# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 06:41:46 2021
#   Inital geometry file: a 127 line input string
#   Ligand name: (2~{S})-4-[(2~{R})-2-azanyl-3-oxidanyl-3-oxidanylidene-propyl]sulfanyl-2-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(C=N[C@@H](CCSC[C@H](N)C(O)=O)C(O)=O)c1O
#
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
 E9U  E9U  '(2~{S})-4-[(2~{R})-2-azanyl-3-oxidanyl-3-oxidanylidene-propyl]sulfanyl-2-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]butanoic acid'  ligand  51  29  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_E9U
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
 E9U  N1   N  N     0  -0.399  -7.9733  -45.7816  -25.4187
 E9U  C2   C  CR6   0   0.139  -6.8904  -45.4272  -26.0820
 E9U  C3   C  CR6   0   0.300  -5.8166  -44.7837  -25.4316
 E9U  N    N  N     0  -0.462  -3.8089  -43.4008  -23.9436
 E9U  CA   C  CH1   0  -0.178  -2.8002  -42.6895  -23.1772
 E9U  C    C  C     0   0.549  -1.5271  -43.5076  -23.0562
 E9U  O    O  OH1   0  -0.576  -1.7679  -44.7991  -22.9184
 E9U  CB   C  CH2   0  -0.520  -3.2805  -42.2629  -21.7827
 E9U  CG   C  CH2   0  -0.566  -2.3893  -41.3198  -20.9977
 E9U  SD   S  S2    0  -0.036  -3.2741  -40.7767  -19.4936
 E9U  CE   C  CH2   0  -0.565  -4.2709  -39.4032  -20.1581
 E9U  CZ   C  CH1   0  -0.215  -3.6463  -38.0480  -19.8759
 E9U  CH   C  C     0   0.548  -3.6580  -37.7625  -18.3756
 E9U  NH   N  NH2   0  -0.778  -2.3567  -37.9209  -20.5199
 E9U  C2A  C  CH3   0  -0.722  -6.8161  -45.7126  -27.5482
 E9U  C4   C  CR6   0  -0.001  -5.9045  -44.5438  -24.0588
 E9U  C4A  C  C1    0   0.069  -4.8175  -43.8912  -23.3449
 E9U  C5   C  CR6   0  -0.005  -7.0753  -44.9218  -23.3799
 E9U  C5A  C  CH2   0  -0.319  -7.2735  -44.6706  -21.9131
 E9U  C6   C  CR16  0  -0.146  -8.0715  -45.5303  -24.1130
 E9U  O1P  O  OH1   0  -0.760  -5.7638  -43.0533  -19.6389
 E9U  O2P  O  O     0  -0.690  -7.3595  -41.1196  -20.3580
 E9U  O3   O  OH1   0  -0.621  -4.7586  -44.4333  -26.1541
 E9U  O3P  O  OH1   0  -0.739  -8.1256  -43.4038  -19.2835
 E9U  O4P  O  O2    0  -0.589  -7.2877  -43.2508  -21.6933
 E9U  OT   O  O     0  -0.433  -0.4283  -43.0149  -23.0349
 E9U  OX1  O  O     0  -0.440  -4.3135  -38.3725  -17.5681
 E9U  OX2  O  OH1   0  -0.590  -2.8789  -36.7385  -18.0583
 E9U  P    P  P     0   1.474  -7.1573  -42.5758  -20.2439
 E9U  H1   H  HCH1  0   0.304  -2.5400  -41.7958  -23.7492
 E9U  H2   H  HOH1  0   0.489  -0.9381  -45.2834  -22.7877
 E9U  H3   H  HCH2  0   0.268  -4.2459  -41.7732  -21.9383
 E9U  H4   H  HCH2  0   0.266  -3.4516  -43.1426  -21.1614
 E9U  H5   H  HCH2  0   0.294  -1.4768  -41.8068  -20.6552
 E9U  H6   H  HCH2  0   0.284  -2.1041  -40.4345  -21.5664
 E9U  H7   H  HCH2  0   0.294  -4.3706  -39.5412  -21.2348
 E9U  H8   H  HCH2  0   0.297  -5.2678  -39.4796  -19.7308
 E9U  H9   H  HCH1  0   0.303  -4.3127  -37.2995  -20.3233
 E9U  H10  H  HNH2  0   0.365  -2.0353  -36.9628  -20.4931
 E9U  H11  H  HNH2  0   0.352  -1.6591  -38.4742  -20.0371
 E9U  H13  H  HCH3  0   0.252  -7.7487  -46.1577  -27.8875
 E9U  H14  H  HCH3  0   0.251  -6.6358  -44.8044  -28.1253
 E9U  H15  H  HCH3  0   0.252  -6.0024  -46.4027  -27.7792
 E9U  H16  H  H     0   0.250  -4.9252  -43.8388  -22.2676
 E9U  H17  H  HCH2  0   0.281  -8.2233  -45.1047  -21.5957
 E9U  H18  H  HCH2  0   0.263  -6.4830  -45.1444  -21.3244
 E9U  H19  H  HCR6  0   0.264  -8.9949  -45.8336  -23.6316
 E9U  H20  H  HOH1  0   0.481  -5.0939  -42.3472  -19.5220
 E9U  H21  H  HOH1  0   0.476  -4.1286  -43.9442  -25.5641
 E9U  H22  H  HOH1  0   0.503  -9.0677  -43.3013  -19.4758
 E9U  H23  H  HOH1  0   0.482  -2.9291  -36.5636  -17.1066

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
 E9U  C2A  C2   single    1.496  0.020  1.496
 E9U  O3   C3   single    1.328  0.020  1.328
 E9U  OT   C    double    1.204  0.020  1.204
 E9U  C2   C3   aromatic  1.411  0.020  1.411
 E9U  C2   N1   aromatic  1.318  0.020  1.318
 E9U  C3   C4   aromatic  1.396  0.020  1.396
 E9U  C    O    single    1.321  0.020  1.321
 E9U  C    CA   single    1.518  0.020  1.518
 E9U  N    CA   single    1.453  0.020  1.453
 E9U  N    C4A  double    1.271  0.020  1.271
 E9U  N1   C6   aromatic  1.333  0.020  1.333
 E9U  CA   CB   single    1.535  0.020  1.535
 E9U  C4   C4A  single    1.455  0.020  1.455
 E9U  C4   C5   aromatic  1.405  0.020  1.405
 E9U  O2P  P    double    1.475  0.020  1.475
 E9U  C6   C5   aromatic  1.379  0.020  1.379
 E9U  C5   C5A  single    1.501  0.020  1.501
 E9U  O4P  P    single    1.604  0.020  1.604
 E9U  O4P  C5A  single    1.437  0.020  1.437
 E9U  CB   CG   single    1.517  0.020  1.517
 E9U  P    O1P  single    1.592  0.020  1.592
 E9U  P    O3P  single    1.595  0.020  1.595
 E9U  CG   SD   single    1.828  0.020  1.828
 E9U  SD   CE   single    1.823  0.020  1.823
 E9U  CE   CZ   single    1.519  0.020  1.519
 E9U  NH   CZ   single    1.447  0.020  1.447
 E9U  CZ   CH   single    1.527  0.020  1.527
 E9U  CH   OX1  double    1.206  0.020  1.206
 E9U  CH   OX2  single    1.325  0.020  1.325
 E9U  CA   H1   single    0.970  0.020  1.090
 E9U  O    H2   single    0.850  0.020  0.980
 E9U  CB   H3   single    0.970  0.020  1.090
 E9U  CB   H4   single    0.970  0.020  1.090
 E9U  CG   H5   single    0.970  0.020  1.090
 E9U  CG   H6   single    0.970  0.020  1.090
 E9U  CE   H7   single    0.970  0.020  1.090
 E9U  CE   H8   single    0.970  0.020  1.090
 E9U  CZ   H9   single    0.970  0.020  1.090
 E9U  NH   H10  single    0.890  0.020  1.040
 E9U  NH   H11  single    0.890  0.020  1.040
 E9U  C2A  H13  single    0.970  0.020  1.090
 E9U  C2A  H14  single    0.970  0.020  1.090
 E9U  C2A  H15  single    0.970  0.020  1.090
 E9U  C4A  H16  single    0.930  0.020  1.080
 E9U  C5A  H17  single    0.970  0.020  1.090
 E9U  C5A  H18  single    0.970  0.020  1.090
 E9U  C6   H19  single    0.930  0.020  1.080
 E9U  O1P  H20  single    0.850  0.020  0.980
 E9U  O3   H21  single    0.850  0.020  0.980
 E9U  O3P  H22  single    0.850  0.020  0.980
 E9U  OX2  H23  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
 E9U  C6   N1   C2   120.17  3.000
 E9U  C2A  C2   C3   120.08  3.000
 E9U  C3   C2   N1   121.05  3.000
 E9U  C2A  C2   N1   118.86  3.000
 E9U  O3   C3   C4   122.66  3.000
 E9U  C4   C3   C2   118.93  3.000
 E9U  O3   C3   C2   118.42  3.000
 E9U  C4A  N    CA   119.43  3.000
 E9U  H1   CA   CB   108.83  3.000
 E9U  H1   CA   C    106.43  3.000
 E9U  CB   CA   C    109.86  3.000
 E9U  H1   CA   N    106.84  3.000
 E9U  CB   CA   N    113.45  3.000
 E9U  C    CA   N    111.13  3.000
 E9U  OT   C    O    124.36  3.000
 E9U  O    C    CA   112.48  3.000
 E9U  OT   C    CA   123.10  3.000
 E9U  H2   O    C    110.27  3.000
 E9U  H4   CB   H3   107.69  3.000
 E9U  H4   CB   CG   107.40  3.000
 E9U  H3   CB   CG   108.29  3.000
 E9U  H4   CB   CA   110.03  3.000
 E9U  H3   CB   CA   105.74  3.000
 E9U  CG   CB   CA   117.33  3.000
 E9U  H6   CG   H5   107.93  3.000
 E9U  H6   CG   SD   108.34  3.000
 E9U  H5   CG   SD   106.23  3.000
 E9U  H6   CG   CB   112.88  3.000
 E9U  H5   CG   CB   112.14  3.000
 E9U  SD   CG   CB   109.05  3.000
 E9U  CE   SD   CG   100.87  3.000
 E9U  H8   CE   H7   107.18  3.000
 E9U  H8   CE   CZ   111.52  3.000
 E9U  H7   CE   CZ   109.52  3.000
 E9U  H8   CE   SD   107.77  3.000
 E9U  H7   CE   SD   108.35  3.000
 E9U  CZ   CE   SD   112.32  3.000
 E9U  H9   CZ   NH   107.45  3.000
 E9U  H9   CZ   CH   105.57  3.000
 E9U  NH   CZ   CH   115.31  3.000
 E9U  H9   CZ   CE   106.44  3.000
 E9U  CH   CZ   CE   110.26  3.000
 E9U  NH   CZ   CE   111.24  3.000
 E9U  OX2  CH   OX1  123.38  3.000
 E9U  OX2  CH   CZ   112.03  3.000
 E9U  OX1  CH   CZ   124.57  3.000
 E9U  H11  NH   H10  106.63  3.000
 E9U  H11  NH   CZ   110.72  3.000
 E9U  H10  NH   CZ   110.78  3.000
 E9U  H15  C2A  H14  106.92  3.000
 E9U  H15  C2A  H13  108.33  3.000
 E9U  H14  C2A  H13  108.51  3.000
 E9U  H15  C2A  C2   111.41  3.000
 E9U  H14  C2A  C2   111.59  3.000
 E9U  H13  C2A  C2   109.96  3.000
 E9U  C5   C4   C4A  120.40  3.000
 E9U  C5   C4   C3   118.77  3.000
 E9U  C4A  C4   C3   120.82  3.000
 E9U  H16  C4A  C4   115.79  3.000
 E9U  H16  C4A  N    121.89  3.000
 E9U  C4   C4A  N    122.32  3.000
 E9U  C6   C5   C5A  119.87  3.000
 E9U  C5A  C5   C4   122.49  3.000
 E9U  C6   C5   C4   117.64  3.000
 E9U  H18  C5A  H17  107.47  3.000
 E9U  H18  C5A  O4P  110.67  3.000
 E9U  H17  C5A  O4P  109.87  3.000
 E9U  H18  C5A  C5   110.98  3.000
 E9U  H17  C5A  C5   109.42  3.000
 E9U  O4P  C5A  C5   108.43  3.000
 E9U  H19  C6   C5   120.17  3.000
 E9U  H19  C6   N1   116.41  3.000
 E9U  C5   C6   N1   123.42  3.000
 E9U  H20  O1P  P    115.30  3.000
 E9U  H21  O3   C3   108.20  3.000
 E9U  H22  O3P  P    114.62  3.000
 E9U  P    O4P  C5A  123.59  3.000
 E9U  H23  OX2  CH   110.13  3.000
 E9U  O4P  P    O3P  106.03  3.000
 E9U  O3P  P    O2P  118.42  3.000
 E9U  O4P  P    O2P  109.54  3.000
 E9U  O3P  P    O1P   98.44  3.000
 E9U  O4P  P    O1P  106.75  3.000
 E9U  O2P  P    O1P  116.45  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
 E9U  CONST_01  C4   C3   C2   N1      0.00   0.0  0
 E9U  CONST_02  C4   C5   C6   N1      0.00   0.0  0
 E9U  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 E9U  CONST_04  C5   C6   N1   C2      0.00   0.0  0
 E9U  CONST_05  C6   N1   C2   C3      0.00   0.0  0
 E9U  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 E9U  CONST_07  O3   C3   C2   N1    180.00   0.0  0
 E9U  CONST_08  C5A  C5   C6   N1    180.00   0.0  0
 E9U  CONST_09  C4A  C4   C3   C2    180.00   0.0  0
 E9U  CONST_10  C5A  C5   C4   C3    180.00   0.0  0
 E9U  CONST_11  C4   C3   C2   C2A   180.00   0.0  0
 E9U  CONST_12  C6   N1   C2   C2A   180.00   0.0  0
 E9U  CONST_13  C6   C5   C4   C4A   180.00   0.0  0
 E9U  CONST_14  O3   C3   C4   C5    180.00   0.0  0
 E9U  CONST_15  H19  C6   N1   C2    180.00   0.0  0
 E9U  CONST_16  H2   O    C    CA    180.00   0.0  0
 E9U  CONST_17  H23  OX2  CH   CZ    180.00   0.0  0
 E9U  Var_01    N    C4A  C4   C3      6.81  30.0  2
 E9U  Var_02    O4P  C5A  C5   C4     63.80  30.0  2
 E9U  Var_03    H13  C2A  C2   N1      2.92  30.0  2
 E9U  Var_04    C4   C4A  N    CA    176.18   0.0  2
 E9U  Var_05    SD   CG   CB   CA    172.06  30.0  3
 E9U  Var_06    CZ   CE   SD   CG    -99.34  30.0  3
 E9U  Var_07    O2P  P    O4P  C5A  -173.72  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
 E9U  chir_01  CA  C   N   CB  negativ
 E9U  chir_02  CZ  NH  CE  CH  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
 E9U  plan-1  N1   0.020
 E9U  plan-1  C2   0.020
 E9U  plan-1  C3   0.020
 E9U  plan-1  C2A  0.020
 E9U  plan-1  C4   0.020
 E9U  plan-1  C4A  0.020
 E9U  plan-1  C5   0.020
 E9U  plan-1  C5A  0.020
 E9U  plan-1  C6   0.020
 E9U  plan-1  O3   0.020
 E9U  plan-1  H19  0.020
 E9U  plan-2  CA   0.020
 E9U  plan-2  C    0.020
 E9U  plan-2  O    0.020
 E9U  plan-2  OT   0.020
 E9U  plan-2  H2   0.020
 E9U  plan-3  CZ   0.020
 E9U  plan-3  CH   0.020
 E9U  plan-3  OX1  0.020
 E9U  plan-3  OX2  0.020
 E9U  plan-3  H23  0.020
 E9U  plan-4  N    0.020
 E9U  plan-4  CA   0.020
 E9U  plan-4  C4   0.020
 E9U  plan-4  C4A  0.020
 E9U  plan-4  H16  0.020

