# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 14:27:42 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: 1-carboxy-1-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]azaniumyl}-2-[(3R)-2-oxo-2,3-dihydro-1H-indol-3-yl]ethan-1-ide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(C=[NH+][C-](C[C@H]2C(=O)Nc3ccccc23)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
 9TD  9TD  1-carboxy-1-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]azaniumyl}-2-[(3R)-2-oxo-2,3-dihydro-1H-indol-3-yl]ethan-1-ide  ligand  51  31  .  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_9TD
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
 9TD  C05  C  CH2    0  -0.215   3.5441   0.2298   0.1387
 9TD  C06  C  CR6    0  -0.101   2.8846  -1.1052  -0.0555
 9TD  C07  C  CR6    0   0.069   1.4973  -1.1621  -0.3129
 9TD  C08  C  C1     0  -0.096   0.7434   0.0635  -0.3585
 9TD  C10  C  C     -1   0.123  -1.4293   1.1246  -0.7865
 9TD  C11  C  CH2    0  -0.541  -2.8371   0.7156  -1.0795
 9TD  C12  C  CR15   0  -0.452  -3.6033   0.1433   0.1399
 9TD  C13  C  CR56   0   0.067  -5.0481  -0.1104  -0.1633
 9TD  C14  C  CR56   0   0.379  -5.8221   0.7121   0.6546
 9TD  C16  C  CR5    0   0.558  -3.6705   1.1441   1.2908
 9TD  C18  C  CR16   0  -0.308  -7.2022   0.7248   0.5846
 9TD  C19  C  CR16   0  -0.266  -7.8058  -0.1218  -0.3434
 9TD  C20  C  CR16   0  -0.265  -7.0497  -0.9468  -1.1663
 9TD  C21  C  CR16   0  -0.330  -5.6568  -0.9421  -1.0797
 9TD  C22  C  C      0   0.491  -1.0279   2.4717  -0.5333
 9TD  C25  C  CR6    0   0.286   0.9522  -2.4427  -0.4953
 9TD  C27  C  CR6    0   0.136   1.7554  -3.5795  -0.4152
 9TD  C28  C  CH3    0  -0.787   1.1632  -4.9445  -0.6047
 9TD  C30  C  CR16   0  -0.131   3.5976  -2.2874   0.0030
 9TD  N09  N  NC1    1  -0.549  -0.5357   0.1217  -0.6771
 9TD  N15  N  NR15   0  -0.737  -4.9856   1.4448   1.4865
 9TD  N29  N  N      0  -0.417   3.0540  -3.4883  -0.1696
 9TD  O01  O  OH1    0  -0.728   7.2560   0.5343   0.6298
 9TD  O03  O  O      0  -0.707   5.7701   2.4065  -0.4650
 9TD  O04  O  O2     0  -0.593   4.9441   0.0514   0.3120
 9TD  O17  O  O      0  -0.448  -2.7394   1.6000   1.9191
 9TD  O23  O  O      0  -0.499   0.1043   2.8309  -0.2339
 9TD  O24  O  OH1    0  -0.618  -2.0274   3.3543  -0.6716
 9TD  O26  O  OH1    0  -0.660  -0.3751  -2.5260  -0.7412
 9TD  O31  O  OH1    0  -0.742   5.5366   1.9019   1.9852
 9TD  P02  P  P      0   1.465   5.8803   1.3293   0.5349
 9TD  H1   H  HCH2   0   0.260   3.3571   0.8727  -0.7275
 9TD  H2   H  HCH2   0   0.258   3.1217   0.7313   1.0168
 9TD  H3   H  H      0   0.299   1.2190   0.9988  -0.1256
 9TD  H5   H  HCH2   0   0.286  -3.3993   1.5556  -1.4834
 9TD  H6   H  HCH2   0   0.276  -2.8539  -0.0503  -1.8616
 9TD  H7   H  HCR5   0   0.305  -3.0954  -0.7611   0.4906
 9TD  H8   H  HCR6   0   0.267  -7.7962   1.3651   1.2234
 9TD  H9   H  HCR6   0   0.259  -8.8854  -0.1335  -0.4210
 9TD  H10  H  HCR6   0   0.255  -7.5437  -1.5955  -1.8774
 9TD  H11  H  HCR6   0   0.254  -5.0650  -1.5851  -1.7198
 9TD  H12  H  HCH3   0   0.259   0.7362  -5.0728  -1.6027
 9TD  H13  H  HCH3   0   0.274   1.9369  -5.6983  -0.4807
 9TD  H14  H  HCH3   0   0.260   0.3751  -5.1573   0.1218
 9TD  H15  H  HCR6   0   0.261   4.6621  -2.2779   0.1967
 9TD  H16  H  HNR5   0   0.410  -5.3064   2.0846   2.1978
 9TD  H17  H  HOH1   0   0.506   8.0390   1.1005   0.5971
 9TD  H18  H  HOH1   0   0.475  -1.6873   4.2416  -0.4928
 9TD  H19  H  HOH1   0   0.502  -0.6657  -3.4307  -0.9065
 9TD  H20  H  HOH1   0   0.498   5.6489   1.2841   2.7206
 9TD  H21  H  HNC1   0   0.451  -0.9354  -0.7917  -0.8908

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
 9TD  O03  P02  double    1.474  0.020  1.474
 9TD  P02  O31  single    1.597  0.020  1.597
 9TD  P02  O01  single    1.592  0.020  1.592
 9TD  P02  O04  single    1.600  0.020  1.600
 9TD  O04  C05  single    1.422  0.020  1.422
 9TD  C05  C06  single    1.502  0.020  1.502
 9TD  C11  C10  single    1.495  0.020  1.495
 9TD  C11  C12  single    1.550  0.020  1.550
 9TD  C06  C30  aromatic  1.382  0.020  1.382
 9TD  C06  C07  aromatic  1.412  0.020  1.412
 9TD  C08  C07  single    1.440  0.020  1.440
 9TD  C08  N09  double    1.320  0.020  1.320
 9TD  O23  C22  double    1.225  0.020  1.225
 9TD  C30  N29  aromatic  1.329  0.020  1.329
 9TD  C10  N09  single    1.348  0.020  1.348
 9TD  C10  C22  single    1.428  0.020  1.428
 9TD  C07  C25  aromatic  1.404  0.020  1.404
 9TD  C12  C13  single    1.498  0.020  1.498
 9TD  C12  C16  single    1.527  0.020  1.527
 9TD  C22  O24  single    1.341  0.020  1.341
 9TD  N29  C27  aromatic  1.325  0.020  1.325
 9TD  C21  C13  aromatic  1.379  0.020  1.379
 9TD  C21  C20  aromatic  1.396  0.020  1.396
 9TD  C25  C27  aromatic  1.394  0.020  1.394
 9TD  C25  O26  single    1.352  0.020  1.352
 9TD  O17  C16  double    1.212  0.020  1.212
 9TD  C27  C28  single    1.500  0.020  1.500
 9TD  C13  C14  aromatic  1.394  0.020  1.394
 9TD  C16  N15  single    1.363  0.020  1.363
 9TD  C20  C19  aromatic  1.389  0.020  1.389
 9TD  C14  N15  single    1.389  0.020  1.389
 9TD  C14  C18  aromatic  1.382  0.020  1.382
 9TD  C19  C18  aromatic  1.394  0.020  1.394
 9TD  C05  H1   single    0.970  0.020  1.090
 9TD  C05  H2   single    0.970  0.020  1.090
 9TD  C08  H3   single    0.930  0.020  1.080
 9TD  C11  H5   single    0.970  0.020  1.090
 9TD  C11  H6   single    0.970  0.020  1.090
 9TD  C12  H7   single    0.970  0.020  1.090
 9TD  C18  H8   single    0.930  0.020  1.080
 9TD  C19  H9   single    0.930  0.020  1.080
 9TD  C20  H10  single    0.930  0.020  1.080
 9TD  C21  H11  single    0.930  0.020  1.080
 9TD  C28  H12  single    0.970  0.020  1.090
 9TD  C28  H13  single    0.970  0.020  1.090
 9TD  C28  H14  single    0.970  0.020  1.090
 9TD  C30  H15  single    0.930  0.020  1.080
 9TD  N15  H16  single    0.860  0.020  1.020
 9TD  O01  H17  single    0.850  0.020  0.980
 9TD  O24  H18  single    0.850  0.020  0.980
 9TD  O26  H19  single    0.850  0.020  0.980
 9TD  O31  H20  single    0.850  0.020  0.980
 9TD  N09  H21  single    0.860  0.020  1.020

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
 9TD  H2   C05  H1   107.42  3.000
 9TD  H2   C05  O04  109.83  3.000
 9TD  H1   C05  O04  109.77  3.000
 9TD  H2   C05  C06  109.95  3.000
 9TD  H1   C05  C06  110.17  3.000
 9TD  O04  C05  C06  109.67  3.000
 9TD  C30  C06  C07  118.70  3.000
 9TD  C07  C06  C05  119.39  3.000
 9TD  C30  C06  C05  121.91  3.000
 9TD  C25  C07  C08  124.69  3.000
 9TD  C25  C07  C06  116.23  3.000
 9TD  C08  C07  C06  119.08  3.000
 9TD  H3   C08  N09  116.28  3.000
 9TD  H3   C08  C07  120.15  3.000
 9TD  N09  C08  C07  123.57  3.000
 9TD  N09  C10  C22  120.07  3.000
 9TD  C22  C10  C11  123.88  3.000
 9TD  N09  C10  C11  115.90  3.000
 9TD  H6   C11  H5   105.48  3.000
 9TD  H6   C11  C12  107.23  3.000
 9TD  H5   C11  C12  108.76  3.000
 9TD  H6   C11  C10  110.23  3.000
 9TD  H5   C11  C10  110.36  3.000
 9TD  C12  C11  C10  114.35  3.000
 9TD  H7   C12  C16  108.69  3.000
 9TD  H7   C12  C13  111.86  3.000
 9TD  C16  C12  C13  102.78  3.000
 9TD  H7   C12  C11  109.13  3.000
 9TD  C16  C12  C11  111.89  3.000
 9TD  C13  C12  C11  112.34  3.000
 9TD  C21  C13  C14  120.03  3.000
 9TD  C14  C13  C12  108.46  3.000
 9TD  C21  C13  C12  131.48  3.000
 9TD  N15  C14  C18  128.83  3.000
 9TD  C18  C14  C13  122.01  3.000
 9TD  N15  C14  C13  109.16  3.000
 9TD  O17  C16  N15  125.70  3.000
 9TD  N15  C16  C12  107.18  3.000
 9TD  O17  C16  C12  127.12  3.000
 9TD  H8   C18  C19  120.99  3.000
 9TD  H8   C18  C14  121.58  3.000
 9TD  C19  C18  C14  117.43  3.000
 9TD  H9   C19  C20  119.60  3.000
 9TD  H9   C19  C18  119.10  3.000
 9TD  C20  C19  C18  121.30  3.000
 9TD  H10  C20  C21  119.91  3.000
 9TD  H10  C20  C19  119.80  3.000
 9TD  C21  C20  C19  120.30  3.000
 9TD  H11  C21  C20  120.44  3.000
 9TD  H11  C21  C13  120.63  3.000
 9TD  C20  C21  C13  118.94  3.000
 9TD  O24  C22  O23  121.42  3.000
 9TD  O24  C22  C10  113.15  3.000
 9TD  O23  C22  C10  125.43  3.000
 9TD  O26  C25  C27  121.71  3.000
 9TD  O26  C25  C07  117.45  3.000
 9TD  C27  C25  C07  120.84  3.000
 9TD  N29  C27  C28  118.24  3.000
 9TD  C28  C27  C25  120.48  3.000
 9TD  N29  C27  C25  121.28  3.000
 9TD  H14  C28  H13  107.60  3.000
 9TD  H14  C28  H12  107.61  3.000
 9TD  H13  C28  H12  107.50  3.000
 9TD  H14  C28  C27  112.21  3.000
 9TD  H13  C28  C27  109.60  3.000
 9TD  H12  C28  C27  112.11  3.000
 9TD  H15  C30  N29  115.68  3.000
 9TD  H15  C30  C06  120.51  3.000
 9TD  N29  C30  C06  123.81  3.000
 9TD  H21  N09  C10  112.94  3.000
 9TD  H21  N09  C08  113.02  3.000
 9TD  C10  N09  C08  134.05  3.000
 9TD  H16  N15  C16  123.22  3.000
 9TD  H16  N15  C14  124.42  3.000
 9TD  C16  N15  C14  112.25  3.000
 9TD  C30  N29  C27  119.15  3.000
 9TD  H17  O01  P02  113.92  3.000
 9TD  P02  O04  C05  119.53  3.000
 9TD  H18  O24  C22  108.83  3.000
 9TD  H19  O26  C25  112.62  3.000
 9TD  H20  O31  P02  115.89  3.000
 9TD  O31  P02  O04  106.68  3.000
 9TD  O04  P02  O03  116.46  3.000
 9TD  O31  P02  O03  109.76  3.000
 9TD  O04  P02  O01   96.61  3.000
 9TD  O31  P02  O01  108.12  3.000
 9TD  O03  P02  O01  118.04  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
 9TD  CONST_01  C27  N29  C30  C06     0.00   0.0  0
 9TD  CONST_02  C27  C25  C07  C06     0.00   0.0  0
 9TD  CONST_03  N29  C30  C06  C07     0.00   0.0  0
 9TD  CONST_04  N29  C27  C25  C07     0.00   0.0  0
 9TD  CONST_05  C19  C20  C21  C13     0.00   0.0  0
 9TD  CONST_06  C19  C18  C14  C13     0.00   0.0  0
 9TD  CONST_07  C20  C21  C13  C14     0.00   0.0  0
 9TD  CONST_08  C20  C19  C18  C14     0.00   0.0  0
 9TD  CONST_09  C21  C13  C14  C18     0.00   0.0  0
 9TD  CONST_10  C21  C20  C19  C18     0.00   0.0  0
 9TD  CONST_11  C30  C06  C07  C25     0.00   0.0  0
 9TD  CONST_12  C30  N29  C27  C25     0.00   0.0  0
 9TD  CONST_13  C14  N15  C16  C12     0.00   0.0  0
 9TD  CONST_14  N29  C30  C06  C05   180.00   0.0  0
 9TD  CONST_15  C25  C07  C06  C05   180.00   0.0  0
 9TD  CONST_16  O26  C25  C07  C06   180.00   0.0  0
 9TD  CONST_17  C28  C27  C25  C07   180.00   0.0  0
 9TD  CONST_18  C30  C06  C07  C08   180.00   0.0  0
 9TD  CONST_19  C27  C25  C07  C08   180.00   0.0  0
 9TD  CONST_20  C30  N29  C27  C28   180.00   0.0  0
 9TD  CONST_21  O26  C25  C27  N29   180.00   0.0  0
 9TD  CONST_22  O17  C16  N15  C14   180.00   0.0  0
 9TD  CONST_23  H15  C30  C06  C07   180.00   0.0  0
 9TD  CONST_24  H11  C21  C13  C12     0.00   0.0  0
 9TD  CONST_25  H10  C20  C21  C13   180.00   0.0  0
 9TD  CONST_26  H8   C18  C14  C13   180.00   0.0  0
 9TD  CONST_27  H9   C19  C18  C14   180.00   0.0  0
 9TD  CONST_28  H16  N15  C16  C12   180.00   0.0  0
 9TD  CONST_29  C10  N09  C08  C07   180.00   0.0  0
 9TD  CONST_30  H21  N09  C08  C07     0.00   0.0  0
 9TD  CONST_31  H3   C08  N09  C10     0.00   0.0  0
 9TD  CONST_32  H18  O24  C22  C10   180.00   0.0  0
 9TD  Var_01    N09  C08  C07  C06   175.42  30.0  2
 9TD  Var_02    O04  C05  C06  C07  -176.91  30.0  2
 9TD  Var_03    H12  C28  C27  C25    62.17  30.0  2
 9TD  Var_04    N09  C10  C11  C12    76.53  30.0  3
 9TD  Var_05    O03  P02  O04  C05   -53.11  30.0  2
 9TD  Var_06    C11  C10  N09  C08  -175.35  30.0  2
 9TD  Var_07    O23  C22  C10  C11   176.66  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
 9TD  chir_01  C12  C11  C13  C16  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
 9TD  plan-1  C05  0.020
 9TD  plan-1  C06  0.020
 9TD  plan-1  C07  0.020
 9TD  plan-1  C08  0.020
 9TD  plan-1  C25  0.020
 9TD  plan-1  C27  0.020
 9TD  plan-1  C28  0.020
 9TD  plan-1  C30  0.020
 9TD  plan-1  N29  0.020
 9TD  plan-1  O26  0.020
 9TD  plan-1  H15  0.020
 9TD  plan-2  C12  0.020
 9TD  plan-2  C13  0.020
 9TD  plan-2  C14  0.020
 9TD  plan-2  C16  0.020
 9TD  plan-2  C18  0.020
 9TD  plan-2  C19  0.020
 9TD  plan-2  C20  0.020
 9TD  plan-2  C21  0.020
 9TD  plan-2  N15  0.020
 9TD  plan-2  O17  0.020
 9TD  plan-2  H8   0.020
 9TD  plan-2  H9   0.020
 9TD  plan-2  H10  0.020
 9TD  plan-2  H11  0.020
 9TD  plan-2  H16  0.020
 9TD  plan-3  C10  0.020
 9TD  plan-3  C22  0.020
 9TD  plan-3  O23  0.020
 9TD  plan-3  O24  0.020
 9TD  plan-3  H18  0.020
 9TD  plan-4  C07  0.020
 9TD  plan-4  C08  0.020
 9TD  plan-4  C10  0.020
 9TD  plan-4  N09  0.020
 9TD  plan-4  H3   0.020
 9TD  plan-4  H21  0.020

