# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 23 04:29:02 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(C=N[C@@H](Cc2ccccc2)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
 P70  P70  (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-phenylalanine  ligand  46  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_P70
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
 P70  C02   C  C     0   0.548   4.4821  -0.6082  -1.8335
 P70  C03   C  CH1   0  -0.234   3.2786   0.1041  -1.2480
 P70  C05   C  C1    0   0.066   1.1173  -0.5914  -0.7400
 P70  C06   C  CR6   0  -0.012   0.1504  -1.4895  -0.1180
 P70  C07   C  CR6   0   0.292   0.5704  -2.7255   0.3881
 P70  C08   C  CR6   0   0.132  -0.3833  -3.5825   0.9730
 P70  C09   C  CH3   0  -0.722   0.0339  -4.9173   1.5061
 P70  C11   C  CR16  0  -0.141  -2.0515  -2.0384   0.6085
 P70  C12   C  CR6   0  -0.049  -1.2015  -1.1293   0.0130
 P70  C13   C  CH2   0  -0.251  -1.6797   0.2062  -0.4920
 P70  C20   C  CH2   0  -0.514   3.7308   1.0475  -0.0976
 P70  C21   C  CR6   0   0.099   2.5502   1.7543   0.5008
 P70  C22   C  CR16  0  -0.293   2.0324   2.8978  -0.1044
 P70  C23   C  CR16  0  -0.242   0.8753   3.4941   0.3782
 P70  C24   C  CR16  0  -0.267   0.2143   2.9495   1.4721
 P70  C25   C  CR16  0  -0.236   0.7256   1.8151   2.0876
 P70  C26   C  CR16  0  -0.294   1.8872   1.2259   1.6064
 P70  N04   N  N     0  -0.444   2.3583  -0.8679  -0.7382
 P70  N10   N  N     0  -0.398  -1.6479  -3.2259   1.0649
 P70  O01   O  OH1   0  -0.591   5.2644   0.2395  -2.4847
 P70  O14   O  O2    0  -0.589  -3.0570   0.4137  -0.2098
 P70  O16   O  OH1   0  -0.734  -3.2694   2.8823   0.4461
 P70  O17   O  OH1   0  -0.729  -5.0487   1.0735   0.9039
 P70  O18   O  O     0  -0.691  -2.8035   1.2157   2.2736
 P70  O19   O  OH1   0  -0.625   1.8332  -3.1319   0.3384
 P70  O27   O  O     0  -0.420   4.7128  -1.7818  -1.7104
 P70  P15   P  P     0   1.457  -3.4893   1.3938   0.9829
 P70  H031  H  HCH1  0   0.290   2.8240   0.7225  -2.0330
 P70  H051  H  H     0   0.265   0.7462   0.3215  -1.2088
 P70  H091  H  HCH3  0   0.249   0.7760  -4.8172   2.3000
 P70  H093  H  HCH3  0   0.249  -0.8290  -5.4433   1.9084
 P70  H092  H  HCH3  0   0.249   0.4827  -5.5375   0.7282
 P70  H111  H  HCR6  0   0.257  -3.1033  -1.8199   0.7347
 P70  H131  H  HCH2  0   0.255  -1.0652   1.0094  -0.0725
 P70  H132  H  HCH2  0   0.285  -1.5744   0.2607  -1.5778
 P70  H202  H  HCH2  0   0.273   4.2533   0.4579   0.6580
 P70  H201  H  HCH2  0   0.279   4.4405   1.7676  -0.5057
 P70  H221  H  HCR6  0   0.252   2.5352   3.3198  -0.9673
 P70  H231  H  HCR6  0   0.256   0.4849   4.3800  -0.1061
 P70  H241  H  HCR6  0   0.254  -0.7003   3.3979   1.8351
 P70  H251  H  HCR6  0   0.255   0.2077   1.3790   2.9313
 P70  H261  H  HCR6  0   0.255   2.2713   0.3331   2.0859
 P70  H4    H  HOH1  0   0.488   6.0464  -0.2186  -2.8282
 P70  H5    H  HOH1  0   0.496  -3.7030   3.0943  -0.3915
 P70  H6    H  HOH1  0   0.505  -5.5671   1.4698   1.6168
 P70  H1    H  HOH1  0   0.474   2.3747  -2.3943  -0.0616

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
 P70  O18  P15   double    1.472  0.020  1.472
 P70  O16  P15   single    1.598  0.020  1.598
 P70  P15  O17   single    1.594  0.020  1.594
 P70  P15  O14   single    1.603  0.020  1.603
 P70  O14  C13   single    1.421  0.020  1.421
 P70  C13  C12   single    1.506  0.020  1.506
 P70  C12  C11   aromatic  1.380  0.020  1.380
 P70  C12  C06   aromatic  1.405  0.020  1.405
 P70  C11  N10   aromatic  1.335  0.020  1.335
 P70  C20  C21   single    1.500  0.020  1.500
 P70  C20  C03   single    1.555  0.020  1.555
 P70  C05  C06   single    1.459  0.020  1.459
 P70  C05  N04   double    1.271  0.020  1.271
 P70  C22  C21   aromatic  1.394  0.020  1.394
 P70  C22  C23   aromatic  1.388  0.020  1.388
 P70  C06  C07   aromatic  1.400  0.020  1.400
 P70  C21  C26   aromatic  1.393  0.020  1.393
 P70  C23  C24   aromatic  1.389  0.020  1.389
 P70  C03  N04   single    1.432  0.020  1.432
 P70  C03  C02   single    1.516  0.020  1.516
 P70  N10  C08   aromatic  1.317  0.020  1.317
 P70  C26  C25   aromatic  1.388  0.020  1.388
 P70  C24  C25   aromatic  1.388  0.020  1.388
 P70  C07  C08   aromatic  1.409  0.020  1.409
 P70  C07  O19   single    1.327  0.020  1.327
 P70  C08  C09   single    1.497  0.020  1.497
 P70  C02  O27   double    1.202  0.020  1.202
 P70  C02  O01   single    1.325  0.020  1.325
 P70  C03  H031  single    0.970  0.020  1.090
 P70  C05  H051  single    0.930  0.020  1.080
 P70  C09  H091  single    0.970  0.020  1.090
 P70  C09  H093  single    0.970  0.020  1.090
 P70  C09  H092  single    0.970  0.020  1.090
 P70  C11  H111  single    0.930  0.020  1.080
 P70  C13  H131  single    0.970  0.020  1.090
 P70  C13  H132  single    0.970  0.020  1.090
 P70  C20  H202  single    0.970  0.020  1.090
 P70  C20  H201  single    0.970  0.020  1.090
 P70  C22  H221  single    0.930  0.020  1.080
 P70  C23  H231  single    0.930  0.020  1.080
 P70  C24  H241  single    0.930  0.020  1.080
 P70  C25  H251  single    0.930  0.020  1.080
 P70  C26  H261  single    0.930  0.020  1.080
 P70  O01  H4    single    0.850  0.020  0.980
 P70  O16  H5    single    0.850  0.020  0.980
 P70  O17  H6    single    0.850  0.020  0.980
 P70  O19  H1    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
 P70  O27   C02  O01   124.17  3.000
 P70  O01   C02  C03   110.98  3.000
 P70  O27   C02  C03   124.85  3.000
 P70  H031  C03  N04   111.76  3.000
 P70  H031  C03  C20   107.92  3.000
 P70  N04   C03  C20   109.59  3.000
 P70  H031  C03  C02   108.49  3.000
 P70  N04   C03  C02   109.19  3.000
 P70  C20   C03  C02   109.87  3.000
 P70  H051  C05  N04   120.96  3.000
 P70  H051  C05  C06   118.22  3.000
 P70  N04   C05  C06   120.83  3.000
 P70  C12   C06  C07   118.76  3.000
 P70  C07   C06  C05   119.92  3.000
 P70  C12   C06  C05   121.31  3.000
 P70  O19   C07  C08   118.24  3.000
 P70  O19   C07  C06   122.82  3.000
 P70  C08   C07  C06   118.93  3.000
 P70  N10   C08  C09   118.96  3.000
 P70  C09   C08  C07   120.10  3.000
 P70  N10   C08  C07   120.94  3.000
 P70  H092  C09  H093  108.37  3.000
 P70  H092  C09  H091  106.92  3.000
 P70  H093  C09  H091  108.35  3.000
 P70  H092  C09  C08   111.56  3.000
 P70  H093  C09  C08   109.99  3.000
 P70  H091  C09  C08   111.52  3.000
 P70  H111  C11  N10   115.71  3.000
 P70  H111  C11  C12   121.09  3.000
 P70  N10   C11  C12   123.20  3.000
 P70  C13   C12  C11   122.24  3.000
 P70  C11   C12  C06   117.65  3.000
 P70  C13   C12  C06   120.11  3.000
 P70  H132  C13  H131  106.86  3.000
 P70  H132  C13  O14   106.47  3.000
 P70  H131  C13  O14   111.14  3.000
 P70  H132  C13  C12   110.31  3.000
 P70  H131  C13  C12   110.12  3.000
 P70  O14   C13  C12   111.76  3.000
 P70  H201  C20  H202  107.71  3.000
 P70  H201  C20  C21   110.51  3.000
 P70  H202  C20  C21   110.79  3.000
 P70  H201  C20  C03   108.24  3.000
 P70  H202  C20  C03   108.88  3.000
 P70  C21   C20  C03   110.61  3.000
 P70  C26   C21  C22   118.62  3.000
 P70  C26   C21  C20   120.82  3.000
 P70  C22   C21  C20   120.37  3.000
 P70  H221  C22  C23   119.73  3.000
 P70  H221  C22  C21   119.52  3.000
 P70  C23   C22  C21   120.74  3.000
 P70  H231  C23  C24   120.10  3.000
 P70  H231  C23  C22   119.78  3.000
 P70  C24   C23  C22   120.13  3.000
 P70  H241  C24  C25   120.10  3.000
 P70  H241  C24  C23   120.28  3.000
 P70  C25   C24  C23   119.62  3.000
 P70  H251  C25  C26   119.98  3.000
 P70  H251  C25  C24   119.93  3.000
 P70  C26   C25  C24   120.08  3.000
 P70  H261  C26  C25   119.52  3.000
 P70  H261  C26  C21   119.66  3.000
 P70  C25   C26  C21   120.81  3.000
 P70  C05   N04  C03   118.62  3.000
 P70  C11   N10  C08   120.49  3.000
 P70  H4    O01  C02   110.38  3.000
 P70  P15   O14  C13   119.90  3.000
 P70  H5    O16  P15   115.70  3.000
 P70  H6    O17  P15   113.94  3.000
 P70  H1    O19  C07   107.74  3.000
 P70  O18   P15  O17   118.35  3.000
 P70  O17   P15  O16   107.78  3.000
 P70  O18   P15  O16   110.07  3.000
 P70  O17   P15  O14    95.98  3.000
 P70  O16   P15  O14   106.41  3.000
 P70  O18   P15  O14   116.91  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
 P70  CONST_01  N10   C11  C12  C06     0.00   0.0  0
 P70  CONST_02  N10   C08  C07  C06     0.00   0.0  0
 P70  CONST_03  C11   C12  C06  C07     0.00   0.0  0
 P70  CONST_04  C11   N10  C08  C07     0.00   0.0  0
 P70  CONST_05  C12   C11  N10  C08     0.00   0.0  0
 P70  CONST_06  C12   C06  C07  C08     0.00   0.0  0
 P70  CONST_07  C24   C23  C22  C21     0.00   0.0  0
 P70  CONST_08  C24   C25  C26  C21     0.00   0.0  0
 P70  CONST_09  C25   C26  C21  C22     0.00   0.0  0
 P70  CONST_10  C25   C24  C23  C22     0.00   0.0  0
 P70  CONST_11  C26   C21  C22  C23     0.00   0.0  0
 P70  CONST_12  C26   C25  C24  C23     0.00   0.0  0
 P70  CONST_13  C11   C12  C06  C05   180.00   0.0  0
 P70  CONST_14  C08   C07  C06  C05   180.00   0.0  0
 P70  CONST_15  C09   C08  C07  C06   180.00   0.0  0
 P70  CONST_16  C13   C12  C06  C07   180.00   0.0  0
 P70  CONST_17  C11   N10  C08  C09   180.00   0.0  0
 P70  CONST_18  O19   C07  C06  C12   180.00   0.0  0
 P70  CONST_19  N10   C11  C12  C13   180.00   0.0  0
 P70  CONST_20  C23   C22  C21  C20   180.00   0.0  0
 P70  CONST_21  C25   C26  C21  C20   180.00   0.0  0
 P70  CONST_22  O19   C07  C08  N10   180.00   0.0  0
 P70  CONST_23  H111  C11  C12  C06   180.00   0.0  0
 P70  CONST_24  H231  C23  C22  C21   180.00   0.0  0
 P70  CONST_25  H251  C25  C26  C21   180.00   0.0  0
 P70  CONST_26  H261  C26  C21  C22   180.00   0.0  0
 P70  CONST_27  H241  C24  C23  C22   180.00   0.0  0
 P70  CONST_28  H221  C22  C23  C24   180.00   0.0  0
 P70  CONST_29  H4    O01  C02  C03   180.00   0.0  0
 P70  Var_01    C22   C21  C20  C03   -82.21  30.0  2
 P70  Var_02    O14   C13  C12  C06  -177.05  30.0  2
 P70  Var_03    N04   C05  C06  C07    -5.50  30.0  1
 P70  Var_04    H091  C09  C08  C07    60.36  30.0  2
 P70  Var_05    C06   C05  N04  C03  -174.14   0.0  2
 P70  Var_06    O18   P15  O14  C13   -47.67  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
 P70  chir_01  C03  C20  N04  C02  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
 P70  plan-1  C05   0.020
 P70  plan-1  C06   0.020
 P70  plan-1  C07   0.020
 P70  plan-1  C08   0.020
 P70  plan-1  C09   0.020
 P70  plan-1  C11   0.020
 P70  plan-1  C12   0.020
 P70  plan-1  C13   0.020
 P70  plan-1  N10   0.020
 P70  plan-1  O19   0.020
 P70  plan-1  H111  0.020
 P70  plan-2  C20   0.020
 P70  plan-2  C21   0.020
 P70  plan-2  C22   0.020
 P70  plan-2  C23   0.020
 P70  plan-2  C24   0.020
 P70  plan-2  C25   0.020
 P70  plan-2  C26   0.020
 P70  plan-2  H221  0.020
 P70  plan-2  H231  0.020
 P70  plan-2  H241  0.020
 P70  plan-2  H251  0.020
 P70  plan-2  H261  0.020
 P70  plan-3  C02   0.020
 P70  plan-3  C03   0.020
 P70  plan-3  O01   0.020
 P70  plan-3  O27   0.020
 P70  plan-3  H4    0.020
 P70  plan-4  C03   0.020
 P70  plan-4  C05   0.020
 P70  plan-4  C06   0.020
 P70  plan-4  N04   0.020
 P70  plan-4  H051  0.020

