# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 11:35:38 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: 3-[(3aS,4R,5S,8aS,8bR)-4-[5-(5-chlorothiophen-2-yl)-1,3-oxazol-2-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)c4oc(cn4)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
 FJD  FJD  3-[(3aS,4R,5S,8aS,8bR)-4-[5-(5-chlorothiophen-2-yl)-1,3-oxazol-2-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  .  2021-08-09  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_FJD
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
 FJD  CL1   CL  CL    0  -0.072  -7.0307   0.7006  -1.2094
 FJD  C25   C   CR5   0  -0.264  -5.5224   0.9910  -0.4685
 FJD  C24   C   CR15  0  -0.106  -5.1681   2.0726   0.2752
 FJD  C22   C   CR15  0  -0.265  -3.8327   1.9778   0.7360
 FJD  S1    S   S2    0   0.309  -4.2516  -0.1563  -0.6246
 FJD  C20   C   CR5   0  -0.319  -3.2061   0.8308   0.3331
 FJD  C17   C   CR5   0   0.444  -1.8638   0.4069   0.6141
 FJD  O16   O   O     0  -0.431  -1.4708  -0.8080   0.1591
 FJD  C10   C   CR15  0  -0.249  -0.8113   0.9373   1.2847
 FJD  N9    N   N     0  -0.400   0.2369   0.0499   1.2405
 FJD  C4    C   CR5   0   0.521  -0.2011  -0.9542   0.5652
 FJD  C1    C   CH1   0  -0.169   0.5168  -2.1923   0.1508
 FJD  N3    N   NT    0  -0.402   1.6175  -2.4746   1.0574
 FJD  C7    C   CH1   0  -0.123   2.5099  -3.3713   0.3305
 FJD  C14   C   CH2   0  -0.461   1.8831  -4.7693   0.4537
 FJD  C15   C   CH2   0  -0.475   1.1547  -4.7190   1.8103
 FJD  C8    C   CH2   0  -0.339   1.2173  -3.2307   2.2378
 FJD  C5    C   CR15  0  -0.395   2.5481  -2.7720  -1.0653
 FJD  C2    C   CR15  0  -0.430   1.1846  -2.1019  -1.2527
 FJD  C6    C   CR5   0   0.605   1.5049  -0.6821  -1.6481
 FJD  O13   O   O     0  -0.422   0.7245   0.1701  -1.9926
 FJD  C11   C   CR5   0   0.597   3.5369  -1.6300  -1.1459
 FJD  O18   O   O     0  -0.424   4.7206  -1.6758  -0.9236
 FJD  N12   N   NR5   0  -0.529   2.8608  -0.4899  -1.5218
 FJD  C19   C   CH2   0  -0.312   3.4774   0.8120  -1.6501
 FJD  C21   C   CH2   0  -0.497   3.3411   1.6010  -0.3494
 FJD  C23   C   CH2   0  -0.312   3.9008   2.9944  -0.5574
 FJD  N29   N   NT    1  -0.385   3.7611   3.9165   0.6233
 FJD  C32   C   CH3   0  -0.547   4.3928   5.2172   0.2599
 FJD  C31   C   CH3   0  -0.550   2.3272   4.1567   0.9450
 FJD  C30   C   CH3   0  -0.552   4.4515   3.3589   1.8190
 FJD  H24   H   HCR5  0   0.294  -5.8292   2.8990   0.4889
 FJD  H22   H   HCR5  0   0.275  -3.3572   2.7328   1.3459
 FJD  H10   H   HCR5  0   0.274  -0.7459   1.8845   1.7954
 FJD  H1    H   HCH1  0   0.286  -0.2228  -3.0046   0.1004
 FJD  H7    H   HCH1  0   0.273   3.4973  -3.3716   0.7999
 FJD  H82   H   HCH2  0   0.250   1.9737  -3.0900   3.0123
 FJD  H81   H   HCH2  0   0.250   0.2763  -2.8559   2.6420
 FJD  H5    H   HCR5  0   0.333   2.7840  -3.5085  -1.8357
 FJD  H2    H   HCR5  0   0.333   0.5532  -2.5631  -2.0104
 FJD  H141  H   HCH2  0   0.242   1.1756  -4.9524  -0.3587
 FJD  H142  H   HCH2  0   0.256   2.6374  -5.5534   0.4033
 FJD  H151  H   HCH2  0   0.243   0.1262  -5.0669   1.7164
 FJD  H152  H   HCH2  0   0.247   1.6372  -5.3521   2.5547
 FJD  H191  H   HCH2  0   0.285   4.5239   0.6722  -1.9161
 FJD  H192  H   HCH2  0   0.281   2.9965   1.3381  -2.4747
 FJD  H211  H   HCH2  0   0.272   2.2872   1.6359  -0.0716
 FJD  H212  H   HCH2  0   0.273   3.8758   1.0718   0.4409
 FJD  H231  H   HCH2  0   0.310   4.9658   2.9512  -0.7863
 FJD  H232  H   HCH2  0   0.307   3.3991   3.4904  -1.3890
 FJD  H321  H   HCH3  0   0.298   3.8857   5.6268  -0.6094
 FJD  H322  H   HCH3  0   0.296   4.3016   5.9016   1.0982
 FJD  H323  H   HCH3  0   0.298   5.4421   5.0527   0.0313
 FJD  H311  H   HCH3  0   0.284   1.8648   3.2363   1.2871
 FJD  H312  H   HCH3  0   0.302   2.2627   4.8986   1.7360
 FJD  H313  H   HCH3  0   0.300   1.8156   4.5195   0.0574
 FJD  H301  H   HCH3  0   0.298   5.4807   3.1237   1.5616
 FJD  H302  H   HCH3  0   0.301   4.4308   4.1006   2.6127
 FJD  H303  H   HCH3  0   0.295   3.9395   2.4624   2.1528

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
 FJD  C1   C2    single    1.557  0.020  1.557
 FJD  C1   N3    single    1.454  0.020  1.454
 FJD  C1   C4    single    1.490  0.020  1.490
 FJD  S1   C20   aromatic  1.728  0.020  1.728
 FJD  S1   C25   aromatic  1.719  0.020  1.719
 FJD  CL1  C25   single    1.705  0.020  1.705
 FJD  C2   C5    single    1.531  0.020  1.531
 FJD  C2   C6    single    1.508  0.020  1.508
 FJD  N3   C7    single    1.459  0.020  1.459
 FJD  N3   C8    single    1.458  0.020  1.458
 FJD  C4   N9    aromatic  1.287  0.020  1.287
 FJD  C4   O16   aromatic  1.341  0.020  1.341
 FJD  C5   C7    single    1.520  0.020  1.520
 FJD  C5   C11   single    1.513  0.020  1.513
 FJD  C6   N12   single    1.375  0.020  1.375
 FJD  C6   O13   double    1.206  0.020  1.206
 FJD  C7   C14   single    1.537  0.020  1.537
 FJD  C8   C15   single    1.550  0.020  1.550
 FJD  N9   C10   aromatic  1.374  0.020  1.374
 FJD  C10  C17   aromatic  1.356  0.020  1.356
 FJD  C11  N12   single    1.378  0.020  1.378
 FJD  C11  O18   double    1.205  0.020  1.205
 FJD  N12  C19   single    1.446  0.020  1.446
 FJD  C14  C15   single    1.541  0.020  1.541
 FJD  O16  C17   aromatic  1.355  0.020  1.355
 FJD  C17  C20   single    1.435  0.020  1.435
 FJD  C19  C21   single    1.527  0.020  1.527
 FJD  C20  C22   aromatic  1.368  0.020  1.368
 FJD  C21  C23   single    1.516  0.020  1.516
 FJD  C22  C24   aromatic  1.416  0.020  1.416
 FJD  C23  N29   single    1.505  0.020  1.505
 FJD  C24  C25   aromatic  1.360  0.020  1.360
 FJD  N29  C30   single    1.489  0.020  1.489
 FJD  N29  C31   single    1.489  0.020  1.489
 FJD  N29  C32   single    1.491  0.020  1.491
 FJD  C24  H24   single    0.930  0.020  1.080
 FJD  C22  H22   single    0.930  0.020  1.080
 FJD  C10  H10   single    0.930  0.020  1.080
 FJD  C1   H1    single    0.970  0.020  1.090
 FJD  C7   H7    single    0.970  0.020  1.090
 FJD  C8   H82   single    0.970  0.020  1.090
 FJD  C8   H81   single    0.970  0.020  1.090
 FJD  C5   H5    single    0.970  0.020  1.090
 FJD  C2   H2    single    0.970  0.020  1.090
 FJD  C14  H141  single    0.970  0.020  1.090
 FJD  C14  H142  single    0.970  0.020  1.090
 FJD  C15  H151  single    0.970  0.020  1.090
 FJD  C15  H152  single    0.970  0.020  1.090
 FJD  C19  H191  single    0.970  0.020  1.090
 FJD  C19  H192  single    0.970  0.020  1.090
 FJD  C21  H211  single    0.970  0.020  1.090
 FJD  C21  H212  single    0.970  0.020  1.090
 FJD  C23  H231  single    0.970  0.020  1.090
 FJD  C23  H232  single    0.970  0.020  1.090
 FJD  C32  H321  single    0.970  0.020  1.090
 FJD  C32  H322  single    0.970  0.020  1.090
 FJD  C32  H323  single    0.970  0.020  1.090
 FJD  C31  H311  single    0.970  0.020  1.090
 FJD  C31  H312  single    0.970  0.020  1.090
 FJD  C31  H313  single    0.970  0.020  1.090
 FJD  C30  H301  single    0.970  0.020  1.090
 FJD  C30  H302  single    0.970  0.020  1.090
 FJD  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
 FJD  S1    C25  C24   112.82  3.000
 FJD  C24   C25  CL1   127.13  3.000
 FJD  S1    C25  CL1   120.05  3.000
 FJD  H24   C24  C22   124.36  3.000
 FJD  H24   C24  C25   123.89  3.000
 FJD  C22   C24  C25   111.75  3.000
 FJD  H22   C22  C20   123.41  3.000
 FJD  H22   C22  C24   123.49  3.000
 FJD  C20   C22  C24   113.10  3.000
 FJD  C20   S1   C25    90.90  3.000
 FJD  C17   C20  S1    120.38  3.000
 FJD  C17   C20  C22   128.20  3.000
 FJD  S1    C20  C22   111.42  3.000
 FJD  C10   C17  O16   106.95  3.000
 FJD  O16   C17  C20   118.04  3.000
 FJD  C10   C17  C20   135.00  3.000
 FJD  C4    O16  C17   105.70  3.000
 FJD  H10   C10  N9    122.43  3.000
 FJD  H10   C10  C17   128.69  3.000
 FJD  N9    C10  C17   108.88  3.000
 FJD  C4    N9   C10   105.13  3.000
 FJD  C1    C4   N9    129.07  3.000
 FJD  N9    C4   O16   113.34  3.000
 FJD  C1    C4   O16   117.55  3.000
 FJD  H1    C1   C2    106.86  3.000
 FJD  H1    C1   N3    113.23  3.000
 FJD  C2    C1   N3    104.40  3.000
 FJD  H1    C1   C4    107.61  3.000
 FJD  N3    C1   C4    110.65  3.000
 FJD  C2    C1   C4    114.15  3.000
 FJD  C8    N3   C7    104.62  3.000
 FJD  C8    N3   C1    113.44  3.000
 FJD  C7    N3   C1    105.77  3.000
 FJD  H7    C7   C5    111.82  3.000
 FJD  H7    C7   C14   109.49  3.000
 FJD  C5    C7   C14   116.27  3.000
 FJD  H7    C7   N3    109.79  3.000
 FJD  C14   C7   N3    105.64  3.000
 FJD  C5    C7   N3    103.33  3.000
 FJD  H142  C14  H141  107.06  3.000
 FJD  H142  C14  C15   113.06  3.000
 FJD  H141  C14  C15   110.73  3.000
 FJD  H142  C14  C7    111.63  3.000
 FJD  H141  C14  C7    110.91  3.000
 FJD  C15   C14  C7    103.51  3.000
 FJD  H152  C15  H151  106.93  3.000
 FJD  H152  C15  C8    110.58  3.000
 FJD  H151  C15  C8    111.62  3.000
 FJD  H152  C15  C14   111.91  3.000
 FJD  H151  C15  C14   111.09  3.000
 FJD  C8    C15  C14   104.78  3.000
 FJD  H81   C8   H82   106.89  3.000
 FJD  H81   C8   C15   113.42  3.000
 FJD  H82   C8   C15   110.33  3.000
 FJD  H81   C8   N3    111.02  3.000
 FJD  H82   C8   N3    108.50  3.000
 FJD  C15   C8   N3    106.61  3.000
 FJD  H5    C5   C11   109.30  3.000
 FJD  H5    C5   C2    113.67  3.000
 FJD  C11   C5   C2    104.19  3.000
 FJD  H5    C5   C7    112.81  3.000
 FJD  C11   C5   C7    111.29  3.000
 FJD  C2    C5   C7    105.23  3.000
 FJD  H2    C2   C6    109.84  3.000
 FJD  H2    C2   C5    114.60  3.000
 FJD  C6    C2   C5    104.77  3.000
 FJD  H2    C2   C1    110.73  3.000
 FJD  C6    C2   C1    112.46  3.000
 FJD  C5    C2   C1    104.26  3.000
 FJD  N12   C6   O13   124.44  3.000
 FJD  O13   C6   C2    127.07  3.000
 FJD  N12   C6   C2    108.48  3.000
 FJD  N12   C11  O18   124.31  3.000
 FJD  O18   C11  C5    127.12  3.000
 FJD  N12   C11  C5    108.57  3.000
 FJD  C19   N12  C11   124.05  3.000
 FJD  C19   N12  C6    122.55  3.000
 FJD  C11   N12  C6    113.15  3.000
 FJD  H192  C19  H191  107.54  3.000
 FJD  H192  C19  C21   110.83  3.000
 FJD  H191  C19  C21   111.10  3.000
 FJD  H192  C19  N12   108.27  3.000
 FJD  H191  C19  N12   108.42  3.000
 FJD  C21   C19  N12   110.57  3.000
 FJD  H212  C21  H211  107.74  3.000
 FJD  H212  C21  C23   111.36  3.000
 FJD  H211  C21  C23   111.24  3.000
 FJD  H212  C21  C19   108.82  3.000
 FJD  H211  C21  C19   108.65  3.000
 FJD  C23   C21  C19   108.97  3.000
 FJD  H232  C23  H231  107.90  3.000
 FJD  H232  C23  N29   106.08  3.000
 FJD  H231  C23  N29   106.24  3.000
 FJD  H232  C23  C21   110.66  3.000
 FJD  H231  C23  C21   110.67  3.000
 FJD  N29   C23  C21   114.92  3.000
 FJD  C30   N29  C31   109.47  3.000
 FJD  C31   N29  C32   108.66  3.000
 FJD  C30   N29  C32   109.02  3.000
 FJD  C32   N29  C23   107.70  3.000
 FJD  C31   N29  C23   110.96  3.000
 FJD  C30   N29  C23   110.95  3.000
 FJD  H323  C32  H322  109.81  3.000
 FJD  H323  C32  H321  109.84  3.000
 FJD  H322  C32  H321  109.93  3.000
 FJD  H323  C32  N29   109.17  3.000
 FJD  H322  C32  N29   109.03  3.000
 FJD  H321  C32  N29   109.03  3.000
 FJD  H313  C31  H312  109.80  3.000
 FJD  H313  C31  H311  109.87  3.000
 FJD  H312  C31  H311  108.92  3.000
 FJD  H313  C31  N29   109.31  3.000
 FJD  H312  C31  N29   108.94  3.000
 FJD  H311  C31  N29   109.97  3.000
 FJD  H303  C30  H302  109.29  3.000
 FJD  H303  C30  H301  109.93  3.000
 FJD  H302  C30  H301  109.81  3.000
 FJD  H303  C30  N29   109.74  3.000
 FJD  H302  C30  N29   108.79  3.000
 FJD  H301  C30  N29   109.26  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
 FJD  CONST_01  C17   C20  S1   C25   180.00   0.0  0
 FJD  CONST_02  C22   C20  S1   C25     0.00   0.0  0
 FJD  CONST_03  C20   C22  C24  C25     0.00   0.0  0
 FJD  CONST_04  S1    C20  C22  C24     0.00   0.0  0
 FJD  CONST_05  C17   C20  C22  C24   180.00   0.0  0
 FJD  CONST_06  C20   S1   C25  C24     0.00   0.0  0
 FJD  CONST_07  C10   C17  C20  C22     0.00   0.0  0
 FJD  CONST_08  O16   C17  C20  C22   180.00   0.0  0
 FJD  CONST_09  S1    C25  C24  C22     0.00   0.0  0
 FJD  CONST_10  C10   C17  C20  S1    180.00   0.0  0
 FJD  CONST_11  O16   C17  C20  S1      0.00   0.0  0
 FJD  CONST_12  N9    C10  C17  C20   180.00   0.0  0
 FJD  CONST_13  C4    O16  C17  C20   180.00   0.0  0
 FJD  CONST_14  C4    N9   C10  C17     0.00   0.0  0
 FJD  CONST_15  N9    C4   O16  C17     0.00   0.0  0
 FJD  CONST_16  C10   N9   C4   O16     0.00   0.0  0
 FJD  CONST_17  N9    C10  C17  O16     0.00   0.0  0
 FJD  CONST_18  C4    O16  C17  C10     0.00   0.0  0
 FJD  CONST_19  C1    C4   O16  C17   180.00   0.0  0
 FJD  CONST_20  C1    C4   N9   C10   180.00   0.0  0
 FJD  CONST_21  C11   N12  C6   C2      0.00   0.0  0
 FJD  CONST_22  C20   S1   C25  CL1   180.00   0.0  0
 FJD  CONST_23  C22   C24  C25  CL1   180.00   0.0  0
 FJD  CONST_24  C19   N12  C6   C2    180.00   0.0  0
 FJD  CONST_25  C11   N12  C6   O13   180.00   0.0  0
 FJD  CONST_26  H22   C22  C24  C25   180.00   0.0  0
 FJD  CONST_27  H24   C24  C25  S1    180.00   0.0  0
 FJD  CONST_28  H10   C10  C17  C20     0.00   0.0  0
 FJD  CONST_29  C19   N12  C6   O13     0.00   0.0  0
 FJD  Var_01    C15   C8   N3   C1     81.50  30.0  1
 FJD  Var_02    C14   C15  C8   N3     14.06  30.0  1
 FJD  Var_03    C8    C15  C14  C7      9.41  30.0  1
 FJD  Var_04    C6    N12  C11  C5      3.11  30.0  1
 FJD  Var_05    C21   C19  N12  C6     80.77  30.0  3
 FJD  Var_06    C23   C21  C19  N12  -175.61  30.0  3
 FJD  Var_07    N29   C23  C21  C19   176.63  30.0  3
 FJD  Var_08    C30   N29  C23  C21    59.18  30.0  3
 FJD  Var_09    H301  C30  N29  C23    53.49  30.0  3
 FJD  Var_10    H311  C31  N29  C23    66.14  30.0  3
 FJD  Var_11    H321  C32  N29  C23    59.82  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
 FJD  chir_01  C1  C2  N3  C4   negativ
 FJD  chir_02  C7  N3  C5  C14  positiv
 FJD  chir_03  C5  C2  C7  C11  positiv
 FJD  chir_04  C2  C6  C5  C1   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
 FJD  plan-1  CL1  0.020
 FJD  plan-1  C25  0.020
 FJD  plan-1  C24  0.020
 FJD  plan-1  C22  0.020
 FJD  plan-1  S1   0.020
 FJD  plan-1  C20  0.020
 FJD  plan-1  C17  0.020
 FJD  plan-1  H24  0.020
 FJD  plan-1  H22  0.020
 FJD  plan-2  C20  0.020
 FJD  plan-2  C17  0.020
 FJD  plan-2  O16  0.020
 FJD  plan-2  C10  0.020
 FJD  plan-2  N9   0.020
 FJD  plan-2  C4   0.020
 FJD  plan-2  C1   0.020
 FJD  plan-2  H10  0.020
 FJD  plan-3  C5   0.020
 FJD  plan-3  C11  0.020
 FJD  plan-3  O18  0.020
 FJD  plan-3  N12  0.020
 FJD  plan-4  C2   0.020
 FJD  plan-4  C6   0.020
 FJD  plan-4  O13  0.020
 FJD  plan-4  C11  0.020
 FJD  plan-4  N12  0.020
 FJD  plan-4  C19  0.020

