# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 08:52:32 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: 1-[(3S,5S)-5-({(2S)-2-[(Z)-hydroxy(imino)methyl]pyrrolidin-1-yl}carbonyl)-1-(4-phenylbutanoyl)pyrrolidin-3-yl]triaza-1,2-dien-2-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=N)[C@@H]1CCCN1C(=O)[C@@H]2C[C@@H](CN2C(=O)CCCc3ccccc3)N=[N+]=N
#
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
 4I4  4I4  1-[(3S,5S)-5-({(2S)-2-[(Z)-hydroxy(imino)methyl]pyrrolidin-1-yl}carbonyl)-1-(4-phenylbutanoyl)pyrrolidin-3-yl]triaza-1,2-dien-2-ium  ligand  56  29  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_4I4
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
 4I4  C14   C  CH2   0  -0.612  -2.0122  -1.0578   0.0684
 4I4  C15   C  CH2   0  -0.406  -3.2259  -0.1755   0.3104
 4I4  C16   C  CH2   0  -0.508  -4.4948  -0.7950  -0.2764
 4I4  C17   C  CR6   0   0.137  -5.6971   0.0789  -0.0523
 4I4  C22   C  CR16  0  -0.317  -6.1456   0.9483  -1.0439
 4I4  C18   C  CR16  0  -0.309  -6.3633   0.0703   1.1722
 4I4  C21   C  CR16  0  -0.239  -7.2301   1.7875  -0.8210
 4I4  C19   C  CR16  0  -0.240  -7.4467   0.9074   1.4009
 4I4  C20   C  CR16  0  -0.275  -7.8846   1.7700   0.4033
 4I4  C12   C  C     0   0.591  -0.7324  -0.4762   0.6187
 4I4  O13   O  O     0  -0.485  -0.6889   0.5661   1.2528
 4I4  O9    O  O     0  -0.487   1.4684   0.8762  -1.0668
 4I4  C8    C  C     0   0.574   1.9780   0.6661   0.0233
 4I4  C10   C  CR15  0  -0.192   1.6822  -0.6280   0.7773
 4I4  C25   C  CH2   0  -0.478   2.7015  -1.7022   0.3494
 4I4  C24   C  CR15  0  -0.182   1.8271  -2.9381   0.1626
 4I4  N26   N  N     0  -0.110   2.4426  -3.8398  -0.8269
 4I4  N27   N  N     1   0.533   2.8867  -4.8815  -0.6033
 4I4  N28   N  N     0  -0.328   3.2296  -5.9937  -0.5167
 4I4  C23   C  CH2   0  -0.251   0.5265  -2.3796  -0.4024
 4I4  N11   N  NR5   0  -0.492   0.4026  -1.1730   0.3792
 4I4  N7    N  NR5   0  -0.490   2.8799   1.4909   0.5669
 4I4  C6    C  CH2   0  -0.285   3.5135   1.3717   1.8778
 4I4  C5    C  CH2   0  -0.471   4.0612   2.7717   2.1102
 4I4  C4    C  CH2   0  -0.487   4.4724   3.2142   0.7119
 4I4  C3    C  CR15  0  -0.089   3.3705   2.6355  -0.1902
 4I4  C1    C  C     0   0.415   3.9101   2.2601  -1.5474
 4I4  N2    N  N     0  -0.646   3.7775   3.0528  -2.5210
 4I4  OXT   O  OH1   0  -0.601   4.5647   1.0928  -1.5164
 4I4  H141  H  HCH2  0   0.277  -2.1728  -2.0478   0.5099
 4I4  H142  H  HCH2  0   0.273  -1.8849  -1.2328  -1.0052
 4I4  H151  H  HCH2  0   0.235  -3.3651  -0.0155   1.3818
 4I4  H152  H  HCH2  0   0.236  -3.0659   0.8096  -0.1343
 4I4  H161  H  HCH2  0   0.241  -4.3567  -0.9633  -1.3479
 4I4  H162  H  HCH2  0   0.241  -4.6610  -1.7776   0.1747
 4I4  H22   H  HCR6  0   0.245  -5.6428   0.9660  -2.0041
 4I4  H18   H  HCR6  0   0.245  -6.0310  -0.6015   1.9558
 4I4  H21   H  HCR6  0   0.252  -7.5655   2.4533  -1.6060
 4I4  H19   H  HCR6  0   0.252  -7.9521   0.8851   2.3582
 4I4  H20   H  HCR6  0   0.253  -8.7319   2.4207   0.5772
 4I4  H10   H  HCR5  0   0.306   1.7066  -0.4845   1.8582
 4I4  H251  H  HCH2  0   0.299   3.1727  -1.4383  -0.5992
 4I4  H252  H  HCH2  0   0.308   3.4837  -1.8532   1.0893
 4I4  H24   H  HCR5  0   0.351   1.6677  -3.4846   1.0923
 4I4  H231  H  HCH2  0   0.276   0.6295  -2.1766  -1.4734
 4I4  H232  H  HCH2  0   0.299  -0.3089  -3.0596  -0.2518
 4I4  H28   H  H     0   0.499   4.2202  -6.1434  -0.2890
 4I4  H61C  H  HCH2  0   0.266   2.7963   1.0791   2.6435
 4I4  H62C  H  HCH2  0   0.249   4.3196   0.6322   1.8591
 4I4  H3    H  HCR5  0   0.283   2.5744   3.3679  -0.3405
 4I4  H51C  H  HCH2  0   0.249   3.2737   3.4179   2.5023
 4I4  H52C  H  HCH2  0   0.260   4.8881   2.7770   2.8182
 4I4  H41C  H  HCH2  0   0.268   4.5480   4.2942   0.6015
 4I4  H42C  H  HCH2  0   0.253   5.4433   2.7848   0.4565
 4I4  H21N  H  H     0   0.337   4.2466   2.7311  -3.3639
 4I4  HXT   H  HOH1  0   0.477   4.9425   0.8861  -2.3812

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
 4I4  O9   C8    double    1.222  0.020  1.222
 4I4  C8   N7    single    1.338  0.020  1.338
 4I4  C8   C10   single    1.527  0.020  1.527
 4I4  N7   C6    single    1.461  0.020  1.461
 4I4  N7   C3    single    1.457  0.020  1.457
 4I4  C6   C5    single    1.521  0.020  1.521
 4I4  C5   C4    single    1.523  0.020  1.523
 4I4  C4   C3    single    1.537  0.020  1.537
 4I4  C3   C1    single    1.508  0.020  1.508
 4I4  C1   N2    double    1.263  0.020  1.263
 4I4  C1   OXT   single    1.339  0.020  1.339
 4I4  C10  C25   single    1.541  0.020  1.541
 4I4  C10  N11   single    1.447  0.020  1.447
 4I4  C25  C24   single    1.525  0.020  1.525
 4I4  C24  N26   single    1.473  0.020  1.473
 4I4  C24  C23   single    1.524  0.020  1.524
 4I4  N26  N27   double    1.154  0.020  1.154
 4I4  N27  N28   double    1.167  0.020  1.167
 4I4  C23  N11   single    1.443  0.020  1.443
 4I4  N11  C12   single    1.353  0.020  1.353
 4I4  C12  O13   double    1.221  0.020  1.221
 4I4  C12  C14   single    1.510  0.020  1.510
 4I4  C14  C15   single    1.520  0.020  1.520
 4I4  C15  C16   single    1.529  0.020  1.529
 4I4  C16  C17   single    1.503  0.020  1.503
 4I4  C17  C22   aromatic  1.393  0.020  1.393
 4I4  C17  C18   aromatic  1.394  0.020  1.394
 4I4  C22  C21   aromatic  1.389  0.020  1.389
 4I4  C21  C20   aromatic  1.388  0.020  1.388
 4I4  C20  C19   aromatic  1.390  0.020  1.390
 4I4  C19  C18   aromatic  1.388  0.020  1.388
 4I4  C10  H10   single    0.970  0.020  1.090
 4I4  C6   H61C  single    0.970  0.020  1.090
 4I4  C6   H62C  single    0.970  0.020  1.090
 4I4  C3   H3    single    0.970  0.020  1.090
 4I4  C5   H51C  single    0.970  0.020  1.090
 4I4  C5   H52C  single    0.970  0.020  1.090
 4I4  C4   H41C  single    0.970  0.020  1.090
 4I4  C4   H42C  single    0.970  0.020  1.090
 4I4  N2   H21N  single    0.890  0.020  1.040
 4I4  C25  H251  single    0.970  0.020  1.090
 4I4  C25  H252  single    0.970  0.020  1.090
 4I4  C24  H24   single    0.970  0.020  1.090
 4I4  C23  H231  single    0.970  0.020  1.090
 4I4  C23  H232  single    0.970  0.020  1.090
 4I4  N28  H28   single    0.890  0.020  1.040
 4I4  C14  H141  single    0.970  0.020  1.090
 4I4  C14  H142  single    0.970  0.020  1.090
 4I4  C15  H151  single    0.970  0.020  1.090
 4I4  C15  H152  single    0.970  0.020  1.090
 4I4  C16  H161  single    0.970  0.020  1.090
 4I4  C16  H162  single    0.970  0.020  1.090
 4I4  C22  H22   single    0.930  0.020  1.080
 4I4  C18  H18   single    0.930  0.020  1.080
 4I4  C21  H21   single    0.930  0.020  1.080
 4I4  C20  H20   single    0.930  0.020  1.080
 4I4  C19  H19   single    0.930  0.020  1.080
 4I4  OXT  HXT   single    0.850  0.020  0.980

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
 4I4  H142  C14  H141  105.53  3.000
 4I4  H142  C14  C12   108.69  3.000
 4I4  H141  C14  C12   108.99  3.000
 4I4  H142  C14  C15   109.98  3.000
 4I4  H141  C14  C15   110.08  3.000
 4I4  C12   C14  C15   113.28  3.000
 4I4  H152  C15  H151  106.61  3.000
 4I4  H152  C15  C16   109.30  3.000
 4I4  H151  C15  C16   109.27  3.000
 4I4  H152  C15  C14   109.98  3.000
 4I4  H151  C15  C14   110.06  3.000
 4I4  C16   C15  C14   111.49  3.000
 4I4  H162  C16  H161  106.56  3.000
 4I4  H162  C16  C17   109.83  3.000
 4I4  H161  C16  C17   109.67  3.000
 4I4  H162  C16  C15   109.38  3.000
 4I4  H161  C16  C15   109.49  3.000
 4I4  C17   C16  C15   111.78  3.000
 4I4  C18   C17  C22   118.37  3.000
 4I4  C18   C17  C16   120.64  3.000
 4I4  C22   C17  C16   120.95  3.000
 4I4  H22   C22  C21   119.62  3.000
 4I4  H22   C22  C17   119.43  3.000
 4I4  C21   C22  C17   120.94  3.000
 4I4  H18   C18  C19   119.59  3.000
 4I4  H18   C18  C17   119.48  3.000
 4I4  C19   C18  C17   120.94  3.000
 4I4  H21   C21  C20   120.07  3.000
 4I4  H21   C21  C22   119.80  3.000
 4I4  C20   C21  C22   120.13  3.000
 4I4  H19   C19  C20   120.03  3.000
 4I4  H19   C19  C18   119.84  3.000
 4I4  C20   C19  C18   120.13  3.000
 4I4  H20   C20  C19   120.30  3.000
 4I4  H20   C20  C21   120.21  3.000
 4I4  C19   C20  C21   119.50  3.000
 4I4  N11   C12  O13   120.11  3.000
 4I4  O13   C12  C14   123.27  3.000
 4I4  N11   C12  C14   116.63  3.000
 4I4  N7    C8   C10   116.91  3.000
 4I4  C10   C8   O9    120.38  3.000
 4I4  N7    C8   O9    122.54  3.000
 4I4  H10   C10  N11   110.00  3.000
 4I4  H10   C10  C25   110.61  3.000
 4I4  N11   C10  C25   104.24  3.000
 4I4  H10   C10  C8    111.94  3.000
 4I4  N11   C10  C8    110.79  3.000
 4I4  C25   C10  C8    108.99  3.000
 4I4  H252  C25  H251  108.33  3.000
 4I4  H252  C25  C24   112.53  3.000
 4I4  H251  C25  C24   109.69  3.000
 4I4  H252  C25  C10   112.56  3.000
 4I4  H251  C25  C10   110.99  3.000
 4I4  C24   C25  C10   102.68  3.000
 4I4  H24   C24  C23   112.03  3.000
 4I4  H24   C24  N26   109.09  3.000
 4I4  C23   C24  N26   109.38  3.000
 4I4  H24   C24  C25   112.68  3.000
 4I4  C23   C24  C25   103.75  3.000
 4I4  N26   C24  C25   109.79  3.000
 4I4  N27   N26  C24   125.66  3.000
 4I4  N28   N27  N26   170.91  3.000
 4I4  H28   N28  N27   116.01  3.000
 4I4  H232  C23  H231  108.88  3.000
 4I4  H232  C23  N11   112.45  3.000
 4I4  H231  C23  N11   112.51  3.000
 4I4  H232  C23  C24   112.03  3.000
 4I4  H231  C23  C24   110.50  3.000
 4I4  N11   C23  C24   100.30  3.000
 4I4  C23   N11  C10   112.84  3.000
 4I4  C23   N11  C12   126.76  3.000
 4I4  C10   N11  C12   119.95  3.000
 4I4  C3    N7   C6    112.60  3.000
 4I4  C3    N7   C8    120.01  3.000
 4I4  C6    N7   C8    127.36  3.000
 4I4  H62C  C6   H61C  108.40  3.000
 4I4  H62C  C6   C5    111.06  3.000
 4I4  H61C  C6   C5    112.14  3.000
 4I4  H62C  C6   N7    111.06  3.000
 4I4  H61C  C6   N7    111.54  3.000
 4I4  C5    C6   N7    102.60  3.000
 4I4  H52C  C5   H51C  108.15  3.000
 4I4  H52C  C5   C4    112.99  3.000
 4I4  H51C  C5   C4    110.64  3.000
 4I4  H52C  C5   C6    112.17  3.000
 4I4  H51C  C5   C6    109.88  3.000
 4I4  C4    C5   C6    102.96  3.000
 4I4  H42C  C4   H41C  107.74  3.000
 4I4  H42C  C4   C3    110.61  3.000
 4I4  H41C  C4   C3    111.34  3.000
 4I4  H42C  C4   C5    109.91  3.000
 4I4  H41C  C4   C5    113.59  3.000
 4I4  C3    C4   C5    103.64  3.000
 4I4  H3    C3   C1    107.69  3.000
 4I4  H3    C3   C4    110.53  3.000
 4I4  C1    C3   C4    111.43  3.000
 4I4  H3    C3   N7    110.67  3.000
 4I4  C1    C3   N7    113.11  3.000
 4I4  C4    C3   N7    103.42  3.000
 4I4  OXT   C1   N2    128.08  3.000
 4I4  OXT   C1   C3    111.79  3.000
 4I4  N2    C1   C3    120.01  3.000
 4I4  H21N  N2   C1    113.09  3.000
 4I4  HXT   OXT  C1    110.92  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
 4I4  CONST_01  C20  C21  C22  C17     0.00   0.0  0
 4I4  CONST_02  C20  C19  C18  C17     0.00   0.0  0
 4I4  CONST_03  C19  C18  C17  C22     0.00   0.0  0
 4I4  CONST_04  C19  C20  C21  C22     0.00   0.0  0
 4I4  CONST_05  C21  C22  C17  C18     0.00   0.0  0
 4I4  CONST_06  C21  C20  C19  C18     0.00   0.0  0
 4I4  CONST_07  C21  C22  C17  C16   180.00   0.0  0
 4I4  CONST_08  C19  C18  C17  C16   180.00   0.0  0
 4I4  CONST_09  C6   N7   C8   C10     0.00   0.0  0
 4I4  CONST_10  C3   N7   C8   C10   180.00   0.0  0
 4I4  CONST_11  H21  C21  C22  C17   180.00   0.0  0
 4I4  CONST_12  H19  C19  C18  C17   180.00   0.0  0
 4I4  CONST_13  H18  C18  C17  C22   180.00   0.0  0
 4I4  CONST_14  H20  C20  C21  C22   180.00   0.0  0
 4I4  CONST_15  H22  C22  C17  C18   180.00   0.0  0
 4I4  CONST_16  C10  N11  C12  C14   180.00   0.0  0
 4I4  CONST_17  C23  N11  C12  C14     0.00   0.0  0
 4I4  CONST_18  C10  N11  C12  O13     0.00   0.0  0
 4I4  CONST_19  C23  N11  C12  O13   180.00   0.0  0
 4I4  CONST_20  C6   N7   C8   O9    180.00   0.0  0
 4I4  CONST_21  C3   N7   C8   O9      0.00   0.0  0
 4I4  Var_01    C24  C23  N11  C10    29.62  30.0  1
 4I4  Var_02    C4   C5   C6   N7    -34.97  30.0  1
 4I4  Var_03    C3   C4   C5   C6     37.91  30.0  1
 4I4  Var_04    C3   N7   C6   C5     19.66  30.0  1
 4I4  Var_05    C22  C17  C16  C15    96.97  30.0  2
 4I4  Var_06    C17  C16  C15  C14  -179.44  30.0  3
 4I4  Var_07    N11  C12  C14  C15  -176.64  30.0  1
 4I4  Var_08    C12  C14  C15  C16   179.36  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
 4I4  chir_01  C10  C8   C25  N11  positiv
 4I4  chir_02  C24  N26  C23  C25  positiv
 4I4  chir_03  C3   N7   C1   C4   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
 4I4  plan-1  C14   0.020
 4I4  plan-1  C12   0.020
 4I4  plan-1  O13   0.020
 4I4  plan-1  C10   0.020
 4I4  plan-1  C23   0.020
 4I4  plan-1  N11   0.020
 4I4  plan-2  C16   0.020
 4I4  plan-2  C17   0.020
 4I4  plan-2  C22   0.020
 4I4  plan-2  C18   0.020
 4I4  plan-2  C21   0.020
 4I4  plan-2  C19   0.020
 4I4  plan-2  C20   0.020
 4I4  plan-2  H22   0.020
 4I4  plan-2  H18   0.020
 4I4  plan-2  H21   0.020
 4I4  plan-2  H19   0.020
 4I4  plan-2  H20   0.020
 4I4  plan-3  C25   0.020
 4I4  plan-3  C24   0.020
 4I4  plan-3  N26   0.020
 4I4  plan-3  N27   0.020
 4I4  plan-3  N28   0.020
 4I4  plan-3  C23   0.020
 4I4  plan-3  H24   0.020
 4I4  plan-3  H28   0.020
 4I4  plan-4  O9    0.020
 4I4  plan-4  C8    0.020
 4I4  plan-4  C10   0.020
 4I4  plan-4  N7    0.020
 4I4  plan-4  C6    0.020
 4I4  plan-4  C3    0.020
 4I4  plan-5  C3    0.020
 4I4  plan-5  C1    0.020
 4I4  plan-5  N2    0.020
 4I4  plan-5  OXT   0.020
 4I4  plan-5  H21N  0.020

