# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 19:18:29 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: [(3~{S},5~{S})-3-methyl-1,5-bis(oxidanyl)-2-oxidanylidene-pyrrolidin-3-yl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@]1(C[C@H](O)N(O)C1=O)[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
 5TX  5TX  '[(3~{S},5~{S})-3-methyl-1,5-bis(oxidanyl)-2-oxidanylidene-pyrrolidin-3-yl]phosphonic acid'  ligand  23  13  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5TX
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
 5TX  C01  C  CR15  0   0.184   2.0412   0.7323   0.6298
 5TX  C02  C  CH2   0  -0.477   0.6215   1.2976   0.6518
 5TX  C03  C  CR5   0  -0.552  -0.1613   0.4502  -0.3678
 5TX  C04  C  CR5   0   0.602   0.6315  -0.8437  -0.4404
 5TX  P05  P  P     0   1.404  -1.8638   0.0901   0.1703
 5TX  O06  O  OH1   0  -0.744  -1.5769  -0.7216   1.5260
 5TX  O07  O  O     0  -0.700  -2.7633   1.2593   0.2922
 5TX  O08  O  OH1   0  -0.755  -2.4279  -0.9626  -0.8989
 5TX  C09  C  CH3   0  -0.652  -0.2031   1.1048  -1.7572
 5TX  O10  O  O     0  -0.472   0.2854  -1.8726  -0.9943
 5TX  N12  N  NR5   0  -0.207   1.7804  -0.6334   0.2190
 5TX  O13  O  OH1   0  -0.647   2.8361   1.4245  -0.2788
 5TX  O11  O  OH1   0  -0.542   2.7986  -1.5274   0.1415
 5TX  H1   H  HCR5  0   0.266   2.4942   0.7185   1.6246
 5TX  H2   H  HCH2  0   0.289   0.2240   1.1966   1.6612
 5TX  H3   H  HCH2  0   0.284   0.6150   2.3559   0.3986
 5TX  H4   H  HOH1  0   0.498  -2.3558  -0.8680   2.0808
 5TX  H5   H  HOH1  0   0.486  -1.7621  -1.6310  -1.1437
 5TX  H6   H  HCH3  0   0.265   0.8062   1.3387  -2.0937
 5TX  H7   H  HCH3  0   0.254  -0.6690   0.4620  -2.5027
 5TX  H8   H  HCH3  0   0.262  -0.7638   2.0380  -1.7136
 5TX  H9   H  HOH1  0   0.466   3.7597   1.1903  -0.1381
 5TX  H10  H  HOH1  0   0.486   2.7868  -2.0257   0.9708

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
 5TX  O11  N12  single  1.357  0.020  1.357
 5TX  N12  C01  single  1.450  0.020  1.450
 5TX  N12  C04  single  1.341  0.020  1.341
 5TX  O13  C01  single  1.392  0.020  1.392
 5TX  O10  C04  double  1.219  0.020  1.219
 5TX  C01  C02  single  1.528  0.020  1.528
 5TX  C04  C03  single  1.519  0.020  1.519
 5TX  O07  P05  double  1.480  0.020  1.480
 5TX  C02  C03  single  1.540  0.020  1.540
 5TX  C03  P05  single  1.821  0.020  1.821
 5TX  C03  C09  single  1.536  0.020  1.536
 5TX  O06  P05  single  1.606  0.020  1.606
 5TX  P05  O08  single  1.603  0.020  1.603
 5TX  C01  H1   single  0.970  0.020  1.090
 5TX  C02  H2   single  0.970  0.020  1.090
 5TX  C02  H3   single  0.970  0.020  1.090
 5TX  O06  H4   single  0.850  0.020  0.980
 5TX  O08  H5   single  0.850  0.020  0.980
 5TX  C09  H6   single  0.970  0.020  1.090
 5TX  C09  H7   single  0.970  0.020  1.090
 5TX  C09  H8   single  0.970  0.020  1.090
 5TX  O13  H9   single  0.850  0.020  0.980
 5TX  O11  H10  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
 5TX  H1   C01  O13  111.33  3.000
 5TX  H1   C01  N12  108.69  3.000
 5TX  O13  C01  N12  112.73  3.000
 5TX  H1   C01  C02  112.11  3.000
 5TX  O13  C01  C02  110.86  3.000
 5TX  N12  C01  C02  100.69  3.000
 5TX  H3   C02  H2   107.67  3.000
 5TX  H3   C02  C03  112.21  3.000
 5TX  H2   C02  C03  112.15  3.000
 5TX  H3   C02  C01  111.22  3.000
 5TX  H2   C02  C01  108.54  3.000
 5TX  C03  C02  C01  105.02  3.000
 5TX  C09  C03  P05  109.02  3.000
 5TX  C09  C03  C04  109.50  3.000
 5TX  P05  C03  C04  109.48  3.000
 5TX  C09  C03  C02  112.23  3.000
 5TX  P05  C03  C02  112.85  3.000
 5TX  C04  C03  C02  103.59  3.000
 5TX  N12  C04  O10  126.81  3.000
 5TX  O10  C04  C03  126.34  3.000
 5TX  N12  C04  C03  106.85  3.000
 5TX  O08  P05  O07  111.09  3.000
 5TX  O08  P05  O06  107.09  3.000
 5TX  O07  P05  O06  116.00  3.000
 5TX  O08  P05  C03  105.17  3.000
 5TX  O06  P05  C03  100.51  3.000
 5TX  O07  P05  C03  115.86  3.000
 5TX  H4   O06  P05  114.63  3.000
 5TX  H5   O08  P05  112.17  3.000
 5TX  H8   C09  H7   108.23  3.000
 5TX  H8   C09  H6   107.77  3.000
 5TX  H7   C09  H6   108.16  3.000
 5TX  H8   C09  C03  110.04  3.000
 5TX  H7   C09  C03  112.29  3.000
 5TX  H6   C09  C03  110.22  3.000
 5TX  O11  N12  C04  120.74  3.000
 5TX  C04  N12  C01  116.18  3.000
 5TX  O11  N12  C01  120.11  3.000
 5TX  H9   O13  C01  109.35  3.000
 5TX  H10  O11  N12  106.33  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
 5TX  CONST_01  C03  C04  N12  C01    0.00  0.0  0
 5TX  CONST_02  O10  C04  N12  C01  180.00  0.0  0
 5TX  CONST_03  O11  N12  C04  C03  180.00  0.0  0
 5TX  CONST_04  O11  N12  C04  O10    0.00  0.0  0

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
 5TX  chir_01  C01  N12  O13  C02  negativ
 5TX  chir_02  C03  C09  C02  C04  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
 5TX  plan-1  C01  0.020
 5TX  plan-1  C03  0.020
 5TX  plan-1  C04  0.020
 5TX  plan-1  O10  0.020
 5TX  plan-1  N12  0.020
 5TX  plan-1  O11  0.020

