# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 10:12:55 2021
#   Inital geometry file: a 131 line input string
#   Ligand name: (2~{S})-2-azanyl-4-[(3~{S})-3-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonomethyl)pyridin-4-yl]methylideneamino]-4-oxidanyl-4-oxidanylidene-butyl]sulfanyl-butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(C[P](O)(O)=O)c(C=N[C@@H](CCSCC[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
 EBO  EBO  '(2~{S})-2-azanyl-4-[(3~{S})-3-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonomethyl)pyridin-4-yl]methylideneamino]-4-oxidanyl-4-oxidanylidene-butyl]sulfanyl-butanoic acid'  ligand  53  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_EBO
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
 EBO  O6   O  OH1   0  -0.615  -23.4891  54.8902  -18.1170
 EBO  C15  C  C     0   0.595  -23.5635  54.9800  -19.4447
 EBO  O5   O  O     0  -0.421  -22.8227  55.6669  -20.0946
 EBO  C8   C  CH1   0  -0.276  -24.6264  54.0674  -20.0308
 EBO  C9   C  CH2   0  -0.423  -25.1542  54.5938  -21.3659
 EBO  C10  C  CH2   0  -0.548  -26.0233  55.8359  -21.2281
 EBO  S    S  S2    0  -0.041  -26.4958  56.4025  -22.8848
 EBO  C11  C  CH2   0  -0.542  -27.5388  57.8227  -22.4441
 EBO  C12  C  CH2   0  -0.468  -28.0387  58.5316  -23.6933
 EBO  C13  C  CH1   0  -0.172  -28.9760  57.7293  -24.6113
 EBO  C14  C  C     0   0.536  -30.3031  57.5204  -23.9083
 EBO  O4   O  O     0  -0.437  -31.2422  58.2717  -23.9768
 EBO  O3   O  OH1   0  -0.587  -30.3066  56.4139  -23.1741
 EBO  N2   N  NH2   0  -0.798  -29.1950  58.5035  -25.8168
 EBO  N1   N  N     0  -0.300  -25.7162  53.9037  -19.1006
 EBO  C7   C  C1    0  -0.083  -26.0778  52.7283  -18.8277
 EBO  C3   C  CR6   0   0.004  -27.2297  52.4591  -17.9394
 EBO  C2   C  CR6   0   0.274  -28.5183  52.8119  -18.3273
 EBO  O7   O  OH1   0  -0.604  -28.6787  53.4275  -19.5100
 EBO  C4   C  CR6   0   0.051  -27.0505  51.8022  -16.7219
 EBO  C6   C  CH2   0  -0.866  -25.6839  51.4418  -16.2268
 EBO  P    P  P     0   1.358  -24.8821  52.7663  -15.2794
 EBO  O2   O  OH1   0  -0.742  -25.7917  52.7967  -13.9611
 EBO  O1   O  O     0  -0.709  -23.4261  52.5610  -15.0815
 EBO  O    O  OH1   0  -0.766  -25.2847  54.1563  -15.9692
 EBO  C5   C  CR16  0  -0.128  -28.1776  51.5399  -15.9587
 EBO  N    N  N     0  -0.404  -29.4043  51.8728  -16.3339
 EBO  C1   C  CR6   0   0.126  -29.5958  52.4967  -17.4865
 EBO  C    C  CH3   0  -0.784  -30.9986  52.8501  -17.8804
 EBO  H1   H  HOH1  0   0.497  -22.7676  55.4459  -17.7807
 EBO  H2   H  HCH1  0   0.296  -24.1091  53.1144  -20.2343
 EBO  H3   H  HCH2  0   0.262  -25.7350  53.7937  -21.8290
 EBO  H4   H  HCH2  0   0.257  -24.3067  54.7881  -22.0251
 EBO  H5   H  HCH2  0   0.262  -25.4909  56.6398  -20.7156
 EBO  H6   H  HCH2  0   0.271  -26.9230  55.6072  -20.6565
 EBO  H7   H  HCH2  0   0.275  -26.9417  58.5219  -21.8567
 EBO  H8   H  HCH2  0   0.266  -28.3603  57.4835  -21.8117
 EBO  H9   H  HCH2  0   0.258  -27.1762  58.8378  -24.2921
 EBO  H10  H  HCH2  0   0.261  -28.5461  59.4526  -23.3952
 EBO  H11  H  HCH1  0   0.248  -28.5332  56.7416  -24.7976
 EBO  H12  H  HOH1  0   0.479  -31.1439  56.3420  -22.6909
 EBO  H13  H  HNH2  0   0.354  -28.3058  58.6309  -26.2839
 EBO  H14  H  HNH2  0   0.353  -29.7753  57.9885  -26.4673
 EBO  H16  H  H     0   0.267  -25.5629  51.8481  -19.2322
 EBO  H17  H  HOH1  0   0.487  -29.6123  53.5516  -19.7143
 EBO  H18  H  HCH2  0   0.310  -25.0066  51.1855  -17.0453
 EBO  H19  H  HCH2  0   0.324  -25.7177  50.5618  -15.5801
 EBO  H20  H  HOH1  0   0.497  -25.4727  53.3944  -13.2708
 EBO  H21  H  HOH1  0   0.497  -24.7479  54.4079  -16.7401
 EBO  H22  H  HCR6  0   0.259  -28.0823  51.0321  -15.0048
 EBO  H23  H  HCH3  0   0.273  -31.6903  52.5377  -17.1017
 EBO  H24  H  HCH3  0   0.261  -31.1257  53.9255  -18.0266
 EBO  H25  H  HCH3  0   0.258  -31.3010  52.3552  -18.8073

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
 EBO  N2   C13  single    1.449  0.020  1.449
 EBO  O4   C14  double    1.205  0.020  1.205
 EBO  C13  C14  single    1.516  0.020  1.516
 EBO  C13  C12  single    1.538  0.020  1.538
 EBO  C14  O3   single    1.328  0.020  1.328
 EBO  C12  C11  single    1.521  0.020  1.521
 EBO  C11  S    single    1.816  0.020  1.816
 EBO  S    C10  single    1.813  0.020  1.813
 EBO  C10  C9   single    1.522  0.020  1.522
 EBO  C9   C8   single    1.529  0.020  1.529
 EBO  O1   P    double    1.484  0.020  1.484
 EBO  O    P    single    1.603  0.020  1.603
 EBO  P    O2   single    1.602  0.020  1.602
 EBO  P    C6   single    1.815  0.020  1.815
 EBO  O5   C15  double    1.201  0.020  1.201
 EBO  C8   C15  single    1.519  0.020  1.519
 EBO  C8   N1   single    1.442  0.020  1.442
 EBO  C15  O6   single    1.333  0.020  1.333
 EBO  C6   C4   single    1.498  0.020  1.498
 EBO  C7   N1   double    1.260  0.020  1.260
 EBO  C7   C3   single    1.479  0.020  1.479
 EBO  C4   C3   aromatic  1.395  0.020  1.395
 EBO  C4   C5   aromatic  1.386  0.020  1.386
 EBO  C3   C2   aromatic  1.391  0.020  1.391
 EBO  C5   N    aromatic  1.325  0.020  1.325
 EBO  C2   O7   single    1.343  0.020  1.343
 EBO  C2   C1   aromatic  1.403  0.020  1.403
 EBO  N    C1   aromatic  1.324  0.020  1.324
 EBO  C1   C    single    1.499  0.020  1.499
 EBO  O6   H1   single    0.850  0.020  0.980
 EBO  C8   H2   single    0.970  0.020  1.090
 EBO  C9   H3   single    0.970  0.020  1.090
 EBO  C9   H4   single    0.970  0.020  1.090
 EBO  C10  H5   single    0.970  0.020  1.090
 EBO  C10  H6   single    0.970  0.020  1.090
 EBO  C11  H7   single    0.970  0.020  1.090
 EBO  C11  H8   single    0.970  0.020  1.090
 EBO  C12  H9   single    0.970  0.020  1.090
 EBO  C12  H10  single    0.970  0.020  1.090
 EBO  C13  H11  single    0.970  0.020  1.090
 EBO  O3   H12  single    0.850  0.020  0.980
 EBO  N2   H13  single    0.890  0.020  1.040
 EBO  N2   H14  single    0.890  0.020  1.040
 EBO  C7   H16  single    0.930  0.020  1.080
 EBO  O7   H17  single    0.850  0.020  0.980
 EBO  C6   H18  single    0.970  0.020  1.090
 EBO  C6   H19  single    0.970  0.020  1.090
 EBO  O2   H20  single    0.850  0.020  0.980
 EBO  O    H21  single    0.850  0.020  0.980
 EBO  C5   H22  single    0.930  0.020  1.080
 EBO  C    H23  single    0.970  0.020  1.090
 EBO  C    H24  single    0.970  0.020  1.090
 EBO  C    H25  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
 EBO  H1   O6   C15  110.37  3.000
 EBO  C8   C15  O5   124.51  3.000
 EBO  C8   C15  O6   112.52  3.000
 EBO  O5   C15  O6   122.89  3.000
 EBO  H2   C8   N1   112.04  3.000
 EBO  H2   C8   C9   107.35  3.000
 EBO  N1   C8   C9   109.96  3.000
 EBO  H2   C8   C15  105.20  3.000
 EBO  N1   C8   C15  110.38  3.000
 EBO  C9   C8   C15  111.82  3.000
 EBO  H4   C9   H3   106.71  3.000
 EBO  H4   C9   C10  110.66  3.000
 EBO  H3   C9   C10  109.43  3.000
 EBO  H4   C9   C8   108.71  3.000
 EBO  H3   C9   C8   107.56  3.000
 EBO  C10  C9   C8   113.51  3.000
 EBO  H6   C10  H5   108.10  3.000
 EBO  H6   C10  S    109.24  3.000
 EBO  H5   C10  S    109.01  3.000
 EBO  H6   C10  C9   110.33  3.000
 EBO  H5   C10  C9   111.40  3.000
 EBO  S    C10  C9   108.73  3.000
 EBO  C11  S    C10   99.92  3.000
 EBO  H8   C11  H7   107.42  3.000
 EBO  H8   C11  C12  111.94  3.000
 EBO  H7   C11  C12  108.87  3.000
 EBO  H8   C11  S    109.27  3.000
 EBO  H7   C11  S    108.51  3.000
 EBO  C12  C11  S    110.73  3.000
 EBO  H10  C12  H9   106.23  3.000
 EBO  H10  C12  C13  108.63  3.000
 EBO  H9   C12  C13  107.45  3.000
 EBO  H10  C12  C11  108.75  3.000
 EBO  H9   C12  C11  108.73  3.000
 EBO  C13  C12  C11  116.58  3.000
 EBO  H11  C13  N2   113.59  3.000
 EBO  H11  C13  C14  107.92  3.000
 EBO  N2   C13  C14  109.09  3.000
 EBO  H11  C13  C12  108.94  3.000
 EBO  C14  C13  C12  109.18  3.000
 EBO  N2   C13  C12  108.06  3.000
 EBO  O3   C14  O4   123.30  3.000
 EBO  O3   C14  C13  111.93  3.000
 EBO  O4   C14  C13  124.76  3.000
 EBO  H12  O3   C14  109.86  3.000
 EBO  H14  N2   H13  105.73  3.000
 EBO  H14  N2   C13  110.44  3.000
 EBO  H13  N2   C13  108.56  3.000
 EBO  C7   N1   C8   117.55  3.000
 EBO  H16  C7   C3   116.16  3.000
 EBO  H16  C7   N1   122.28  3.000
 EBO  C3   C7   N1   121.56  3.000
 EBO  C4   C3   C2   118.80  3.000
 EBO  C2   C3   C7   120.51  3.000
 EBO  C4   C3   C7   120.64  3.000
 EBO  C1   C2   O7   122.63  3.000
 EBO  C1   C2   C3   119.17  3.000
 EBO  O7   C2   C3   118.20  3.000
 EBO  H17  O7   C2   111.19  3.000
 EBO  C5   C4   C6   120.96  3.000
 EBO  C5   C4   C3   117.72  3.000
 EBO  C6   C4   C3   121.27  3.000
 EBO  H19  C6   H18  105.88  3.000
 EBO  H19  C6   P    107.01  3.000
 EBO  H18  C6   P    106.76  3.000
 EBO  H19  C6   C4   111.18  3.000
 EBO  H18  C6   C4   111.98  3.000
 EBO  P    C6   C4   113.58  3.000
 EBO  O    P    O1   115.08  3.000
 EBO  O    P    O2   101.25  3.000
 EBO  O1   P    O2   116.75  3.000
 EBO  O2   P    C6   101.10  3.000
 EBO  O    P    C6   107.29  3.000
 EBO  O1   P    C6   113.71  3.000
 EBO  H20  O2   P    114.31  3.000
 EBO  H21  O    P    115.26  3.000
 EBO  H22  C5   N    116.61  3.000
 EBO  H22  C5   C4   120.08  3.000
 EBO  N    C5   C4   123.31  3.000
 EBO  C1   N    C5   119.90  3.000
 EBO  C    C1   N    118.35  3.000
 EBO  C    C1   C2   120.55  3.000
 EBO  N    C1   C2   121.10  3.000
 EBO  H25  C    H24  107.45  3.000
 EBO  H25  C    H23  107.53  3.000
 EBO  H24  C    H23  107.73  3.000
 EBO  H25  C    C1   112.01  3.000
 EBO  H24  C    C1   112.08  3.000
 EBO  H23  C    C1   109.83  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
 EBO  CONST_01  N    C5   C4   C3      0.00   0.0  0
 EBO  CONST_02  N    C1   C2   C3      0.00   0.0  0
 EBO  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 EBO  CONST_04  C5   N    C1   C2      0.00   0.0  0
 EBO  CONST_05  C1   C2   C3   C4      0.00   0.0  0
 EBO  CONST_06  C1   N    C5   C4      0.00   0.0  0
 EBO  CONST_07  C5   C4   C3   C7    180.00   0.0  0
 EBO  CONST_08  C1   C2   C3   C7    180.00   0.0  0
 EBO  CONST_09  C    C1   C2   C3    180.00   0.0  0
 EBO  CONST_10  C6   C4   C3   C2    180.00   0.0  0
 EBO  CONST_11  C4   C3   C2   O7    180.00   0.0  0
 EBO  CONST_12  N    C1   C2   O7    180.00   0.0  0
 EBO  CONST_13  N    C5   C4   C6    180.00   0.0  0
 EBO  CONST_14  C    C1   N    C5    180.00   0.0  0
 EBO  CONST_15  H22  C5   C4   C3    180.00   0.0  0
 EBO  CONST_16  H1   O6   C15  O5      0.00   0.0  0
 EBO  CONST_17  H12  O3   C14  C13   180.00   0.0  0
 EBO  Var_01    C4   C3   C7   N1   -116.30  30.0  2
 EBO  Var_02    P    C6   C4   C3     87.14  30.0  3
 EBO  Var_03    H23  C    C1   C2   -179.38  30.0  2
 EBO  Var_04    C3   C7   N1   C8   -176.83   0.0  2
 EBO  Var_05    O1   P    C6   C4   -165.42  30.0  2
 EBO  Var_06    S    C10  C9   C8    176.73  30.0  1
 EBO  Var_07    C12  C11  S    C10   177.87  30.0  1
 EBO  Var_08    C13  C12  C11  S      64.42  30.0  2

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
 EBO  chir_01  C8   C9  C15  N1   negativ
 EBO  chir_02  C13  N2  C14  C12  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
 EBO  plan-1  C7   0.020
 EBO  plan-1  C3   0.020
 EBO  plan-1  C2   0.020
 EBO  plan-1  O7   0.020
 EBO  plan-1  C4   0.020
 EBO  plan-1  C6   0.020
 EBO  plan-1  C5   0.020
 EBO  plan-1  N    0.020
 EBO  plan-1  C1   0.020
 EBO  plan-1  C    0.020
 EBO  plan-1  H22  0.020
 EBO  plan-2  O6   0.020
 EBO  plan-2  C15  0.020
 EBO  plan-2  O5   0.020
 EBO  plan-2  C8   0.020
 EBO  plan-2  H1   0.020
 EBO  plan-3  C13  0.020
 EBO  plan-3  C14  0.020
 EBO  plan-3  O4   0.020
 EBO  plan-3  O3   0.020
 EBO  plan-3  H12  0.020
 EBO  plan-4  C8   0.020
 EBO  plan-4  N1   0.020
 EBO  plan-4  C7   0.020
 EBO  plan-4  C3   0.020
 EBO  plan-4  H16  0.020

