# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:35:02 2022
#   Inital geometry file: a 92 line input string
#   Ligand name: (3S,5S)-3-({[(aminomethyl)amino]methyl}sulfanyl)-5-[(2S)-1,3-dioxobutan-2-yl]-L-proline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)[C@H](C=O)[C@@H]1C[C@H](SCNCN)[C@H](N1)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
 3V5  3V5  (3S,5S)-3-({[(aminomethyl)amino]methyl}sulfanyl)-5-[(2S)-1,3-dioxobutan-2-yl]-L-proline  ligand  37  19  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3V5
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
 3V5  OAF  O  O      0  -0.598  -0.2497  -2.8819   0.7226
 3V5  CAS  C  C      0   0.409   0.3602  -2.5561  -0.3129
 3V5  OAH  O  OC    -1  -0.616   1.2437  -3.2118  -0.9008
 3V5  CAX  C  CH1    0  -0.196   0.0467  -1.1722  -0.9082
 3V5  CAW  C  CH1    0  -0.415   0.9280  -0.0985  -0.1820
 3V5  SAQ  S  S2     0  -0.069   2.1811   0.5540  -1.3150
 3V5  CAK  C  CH2    0  -0.414   2.9881   1.8280  -0.2480
 3V5  NAN  N  NH1    0  -0.577   3.5123   1.3909   1.0049
 3V5  CAJ  C  CH2    0  -0.144   4.5045   0.3395   0.9582
 3V5  NAB  N  NH2    0  -0.793   5.7229   0.8488   0.3688
 3V5  CAM  C  CH2    0  -0.413  -0.0755   0.9317   0.3349
 3V5  NAO  N  NH1    0  -0.577  -1.3470  -0.7617  -0.7251
 3V5  CAV  C  CH1    0  -0.095  -1.3524   0.0954   0.4533
 3V5  CAY  C  CH1    0  -0.510  -2.6329   0.9151   0.6309
 3V5  CAR  C  C      0   0.430  -3.8356   0.0785   1.0661
 3V5  CAA  C  CH3    0  -0.796  -5.1749   0.7421   0.9169
 3V5  OAE  O  O      0  -0.375  -3.7045  -1.0193   1.5469
 3V5  CAT  C  C1     0   0.163  -2.9474   1.7375  -0.5964
 3V5  OAG  O  O      0  -0.355  -2.7496   2.9228  -0.6817
 3V5  H2   H  HCH1   0   0.234   0.2627  -1.1902  -1.9790
 3V5  H3   H  HCH1   0   0.277   1.4467  -0.5549   0.6644
 3V5  H4   H  HCH2   0   0.272   3.7909   2.2234  -0.8697
 3V5  H5   H  HCH2   0   0.269   2.2703   2.6294  -0.0745
 3V5  H6   H  HNH1   0   0.360   2.7731   1.1559   1.6526
 3V5  H8   H  HCH2   0   0.208   4.6210  -0.0242   1.9865
 3V5  H9   H  HCH2   0   0.202   4.1777  -0.5163   0.3516
 3V5  H10  H  HNH2   0   0.340   6.2019   1.4466   1.0301
 3V5  H11  H  HNH2   0   0.348   6.3501   0.0829   0.1617
 3V5  H13  H  HCH2   0   0.244   0.2257   1.3795   1.2839
 3V5  H14  H  HCH2   0   0.233  -0.1991   1.7392  -0.3922
 3V5  H15  H  HNH1   0   0.339  -1.5959  -0.2098  -1.5382
 3V5  H17  H  HCH1   0   0.261  -1.2629  -0.5529   1.3270
 3V5  H18  H  HCH1   0   0.316  -2.4640   1.6250   1.4513
 3V5  H19  H  HCH3   0   0.274  -5.4495   0.7916  -0.1407
 3V5  H20  H  HCH3   0   0.276  -5.9503   0.1920   1.4453
 3V5  H21  H  HCH3   0   0.272  -5.1431   1.7692   1.2846
 3V5  H22  H  H      0   0.215  -3.3677   1.1789  -1.4518

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
 3V5  NAN  CAJ  single  1.446  0.020  1.446
 3V5  NAN  CAK  single  1.427  0.020  1.427
 3V5  CAJ  NAB  single  1.446  0.020  1.446
 3V5  CAK  SAQ  single  1.847  0.020  1.847
 3V5  SAQ  CAW  single  1.811  0.020  1.811
 3V5  CAW  CAX  single  1.567  0.020  1.567
 3V5  CAW  CAM  single  1.528  0.020  1.528
 3V5  OAF  CAS  deloc   1.245  0.020  1.245
 3V5  CAX  CAS  single  1.539  0.020  1.539
 3V5  CAX  NAO  single  1.464  0.020  1.464
 3V5  CAS  OAH  deloc   1.247  0.020  1.247
 3V5  CAM  CAV  single  1.531  0.020  1.531
 3V5  NAO  CAV  single  1.457  0.020  1.457
 3V5  CAV  CAY  single  1.531  0.020  1.531
 3V5  CAY  CAT  single  1.511  0.020  1.511
 3V5  CAY  CAR  single  1.528  0.020  1.528
 3V5  CAT  OAG  double  1.205  0.020  1.205
 3V5  CAR  CAA  single  1.502  0.020  1.502
 3V5  CAR  OAE  double  1.206  0.020  1.206
 3V5  CAX  H2   single  0.970  0.020  1.090
 3V5  CAW  H3   single  0.970  0.020  1.090
 3V5  CAK  H4   single  0.970  0.020  1.090
 3V5  CAK  H5   single  0.970  0.020  1.090
 3V5  NAN  H6   single  0.890  0.020  1.040
 3V5  CAJ  H8   single  0.970  0.020  1.090
 3V5  CAJ  H9   single  0.970  0.020  1.090
 3V5  NAB  H10  single  0.890  0.020  1.040
 3V5  NAB  H11  single  0.890  0.020  1.040
 3V5  CAM  H13  single  0.970  0.020  1.090
 3V5  CAM  H14  single  0.970  0.020  1.090
 3V5  NAO  H15  single  0.890  0.020  1.040
 3V5  CAV  H17  single  0.970  0.020  1.090
 3V5  CAY  H18  single  0.970  0.020  1.090
 3V5  CAA  H19  single  0.970  0.020  1.090
 3V5  CAA  H20  single  0.970  0.020  1.090
 3V5  CAA  H21  single  0.970  0.020  1.090
 3V5  CAT  H22  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
 3V5  CAX  CAS  OAH  115.77  3.000
 3V5  OAH  CAS  OAF  126.96  3.000
 3V5  CAX  CAS  OAF  117.21  3.000
 3V5  H2   CAX  NAO  108.38  3.000
 3V5  H2   CAX  CAW  110.75  3.000
 3V5  NAO  CAX  CAW  106.57  3.000
 3V5  H2   CAX  CAS  108.91  3.000
 3V5  NAO  CAX  CAS  113.43  3.000
 3V5  CAW  CAX  CAS  108.80  3.000
 3V5  H3   CAW  CAM  109.35  3.000
 3V5  H3   CAW  SAQ  107.86  3.000
 3V5  CAM  CAW  SAQ  115.03  3.000
 3V5  H3   CAW  CAX  109.86  3.000
 3V5  CAM  CAW  CAX  104.43  3.000
 3V5  SAQ  CAW  CAX  110.24  3.000
 3V5  CAK  SAQ  CAW  100.92  3.000
 3V5  H5   CAK  H4   108.02  3.000
 3V5  H5   CAK  NAN  109.11  3.000
 3V5  H4   CAK  NAN  109.96  3.000
 3V5  H5   CAK  SAQ  108.14  3.000
 3V5  H4   CAK  SAQ  104.04  3.000
 3V5  NAN  CAK  SAQ  117.15  3.000
 3V5  H6   NAN  CAJ  110.70  3.000
 3V5  H6   NAN  CAK  111.43  3.000
 3V5  CAJ  NAN  CAK  116.52  3.000
 3V5  H9   CAJ  H8   106.92  3.000
 3V5  H9   CAJ  NAB  107.45  3.000
 3V5  H8   CAJ  NAB  114.17  3.000
 3V5  H9   CAJ  NAN  112.32  3.000
 3V5  H8   CAJ  NAN  106.48  3.000
 3V5  NAB  CAJ  NAN  109.58  3.000
 3V5  H11  NAB  H10  106.71  3.000
 3V5  H11  NAB  CAJ  109.83  3.000
 3V5  H10  NAB  CAJ  109.91  3.000
 3V5  H14  CAM  H13  107.83  3.000
 3V5  H14  CAM  CAV  111.13  3.000
 3V5  H13  CAM  CAV  112.77  3.000
 3V5  H14  CAM  CAW  110.31  3.000
 3V5  H13  CAM  CAW  112.92  3.000
 3V5  CAV  CAM  CAW  101.87  3.000
 3V5  H15  NAO  CAV  109.12  3.000
 3V5  H15  NAO  CAX  106.62  3.000
 3V5  CAV  NAO  CAX  105.63  3.000
 3V5  H17  CAV  CAY  107.08  3.000
 3V5  H17  CAV  NAO  107.32  3.000
 3V5  CAY  CAV  NAO  114.32  3.000
 3V5  H17  CAV  CAM  108.54  3.000
 3V5  CAY  CAV  CAM  114.47  3.000
 3V5  NAO  CAV  CAM  104.81  3.000
 3V5  H18  CAY  CAT  106.68  3.000
 3V5  H18  CAY  CAR  105.21  3.000
 3V5  CAT  CAY  CAR  111.44  3.000
 3V5  H18  CAY  CAV  107.71  3.000
 3V5  CAR  CAY  CAV  113.47  3.000
 3V5  CAT  CAY  CAV  111.80  3.000
 3V5  OAE  CAR  CAA  122.60  3.000
 3V5  OAE  CAR  CAY  121.77  3.000
 3V5  CAA  CAR  CAY  115.57  3.000
 3V5  H21  CAA  H20  109.45  3.000
 3V5  H21  CAA  H19  106.88  3.000
 3V5  H20  CAA  H19  108.28  3.000
 3V5  H21  CAA  CAR  110.88  3.000
 3V5  H20  CAA  CAR  111.34  3.000
 3V5  H19  CAA  CAR  109.87  3.000
 3V5  H22  CAT  OAG  120.35  3.000
 3V5  H22  CAT  CAY  115.66  3.000
 3V5  OAG  CAT  CAY  123.98  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
 3V5  Var_01  NAN  CAK  SAQ  CAW  55.73  30.0  1
 3V5  Var_02  CAJ  NAN  CAK  SAQ  57.82  30.0  1
 3V5  Var_03  NAB  CAJ  NAN  CAK  68.73  30.0  3
 3V5  Var_04  H10  NAB  CAJ  NAN  74.29  30.0  3
 3V5  Var_05  H19  CAA  CAR  CAY  72.92  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
 3V5  chir_01  CAX  CAW  CAS  NAO  negativ
 3V5  chir_02  CAW  SAQ  CAX  CAM  positiv
 3V5  chir_03  CAV  NAO  CAY  CAM  positiv
 3V5  chir_04  CAY  CAV  CAT  CAR  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
 3V5  plan-1  CAY  0.020
 3V5  plan-1  CAR  0.020
 3V5  plan-1  CAA  0.020
 3V5  plan-1  OAE  0.020
 3V5  plan-2  OAF  0.020
 3V5  plan-2  CAS  0.020
 3V5  plan-2  OAH  0.020
 3V5  plan-2  CAX  0.020
 3V5  plan-3  CAY  0.020
 3V5  plan-3  CAT  0.020
 3V5  plan-3  OAG  0.020
 3V5  plan-3  H22  0.020

