# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 14:43:50 2022
#   Inital geometry file: a 129 line input string
#   Ligand name: (4R,5S)-3-{[(3S,5S)-5-({[amino(dihydroxy)methyl]amino}methyl)pyrrolidin-3-yl]sulfanyl}-5-[(1S,2R)-1-carboxy-2-hydroxypropyl]-4-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)[C@H]([C@@H]1NC(=C(S[C@@H]2CN[C@H](CNC(N)(O)O)C2)[C@@H]1C)C(O)=O)C(O)=O
#
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
 QP2  QP2  '(4R,5S)-3-{[(3S,5S)-5-({[amino(dihydroxy)methyl]amino}methyl)pyrrolidin-3-yl]sulfanyl}-5-[(1S,2R)-1-carboxy-2-hydroxypropyl]-4-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid'  ligand  54  28  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QP2
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
 QP2  CAC  C  CH3    0  -0.688  28.5933  13.6787  -1.8423
 QP2  CAA  C  CH1    0   0.075  28.1370  13.8114  -0.4001
 QP2  OAB  O  OH1    0  -0.673  27.6955  15.1494  -0.2257
 QP2  CAD  C  CH1    0  -0.449  27.0485  12.8235   0.0581
 QP2  CAE  C  C      0   0.425  25.6656  13.1839  -0.5411
 QP2  OBB  O  O      0  -0.599  25.5159  13.0140  -1.7677
 QP2  OAF  O  OC    -1  -0.606  24.8101  13.6155   0.2585
 QP2  CAG  C  CR15   0  -0.034  27.4086  11.3733  -0.2265
 QP2  CAI  C  CR15   0  -0.272  28.6802  10.8055   0.4444
 QP2  CBA  C  CH3    0  -0.664  28.9854  11.3092   1.8555
 QP2  NAH  N  NR15   0  -0.663  26.3342  10.4471   0.1448
 QP2  CAK  C  CR5    0   0.126  26.9522   9.2314   0.4804
 QP2  CAL  C  C      0   0.356  26.1178   8.0149   0.7888
 QP2  OAN  O  O      0  -0.595  24.8824   8.1488   0.6958
 QP2  OAM  O  OC    -1  -0.584  26.7473   6.9916   1.1265
 QP2  CAJ  C  CR5    0  -0.170  28.2936   9.3408   0.5120
 QP2  SAO  S  S2     0   0.010  29.4299   8.0639   0.8783
 QP2  CAP  C  CH1    0  -0.393  30.9666   8.6860   0.1140
 QP2  CAT  C  CH2    0  -0.476  32.0364   7.6090   0.3034
 QP2  CAQ  C  CH2    0  -0.299  30.8561   8.7415  -1.4099
 QP2  NAR  N  NH1    0  -0.590  30.9698   7.3656  -1.8663
 QP2  CAS  C  CH1    0  -0.073  31.9286   6.7183  -0.9619
 QP2  CAU  C  CH2    0  -0.294  31.5039   5.2871  -0.6635
 QP2  NAV  N  NH1    0  -0.650  32.5249   4.6186   0.1168
 QP2  CAW  C  CT     0   0.723  32.1669   3.4066   0.7840
 QP2  OAX  O  OH1    0  -0.669  31.6609   2.4730  -0.1191
 QP2  OAY  O  OH1    0  -0.662  31.1200   3.6492   1.6911
 QP2  NAZ  N  NH2    0  -0.834  33.3729   2.9016   1.3884
 QP2  H1   H  HCH3   0   0.221  29.0670  12.7114  -2.0105
 QP2  H2   H  HCH3   0   0.230  27.7651  13.7768  -2.5405
 QP2  H3   H  HCH3   0   0.223  29.3378  14.4438  -2.0692
 QP2  H4   H  HCH1   0   0.194  29.0206  13.6379   0.2317
 QP2  H5   H  HOH1   0   0.439  27.2869  15.2182   0.6432
 QP2  H6   H  HCH1   0   0.210  26.9715  12.9357   1.1477
 QP2  H8   H  HCR5   0   0.221  27.5509  11.2556  -1.3073
 QP2  H9   H  HCR5   0   0.245  29.5415  11.0004  -0.1991
 QP2  H10  H  HCH3   0   0.234  29.7801  10.7134   2.3067
 QP2  H11  H  HCH3   0   0.230  29.3128  12.3493   1.8596
 QP2  H12  H  HCH3   0   0.223  28.1069  11.2285   2.4977
 QP2  H13  H  HNR5   0   0.345  25.7058  10.7962   0.8588
 QP2  H15  H  HCH1   0   0.273  31.2514   9.6384   0.5631
 QP2  H16  H  HCH2   0   0.246  31.9156   7.0355   1.2252
 QP2  H17  H  HCH2   0   0.252  33.0170   8.0845   0.3590
 QP2  H18  H  HCH2   0   0.231  31.6908   9.3333  -1.8023
 QP2  H19  H  HCH2   0   0.248  29.9338   9.1982  -1.7720
 QP2  H20  H  HNH1   0   0.342  30.0631   6.9279  -1.7411
 QP2  H22  H  HCH1   0   0.223  32.9061   6.6903  -1.4570
 QP2  H23  H  HCH2   0   0.223  30.5761   5.3149  -0.0875
 QP2  H24  H  HCH2   0   0.217  31.2800   4.7774  -1.6100
 QP2  H25  H  HNH1   0   0.354  33.3645   4.4765  -0.4300
 QP2  H27  H  HOH1   0   0.451  31.3299   1.7016   0.3565
 QP2  H28  H  HOH1   0   0.445  31.4285   4.2823   2.3495
 QP2  H29  H  HNH2   0   0.351  33.7612   3.5843   2.0284
 QP2  H30  H  HNH2   0   0.352  33.1832   2.0645   1.9274

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
 QP2  CAC  CAA  single  1.518  0.020  1.518
 QP2  NAR  CAQ  single  1.454  0.020  1.454
 QP2  NAR  CAS  single  1.468  0.020  1.468
 QP2  OBB  CAE  deloc   1.247  0.020  1.247
 QP2  CAQ  CAP  single  1.529  0.020  1.529
 QP2  CAS  CAU  single  1.522  0.020  1.522
 QP2  CAS  CAT  single  1.551  0.020  1.551
 QP2  CAA  OAB  single  1.420  0.020  1.420
 QP2  CAA  CAD  single  1.540  0.020  1.540
 QP2  CAU  NAV  single  1.449  0.020  1.449
 QP2  OAX  CAW  single  1.394  0.020  1.394
 QP2  CAG  NAH  single  1.466  0.020  1.466
 QP2  CAG  CAD  single  1.521  0.020  1.521
 QP2  CAG  CAI  single  1.546  0.020  1.546
 QP2  CAE  CAD  single  1.550  0.020  1.550
 QP2  CAE  OAF  deloc   1.248  0.020  1.248
 QP2  NAH  CAK  single  1.404  0.020  1.404
 QP2  OAN  CAL  deloc   1.246  0.020  1.246
 QP2  CAI  CAJ  single  1.516  0.020  1.516
 QP2  CAI  CBA  single  1.529  0.020  1.529
 QP2  CAP  CAT  single  1.530  0.020  1.530
 QP2  CAP  SAO  single  1.826  0.020  1.826
 QP2  CAK  CAJ  double  1.346  0.020  1.346
 QP2  CAK  CAL  single  1.507  0.020  1.507
 QP2  CAJ  SAO  single  1.748  0.020  1.748
 QP2  CAL  OAM  deloc   1.248  0.020  1.248
 QP2  NAV  CAW  single  1.429  0.020  1.429
 QP2  CAW  NAZ  single  1.440  0.020  1.440
 QP2  CAW  OAY  single  1.406  0.020  1.406
 QP2  CAC  H1   single  0.970  0.020  1.090
 QP2  CAC  H2   single  0.970  0.020  1.090
 QP2  CAC  H3   single  0.970  0.020  1.090
 QP2  CAA  H4   single  0.970  0.020  1.090
 QP2  OAB  H5   single  0.850  0.020  0.980
 QP2  CAD  H6   single  0.970  0.020  1.090
 QP2  CAG  H8   single  0.970  0.020  1.090
 QP2  CAI  H9   single  0.970  0.020  1.090
 QP2  CBA  H10  single  0.970  0.020  1.090
 QP2  CBA  H11  single  0.970  0.020  1.090
 QP2  CBA  H12  single  0.970  0.020  1.090
 QP2  NAH  H13  single  0.890  0.020  1.040
 QP2  CAP  H15  single  0.970  0.020  1.090
 QP2  CAT  H16  single  0.970  0.020  1.090
 QP2  CAT  H17  single  0.970  0.020  1.090
 QP2  CAQ  H18  single  0.970  0.020  1.090
 QP2  CAQ  H19  single  0.970  0.020  1.090
 QP2  NAR  H20  single  0.890  0.020  1.040
 QP2  CAS  H22  single  0.970  0.020  1.090
 QP2  CAU  H23  single  0.970  0.020  1.090
 QP2  CAU  H24  single  0.970  0.020  1.090
 QP2  NAV  H25  single  0.890  0.020  1.040
 QP2  OAX  H27  single  0.850  0.020  0.980
 QP2  OAY  H28  single  0.850  0.020  0.980
 QP2  NAZ  H29  single  0.890  0.020  1.040
 QP2  NAZ  H30  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
 QP2  H3   CAC  H2   108.83  3.000
 QP2  H3   CAC  H1   107.07  3.000
 QP2  H2   CAC  H1   108.16  3.000
 QP2  H3   CAC  CAA  109.96  3.000
 QP2  H2   CAC  CAA  111.90  3.000
 QP2  H1   CAC  CAA  110.78  3.000
 QP2  H4   CAA  CAD  107.20  3.000
 QP2  H4   CAA  OAB  109.14  3.000
 QP2  CAD  CAA  OAB  110.38  3.000
 QP2  H4   CAA  CAC  106.88  3.000
 QP2  CAD  CAA  CAC  116.04  3.000
 QP2  OAB  CAA  CAC  107.01  3.000
 QP2  H5   OAB  CAA  108.08  3.000
 QP2  H6   CAD  CAG  107.43  3.000
 QP2  H6   CAD  CAE  107.30  3.000
 QP2  CAG  CAD  CAE  111.14  3.000
 QP2  H6   CAD  CAA  106.22  3.000
 QP2  CAE  CAD  CAA  111.51  3.000
 QP2  CAG  CAD  CAA  112.87  3.000
 QP2  OAF  CAE  OBB  126.51  3.000
 QP2  OAF  CAE  CAD  116.39  3.000
 QP2  OBB  CAE  CAD  117.11  3.000
 QP2  H8   CAG  NAH  106.07  3.000
 QP2  H8   CAG  CAI  106.35  3.000
 QP2  NAH  CAG  CAI  105.12  3.000
 QP2  H8   CAG  CAD  108.51  3.000
 QP2  CAI  CAG  CAD  117.63  3.000
 QP2  NAH  CAG  CAD  112.42  3.000
 QP2  H9   CAI  CAJ  113.55  3.000
 QP2  H9   CAI  CBA  109.11  3.000
 QP2  CAJ  CAI  CBA  109.14  3.000
 QP2  H9   CAI  CAG  109.11  3.000
 QP2  CBA  CAI  CAG  116.34  3.000
 QP2  CAJ  CAI  CAG   99.46  3.000
 QP2  H12  CBA  H11  108.06  3.000
 QP2  H12  CBA  H10  107.62  3.000
 QP2  H11  CBA  H10  107.49  3.000
 QP2  H12  CBA  CAI  110.98  3.000
 QP2  H11  CBA  CAI  112.18  3.000
 QP2  H10  CBA  CAI  110.32  3.000
 QP2  H13  NAH  CAK  113.75  3.000
 QP2  H13  NAH  CAG  114.53  3.000
 QP2  CAK  NAH  CAG  106.55  3.000
 QP2  CAJ  CAK  CAL  127.77  3.000
 QP2  CAL  CAK  NAH  120.26  3.000
 QP2  CAJ  CAK  NAH  111.94  3.000
 QP2  OAM  CAL  OAN  127.47  3.000
 QP2  OAM  CAL  CAK  115.97  3.000
 QP2  OAN  CAL  CAK  116.54  3.000
 QP2  SAO  CAJ  CAK  126.39  3.000
 QP2  SAO  CAJ  CAI  123.31  3.000
 QP2  CAK  CAJ  CAI  109.36  3.000
 QP2  CAP  SAO  CAJ  102.16  3.000
 QP2  H15  CAP  CAQ  113.42  3.000
 QP2  H15  CAP  CAT  112.41  3.000
 QP2  CAQ  CAP  CAT  101.51  3.000
 QP2  H15  CAP  SAO  110.17  3.000
 QP2  CAT  CAP  SAO  107.27  3.000
 QP2  CAQ  CAP  SAO  111.64  3.000
 QP2  H17  CAT  H16  106.57  3.000
 QP2  H17  CAT  CAS  110.75  3.000
 QP2  H16  CAT  CAS  112.29  3.000
 QP2  H17  CAT  CAP  109.14  3.000
 QP2  H16  CAT  CAP  113.38  3.000
 QP2  CAS  CAT  CAP  104.75  3.000
 QP2  H19  CAQ  H18  107.40  3.000
 QP2  H19  CAQ  NAR  110.98  3.000
 QP2  H18  CAQ  NAR  109.82  3.000
 QP2  H19  CAQ  CAP  114.02  3.000
 QP2  H18  CAQ  CAP  108.75  3.000
 QP2  NAR  CAQ  CAP  105.83  3.000
 QP2  H20  NAR  CAS  108.50  3.000
 QP2  H20  NAR  CAQ  107.43  3.000
 QP2  CAS  NAR  CAQ  105.96  3.000
 QP2  H22  CAS  CAU  108.26  3.000
 QP2  H22  CAS  NAR  108.38  3.000
 QP2  CAU  CAS  NAR  110.67  3.000
 QP2  H22  CAS  CAT  108.73  3.000
 QP2  CAU  CAS  CAT  113.53  3.000
 QP2  NAR  CAS  CAT  107.14  3.000
 QP2  H24  CAU  H23  107.05  3.000
 QP2  H24  CAU  NAV  113.19  3.000
 QP2  H23  CAU  NAV  109.05  3.000
 QP2  H24  CAU  CAS  108.92  3.000
 QP2  H23  CAU  CAS  108.45  3.000
 QP2  NAV  CAU  CAS  110.05  3.000
 QP2  H25  NAV  CAW  109.94  3.000
 QP2  H25  NAV  CAU  111.01  3.000
 QP2  CAW  NAV  CAU  117.79  3.000
 QP2  NAZ  CAW  OAY  114.40  3.000
 QP2  OAY  CAW  OAX  105.26  3.000
 QP2  NAZ  CAW  OAX  109.93  3.000
 QP2  OAY  CAW  NAV  109.96  3.000
 QP2  NAZ  CAW  NAV  106.47  3.000
 QP2  OAX  CAW  NAV  110.89  3.000
 QP2  H27  OAX  CAW  109.92  3.000
 QP2  H28  OAY  CAW  108.40  3.000
 QP2  H30  NAZ  H29  107.00  3.000
 QP2  H30  NAZ  CAW  110.85  3.000
 QP2  H29  NAZ  CAW  110.47  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
 QP2  Var_01  CAJ  CAK  NAH  CAG    7.28  30.0  1
 QP2  Var_02  NAH  CAK  CAJ  CAI   11.19  30.0  1
 QP2  Var_03  CAS  NAR  CAQ  CAP  -35.60  30.0  1
 QP2  Var_04  OAN  CAL  CAK  NAH    1.68  30.0  2
 QP2  Var_05  CAW  NAV  CAU  CAS  164.01  30.0  3
 QP2  Var_06  OAX  CAW  NAV  CAU   56.02  30.0  3
 QP2  Var_07  H29  NAZ  CAW  NAV   58.33  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
 QP2  chir_01  CAA  CAC  OAB  CAD  negativ
 QP2  chir_02  CAD  CAA  CAG  CAE  positiv
 QP2  chir_03  CAG  NAH  CAD  CAI  negativ
 QP2  chir_04  CAI  CAG  CAJ  CBA  positiv
 QP2  chir_05  CAP  SAO  CAT  CAQ  negativ
 QP2  chir_06  CAS  NAR  CAT  CAU  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
 QP2  plan-1  CAG  0.020
 QP2  plan-1  NAH  0.020
 QP2  plan-1  CAK  0.020
 QP2  plan-1  H13  0.020
 QP2  plan-2  CAD  0.020
 QP2  plan-2  CAE  0.020
 QP2  plan-2  OBB  0.020
 QP2  plan-2  OAF  0.020
 QP2  plan-3  CAK  0.020
 QP2  plan-3  CAL  0.020
 QP2  plan-3  OAN  0.020
 QP2  plan-3  OAM  0.020

