# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jun 25 21:23:44 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: "3-[(3~{a}~{S},4~{R},8~{a}~{S},8~{b}~{R})-4-[5-(5-chloranylthiophen-2-yl)-1,2-oxazol-3-yl]-1,3-bis(oxidanylidene)-4,6,7,8,8~{a},8~{b}-hexahydro-3~{a}~{H}-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)c4cc(on4)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
 BI7  BI7  "3-[(3~{a}~{S},4~{R},8~{a}~{S},8~{b}~{R})-4-[5-(5-chloranylthiophen-2-yl)-1,2-oxazol-3-yl]-1,3-bis(oxidanylidene)-4,6,7,8,8~{a},8~{b}-hexahydro-3~{a}~{H}-pyrrolo[3,4-a]pyrrolizin-2-yl]propyl-trimethyl-azanium"
  ligand  59  31  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BI7
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
 BI7  O13   O   O     0  -0.418   0.9882   0.2243   2.2741
 BI7  C6    C   C     0   0.601   1.7768   0.9282   1.6955
 BI7  N12   N   NT    0  -0.529   3.0391   0.5322   1.3124
 BI7  C19   C   CH2   0  -0.311   3.5015  -0.8318   1.4352
 BI7  C21   C   CH2   0  -0.495   3.1265  -1.6504   0.2012
 BI7  C23   C   CH2   0  -0.314   3.4715  -3.1031   0.4591
 BI7  N29   N   NT    1  -0.385   3.1584  -4.0446  -0.6708
 BI7  C30   C   CH3   0  -0.551   3.9467  -3.7012  -1.8863
 BI7  C31   C   CH3   0  -0.548   3.5341  -5.4181  -0.2304
 BI7  C32   C   CH3   0  -0.552   1.7053  -4.0264  -0.9951
 BI7  C2    C   CH1   0  -0.434   1.5700   2.3520   1.2442
 BI7  C1    C   CH1   0  -0.123   0.6876   2.4589  -0.0349
 BI7  N3    N   NR5   0  -0.406   1.6366   2.6260  -1.1275
 BI7  C8    C   CH2   0  -0.335   1.1089   3.4237  -2.2271
 BI7  C15   C   CH2   0  -0.477   1.2864   4.9069  -1.8190
 BI7  C14   C   CH2   0  -0.460   2.2853   4.8769  -0.6462
 BI7  C7    C   CR15  0  -0.120   2.7441   3.4092  -0.5955
 BI7  C5    C   CH1   0  -0.393   2.9547   2.8189   0.7868
 BI7  C11   C   C     0   0.597   3.7696   1.5448   0.7320
 BI7  O18   O   O     0  -0.426   4.8761   1.4070   0.2731
 BI7  C4    C   CR5   0   0.267  -0.2117   1.2865  -0.2660
 BI7  C16   C   CR15  0  -0.514  -1.5076   1.0902   0.2649
 BI7  N9    N   N     0  -0.156   0.1558   0.2792  -1.0051
 BI7  O10   O   O     0  -0.348  -0.8789  -0.6088  -0.9767
 BI7  C17   C   CR5   0   0.497  -1.8698  -0.1242  -0.2231
 BI7  C20   C   CR5   0  -0.306  -3.0592  -0.9253  -0.0995
 BI7  C22   C   CR15  0  -0.197  -3.3468  -2.1158  -0.7091
 BI7  C24   C   CR15  0  -0.116  -4.6238  -2.6202  -0.3664
 BI7  S1    S   S2    0   0.310  -4.3569  -0.4040   0.9118
 BI7  C25   C   CR5   0  -0.246  -5.2741  -1.7957   0.4981
 BI7  CL1   CL  CL    0  -0.062  -6.8276  -2.0192   1.1591
 BI7  H2    H   HCH1  0   0.328   1.1378   2.9358   2.0549
 BI7  H191  H   HCH2  0   0.284   4.5806  -0.8219   1.5824
 BI7  H192  H   HCH2  0   0.279   3.0547  -1.2578   2.3335
 BI7  H211  H   HCH2  0   0.271   2.0603  -1.5274   0.0077
 BI7  H212  H   HCH2  0   0.272   3.6675  -1.2567  -0.6607
 BI7  H231  H   HCH2  0   0.308   4.5360  -3.2185   0.6657
 BI7  H232  H   HCH2  0   0.308   2.9218  -3.4748   1.3247
 BI7  H301  H   HCH3  0   0.297   5.0030  -3.6767  -1.6317
 BI7  H302  H   HCH3  0   0.299   3.7704  -4.4606  -2.6430
 BI7  H303  H   HCH3  0   0.296   3.6364  -2.7354  -2.2729
 BI7  H311  H   HCH3  0   0.298   2.9428  -5.6886   0.6401
 BI7  H312  H   HCH3  0   0.296   3.3391  -6.1172  -1.0388
 BI7  H313  H   HCH3  0   0.297   4.5904  -5.4336   0.0236
 BI7  H321  H   HCH3  0   0.289   1.4281  -3.0617  -1.4085
 BI7  H322  H   HCH3  0   0.302   1.5024  -4.8000  -1.7306
 BI7  H323  H   HCH3  0   0.299   1.1364  -4.2222  -0.0901
 BI7  H1    H   HCH1  0   0.274   0.0395   3.3362   0.1015
 BI7  H5    H   HCH1  0   0.332   3.4359   3.5142   1.4775
 BI7  H81C  H   HCH2  0   0.247   1.6862   3.2031  -3.1271
 BI7  H82C  H   HCH2  0   0.249   0.0734   3.1559  -2.4391
 BI7  H7    H   HCR5  0   0.270   3.6245   3.2799  -1.2308
 BI7  H151  H   HCH2  0   0.246   1.6579   5.4949  -2.6582
 BI7  H152  H   HCH2  0   0.242   0.3391   5.3534  -1.5155
 BI7  H141  H   HCH2  0   0.253   3.1272   5.5536  -0.7886
 BI7  H142  H   HCH2  0   0.242   1.7995   5.1690   0.2877
 BI7  H16   H   HCR5  0   0.292  -2.0659   1.7569   0.9012
 BI7  H22   H   HCR5  0   0.282  -2.6743  -2.6194  -1.3882
 BI7  H24   H   HCR5  0   0.297  -5.0364  -3.5434  -0.7444

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
 BI7  O13  C6    double    1.205  0.020  1.205
 BI7  C6   N12   single    1.377  0.020  1.377
 BI7  C6   C2    single    1.508  0.020  1.508
 BI7  N12  C19   single    1.445  0.020  1.445
 BI7  N12  C11   single    1.377  0.020  1.377
 BI7  C19  C21   single    1.528  0.020  1.528
 BI7  C21  C23   single    1.515  0.020  1.515
 BI7  C23  N29   single    1.504  0.020  1.504
 BI7  N29  C30   single    1.489  0.020  1.489
 BI7  N29  C31   single    1.490  0.020  1.490
 BI7  N29  C32   single    1.489  0.020  1.489
 BI7  C2   C1    single    1.558  0.020  1.558
 BI7  C2   C5    single    1.531  0.020  1.531
 BI7  C1   N3    single    1.457  0.020  1.457
 BI7  C1   C4    single    1.496  0.020  1.496
 BI7  N3   C8    single    1.457  0.020  1.457
 BI7  N3   C7    single    1.457  0.020  1.457
 BI7  C8   C15   single    1.549  0.020  1.549
 BI7  C15  C14   single    1.541  0.020  1.541
 BI7  C14  C7    single    1.539  0.020  1.539
 BI7  C7   C5    single    1.518  0.020  1.518
 BI7  C5   C11   single    1.513  0.020  1.513
 BI7  C11  O18   double    1.206  0.020  1.206
 BI7  C4   C16   aromatic  1.414  0.020  1.414
 BI7  C4   N9    aromatic  1.302  0.020  1.302
 BI7  C16  C17   aromatic  1.358  0.020  1.358
 BI7  N9   O10   aromatic  1.364  0.020  1.364
 BI7  O10  C17   aromatic  1.336  0.020  1.336
 BI7  C17  C20   single    1.439  0.020  1.439
 BI7  C20  C22   aromatic  1.368  0.020  1.368
 BI7  C20  S1    aromatic  1.726  0.020  1.726
 BI7  C22  C24   aromatic  1.415  0.020  1.415
 BI7  C24  C25   aromatic  1.360  0.020  1.360
 BI7  S1   C25   aromatic  1.717  0.020  1.717
 BI7  C25  CL1   single    1.703  0.020  1.703
 BI7  C2   H2    single    0.970  0.020  1.090
 BI7  C19  H191  single    0.970  0.020  1.090
 BI7  C19  H192  single    0.970  0.020  1.090
 BI7  C21  H211  single    0.970  0.020  1.090
 BI7  C21  H212  single    0.970  0.020  1.090
 BI7  C23  H231  single    0.970  0.020  1.090
 BI7  C23  H232  single    0.970  0.020  1.090
 BI7  C30  H301  single    0.970  0.020  1.090
 BI7  C30  H302  single    0.970  0.020  1.090
 BI7  C30  H303  single    0.970  0.020  1.090
 BI7  C31  H311  single    0.970  0.020  1.090
 BI7  C31  H312  single    0.970  0.020  1.090
 BI7  C31  H313  single    0.970  0.020  1.090
 BI7  C32  H321  single    0.970  0.020  1.090
 BI7  C32  H322  single    0.970  0.020  1.090
 BI7  C32  H323  single    0.970  0.020  1.090
 BI7  C1   H1    single    0.970  0.020  1.090
 BI7  C5   H5    single    0.970  0.020  1.090
 BI7  C8   H81C  single    0.970  0.020  1.090
 BI7  C8   H82C  single    0.970  0.020  1.090
 BI7  C7   H7    single    0.970  0.020  1.090
 BI7  C15  H151  single    0.970  0.020  1.090
 BI7  C15  H152  single    0.970  0.020  1.090
 BI7  C14  H141  single    0.970  0.020  1.090
 BI7  C14  H142  single    0.970  0.020  1.090
 BI7  C16  H16   single    0.930  0.020  1.080
 BI7  C22  H22   single    0.930  0.020  1.080
 BI7  C24  H24   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
 BI7  C2    C6   N12   108.30  3.000
 BI7  C2    C6   O13   127.26  3.000
 BI7  N12   C6   O13   124.43  3.000
 BI7  C11   N12  C19   124.06  3.000
 BI7  C11   N12  C6    113.08  3.000
 BI7  C19   N12  C6    122.74  3.000
 BI7  H192  C19  H191  107.36  3.000
 BI7  H192  C19  C21   110.83  3.000
 BI7  H191  C19  C21   110.93  3.000
 BI7  H192  C19  N12   107.92  3.000
 BI7  H191  C19  N12   108.66  3.000
 BI7  C21   C19  N12   111.01  3.000
 BI7  H212  C21  H211  107.69  3.000
 BI7  H212  C21  C23   111.56  3.000
 BI7  H211  C21  C23   111.15  3.000
 BI7  H212  C21  C19   108.85  3.000
 BI7  H211  C21  C19   108.84  3.000
 BI7  C23   C21  C19   108.69  3.000
 BI7  H232  C23  H231  107.79  3.000
 BI7  H232  C23  N29   106.14  3.000
 BI7  H231  C23  N29   106.22  3.000
 BI7  H232  C23  C21   110.31  3.000
 BI7  H231  C23  C21   110.85  3.000
 BI7  N29   C23  C21   115.15  3.000
 BI7  C32   N29  C31   108.76  3.000
 BI7  C32   N29  C30   109.63  3.000
 BI7  C31   N29  C30   108.68  3.000
 BI7  C32   N29  C23   111.05  3.000
 BI7  C31   N29  C23   107.60  3.000
 BI7  C30   N29  C23   111.03  3.000
 BI7  H303  C30  H302  109.12  3.000
 BI7  H303  C30  H301  109.95  3.000
 BI7  H302  C30  H301  109.67  3.000
 BI7  H303  C30  N29   110.16  3.000
 BI7  H302  C30  N29   108.75  3.000
 BI7  H301  C30  N29   109.18  3.000
 BI7  H313  C31  H312  109.83  3.000
 BI7  H313  C31  H311  109.77  3.000
 BI7  H312  C31  H311  109.77  3.000
 BI7  H313  C31  N29   109.10  3.000
 BI7  H312  C31  N29   109.14  3.000
 BI7  H311  C31  N29   109.21  3.000
 BI7  H323  C32  H322  109.73  3.000
 BI7  H323  C32  H321  110.10  3.000
 BI7  H322  C32  H321  109.11  3.000
 BI7  H323  C32  N29   109.10  3.000
 BI7  H322  C32  N29   108.72  3.000
 BI7  H321  C32  N29   110.06  3.000
 BI7  H2    C2   C5    114.71  3.000
 BI7  H2    C2   C1    110.47  3.000
 BI7  C5    C2   C1    104.25  3.000
 BI7  H2    C2   C6    109.75  3.000
 BI7  C5    C2   C6    104.67  3.000
 BI7  C1    C2   C6    112.85  3.000
 BI7  H1    C1   C4    106.88  3.000
 BI7  H1    C1   N3    112.68  3.000
 BI7  C4    C1   N3    111.45  3.000
 BI7  H1    C1   C2    106.67  3.000
 BI7  C4    C1   C2    114.44  3.000
 BI7  N3    C1   C2    104.75  3.000
 BI7  C7    N3   C8    104.86  3.000
 BI7  C7    N3   C1    106.44  3.000
 BI7  C8    N3   C1    113.13  3.000
 BI7  H82C  C8   H81C  106.99  3.000
 BI7  H82C  C8   C15   113.29  3.000
 BI7  H81C  C8   C15   110.50  3.000
 BI7  H82C  C8   N3    110.86  3.000
 BI7  H81C  C8   N3    108.66  3.000
 BI7  C15   C8   N3    106.49  3.000
 BI7  H152  C15  H151  106.82  3.000
 BI7  H152  C15  C14   111.06  3.000
 BI7  H151  C15  C14   112.06  3.000
 BI7  H152  C15  C8    111.47  3.000
 BI7  H151  C15  C8    110.66  3.000
 BI7  C14   C15  C8    104.85  3.000
 BI7  H142  C14  H141  106.82  3.000
 BI7  H142  C14  C7    111.07  3.000
 BI7  H141  C14  C7    111.49  3.000
 BI7  H142  C14  C15   110.93  3.000
 BI7  H141  C14  C15   112.92  3.000
 BI7  C7    C14  C15   103.71  3.000
 BI7  H7    C7   C5    111.81  3.000
 BI7  H7    C7   C14   109.50  3.000
 BI7  C5    C7   C14   116.25  3.000
 BI7  H7    C7   N3    109.65  3.000
 BI7  C5    C7   N3    103.23  3.000
 BI7  C14   C7   N3    105.90  3.000
 BI7  H5    C5   C11   108.77  3.000
 BI7  H5    C5   C7    112.93  3.000
 BI7  C11   C5   C7    111.66  3.000
 BI7  H5    C5   C2    113.82  3.000
 BI7  C11   C5   C2    103.95  3.000
 BI7  C7    C5   C2    105.38  3.000
 BI7  O18   C11  C5    127.17  3.000
 BI7  O18   C11  N12   124.28  3.000
 BI7  C5    C11  N12   108.55  3.000
 BI7  N9    C4   C16   111.36  3.000
 BI7  N9    C4   C1    121.62  3.000
 BI7  C16   C4   C1    127.00  3.000
 BI7  H16   C16  C17   128.85  3.000
 BI7  H16   C16  C4    127.63  3.000
 BI7  C17   C16  C4    103.51  3.000
 BI7  O10   N9   C4    106.12  3.000
 BI7  C17   O10  N9    109.77  3.000
 BI7  C20   C17  O10   117.35  3.000
 BI7  C20   C17  C16   133.42  3.000
 BI7  O10   C17  C16   109.23  3.000
 BI7  S1    C20  C22   111.46  3.000
 BI7  S1    C20  C17   120.23  3.000
 BI7  C22   C20  C17   128.30  3.000
 BI7  H22   C22  C24   123.22  3.000
 BI7  H22   C22  C20   123.70  3.000
 BI7  C24   C22  C20   113.08  3.000
 BI7  H24   C24  C25   123.94  3.000
 BI7  H24   C24  C22   124.39  3.000
 BI7  C25   C24  C22   111.67  3.000
 BI7  C25   S1   C20    90.90  3.000
 BI7  CL1   C25  S1    120.00  3.000
 BI7  CL1   C25  C24   127.10  3.000
 BI7  S1    C25  C24   112.89  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
 BI7  CONST_01  O10   C17  C16  C4      0.00   0.0  0
 BI7  CONST_02  C20   C17  C16  C4    180.00   0.0  0
 BI7  CONST_03  C17   O10  N9   C4      0.00   0.0  0
 BI7  CONST_04  O10   N9   C4   C16     0.00   0.0  0
 BI7  CONST_05  N9    O10  C17  C16     0.00   0.0  0
 BI7  CONST_06  C22   C20  C17  C16   180.00   0.0  0
 BI7  CONST_07  S1    C20  C17  C16     0.00   0.0  0
 BI7  CONST_08  C17   C16  C4   N9      0.00   0.0  0
 BI7  CONST_09  C20   C17  O10  N9    180.00   0.0  0
 BI7  CONST_10  C22   C20  C17  O10     0.00   0.0  0
 BI7  CONST_11  S1    C20  C17  O10   180.00   0.0  0
 BI7  CONST_12  C24   C22  C20  C17   180.00   0.0  0
 BI7  CONST_13  C25   S1   C20  C17   180.00   0.0  0
 BI7  CONST_14  C25   C24  C22  C20     0.00   0.0  0
 BI7  CONST_15  C24   C25  S1   C20     0.00   0.0  0
 BI7  CONST_16  C25   S1   C20  C22     0.00   0.0  0
 BI7  CONST_17  S1    C25  C24  C22     0.00   0.0  0
 BI7  CONST_18  S1    C20  C22  C24     0.00   0.0  0
 BI7  CONST_19  C17   C16  C4   C1    180.00   0.0  0
 BI7  CONST_20  O10   N9   C4   C1    180.00   0.0  0
 BI7  CONST_21  C11   N12  C6   C2      0.00   0.0  0
 BI7  CONST_22  CL1   C25  S1   C20   180.00   0.0  0
 BI7  CONST_23  CL1   C25  C24  C22   180.00   0.0  0
 BI7  CONST_24  C11   N12  C6   O13   180.00   0.0  0
 BI7  CONST_25  C2    C6   N12  C19   180.00   0.0  0
 BI7  CONST_26  H16   C16  C4   C1      0.00   0.0  0
 BI7  CONST_27  H22   C22  C20  C17     0.00   0.0  0
 BI7  CONST_28  H24   C24  C22  C20   180.00   0.0  0
 BI7  CONST_29  C19   N12  C6   O13     0.00   0.0  0
 BI7  Var_01    C5    C11  N12  C6      3.65  30.0  1
 BI7  Var_02    C15   C8   N3   C1     81.87  30.0  1
 BI7  Var_03    C14   C15  C8   N3     15.66  30.0  1
 BI7  Var_04    C7    C14  C15  C8      7.26  30.0  1
 BI7  Var_05    C21   C19  N12  C6     87.08  30.0  3
 BI7  Var_06    C23   C21  C19  N12  -172.70  30.0  3
 BI7  Var_07    N29   C23  C21  C19   179.95  30.0  3
 BI7  Var_08    C30   N29  C23  C21    62.35  30.0  3
 BI7  Var_09    H301  C30  N29  C23    54.63  30.0  3
 BI7  Var_10    H311  C31  N29  C23    61.29  30.0  3
 BI7  Var_11    H321  C32  N29  C23    67.16  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
 BI7  chir_01  C2  C6   C1  C5   positiv
 BI7  chir_02  C1  N3   C4  C2   negativ
 BI7  chir_03  C7  N3   C5  C14  positiv
 BI7  chir_04  C5  C11  C7  C2   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
 BI7  plan-1  C1   0.020
 BI7  plan-1  C4   0.020
 BI7  plan-1  C16  0.020
 BI7  plan-1  N9   0.020
 BI7  plan-1  O10  0.020
 BI7  plan-1  C17  0.020
 BI7  plan-1  C20  0.020
 BI7  plan-1  H16  0.020
 BI7  plan-2  C17  0.020
 BI7  plan-2  C20  0.020
 BI7  plan-2  C22  0.020
 BI7  plan-2  C24  0.020
 BI7  plan-2  S1   0.020
 BI7  plan-2  C25  0.020
 BI7  plan-2  CL1  0.020
 BI7  plan-2  H22  0.020
 BI7  plan-2  H24  0.020
 BI7  plan-3  N12  0.020
 BI7  plan-3  C5   0.020
 BI7  plan-3  C11  0.020
 BI7  plan-3  O18  0.020
 BI7  plan-4  O13  0.020
 BI7  plan-4  C6   0.020
 BI7  plan-4  N12  0.020
 BI7  plan-4  C19  0.020
 BI7  plan-4  C2   0.020
 BI7  plan-4  C11  0.020

