5H  H313  C31  H311  110.04  3.000
 Y5H  H312  C31  H311  109.17  3.000
 Y5H  H313  C31  N29   109.30  3.000
 Y5H  H312  C31  N29   108.69  3.000
 Y5H  H311  C31  N29   109.78  3.000
 Y5H  H303  C30  H302  109.03  3.000
 Y5H  H303  C30  H301  109.98  3.000
 Y5H  H302  C30  H301  109.80  3.000
 Y5H  H303  C30  N29   110.00  3.000
 Y5H  H302  C30  N29   108.79  3.000
 Y5H  H301  C30  N29   109.22  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
 Y5H  CONST_01  C17   C20  S1   C25   180.00   0.0  0
 Y5H  CONST_02  C22   C20  S1   C25     0.00   0.0  0
 Y5H  CONST_03  C20   C22  C24  C25     0.00   0.0  0
 Y5H  CONST_04  S1    C20  C22  C24     0.00   0.0  0
 Y5H  CONST_05  C17   C20  C22  C24   180.00   0.0  0
 Y5H  CONST_06  C20   S1   C25  C24     0.00   0.0  0
 Y5H  CONST_07  O10   C17  C20  C22     0.00   0.0  0
 Y5H  CONST_08  N16   C17  C20  C22   180.00   0.0  0
 Y5H  CONST_09  S1    C25  C24  C22     0.00   0.0  0
 Y5H  CONST_10  O10   C17  C20  S1    180.00   0.0  0
 Y5H  CONST_11  N16   C17  C20  S1      0.00   0.0  0
 Y5H  CONST_12  C9    O10  C17  C20   180.00   0.0  0
 Y5H  CONST_13  C4    N16  C17  C20   180.00   0.0  0
 Y5H  CONST_14  C4    C9   O10  C17     0.00   0.0  0
 Y5H  CONST_15  C9    C4   N16  C17     0.00   0.0  0
 Y5H  CONST_16  O10   C9   C4   N16     0.00   0.0  0
 Y5H  CONST_17  C9    O10  C17  N16     0.00   0.0  0
 Y5H  CONST_18  C4    N16  C17  O10     0.00   0.0  0
 Y5H  CONST_19  C1    C4   N16  C17   180.00   0.0  0
 Y5H  CONST_20  C1    C4   C9   O10   180.00   0.0  0
 Y5H  CONST_21  C11   N12  C6   C2      0.00   0.0  0
 Y5H  CONST_22  C20   S1   C25  CL1   180.00   0.0  0
 Y5H  CONST_23  C22   C24  C25  CL1   180.00   0.0  0
 Y5H  CONST_24  C19   N12  C6   C2    180.00   0.0  0
 Y5H  CONST_25  C11   N12  C6   O13   180.00   0.0  0
 Y5H  CONST_26  H22   C22  C24  C25   180.00   0.0  0
 Y5H  CONST_27  H24   C24  C25  S1    180.00   0.0  0
 Y5H  CONST_28  H9    C9   O10  C17   180.00   0.0  0
 Y5H  CONST_29  C19   N12  C6   O13     0.00   0.0  0
 Y5H  Var_01    C15   C8   N3   C1     81.90  30.0  1
 Y5H  Var_02    C14   C15  C8   N3     16.35  30.0  1
 Y5H  Var_03    C8    C15  C14  C7      6.61  30.0  1
 Y5H  Var_04    C6    N12  C11  C5      2.22  30.0  1
 Y5H  Var_05    C21   C19  N12  C6    -84.98  30.0  3
 Y5H  Var_06    C23   C21  C19  N12  -177.14  30.0  3
 Y5H  Var_07    N29   C23  C21  C19  -170.50  30.0  3
 Y5H  Var_08    C30   N29  C23  C21    65.94  30.0  3
 Y5H  Var_09    H301  C30  N29  C23    56.00  30.0  3
 Y5H  Var_10    H311  C31  N29  C23    66.05  30.0  3
 Y5H  Var_11    H321  C32  N29  C23    62.09  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
 Y5H  chir_01  C1  C2   N3  C4   negativ
 Y5H  chir_02  C7  N3   C5  C14  positiv
 Y5H  chir_03  C5  C11  C7  C2   negativ
 Y5H  chir_04  C2  C1   C5  C6   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
 Y5H  plan-1  CL1  0.020
 Y5H  plan-1  C25  0.020
 Y5H  plan-1  C24  0.020
 Y5H  plan-1  C22  0.020
 Y5H  plan-1  S1   0.020
 Y5H  plan-1  C20  0.020
 Y5H  plan-1  C17  0.020
 Y5H  plan-1  H24  0.020
 Y5H  plan-1  H22  0.020
 Y5H  plan-2  C20  0.020
 Y5H  plan-2  C17  0.020
 Y5H  plan-2  N16  0.020
 Y5H  plan-2  O10  0.020
 Y5H  plan-2  C9   0.020
 Y5H  plan-2  C4   0.020
 Y5H  plan-2  C1   0.020
 Y5H  plan-2  H9   0.020
 Y5H  plan-3  C5   0.020
 Y5H  plan-3  C11  0.020
 Y5H  plan-3  O18  0.020
 Y5H  plan-3  N12  0.020
 Y5H  plan-4  C2   0.020
 Y5H  plan-4  C6   0.020
 Y5H  plan-4  O13  0.020
 Y5H  plan-4  C11  0.020
 Y5H  plan-4  N12  0.020
 Y5H  plan-4  C19  0.020

