# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 17:07:05 2020
#   Inital geometry file: a 156 line input string
#   Ligand name: N-{(2S)-1-[4-(3-aminopropyl)piperazin-1-yl]-5-[(diaminomethylidene)amino]-1-oxopentan-2-yl}-3-(trifluoromethyl)benzenesulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCN1CCN(CC1)C(=O)[C@H](CCCN=C(N)N)N[S](=O)(=O)c2cccc(c2)C(F)(F)F
#
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
 MIU  MIU  N-{(2S)-1-[4-(3-aminopropyl)piperazin-1-yl]-5-[(diaminomethylidene)amino]-1-oxopentan-2-yl}-3-(trifluoromethyl)benzenesulfonamide  peptide  66  34  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_MIU
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
 MIU  C1    C  CR6   0  -0.193   0.4120  -2.0335   0.2423
 MIU  S11   S  S     0   1.376  -1.1582  -2.3183  -0.5457
 MIU  O24   O  OS    0  -0.645  -0.9194  -2.3405  -1.9784
 MIU  O25   O  OS    0  -0.650  -1.7956  -3.4475   0.1073
 MIU  C2    C  CR16  0  -0.211   0.4606  -1.9588   1.6304
 MIU  C3    C  CR16  0  -0.229   1.6786  -1.7425   2.2463
 MIU  C4    C  CR16  0  -0.267   2.8373  -1.6161   1.4895
 MIU  C5    C  CR6   0  -0.182   2.7744  -1.7012   0.1075
 MIU  C6    C  CT    0   1.064   4.0053  -1.5825  -0.7389
 MIU  F61   F  F     0  -0.299   5.0949  -1.3021  -0.0207
 MIU  F1    F  F     0  -0.309   4.2516  -2.7168  -1.4066
 MIU  F6    F  F     0  -0.309   3.8800  -0.6170  -1.6599
 MIU  C10   C  CR16  0  -0.264   1.5537  -1.9086  -0.5283
 MIU  N12   N  NC1   0  -0.711  -2.1037  -1.0173  -0.2194
 MIU  C13   C  CH1   0  -0.262  -1.6357   0.3141  -0.5770
 MIU  C14   C  C     0   0.575  -1.1349   1.0264   0.6866
 MIU  O15   O  O     0  -0.494  -1.5342   0.6423   1.7791
 MIU  C16   C  CH2   0  -0.405  -2.7604   1.1101  -1.2499
 MIU  C17   C  CH2   0  -0.452  -3.9872   1.3370  -0.3771
 MIU  C18   C  CH2   0  -0.324  -5.0859   2.0833  -1.1364
 MIU  N19   N  N     0  -0.496  -6.2422   2.3663  -0.3254
 MIU  C20   C  C     0   0.569  -7.1277   1.4498  -0.1700
 MIU  N22   N  NH2   0  -0.833  -8.1715   1.6673   0.7074
 MIU  N21   N  NH2   0  -0.845  -7.1435   0.2223  -0.7518
 MIU  N26   N  NT    0  -0.445  -0.3332   2.0932   0.5358
 MIU  C27   C  CH2   0  -0.334   0.2309   2.7642   1.6958
 MIU  C28   C  CH2   0  -0.281   1.7008   2.4051   1.8256
 MIU  N29   N  NT    0  -0.424   2.4383   2.7344   0.6184
 MIU  C30   C  CH2   0  -0.273   1.8441   2.1116  -0.5492
 MIU  C31   C  CH2   0  -0.349   0.3726   2.4677  -0.6763
 MIU  C32   C  CH2   0  -0.256   3.8419   2.3947   0.7795
 MIU  C33   C  CH2   0  -0.460   4.7419   2.8851  -0.3438
 MIU  C8    C  CH2   0  -0.270   6.2034   2.5739  -0.0551
 MIU  N9    N  NH2   0  -0.800   7.0553   3.0354  -1.1414
 MIU  H2    H  HCR6  0   0.296  -0.4338  -2.0624   2.2295
 MIU  H3    H  HCR6  0   0.288   1.7328  -1.6763   3.3237
 MIU  H4    H  HCR6  0   0.289   3.7775  -1.4486   1.9961
 MIU  H10   H  HCR6  0   0.304   1.4905  -1.9711  -1.6068
 MIU  H12   H  HNC1  0   0.414  -2.5231  -1.0652   0.7052
 MIU  H13   H  HCH1  0   0.290  -0.8328   0.1988  -1.3074
 MIU  H161  H  HCH2  0   0.245  -2.3635   2.0743  -1.5798
 MIU  H162  H  HCH2  0   0.252  -3.0421   0.5661  -2.1550
 MIU  H171  H  HCH2  0   0.222  -4.3761   0.3792  -0.0194
 MIU  H172  H  HCH2  0   0.230  -3.7263   1.9186   0.5107
 MIU  H181  H  HCH2  0   0.221  -4.6706   3.0361  -1.4802
 MIU  H182  H  HCH2  0   0.186  -5.3192   1.5293  -2.0605
 MIU  H221  H  HNH2  0   0.373  -8.2748   2.6378   0.9580
 MIU  H222  H  HNH2  0   0.376  -9.0544   1.2482   0.4583
 MIU  H211  H  HNH2  0   0.403  -6.4462  -0.0525  -1.4180
 MIU  H212  H  HNH2  0   0.397  -7.8623  -0.4478  -0.5480
 MIU  H271  H  HCH2  0   0.254   0.1146   3.8423   1.5577
 MIU  H272  H  HCH2  0   0.272  -0.3087   2.4778   2.5939
 MIU  H281  H  HCH2  0   0.248   2.1302   2.9600   2.6632
 MIU  H282  H  HCH2  0   0.202   1.7799   1.3332   2.0782
 MIU  H301  H  HCH2  0   0.253   2.3518   2.4547  -1.4510
 MIU  H302  H  HCH2  0   0.195   1.9371   1.0129  -0.5227
 MIU  H311  H  HCH2  0   0.275  -0.0421   1.9864  -1.5567
 MIU  H312  H  HCH2  0   0.264   0.2577   3.5449  -0.8183
 MIU  H321  H  HCH2  0   0.231   4.1796   2.8446   1.7182
 MIU  H322  H  HCH2  0   0.182   3.9755   1.3048   0.9009
 MIU  H331  H  HCH2  0   0.224   4.4763   2.4191  -1.2953
 MIU  H332  H  HCH2  0   0.221   4.6078   3.9645  -0.4683
 MIU  H8C1  H  HCH2  0   0.191   6.4751   2.9959   0.9232
 MIU  H8C2  H  HCH2  0   0.211   6.3221   1.4905   0.0356
 MIU  H9N1  H  HNH2  0   0.338   7.0535   4.0482  -1.1555
 MIU  H9N2  H  HNH2  0   0.346   8.0136   2.7703  -0.9528

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
 MIU  C1   S11   single    1.780  0.020  1.780
 MIU  C1   C2    aromatic  1.391  0.020  1.391
 MIU  C1   C10   aromatic  1.383  0.020  1.383
 MIU  S11  N12   single    1.641  0.020  1.641
 MIU  S11  O24   double    1.453  0.020  1.453
 MIU  S11  O25   double    1.452  0.020  1.452
 MIU  N12  C13   single    1.456  0.020  1.456
 MIU  N12  H12   single    0.890  0.020  1.040
 MIU  C13  C14   single    1.535  0.020  1.535
 MIU  C13  C16   single    1.533  0.020  1.533
 MIU  C13  H13   single    0.970  0.020  1.090
 MIU  C2   C3    aromatic  1.382  0.020  1.382
 MIU  C2   H2    single    0.930  0.020  1.080
 MIU  C3   C4    aromatic  1.390  0.020  1.390
 MIU  C3   H3    single    0.930  0.020  1.080
 MIU  C4   C5    aromatic  1.386  0.020  1.386
 MIU  C4   H4    single    0.930  0.020  1.080
 MIU  C5   C6    single    1.499  0.020  1.499
 MIU  C5   C10   aromatic  1.392  0.020  1.392
 MIU  C6   F61   single    1.335  0.020  1.335
 MIU  C6   F1    single    1.339  0.020  1.339
 MIU  C6   F6    single    1.340  0.020  1.340
 MIU  C10  H10   single    0.930  0.020  1.080
 MIU  C14  O15   double    1.225  0.020  1.225
 MIU  C14  N26   single    1.343  0.020  1.343
 MIU  N26  C27   single    1.454  0.020  1.454
 MIU  N26  C31   single    1.452  0.020  1.452
 MIU  C27  C28   single    1.519  0.020  1.519
 MIU  C27  H271  single    0.970  0.020  1.090
 MIU  C27  H272  single    0.970  0.020  1.090
 MIU  C28  N29   single    1.453  0.020  1.453
 MIU  C28  H281  single    0.970  0.020  1.090
 MIU  C28  H282  single    0.970  0.020  1.090
 MIU  N29  C30   single    1.451  0.020  1.451
 MIU  N29  C32   single    1.453  0.020  1.453
 MIU  C30  C31   single    1.519  0.020  1.519
 MIU  C30  H301  single    0.970  0.020  1.090
 MIU  C30  H302  single    0.970  0.020  1.090
 MIU  C31  H311  single    0.970  0.020  1.090
 MIU  C31  H312  single    0.970  0.020  1.090
 MIU  C32  C33   single    1.521  0.020  1.521
 MIU  C32  H321  single    0.970  0.020  1.090
 MIU  C32  H322  single    0.970  0.020  1.090
 MIU  C16  C17   single    1.523  0.020  1.523
 MIU  C16  H161  single    0.970  0.020  1.090
 MIU  C16  H162  single    0.970  0.020  1.090
 MIU  C17  C18   single    1.530  0.020  1.530
 MIU  C17  H171  single    0.970  0.020  1.090
 MIU  C17  H172  single    0.970  0.020  1.090
 MIU  C18  N19   single    1.440  0.020  1.440
 MIU  C18  H181  single    0.970  0.020  1.090
 MIU  C18  H182  single    0.970  0.020  1.090
 MIU  N19  C20   double    1.284  0.020  1.284
 MIU  C20  N21   single    1.358  0.020  1.358
 MIU  C20  N22   single    1.381  0.020  1.381
 MIU  N21  H211  single    0.860  0.020  1.020
 MIU  N21  H212  single    0.860  0.020  1.020
 MIU  N22  H221  single    0.890  0.020  1.040
 MIU  N22  H222  single    0.890  0.020  1.040
 MIU  C33  C8    single    1.522  0.020  1.522
 MIU  C33  H331  single    0.970  0.020  1.090
 MIU  C33  H332  single    0.970  0.020  1.090
 MIU  C8   N9    single    1.456  0.020  1.456
 MIU  C8   H8C1  single    0.970  0.020  1.090
 MIU  C8   H8C2  single    0.970  0.020  1.090
 MIU  N9   H9N1  single    0.890  0.020  1.040
 MIU  N9   H9N2  single    0.890  0.020  1.040

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
 MIU  C10   C1   C2    121.49  3.000
 MIU  C10   C1   S11   119.74  3.000
 MIU  C2    C1   S11   118.77  3.000
 MIU  N12   S11  O25   105.92  3.000
 MIU  O25   S11  O24   120.25  3.000
 MIU  N12   S11  O24   107.64  3.000
 MIU  O25   S11  C1    108.22  3.000
 MIU  O24   S11  C1    107.10  3.000
 MIU  N12   S11  C1    107.06  3.000
 MIU  H2    C2   C3    119.80  3.000
 MIU  H2    C2   C1    121.25  3.000
 MIU  C3    C2   C1    118.95  3.000
 MIU  H3    C3   C4    119.70  3.000
 MIU  H3    C3   C2    119.87  3.000
 MIU  C4    C3   C2    120.43  3.000
 MIU  H4    C4   C5    121.08  3.000
 MIU  H4    C4   C3    118.95  3.000
 MIU  C5    C4   C3    119.97  3.000
 MIU  C10   C5   C6    118.30  3.000
 MIU  C10   C5   C4    120.29  3.000
 MIU  C6    C5   C4    121.40  3.000
 MIU  F6    C6   F1    106.55  3.000
 MIU  F6    C6   F61   107.14  3.000
 MIU  F1    C6   F61   107.22  3.000
 MIU  F6    C6   C5    111.62  3.000
 MIU  F1    C6   C5    111.45  3.000
 MIU  F61   C6   C5    112.53  3.000
 MIU  H10   C10  C5    121.00  3.000
 MIU  H10   C10  C1    120.12  3.000
 MIU  C5    C10  C1    118.88  3.000
 MIU  H12   N12  C13   113.53  3.000
 MIU  H12   N12  S11   112.41  3.000
 MIU  C13   N12  S11   119.41  3.000
 MIU  H13   C13  C16   107.50  3.000
 MIU  H13   C13  C14   111.10  3.000
 MIU  C16   C13  C14   111.08  3.000
 MIU  H13   C13  N12   107.71  3.000
 MIU  C16   C13  N12   110.29  3.000
 MIU  C14   C13  N12   109.09  3.000
 MIU  N26   C14  O15   122.94  3.000
 MIU  N26   C14  C13   118.10  3.000
 MIU  O15   C14  C13   118.85  3.000
 MIU  H162  C16  H161  106.41  3.000
 MIU  H162  C16  C17   109.95  3.000
 MIU  H161  C16  C17   109.51  3.000
 MIU  H162  C16  C13   107.10  3.000
 MIU  H161  C16  C13   108.90  3.000
 MIU  C17   C16  C13   114.63  3.000
 MIU  H172  C17  H171  106.57  3.000
 MIU  H172  C17  C18   108.36  3.000
 MIU  H171  C17  C18   109.52  3.000
 MIU  H172  C17  C16   110.65  3.000
 MIU  H171  C17  C16   110.09  3.000
 MIU  C18   C17  C16   111.52  3.000
 MIU  H182  C18  H181  104.74  3.000
 MIU  H182  C18  N19   113.63  3.000
 MIU  H181  C18  N19   108.08  3.000
 MIU  H182  C18  C17   108.84  3.000
 MIU  H181  C18  C17   107.94  3.000
 MIU  N19   C18  C17   113.13  3.000
 MIU  C20   N19  C18   118.79  3.000
 MIU  N21   C20  N22   113.94  3.000
 MIU  N22   C20  N19   119.07  3.000
 MIU  N21   C20  N19   126.95  3.000
 MIU  H222  N22  H221  111.84  3.000
 MIU  H222  N22  C20   116.06  3.000
 MIU  H221  N22  C20   112.79  3.000
 MIU  H212  N21  H211  116.74  3.000
 MIU  H212  N21  C20   121.64  3.000
 MIU  H211  N21  C20   121.61  3.000
 MIU  C31   N26  C27   111.01  3.000
 MIU  C31   N26  C14   126.08  3.000
 MIU  C27   N26  C14   120.57  3.000
 MIU  H272  C27  H271  108.17  3.000
 MIU  H272  C27  C28   110.35  3.000
 MIU  H271  C27  C28   110.30  3.000
 MIU  H272  C27  N26   110.20  3.000
 MIU  H271  C27  N26   108.24  3.000
 MIU  C28   C27  N26   109.54  3.000
 MIU  H282  C28  H281  106.83  3.000
 MIU  H282  C28  N29   111.95  3.000
 MIU  H281  C28  N29   108.81  3.000
 MIU  H282  C28  C27   108.57  3.000
 MIU  H281  C28  C27   109.01  3.000
 MIU  N29   C28  C27   111.52  3.000
 MIU  C32   N29  C30   112.62  3.000
 MIU  C32   N29  C28   110.20  3.000
 MIU  C30   N29  C28   111.32  3.000
 MIU  H302  C30  H301  107.10  3.000
 MIU  H302  C30  C31   108.49  3.000
 MIU  H301  C30  C31   107.94  3.000
 MIU  H302  C30  N29   111.96  3.000
 MIU  H301  C30  N29   109.87  3.000
 MIU  C31   C30  N29   111.31  3.000
 MIU  H312  C31  H311  106.95  3.000
 MIU  H312  C31  C30   110.11  3.000
 MIU  H311  C31  C30   109.51  3.000
 MIU  H312  C31  N26   108.16  3.000
 MIU  H311  C31  N26   112.15  3.000
 MIU  C30   C31  N26   109.91  3.000
 MIU  H322  C32  H321  105.91  3.000
 MIU  H322  C32  C33   109.13  3.000
 MIU  H321  C32  C33   108.56  3.000
 MIU  H322  C32  N29   111.08  3.000
 MIU  H321  C32  N29   107.29  3.000
 MIU  C33   C32  N29   114.48  3.000
 MIU  H332  C33  H331  106.96  3.000
 MIU  H332  C33  C8    109.92  3.000
 MIU  H331  C33  C8    108.15  3.000
 MIU  H332  C33  C32   109.23  3.000
 MIU  H331  C33  C32   111.22  3.000
 MIU  C8    C33  C32   111.25  3.000
 MIU  H8C2  C8   H8C1  106.23  3.000
 MIU  H8C2  C8   N9    108.21  3.000
 MIU  H8C1  C8   N9    113.43  3.000
 MIU  H8C2  C8   C33   108.81  3.000
 MIU  H8C1  C8   C33   109.13  3.000
 MIU  N9    C8   C33   110.83  3.000
 MIU  H9N2  N9   H9N1  105.44  3.000
 MIU  H9N2  N9   C8    109.39  3.000
 MIU  H9N1  N9   C8    109.05  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
 MIU  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 MIU  CONST_02  C4    C5   C10  C1      0.00   0.0  0
 MIU  CONST_03  C5    C10  C1   C2      0.00   0.0  0
 MIU  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 MIU  CONST_05  C10   C1   C2   C3      0.00   0.0  0
 MIU  CONST_06  C10   C5   C4   C3      0.00   0.0  0
 MIU  CONST_07  C6    C5   C10  C1    180.00   0.0  0
 MIU  CONST_08  C3    C2   C1   S11   180.00   0.0  0
 MIU  CONST_09  C5    C10  C1   S11   180.00   0.0  0
 MIU  CONST_10  C6    C5   C4   C3    180.00   0.0  0
 MIU  CONST_11  H3    C3   C2   C1    180.00   0.0  0
 MIU  CONST_12  H10   C10  C1   C2    180.00   0.0  0
 MIU  CONST_13  H4    C4   C3   C2    180.00   0.0  0
 MIU  CONST_14  H2    C2   C3   C4    180.00   0.0  0
 MIU  CONST_15  C27   N26  C14  C13   180.00   0.0  0
 MIU  CONST_17  C27   N26  C14  O15     0.00   0.0  0
 MIU  CONST_18  C31   N26  C14  O15   180.00   0.0  0
 MIU  CONST_19  N21   C20  N19  C18     0.00   0.0  0
 MIU  CONST_20  N22   C20  N19  C18   180.00   0.0  0
 MIU  CONST_21  H211  N21  C20  N19     0.00   0.0  0
 MIU  CONST_22  H212  N21  C20  N19   180.00   0.0  0
 MIU  Var_01    N29   C28  C27  N26    56.47  30.0  1
 MIU  Var_02    N29   C30  C31  N26   -56.31  30.0  1
 MIU  Var_03    C30   C31  N26  C27    58.67  30.0  1
 MIU  Var_04    C30   N29  C28  C27   -55.00  30.0  1
 MIU  Var_05    C31   N26  C27  C28   -58.62  30.0  1
 MIU  Var_06    C31   C30  N29  C28    54.72  30.0  1
 MIU  Var_07    C2    C1   S11  O24   179.61  30.0  3
 MIU  Var_08    F61   C6   C5   C4     -4.32  30.0  2
 MIU  Var_09    C33   C32  N29  C28  -171.40  30.0  3
 MIU  Var_10    C13   N12  S11  C1     56.04  30.0  3
 MIU  Var_11    C8    C33  C32  N29   176.11  30.0  3
 MIU  Var_12    C18   C17  C16  C13  -177.53  30.0  3
 MIU  Var_13    N19   C18  C17  C16  -177.54  30.0  3
 MIU  Var_14    N9    C8   C33  C32   179.45  30.0  3
 MIU  Var_15    H9N1  N9   C8   C33    68.43  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
 MIU  chir_01  C13  N12  C14  C16  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
 MIU  plan-1  C1    0.020
 MIU  plan-1  S11   0.020
 MIU  plan-1  C2    0.020
 MIU  plan-1  C3    0.020
 MIU  plan-1  C4    0.020
 MIU  plan-1  C5    0.020
 MIU  plan-1  C6    0.020
 MIU  plan-1  C10   0.020
 MIU  plan-1  H2    0.020
 MIU  plan-1  H3    0.020
 MIU  plan-1  H4    0.020
 MIU  plan-1  H10   0.020
 MIU  plan-2  C13   0.020
 MIU  plan-2  C14   0.020
 MIU  plan-2  O15   0.020
 MIU  plan-2  N26   0.020
 MIU  plan-2  C27   0.020
 MIU  plan-2  C31   0.020
 MIU  plan-3  C18   0.020
 MIU  plan-3  N19   0.020
 MIU  plan-3  C20   0.020
 MIU  plan-3  N22   0.020
 MIU  plan-3  N21   0.020
 MIU  plan-3  H221  0.020
 MIU  plan-3  H222  0.020
 MIU  plan-3  H211  0.020
 MIU  plan-3  H212  0.020

