# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jul 20 23:57:07 2021
#   Inital geometry file: a 120 line input string
#   Ligand name: [(4~{Z})-4-[[(~{Z})-2-(4-hydroxyphenyl)ethylideneamino]methylidene]-6-methyl-5-oxidanyl-1~{H}-pyridin-3-yl]methyl dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=C(O)\C(=C/N=CCc2ccc(O)cc2)C(=CN1)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
 EBR  EBR  '[(4~{Z})-4-[[(~{Z})-2-(4-hydroxyphenyl)ethylideneamino]methylidene]-6-methyl-5-oxidanyl-1~{H}-pyridin-3-yl]methyl dihydrogen phosphate'  ligand  44  25  .  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_EBR
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
 EBR  CA   C  C1    0  -0.050  -15.4973  -21.9531  -14.2062
 EBR  CB   C  CH2   0  -0.608  -14.8429  -22.0043  -12.8531
 EBR  CG   C  CR6   0   0.102  -13.3438  -22.0365  -12.9343
 EBR  CD1  C  CR16  0  -0.306  -12.5722  -20.9417  -12.5645
 EBR  CD2  C  CR16  0  -0.283  -12.6793  -23.1677  -13.4065
 EBR  CE1  C  CR16  0  -0.368  -11.1864  -20.9656  -12.6541
 EBR  CE2  C  CR16  0  -0.323  -11.2987  -23.2096  -13.5054
 EBR  CZ   C  CR6   0   0.337  -10.5404  -22.1032  -13.1265
 EBR  NH   N  N     0  -0.461  -16.7590  -21.9263  -14.4149
 EBR  OH   O  OH1   0  -0.635   -9.1980  -22.1900  -13.2357
 EBR  C1   C  CR6   0   0.209  -20.8900  -21.9363  -15.2945
 EBR  C2A  C  CH3   0  -0.720  -21.4472  -21.9362  -16.6800
 EBR  C3   C  CR6   0   0.232  -19.5525  -21.9236  -15.0370
 EBR  C4   C  CR6   0   0.058  -19.0353  -21.9241  -13.6821
 EBR  C4A  C  C1    0  -0.151  -17.6869  -21.9219  -13.3981
 EBR  C5   C  CR6   0  -0.086  -20.0417  -21.9399  -12.6468
 EBR  C5A  C  CH2   0  -0.310  -19.6630  -21.9435  -11.2065
 EBR  C6   C  CR16  0  -0.017  -21.3617  -21.9492  -12.9713
 EBR  N1   N  NR16  0  -0.653  -21.7737  -21.9501  -14.2481
 EBR  O1P  O  O     0  -0.701  -16.8318  -21.2322   -9.8712
 EBR  O2P  O  OH1   0  -0.738  -18.9192  -20.7203   -8.3890
 EBR  O3P  O  OH1   0  -0.729  -17.9005  -18.8588   -9.6989
 EBR  O4P  O  O2    0  -0.583  -19.1798  -20.6319  -10.8428
 EBR  P    P  P     0   1.452  -18.0726  -20.4445   -9.7128
 EBR  H1   H  H     0   0.240  -14.8522  -21.9456  -15.0808
 EBR  H2   H  HCH2  0   0.270  -15.1716  -21.1511  -12.2497
 EBR  H3   H  HCH2  0   0.265  -15.2105  -22.8869  -12.3147
 EBR  H4   H  HCR6  0   0.252  -13.0560  -20.0458  -12.1938
 EBR  H5   H  HCR6  0   0.250  -13.2495  -24.0407  -13.7032
 EBR  H6   H  HCR6  0   0.268  -10.6137  -20.0957  -12.3520
 EBR  H7   H  HCR6  0   0.261  -10.8046  -24.1006  -13.8725
 EBR  H8   H  HOH1  0   0.473   -8.7846  -21.3738  -12.9333
 EBR  H10  H  HCH3  0   0.252  -22.5364  -21.9562  -16.6704
 EBR  H11  H  HCH3  0   0.260  -21.1372  -21.0481  -17.2314
 EBR  H12  H  HCH3  0   0.259  -21.1045  -22.8037  -17.2447
 EBR  H13  H  H     0   0.240  -17.3468  -21.9061  -12.3694
 EBR  H15  H  HCH2  0   0.268  -20.5276  -22.1774  -10.5832
 EBR  H16  H  HCH2  0   0.245  -18.8957  -22.6979  -11.0091
 EBR  H17  H  HCR6  0   0.305  -22.1403  -21.9605  -12.2221
 EBR  H18  H  HOH1  0   0.500  -18.3850  -20.8506   -7.5940
 EBR  H19  H  HOH1  0   0.500  -17.1510  -18.5386  -10.2177
 EBR  H9   H  HNR6  0   0.423  -22.7616  -21.9629  -14.4438
 EBR  H14  H  HOH1  0   0.462  -17.7852  -21.9110  -15.7101
 EBR  O3   O  OH1   0  -0.660  -18.7109  -21.9106  -16.0849

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
 EBR  C2A  C1   single    1.493  0.020  1.493
 EBR  O3   C3   single    1.344  0.020  1.344
 EBR  C1   C3   double    1.362  0.020  1.362
 EBR  C1   N1   single    1.370  0.020  1.370
 EBR  C3   C4   single    1.450  0.020  1.450
 EBR  NH   CA   double    1.279  0.020  1.279
 EBR  NH   C4A  single    1.377  0.020  1.377
 EBR  N1   C6   single    1.342  0.020  1.342
 EBR  CA   CB   single    1.504  0.020  1.504
 EBR  C4   C4A  double    1.378  0.020  1.378
 EBR  C4   C5   single    1.444  0.020  1.444
 EBR  CE2  CD2  aromatic  1.385  0.020  1.385
 EBR  CE2  CZ   aromatic  1.394  0.020  1.394
 EBR  CD2  CG   aromatic  1.394  0.020  1.394
 EBR  CZ   OH   single    1.350  0.020  1.350
 EBR  CZ   CE1  aromatic  1.391  0.020  1.391
 EBR  CG   CD1  aromatic  1.389  0.020  1.389
 EBR  CG   CB   single    1.502  0.020  1.502
 EBR  C6   C5   double    1.359  0.020  1.359
 EBR  CE1  CD1  aromatic  1.389  0.020  1.389
 EBR  C5   C5A  single    1.489  0.020  1.489
 EBR  C5A  O4P  single    1.444  0.020  1.444
 EBR  O4P  P    single    1.593  0.020  1.593
 EBR  O1P  P    double    1.478  0.020  1.478
 EBR  P    O3P  single    1.595  0.020  1.595
 EBR  P    O2P  single    1.595  0.020  1.595
 EBR  CA   H1   single    0.930  0.020  1.080
 EBR  CB   H2   single    0.970  0.020  1.090
 EBR  CB   H3   single    0.970  0.020  1.090
 EBR  CD1  H4   single    0.930  0.020  1.080
 EBR  CD2  H5   single    0.930  0.020  1.080
 EBR  CE1  H6   single    0.930  0.020  1.080
 EBR  CE2  H7   single    0.930  0.020  1.080
 EBR  OH   H8   single    0.850  0.020  0.980
 EBR  C2A  H10  single    0.970  0.020  1.090
 EBR  C2A  H11  single    0.970  0.020  1.090
 EBR  C2A  H12  single    0.970  0.020  1.090
 EBR  C4A  H13  single    0.930  0.020  1.080
 EBR  C5A  H15  single    0.970  0.020  1.090
 EBR  C5A  H16  single    0.970  0.020  1.090
 EBR  C6   H17  single    0.930  0.020  1.080
 EBR  O2P  H18  single    0.850  0.020  0.980
 EBR  O3P  H19  single    0.850  0.020  0.980
 EBR  N1   H9   single    0.860  0.020  1.020
 EBR  O3   H14  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
 EBR  H1   CA   NH   117.01  3.000
 EBR  H1   CA   CB   117.77  3.000
 EBR  NH   CA   CB   125.22  3.000
 EBR  H3   CB   H2   104.81  3.000
 EBR  H3   CB   CG   110.10  3.000
 EBR  H2   CB   CG   110.24  3.000
 EBR  H3   CB   CA   108.85  3.000
 EBR  H2   CB   CA   109.79  3.000
 EBR  CG   CB   CA   112.74  3.000
 EBR  CD2  CG   CD1  117.69  3.000
 EBR  CD1  CG   CB   121.54  3.000
 EBR  CD2  CG   CB   120.76  3.000
 EBR  H4   CD1  CE1  118.80  3.000
 EBR  H4   CD1  CG   119.64  3.000
 EBR  CE1  CD1  CG   121.55  3.000
 EBR  H5   CD2  CE2  118.71  3.000
 EBR  H5   CD2  CG   119.70  3.000
 EBR  CE2  CD2  CG   121.59  3.000
 EBR  H6   CE1  CZ   120.36  3.000
 EBR  H6   CE1  CD1  119.68  3.000
 EBR  CZ   CE1  CD1  119.96  3.000
 EBR  H7   CE2  CZ   119.80  3.000
 EBR  H7   CE2  CD2  120.27  3.000
 EBR  CZ   CE2  CD2  119.93  3.000
 EBR  OH   CZ   CE2  117.91  3.000
 EBR  OH   CZ   CE1  122.82  3.000
 EBR  CE2  CZ   CE1  119.27  3.000
 EBR  C4A  NH   CA   122.99  3.000
 EBR  H8   OH   CZ   110.30  3.000
 EBR  N1   C1   C3   119.29  3.000
 EBR  N1   C1   C2A  117.91  3.000
 EBR  C3   C1   C2A  122.80  3.000
 EBR  H12  C2A  H11  107.26  3.000
 EBR  H12  C2A  H10  107.71  3.000
 EBR  H11  C2A  H10  107.67  3.000
 EBR  H12  C2A  C1   111.30  3.000
 EBR  H11  C2A  C1   111.30  3.000
 EBR  H10  C2A  C1   111.40  3.000
 EBR  O3   C3   C4   120.34  3.000
 EBR  C4   C3   C1   121.79  3.000
 EBR  O3   C3   C1   117.87  3.000
 EBR  C5   C4   C4A  122.29  3.000
 EBR  C5   C4   C3   114.92  3.000
 EBR  C4A  C4   C3   122.79  3.000
 EBR  H13  C4A  C4   120.19  3.000
 EBR  H13  C4A  NH   119.32  3.000
 EBR  C4   C4A  NH   120.49  3.000
 EBR  C6   C5   C5A  118.54  3.000
 EBR  C5A  C5   C4   121.08  3.000
 EBR  C6   C5   C4   120.38  3.000
 EBR  H16  C5A  H15  107.76  3.000
 EBR  H16  C5A  O4P  110.25  3.000
 EBR  H15  C5A  O4P  108.41  3.000
 EBR  H16  C5A  C5   110.77  3.000
 EBR  H15  C5A  C5   110.57  3.000
 EBR  O4P  C5A  C5   109.05  3.000
 EBR  H17  C6   N1   116.01  3.000
 EBR  H17  C6   C5   122.29  3.000
 EBR  N1   C6   C5   121.70  3.000
 EBR  H9   N1   C6   119.09  3.000
 EBR  H9   N1   C1   118.98  3.000
 EBR  C6   N1   C1   121.93  3.000
 EBR  H18  O2P  P    114.36  3.000
 EBR  H19  O3P  P    114.11  3.000
 EBR  P    O4P  C5A  121.20  3.000
 EBR  O4P  P    O3P  101.43  3.000
 EBR  O3P  P    O2P  102.82  3.000
 EBR  O4P  P    O2P  101.50  3.000
 EBR  O2P  P    O1P  116.24  3.000
 EBR  O3P  P    O1P  116.11  3.000
 EBR  O4P  P    O1P  116.40  3.000
 EBR  H14  O3   C3   106.73  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
 EBR  CONST_01  CZ   CE2  CD2  CG      0.00   0.0  0
 EBR  CONST_02  CZ   CE1  CD1  CG      0.00   0.0  0
 EBR  CONST_03  CE2  CD2  CG   CD1     0.00   0.0  0
 EBR  CONST_04  CE2  CZ   CE1  CD1     0.00   0.0  0
 EBR  CONST_05  CE1  CZ   CE2  CD2     0.00   0.0  0
 EBR  CONST_06  CE1  CD1  CG   CD2     0.00   0.0  0
 EBR  CONST_07  CE2  CD2  CG   CB    180.00   0.0  0
 EBR  CONST_08  CE1  CD1  CG   CB    180.00   0.0  0
 EBR  CONST_09  OH   CZ   CE1  CD1   180.00   0.0  0
 EBR  CONST_10  OH   CZ   CE2  CD2   180.00   0.0  0
 EBR  CONST_11  H7   CE2  CD2  CG    180.00   0.0  0
 EBR  CONST_12  H6   CE1  CD1  CG    180.00   0.0  0
 EBR  CONST_13  H5   CD2  CG   CD1   180.00   0.0  0
 EBR  CONST_14  H4   CD1  CG   CD2   180.00   0.0  0
 EBR  Var_01    C3   C4   C4A  NH     -0.35   0.0  2
 EBR  Var_02    CD2  CG   CB   CA    -70.28  30.0  2
 EBR  Var_03    O4P  C5A  C5   C4     73.42  30.0  3
 EBR  Var_04    H10  C2A  C1   C3    179.51  30.0  3
 EBR  Var_05    C4   C4A  NH   CA   -178.47  30.0  3
 EBR  Var_06    NH   CA   CB   CG    179.58  30.0  1
 EBR  Var_07    O1P  P    O4P  C5A    53.06  30.0  3

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
 EBR  plan-1  CB   0.020
 EBR  plan-1  CG   0.020
 EBR  plan-1  CD1  0.020
 EBR  plan-1  CD2  0.020
 EBR  plan-1  CE1  0.020
 EBR  plan-1  CE2  0.020
 EBR  plan-1  CZ   0.020
 EBR  plan-1  OH   0.020
 EBR  plan-1  H4   0.020
 EBR  plan-1  H5   0.020
 EBR  plan-1  H6   0.020
 EBR  plan-1  H7   0.020
 EBR  plan-2  NH   0.020
 EBR  plan-2  C1   0.020
 EBR  plan-2  C2A  0.020
 EBR  plan-2  C3   0.020
 EBR  plan-2  C4   0.020
 EBR  plan-2  C4A  0.020
 EBR  plan-2  C5   0.020
 EBR  plan-2  C5A  0.020
 EBR  plan-2  C6   0.020
 EBR  plan-2  N1   0.020
 EBR  plan-2  H13  0.020
 EBR  plan-2  H17  0.020
 EBR  plan-2  H9   0.020
 EBR  plan-2  O3   0.020
 EBR  plan-3  CA   0.020
 EBR  plan-3  CB   0.020
 EBR  plan-3  NH   0.020
 EBR  plan-3  C4A  0.020
 EBR  plan-3  H1   0.020

