# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 26 02:25:06 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] butanethioate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC(=O)SCCNC(=O)CCNC(=O)[C@@H](O)C(C)(C)CO[P](O)(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
 PSR  PSR  'S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] butanethioate'  ligand  56  27  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PSR
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
 PSR  O23   O  OH1   0  -0.746   8.9531   0.0875  -1.7145
 PSR  P24   P  P     0   1.474   8.2709  -1.1452  -0.9695
 PSR  O25   O  O     0  -0.693   9.0926  -1.9087  -0.0111
 PSR  O26   O  OH1   0  -0.745   7.6926  -1.9873  -2.2023
 PSR  O27   O  O2    0  -0.582   7.0369  -0.4507  -0.2513
 PSR  C28   C  CH2   0  -0.150   6.0330   0.2878  -0.9575
 PSR  C29   C  CT    0  -0.163   4.8238   0.4760  -0.0426
 PSR  C30   C  CH3   0  -0.646   4.2922  -0.8793   0.4315
 PSR  C31   C  CH3   0  -0.667   5.2041   1.3190   1.1761
 PSR  C32   C  CH1   0  -0.035   3.6805   1.1738  -0.8317
 PSR  O33   O  OH1   0  -0.660   3.2478   0.4225  -1.9342
 PSR  C34   C  C     0   0.517   4.0477   2.5758  -1.3199
 PSR  O35   O  O     0  -0.498   4.6211   2.7169  -2.3950
 PSR  N36   N  NH1   0  -0.617   3.6853   3.5933  -0.5361
 PSR  C37   C  CH2   0  -0.309   3.9946   4.9759  -0.8313
 PSR  C38   C  CH2   0  -0.590   5.3782   5.3881  -0.3577
 PSR  C39   C  C     0   0.566   5.5358   5.2719   1.1450
 PSR  O40   O  O     0  -0.494   4.5778   5.2357   1.9039
 PSR  N41   N  NH1   0  -0.630   6.8081   5.2411   1.5786
 PSR  C42   C  CH2   0  -0.323   7.1595   5.1762   2.9765
 PSR  C43   C  CH2   0  -0.546   7.1558   3.7608   3.5393
 PSR  S1    S  S2    0  -0.003   8.4472   2.7889   2.7138
 PSR  C1    C  C     0   0.260   8.3236   1.2387   3.5614
 PSR  O1    O  O     0  -0.391   7.5326   1.0490   4.4494
 PSR  C2    C  CH2   0  -0.544   9.2901   0.2098   3.0385
 PSR  C3    C  CH2   0  -0.420   9.4949  -0.9767   3.9716
 PSR  C4    C  CH3   0  -0.675  10.5165  -1.9521   3.4046
 PSR  H231  H  HOH1  0   0.501   9.7824  -0.1187  -2.1659
 PSR  H261  H  HOH1  0   0.498   7.4402  -2.8920  -1.9747
 PSR  H281  H  HCH2  0   0.245   6.4510   1.2513  -1.2555
 PSR  H282  H  HCH2  0   0.236   5.7432  -0.2543  -1.8612
 PSR  H301  H  HCH3  0   0.230   3.4094  -0.7395   1.0588
 PSR  H302  H  HCH3  0   0.240   5.0353  -1.4054   1.0295
 PSR  H303  H  HCH3  0   0.234   4.0117  -1.5236  -0.4017
 PSR  H311  H  HCH3  0   0.249   5.8699   0.7624   1.8345
 PSR  H312  H  HCH3  0   0.235   4.3204   1.5855   1.7610
 PSR  H313  H  HCH3  0   0.228   5.7179   2.2416   0.9028
 PSR  H321  H  HCH1  0   0.258   2.8329   1.2444  -0.1407
 PSR  H331  H  HOH1  0   0.446   3.7841   0.6782  -2.6953
 PSR  H361  H  HNH1  0   0.406   3.2186   3.3940   0.3338
 PSR  H371  H  HCH2  0   0.266   3.9176   5.1338  -1.9060
 PSR  H372  H  HCH2  0   0.264   3.2312   5.5928  -0.3616
 PSR  H381  H  HCH2  0   0.290   5.5548   6.4308  -0.6398
 PSR  H382  H  HCH2  0   0.266   6.1456   4.8026  -0.8694
 PSR  H411  H  HNH1  0   0.406   7.5513   5.2693   0.9003
 PSR  H421  H  HCH2  0   0.273   8.1409   5.6328   3.1035
 PSR  H422  H  HCH2  0   0.274   6.4547   5.7724   3.5562
 PSR  H431  H  HCH2  0   0.290   7.3618   3.7921   4.6089
 PSR  H432  H  HCH2  0   0.286   6.1868   3.2885   3.3834
 PSR  HC21  H  HCH2  0   0.288   8.9098  -0.1351   2.0709
 PSR  HC22  H  HCH2  0   0.264  10.2456   0.6961   2.8199
 PSR  HC31  H  HCH2  0   0.228   9.8265  -0.6229   4.9506
 PSR  HC32  H  HCH2  0   0.229   8.5443  -1.4889   4.1310
 PSR  HC41  H  HCH3  0   0.231  10.6554  -2.8052   4.0689
 PSR  HC42  H  HCH3  0   0.231  10.2010  -2.3302   2.4317
 PSR  HC43  H  HCH3  0   0.219  11.4879  -1.4722   3.2728

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
 PSR  O23  P24   single  1.594  0.020  1.594
 PSR  O23  H231  single  0.850  0.020  0.980
 PSR  P24  O25   double  1.475  0.020  1.475
 PSR  P24  O26   single  1.601  0.020  1.601
 PSR  P24  O27   single  1.588  0.020  1.588
 PSR  O26  H261  single  0.850  0.020  0.980
 PSR  O27  C28   single  1.432  0.020  1.432
 PSR  C28  C29   single  1.528  0.020  1.528
 PSR  C28  H281  single  0.970  0.020  1.090
 PSR  C28  H282  single  0.970  0.020  1.090
 PSR  C29  C30   single  1.531  0.020  1.531
 PSR  C29  C31   single  1.530  0.020  1.530
 PSR  C29  C32   single  1.555  0.020  1.555
 PSR  C30  H301  single  0.970  0.020  1.090
 PSR  C30  H302  single  0.970  0.020  1.090
 PSR  C30  H303  single  0.970  0.020  1.090
 PSR  C31  H311  single  0.970  0.020  1.090
 PSR  C31  H312  single  0.970  0.020  1.090
 PSR  C31  H313  single  0.970  0.020  1.090
 PSR  C32  O33   single  1.403  0.020  1.403
 PSR  C32  C34   single  1.529  0.020  1.529
 PSR  C32  H321  single  0.970  0.020  1.090
 PSR  O33  H331  single  0.850  0.020  0.980
 PSR  C34  O35   double  1.227  0.020  1.227
 PSR  C34  N36   single  1.335  0.020  1.335
 PSR  N36  C37   single  1.447  0.020  1.447
 PSR  N36  H361  single  0.860  0.020  1.020
 PSR  C37  C38   single  1.519  0.020  1.519
 PSR  C37  H371  single  0.970  0.020  1.090
 PSR  C37  H372  single  0.970  0.020  1.090
 PSR  C38  C39   single  1.515  0.020  1.515
 PSR  C38  H381  single  0.970  0.020  1.090
 PSR  C38  H382  single  0.970  0.020  1.090
 PSR  C39  O40   double  1.223  0.020  1.223
 PSR  C39  N41   single  1.344  0.020  1.344
 PSR  N41  C42   single  1.443  0.020  1.443
 PSR  N41  H411  single  0.860  0.020  1.020
 PSR  C42  C43   single  1.523  0.020  1.523
 PSR  C42  H421  single  0.970  0.020  1.090
 PSR  C42  H422  single  0.970  0.020  1.090
 PSR  C43  S1    single  1.815  0.020  1.815
 PSR  C43  H431  single  0.970  0.020  1.090
 PSR  C43  H432  single  0.970  0.020  1.090
 PSR  S1   C1    single  1.771  0.020  1.771
 PSR  C1   O1    double  1.204  0.020  1.204
 PSR  C1   C2    single  1.505  0.020  1.505
 PSR  C2   C3    single  1.523  0.020  1.523
 PSR  C2   HC21  single  0.970  0.020  1.090
 PSR  C2   HC22  single  0.970  0.020  1.090
 PSR  C3   C4    single  1.522  0.020  1.522
 PSR  C3   HC31  single  0.970  0.020  1.090
 PSR  C3   HC32  single  0.970  0.020  1.090
 PSR  C4   HC41  single  0.970  0.020  1.090
 PSR  C4   HC42  single  0.970  0.020  1.090
 PSR  C4   HC43  single  0.970  0.020  1.090

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
 PSR  H231  O23  P24   114.87  3.000
 PSR  O27   P24  O26   107.32  3.000
 PSR  O27   P24  O25   111.43  3.000
 PSR  O26   P24  O25   115.42  3.000
 PSR  O27   P24  O23   101.88  3.000
 PSR  O26   P24  O23   101.62  3.000
 PSR  O25   P24  O23   117.74  3.000
 PSR  H261  O26  P24   113.91  3.000
 PSR  C28   O27  P24   123.17  3.000
 PSR  H282  C28  H281  108.27  3.000
 PSR  H282  C28  C29   110.26  3.000
 PSR  H281  C28  C29   110.96  3.000
 PSR  H282  C28  O27   109.74  3.000
 PSR  H281  C28  O27   108.74  3.000
 PSR  C29   C28  O27   108.84  3.000
 PSR  C32   C29  C31   109.87  3.000
 PSR  C32   C29  C30   107.41  3.000
 PSR  C31   C29  C30   109.11  3.000
 PSR  C32   C29  C28   109.48  3.000
 PSR  C31   C29  C28   110.37  3.000
 PSR  C30   C29  C28   110.56  3.000
 PSR  H303  C30  H302  108.04  3.000
 PSR  H303  C30  H301  107.86  3.000
 PSR  H302  C30  H301  107.34  3.000
 PSR  H303  C30  C29   112.08  3.000
 PSR  H302  C30  C29   111.14  3.000
 PSR  H301  C30  C29   110.20  3.000
 PSR  H313  C31  H312  107.98  3.000
 PSR  H313  C31  H311  107.20  3.000
 PSR  H312  C31  H311  107.18  3.000
 PSR  H313  C31  C29   112.55  3.000
 PSR  H312  C31  C29   111.08  3.000
 PSR  H311  C31  C29   110.61  3.000
 PSR  H321  C32  C34   109.14  3.000
 PSR  H321  C32  O33   106.95  3.000
 PSR  C34   C32  O33   108.31  3.000
 PSR  H321  C32  C29   106.12  3.000
 PSR  C34   C32  C29   113.39  3.000
 PSR  O33   C32  C29   112.67  3.000
 PSR  H331  O33  C32   107.84  3.000
 PSR  N36   C34  O35   123.64  3.000
 PSR  N36   C34  C32   116.51  3.000
 PSR  O35   C34  C32   119.83  3.000
 PSR  H361  N36  C37   117.67  3.000
 PSR  H361  N36  C34   118.83  3.000
 PSR  C37   N36  C34   123.40  3.000
 PSR  H372  C37  H371  107.11  3.000
 PSR  H372  C37  C38   110.52  3.000
 PSR  H371  C37  C38   109.43  3.000
 PSR  H372  C37  N36   107.67  3.000
 PSR  H371  C37  N36   108.96  3.000
 PSR  C38   C37  N36   112.97  3.000
 PSR  H382  C38  H381  106.05  3.000
 PSR  H382  C38  C39   110.50  3.000
 PSR  H381  C38  C39   108.17  3.000
 PSR  H382  C38  C37   110.39  3.000
 PSR  H381  C38  C37   108.97  3.000
 PSR  C39   C38  C37   112.52  3.000
 PSR  N41   C39  O40   122.72  3.000
 PSR  N41   C39  C38   114.84  3.000
 PSR  O40   C39  C38   122.43  3.000
 PSR  H411  N41  C42   118.32  3.000
 PSR  H411  N41  C39   118.73  3.000
 PSR  C42   N41  C39   122.96  3.000
 PSR  H422  C42  H421  106.92  3.000
 PSR  H422  C42  C43   108.08  3.000
 PSR  H421  C42  C43   110.39  3.000
 PSR  H422  C42  N41   109.46  3.000
 PSR  H421  C42  N41   108.26  3.000
 PSR  C43   C42  N41   113.53  3.000
 PSR  H432  C43  H431  108.73  3.000
 PSR  H432  C43  S1    109.62  3.000
 PSR  H431  C43  S1    109.11  3.000
 PSR  H432  C43  C42   110.62  3.000
 PSR  H431  C43  C42   109.60  3.000
 PSR  S1    C43  C42   109.14  3.000
 PSR  C1    S1   C43   101.62  3.000
 PSR  C2    C1   O1    124.76  3.000
 PSR  C2    C1   S1    112.78  3.000
 PSR  O1    C1   S1    122.46  3.000
 PSR  HC22  C2   HC21  105.47  3.000
 PSR  HC22  C2   C3    110.56  3.000
 PSR  HC21  C2   C3    110.03  3.000
 PSR  HC22  C2   C1    109.04  3.000
 PSR  HC21  C2   C1    107.41  3.000
 PSR  C3    C2   C1    113.95  3.000
 PSR  HC32  C3   HC31  106.58  3.000
 PSR  HC32  C3   C4    109.77  3.000
 PSR  HC31  C3   C4    109.73  3.000
 PSR  HC32  C3   C2    109.75  3.000
 PSR  HC31  C3   C2    109.72  3.000
 PSR  C4    C3   C2    111.18  3.000
 PSR  HC43  C4   HC42  107.59  3.000
 PSR  HC43  C4   HC41  107.72  3.000
 PSR  HC42  C4   HC41  108.01  3.000
 PSR  HC43  C4   C3    111.13  3.000
 PSR  HC42  C4   C3    111.13  3.000
 PSR  HC41  C4   C3    111.11  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
 PSR  CONST_01  C37   N36  C34  C32   180.00   0.0  0
 PSR  CONST_02  C37   N36  C34  O35     0.00   0.0  0
 PSR  CONST_03  C42   N41  C39  C38   180.00   0.0  0
 PSR  CONST_04  C42   N41  C39  O40     0.00   0.0  0
 PSR  CONST_05  H361  N36  C34  C32     0.00   0.0  0
 PSR  CONST_06  H411  N41  C39  C38     0.00   0.0  0
 PSR  Var_01    C29   C28  O27  P24   164.43  30.0  3
 PSR  Var_02    C30   C29  C28  O27   -57.27  30.0  3
 PSR  Var_03    C38   C37  N36  C34   -84.61  30.0  3
 PSR  Var_04    C39   C38  C37  N36   -61.73  30.0  3
 PSR  Var_05    O40   C39  C38  C37   -19.84  30.0  3
 PSR  Var_06    C43   C42  N41  C39    84.10  30.0  3
 PSR  Var_07    S1    C43  C42  N41    64.41  30.0  3
 PSR  Var_08    O1    C1   S1   C43    -0.57  30.0  3
 PSR  Var_09    C3    C2   C1   S1    163.60  30.0  3
 PSR  Var_10    C4    C3   C2   C1   -178.08  30.0  3
 PSR  Var_11    H301  C30  C29  C28  -178.20  30.0  3
 PSR  Var_12    H311  C31  C29  C28   -69.50  30.0  3
 PSR  Var_13    HC41  C4   C3   C2   -179.48  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
 PSR  chir_01  C32  C29  O33  C34  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
 PSR  plan-1  C32   0.020
 PSR  plan-1  C34   0.020
 PSR  plan-1  O35   0.020
 PSR  plan-1  N36   0.020
 PSR  plan-1  C37   0.020
 PSR  plan-1  H361  0.020
 PSR  plan-2  C38   0.020
 PSR  plan-2  C39   0.020
 PSR  plan-2  O40   0.020
 PSR  plan-2  N41   0.020
 PSR  plan-2  C42   0.020
 PSR  plan-2  H411  0.020
 PSR  plan-3  S1    0.020
 PSR  plan-3  C1    0.020
 PSR  plan-3  O1    0.020
 PSR  plan-3  C2    0.020

