# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 12:40:09 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: [(1R)-1-{[(1E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}-1-phenylethyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(C=N[C@@](C)(c2ccccc2)[P](O)(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
 ELP  ELP  '[(1R)-1-{[(1E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}-1-phenylethyl]phosphonic acid'  ligand  48  28  .  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_ELP
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
 ELP  C3    C  CR6   0   0.295   2.4429  -0.7332   0.2888
 ELP  C2    C  CR6   0   0.136   3.5176  -0.9061   1.1835
 ELP  N1    N  N     0  -0.397   3.3964  -0.5880   2.4548
 ELP  C6    C  CR16  0  -0.141   2.2458  -0.0994   2.9232
 ELP  C4    C  CR6   0   0.000   1.2342  -0.2115   0.7646
 ELP  C4A   C  C1    0   0.064   0.1059  -0.0165  -0.1418
 ELP  N2    N  N     0  -0.484   0.2178  -0.2682  -1.3826
 ELP  C     C  CT    0  -0.219  -0.8901  -0.1507  -2.3086
 ELP  CA1   C  CH3   0  -0.735  -2.1779   0.4074  -1.7046
 ELP  CA2   C  CR6   0   0.104  -0.4374   0.6318  -3.5394
 ELP  P2    P  P     0   1.396  -1.1454  -1.9313  -2.7595
 ELP  O6    O  O     0  -0.696  -1.4187  -2.8125  -1.6026
 ELP  O7    O  OH1   0  -0.739  -2.2945  -1.8359  -3.8702
 ELP  O8    O  OH1   0  -0.737   0.1972  -2.3935  -3.5063
 ELP  O1    O  OH1   0  -0.626   2.6287  -1.0803  -0.9798
 ELP  C2A   C  CH3   0  -0.721   4.8212  -1.4530   0.6932
 ELP  C5    C  CR6   0  -0.071   1.1353   0.1079   2.1315
 ELP  C5A   C  CH2   0  -0.217  -0.1522   0.6493   2.6890
 ELP  O2    O  O2    0  -0.593  -0.0229   0.8149   4.0938
 ELP  P1    P  P     0   1.464  -1.1750   1.5769   4.9027
 ELP  O3    O  O     0  -0.707  -2.5595   1.2190   4.5462
 ELP  O4    O  OH1   0  -0.727  -0.6465   1.2093   6.3580
 ELP  O5    O  OH1   0  -0.737  -0.9447   3.1395   4.6728
 ELP  CB2   C  CR16  0  -0.282  -1.3653   1.0400  -4.4996
 ELP  CG2   C  CR16  0  -0.239  -0.9644   1.7385  -5.6283
 ELP  CD    C  CR16  0  -0.263   0.3752   2.0413  -5.8283
 ELP  CG1   C  CR16  0  -0.233   1.3064   1.6405  -4.8833
 ELP  CB1   C  CR16  0  -0.289   0.9054   0.9423  -3.7515
 ELP  HC6   H  HCR6  0   0.263   2.2286   0.1306   3.9798
 ELP  H4A   H  H     0   0.271  -0.8241   0.3533   0.2845
 ELP  HA11  H  HCH3  0   0.271  -2.0184   1.4266  -1.3493
 ELP  HA12  H  HCH3  0   0.282  -2.9842   0.4363  -2.4320
 ELP  HA13  H  HCH3  0   0.261  -2.5291  -0.1994  -0.8699
 ELP  HO7   H  HOH1  0   0.502  -2.7634  -2.6675  -4.0296
 ELP  HO8   H  HOH1  0   0.493   0.4187  -1.9170  -4.3175
 ELP  HO1   H  HOH1  0   0.485   1.7807  -0.8997  -1.4653
 ELP  H2A1  H  HCH3  0   0.251   4.7079  -2.4617   0.2918
 ELP  H2A2  H  HCH3  0   0.250   5.2384  -0.8379  -0.1058
 ELP  H2A3  H  HCH3  0   0.251   5.5387  -1.4881   1.5098
 ELP  H5A1  H  HCH2  0   0.262  -0.3928   1.6043   2.2097
 ELP  H5A2  H  HCH2  0   0.266  -0.9733  -0.0418   2.4789
 ELP  HO4   H  HOH1  0   0.506  -1.2284   1.4949   7.0752
 ELP  HO5   H  HOH1  0   0.498  -0.0795   3.4814   4.9364
 ELP  HB2   H  HCR6  0   0.258  -2.4169   0.8218  -4.3802
 ELP  HG2   H  HCR6  0   0.261  -1.7066   2.0452  -6.3537
 ELP  HCD   H  HCR6  0   0.261   0.6878   2.5861  -6.7094
 ELP  HG1   H  HCR6  0   0.261   2.3548   1.8711  -5.0198
 ELP  HB1   H  HCR6  0   0.243   1.6571   0.6598  -3.0295

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
 ELP  C3   C2    aromatic  1.409  0.020  1.409
 ELP  C3   C4    aromatic  1.400  0.020  1.400
 ELP  C3   O1    single    1.328  0.020  1.328
 ELP  C2   N1    aromatic  1.316  0.020  1.316
 ELP  C2   C2A   single    1.496  0.020  1.496
 ELP  N1   C6    aromatic  1.335  0.020  1.335
 ELP  C6   C5    aromatic  1.379  0.020  1.379
 ELP  C6   HC6   single    0.930  0.020  1.080
 ELP  C4   C4A   single    1.460  0.020  1.460
 ELP  C4   C5    aromatic  1.407  0.020  1.407
 ELP  C4A  N2    double    1.271  0.020  1.271
 ELP  C4A  H4A   single    0.930  0.020  1.080
 ELP  N2   C     single    1.449  0.020  1.449
 ELP  C    CA1   single    1.528  0.020  1.528
 ELP  C    CA2   single    1.527  0.020  1.527
 ELP  C    P2    single    1.855  0.020  1.855
 ELP  CA1  HA11  single    0.970  0.020  1.090
 ELP  CA1  HA12  single    0.970  0.020  1.090
 ELP  CA1  HA13  single    0.970  0.020  1.090
 ELP  CA2  CB2   aromatic  1.396  0.020  1.396
 ELP  CA2  CB1   aromatic  1.394  0.020  1.394
 ELP  P2   O6    double    1.480  0.020  1.480
 ELP  P2   O7    single    1.601  0.020  1.601
 ELP  P2   O8    single    1.604  0.020  1.604
 ELP  O7   HO7   single    0.850  0.020  0.980
 ELP  O8   HO8   single    0.850  0.020  0.980
 ELP  O1   HO1   single    0.850  0.020  0.980
 ELP  C2A  H2A1  single    0.970  0.020  1.090
 ELP  C2A  H2A2  single    0.970  0.020  1.090
 ELP  C2A  H2A3  single    0.970  0.020  1.090
 ELP  C5   C5A   single    1.504  0.020  1.504
 ELP  C5A  O2    single    1.420  0.020  1.420
 ELP  C5A  H5A1  single    0.970  0.020  1.090
 ELP  C5A  H5A2  single    0.970  0.020  1.090
 ELP  O2   P1    single    1.601  0.020  1.601
 ELP  P1   O3    double    1.474  0.020  1.474
 ELP  P1   O4    single    1.591  0.020  1.591
 ELP  P1   O5    single    1.596  0.020  1.596
 ELP  O4   HO4   single    0.850  0.020  0.980
 ELP  O5   HO5   single    0.850  0.020  0.980
 ELP  CB2  CG2   aromatic  1.387  0.020  1.387
 ELP  CB2  HB2   single    0.930  0.020  1.080
 ELP  CG2  CD    aromatic  1.388  0.020  1.388
 ELP  CG2  HG2   single    0.930  0.020  1.080
 ELP  CD   CG1   aromatic  1.386  0.020  1.386
 ELP  CD   HCD   single    0.930  0.020  1.080
 ELP  CG1  CB1   aromatic  1.389  0.020  1.389
 ELP  CG1  HG1   single    0.930  0.020  1.080
 ELP  CB1  HB1   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
 ELP  O1    C3   C4    122.88  3.000
 ELP  O1    C3   C2    117.89  3.000
 ELP  C4    C3   C2    119.24  3.000
 ELP  C2A   C2   N1    119.02  3.000
 ELP  C2A   C2   C3    120.08  3.000
 ELP  N1    C2   C3    120.90  3.000
 ELP  C6    N1   C2    120.45  3.000
 ELP  HC6   C6   C5    121.06  3.000
 ELP  HC6   C6   N1    115.75  3.000
 ELP  C5    C6   N1    123.19  3.000
 ELP  C5    C4   C4A   121.22  3.000
 ELP  C5    C4   C3    118.39  3.000
 ELP  C4A   C4   C3    120.39  3.000
 ELP  H4A   C4A  N2    121.68  3.000
 ELP  H4A   C4A  C4    117.56  3.000
 ELP  N2    C4A  C4    120.76  3.000
 ELP  C     N2   C4A   122.72  3.000
 ELP  P2    C    CA2   109.68  3.000
 ELP  P2    C    CA1   109.31  3.000
 ELP  CA2   C    CA1   112.41  3.000
 ELP  P2    C    N2    100.53  3.000
 ELP  CA2   C    N2    109.27  3.000
 ELP  CA1   C    N2    114.93  3.000
 ELP  HA13  CA1  HA12  106.77  3.000
 ELP  HA13  CA1  HA11  108.52  3.000
 ELP  HA12  CA1  HA11  107.56  3.000
 ELP  HA13  CA1  C     111.77  3.000
 ELP  HA12  CA1  C     111.76  3.000
 ELP  HA11  CA1  C     110.28  3.000
 ELP  CB1   CA2  CB2   118.06  3.000
 ELP  CB1   CA2  C     121.47  3.000
 ELP  CB2   CA2  C     120.46  3.000
 ELP  O8    P2   O7    107.15  3.000
 ELP  O8    P2   O6    110.30  3.000
 ELP  O7    P2   O6    116.45  3.000
 ELP  O8    P2   C     105.93  3.000
 ELP  O7    P2   C     102.14  3.000
 ELP  O6    P2   C     114.02  3.000
 ELP  HO7   O7   P2    114.25  3.000
 ELP  HO8   O8   P2    116.13  3.000
 ELP  HO1   O1   C3    107.44  3.000
 ELP  H2A3  C2A  H2A2  108.41  3.000
 ELP  H2A3  C2A  H2A1  108.35  3.000
 ELP  H2A2  C2A  H2A1  106.94  3.000
 ELP  H2A3  C2A  C2    109.91  3.000
 ELP  H2A2  C2A  C2    111.53  3.000
 ELP  H2A1  C2A  C2    111.58  3.000
 ELP  C5A   C5   C4    120.13  3.000
 ELP  C5A   C5   C6    122.04  3.000
 ELP  C4    C5   C6    117.83  3.000
 ELP  H5A2  C5A  H5A1  107.58  3.000
 ELP  H5A2  C5A  O2    109.39  3.000
 ELP  H5A1  C5A  O2    110.56  3.000
 ELP  H5A2  C5A  C5    110.12  3.000
 ELP  H5A1  C5A  C5    109.86  3.000
 ELP  O2    C5A  C5    109.31  3.000
 ELP  P1    O2   C5A   119.33  3.000
 ELP  O5    P1   O4    108.06  3.000
 ELP  O5    P1   O3    109.78  3.000
 ELP  O4    P1   O3    118.49  3.000
 ELP  O5    P1   O2    106.83  3.000
 ELP  O4    P1   O2     96.50  3.000
 ELP  O3    P1   O2    115.99  3.000
 ELP  HO4   O4   P1    114.23  3.000
 ELP  HO5   O5   P1    115.84  3.000
 ELP  HB2   CB2  CG2   118.23  3.000
 ELP  HB2   CB2  CA2   120.78  3.000
 ELP  CG2   CB2  CA2   120.99  3.000
 ELP  HG2   CG2  CD    120.23  3.000
 ELP  HG2   CG2  CB2   119.35  3.000
 ELP  CD    CG2  CB2   120.42  3.000
 ELP  HCD   CD   CG1   120.45  3.000
 ELP  HCD   CD   CG2   120.40  3.000
 ELP  CG1   CD   CG2   119.15  3.000
 ELP  HG1   CG1  CB1   119.32  3.000
 ELP  HG1   CG1  CD    120.22  3.000
 ELP  CB1   CG1  CD    120.47  3.000
 ELP  HB1   CB1  CG1   118.38  3.000
 ELP  HB1   CB1  CA2   120.69  3.000
 ELP  CG1   CB1  CA2   120.92  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
 ELP  CONST_01  C6    N1   C2   C3     0.00   0.0  0
 ELP  CONST_02  C6    C5   C4   C3     0.00   0.0  0
 ELP  CONST_03  C5    C4   C3   C2     0.00   0.0  0
 ELP  CONST_04  C5    C6   N1   C2     0.00   0.0  0
 ELP  CONST_05  C4    C3   C2   N1     0.00   0.0  0
 ELP  CONST_06  C4    C5   C6   N1     0.00   0.0  0
 ELP  CONST_07  CD    CG2  CB2  CA2    0.00   0.0  0
 ELP  CONST_08  CD    CG1  CB1  CA2    0.00   0.0  0
 ELP  CONST_09  CG1   CB1  CA2  CB2    0.00   0.0  0
 ELP  CONST_10  CG1   CD   CG2  CB2    0.00   0.0  0
 ELP  CONST_11  CB1   CA2  CB2  CG2    0.00   0.0  0
 ELP  CONST_12  CB1   CG1  CD   CG2    0.00   0.0  0
 ELP  CONST_13  C5A   C5   C4   C3   180.00   0.0  0
 ELP  CONST_14  C4A   C4   C3   C2   180.00   0.0  0
 ELP  CONST_15  O1    C3   C2   N1   180.00   0.0  0
 ELP  CONST_16  C5A   C5   C6   N1   180.00   0.0  0
 ELP  CONST_17  C2A   C2   N1   C6   180.00   0.0  0
 ELP  CONST_18  C4A   C4   C5   C6   180.00   0.0  0
 ELP  CONST_19  C2A   C2   C3   C4   180.00   0.0  0
 ELP  CONST_20  CG2   CB2  CA2  C    180.00   0.0  0
 ELP  CONST_21  CG1   CB1  CA2  C    180.00   0.0  0
 ELP  CONST_22  C5    C4   C3   O1   180.00   0.0  0
 ELP  CONST_23  HC6   C6   N1   C2   180.00   0.0  0
 ELP  CONST_24  HG2   CG2  CB2  CA2  180.00   0.0  0
 ELP  CONST_25  HG1   CG1  CB1  CA2  180.00   0.0  0
 ELP  CONST_26  HB1   CB1  CA2  CB2  180.00   0.0  0
 ELP  CONST_27  HCD   CD   CG2  CB2  180.00   0.0  0
 ELP  CONST_28  HB2   CB2  CG2  CD   180.00   0.0  0
 ELP  Var_01    N2    C4A  C4   C3    -2.69  30.0  2
 ELP  Var_02    O2    C5A  C5   C6    -3.11  30.0  2
 ELP  Var_03    H2A1  C2A  C2   C3   -61.52  30.0  2
 ELP  Var_04    O3    P1   O2   C5A   43.58  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
 ELP  chir_01  C  CA1  CA2  P2  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
 ELP  plan-1  C3   0.020
 ELP  plan-1  C2   0.020
 ELP  plan-1  N1   0.020
 ELP  plan-1  C6   0.020
 ELP  plan-1  C4   0.020
 ELP  plan-1  C4A  0.020
 ELP  plan-1  O1   0.020
 ELP  plan-1  C2A  0.020
 ELP  plan-1  C5   0.020
 ELP  plan-1  C5A  0.020
 ELP  plan-1  HC6  0.020
 ELP  plan-2  C    0.020
 ELP  plan-2  CA2  0.020
 ELP  plan-2  CB2  0.020
 ELP  plan-2  CG2  0.020
 ELP  plan-2  CD   0.020
 ELP  plan-2  CG1  0.020
 ELP  plan-2  CB1  0.020
 ELP  plan-2  HB2  0.020
 ELP  plan-2  HG2  0.020
 ELP  plan-2  HCD  0.020
 ELP  plan-2  HG1  0.020
 ELP  plan-2  HB1  0.020
 ELP  plan-3  C4   0.020
 ELP  plan-3  C4A  0.020
 ELP  plan-3  N2   0.020
 ELP  plan-3  C    0.020
 ELP  plan-3  H4A  0.020

