# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 10:41:28 2022
#   Inital geometry file: a 143 line input string
#   Ligand name: 4-[(1~{R},3~{S})-3-carboxy-1-[[4-fluoranyl-2-(3-methylimidazol-4-yl)phenyl]methyl]-4-oxidanyl-4-oxidanylidene-1,4$l^{5}-azaphosphinan-1-ium-3-yl]butylazanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cncc1c2cc(F)ccc2C[NH+]3CC[P](O)(=O)[C@@](CCCC[NH3+])(C3)C(O)=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 U9K  U9K  4-[(1~{R},3~{S})-3-carboxy-1-[[4-fluoranyl-2-(3-methylimidazol-4-yl)phenyl]methyl]-4-oxidanyl-4-oxidanylidene-1,4$l^{5}-azaphosphinan-1-ium-3-yl]butylazanium  ligand  59  30  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_U9K
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
 U9K  N1   N  NR5    0  -0.430  -37.0996  -15.0867  15.0902
 U9K  N2   N  N      0  -0.438  -35.3952  -14.1514  16.1321
 U9K  C3   C  CR15   0  -0.238  -35.2727  -13.9369  14.7929
 U9K  N4   N  NT3    1  -0.778  -33.5494  -12.5308   7.7324
 U9K  C6   C  CR16   0  -0.442  -37.0832  -13.3650  12.0866
 U9K  C7   C  CR6    0   0.560  -37.3990  -13.3657  10.7430
 U9K  C9   C  CR16   0  -0.259  -36.8994  -15.6781  10.5790
 U9K  C10  C  CR6    0   0.035  -36.5344  -15.7092  11.9225
 U9K  C11  C  CH2    0  -0.411  -35.9893  -16.9842  12.4933
 U9K  C12  C  CH2    0  -0.321  -34.1749  -18.6389  12.4793
 U9K  C13  C  CH2    0  -0.754  -32.8904  -19.1089  11.8258
 U9K  C14  C  CT     0  -0.541  -32.2604  -16.3081  11.6744
 U9K  C15  C  CH2    0  -0.437  -32.3320  -16.1532  10.1488
 U9K  C16  C  CH2    0  -0.448  -33.1270  -14.9636   9.6161
 U9K  C18  C  CH2    0  -0.330  -34.0372  -13.9163   7.4733
 U9K  C19  C  C      0   0.535  -31.3490  -15.2309  12.3613
 U9K  C20  C  CH2    0  -0.305  -33.6305  -16.2091  12.3603
 U9K  C1   C  CH3    0  -0.533  -38.3551  -15.7776  14.8939
 U9K  C2   C  CR15   0   0.084  -36.4997  -14.8385  16.2729
 U9K  C4   C  CR5    0   0.212  -36.3171  -14.5117  14.1202
 U9K  C5   C  CR6    0   0.063  -36.6486  -14.5418  12.6894
 U9K  C8   C  CR16   0  -0.405  -37.3288  -14.5094   9.9726
 U9K  N3   N  NT1    1  -0.543  -34.6013  -17.2900  11.9841
 U9K  P1   P  P      0   1.259  -31.5137  -17.9551  12.0693
 U9K  O1   O  OH1    0  -0.786  -31.3457  -17.8871  13.6508
 U9K  O2   O  O      0  -0.703  -30.3027  -18.2823  11.2632
 U9K  C17  C  CH2    0  -0.450  -33.1351  -14.9653   8.0905
 U9K  O3   O  O      0  -0.614  -31.1287  -15.4360  13.5935
 U9K  O4   O  OC    -1  -0.494  -30.9170  -14.3003  11.6946
 U9K  H5   H  HCR5   0   0.260  -34.4431  -13.3924  14.3669
 U9K  H24  H  HNT3   0   0.478  -34.1604  -11.8355   7.3029
 U9K  H25  H  HNT3   0   0.473  -33.5110  -12.3133   8.7285
 U9K  H26  H  HNT3   0   0.470  -32.6128  -12.3824   7.3533
 U9K  H6   H  HCR6   0   0.283  -37.1766  -12.4574  12.6684
 U9K  H8   H  HCR6   0   0.285  -36.8371  -16.5828   9.9846
 U9K  H9   H  HCH2   0   0.319  -35.9125  -16.9682  13.5791
 U9K  H10  H  HCH2   0   0.334  -36.6088  -17.8331  12.2059
 U9K  H12  H  HCH2   0   0.319  -34.9862  -19.3306  12.2603
 U9K  H13  H  HCH2   0   0.309  -34.0753  -18.5555  13.5609
 U9K  H15  H  HCH2   0   0.302  -33.0369  -19.2743  10.7562
 U9K  H14  H  HCH2   0   0.322  -32.6201  -20.0749  12.2582
 U9K  H17  H  HCH2   0   0.239  -32.7489  -17.0618   9.6969
 U9K  H16  H  HCH2   0   0.264  -31.3104  -16.0952   9.7699
 U9K  H19  H  HCH2   0   0.248  -32.6958  -14.0412  10.0061
 U9K  H18  H  HCH2   0   0.229  -34.1656  -14.9958   9.9579
 U9K  H23  H  HCH2   0   0.293  -35.0481  -13.9697   7.8738
 U9K  H22  H  HCH2   0   0.302  -34.0877  -14.0247   6.3924
 U9K  H28  H  HCH2   0   0.320  -33.5486  -16.2481  13.4453
 U9K  H27  H  HCH2   0   0.324  -34.0941  -15.2595  12.1006
 U9K  H1   H  HCH3   0   0.276  -38.8221  -15.9393  15.8616
 U9K  H2   H  HCH3   0   0.267  -39.0246  -15.1801  14.2788
 U9K  H3   H  HCH3   0   0.261  -38.2066  -16.7455  14.4172
 U9K  H4   H  HCR5   0   0.281  -36.9223  -15.1806  17.2063
 U9K  H7   H  HCR6   0   0.292  -37.6016  -14.4922   8.9258
 U9K  H11  H  HNT1   0   0.469  -34.6660  -17.3452  10.9636
 U9K  H29  H  HOH1   0   0.482  -31.2361  -16.8739  13.8593
 U9K  H21  H  HCH2   0   0.261  -33.4997  -15.9304   7.7308
 U9K  H20  H  HCH2   0   0.254  -32.1189  -14.8574   7.6998
 U9K  F1   F  F      0  -0.304  -37.7998  -12.2217  10.1787

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
 U9K  N4   C18  single    1.492  0.020  1.492
 U9K  C18  C17  single    1.515  0.020  1.515
 U9K  C17  C16  single    1.526  0.020  1.526
 U9K  C16  C15  single    1.527  0.020  1.527
 U9K  C8   C9   aromatic  1.385  0.020  1.385
 U9K  C8   C7   aromatic  1.381  0.020  1.381
 U9K  C15  C14  single    1.535  0.020  1.535
 U9K  F1   C7   single    1.337  0.020  1.337
 U9K  C9   C10  aromatic  1.392  0.020  1.392
 U9K  C7   C6   aromatic  1.380  0.020  1.380
 U9K  O2   P1   double    1.491  0.020  1.491
 U9K  O3   C19  deloc     1.268  0.020  1.268
 U9K  C14  P1   single    1.851  0.020  1.851
 U9K  C14  C19  single    1.569  0.020  1.569
 U9K  C14  C20  single    1.535  0.020  1.535
 U9K  C10  C11  single    1.500  0.020  1.500
 U9K  C10  C5   aromatic  1.401  0.020  1.401
 U9K  C13  P1   single    1.813  0.020  1.813
 U9K  C13  C12  single    1.516  0.020  1.516
 U9K  P1   O1   single    1.592  0.020  1.592
 U9K  N3   C20  single    1.501  0.020  1.501
 U9K  N3   C11  single    1.510  0.020  1.510
 U9K  N3   C12  single    1.499  0.020  1.499
 U9K  C19  O4   deloc     1.224  0.020  1.224
 U9K  C6   C5   aromatic  1.392  0.020  1.392
 U9K  C5   C4   single    1.469  0.020  1.469
 U9K  C4   C3   aromatic  1.369  0.020  1.369
 U9K  C4   N1   aromatic  1.373  0.020  1.373
 U9K  C1   N1   single    1.446  0.020  1.446
 U9K  C3   N2   aromatic  1.362  0.020  1.362
 U9K  N1   C2   aromatic  1.349  0.020  1.349
 U9K  N2   C2   aromatic  1.308  0.020  1.308
 U9K  C3   H5   single    0.930  0.020  1.080
 U9K  N4   H24  single    0.890  0.020  1.040
 U9K  N4   H25  single    0.890  0.020  1.040
 U9K  N4   H26  single    0.890  0.020  1.040
 U9K  C6   H6   single    0.930  0.020  1.080
 U9K  C9   H8   single    0.930  0.020  1.080
 U9K  C11  H9   single    0.970  0.020  1.090
 U9K  C11  H10  single    0.970  0.020  1.090
 U9K  C12  H12  single    0.970  0.020  1.090
 U9K  C12  H13  single    0.970  0.020  1.090
 U9K  C13  H15  single    0.970  0.020  1.090
 U9K  C13  H14  single    0.970  0.020  1.090
 U9K  C15  H17  single    0.970  0.020  1.090
 U9K  C15  H16  single    0.970  0.020  1.090
 U9K  C16  H19  single    0.970  0.020  1.090
 U9K  C16  H18  single    0.970  0.020  1.090
 U9K  C18  H23  single    0.970  0.020  1.090
 U9K  C18  H22  single    0.970  0.020  1.090
 U9K  C20  H28  single    0.970  0.020  1.090
 U9K  C20  H27  single    0.970  0.020  1.090
 U9K  C1   H1   single    0.970  0.020  1.090
 U9K  C1   H2   single    0.970  0.020  1.090
 U9K  C1   H3   single    0.970  0.020  1.090
 U9K  C2   H4   single    0.930  0.020  1.080
 U9K  C8   H7   single    0.930  0.020  1.080
 U9K  N3   H11  single    0.890  0.020  1.040
 U9K  O1   H29  single    0.850  0.020  0.980
 U9K  C17  H21  single    0.970  0.020  1.090
 U9K  C17  H20  single    0.970  0.020  1.090

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
 U9K  C4   N1   C2   106.80  3.000
 U9K  C2   N1   C1   126.36  3.000
 U9K  C4   N1   C1   126.80  3.000
 U9K  C2   N2   C3   105.33  3.000
 U9K  H5   C3   C4   127.15  3.000
 U9K  H5   C3   N2   122.44  3.000
 U9K  C4   C3   N2   110.40  3.000
 U9K  H26  N4   H25  107.27  3.000
 U9K  H26  N4   H24  107.09  3.000
 U9K  H25  N4   H24  106.75  3.000
 U9K  H26  N4   C18  111.74  3.000
 U9K  H25  N4   C18  112.33  3.000
 U9K  H24  N4   C18  111.34  3.000
 U9K  H6   C6   C5   120.22  3.000
 U9K  H6   C6   C7   120.27  3.000
 U9K  C5   C6   C7   119.51  3.000
 U9K  C8   C7   F1   119.24  3.000
 U9K  F1   C7   C6   118.62  3.000
 U9K  C8   C7   C6   122.14  3.000
 U9K  H8   C9   C8   118.80  3.000
 U9K  H8   C9   C10  119.68  3.000
 U9K  C8   C9   C10  121.51  3.000
 U9K  C5   C10  C11  121.98  3.000
 U9K  C5   C10  C9   119.21  3.000
 U9K  C11  C10  C9   118.79  3.000
 U9K  H10  C11  H9   108.34  3.000
 U9K  H10  C11  N3   106.02  3.000
 U9K  H9   C11  N3   105.93  3.000
 U9K  H10  C11  C10  110.82  3.000
 U9K  H9   C11  C10  113.13  3.000
 U9K  N3   C11  C10  112.21  3.000
 U9K  H13  C12  H12  108.46  3.000
 U9K  H13  C12  N3   106.57  3.000
 U9K  H12  C12  N3   107.06  3.000
 U9K  H13  C12  C13  111.98  3.000
 U9K  H12  C12  C13  110.36  3.000
 U9K  N3   C12  C13  112.19  3.000
 U9K  H14  C13  H15  106.67  3.000
 U9K  H14  C13  P1   108.77  3.000
 U9K  H15  C13  P1   109.25  3.000
 U9K  H14  C13  C12  108.26  3.000
 U9K  H15  C13  C12  110.82  3.000
 U9K  P1   C13  C12  112.85  3.000
 U9K  P1   C14  C20  108.79  3.000
 U9K  C20  C14  C19  106.17  3.000
 U9K  P1   C14  C19  106.45  3.000
 U9K  C20  C14  C15  113.32  3.000
 U9K  C19  C14  C15  113.13  3.000
 U9K  P1   C14  C15  108.70  3.000
 U9K  H16  C15  H17  104.88  3.000
 U9K  H16  C15  C16  108.96  3.000
 U9K  H17  C15  C16  107.68  3.000
 U9K  H16  C15  C14  107.86  3.000
 U9K  H17  C15  C14  110.09  3.000
 U9K  C16  C15  C14  116.72  3.000
 U9K  H18  C16  H19  106.77  3.000
 U9K  H18  C16  C17  107.90  3.000
 U9K  H19  C16  C17  111.15  3.000
 U9K  H18  C16  C15  111.25  3.000
 U9K  H19  C16  C15  109.17  3.000
 U9K  C17  C16  C15  110.54  3.000
 U9K  H22  C18  H23  108.52  3.000
 U9K  H22  C18  C17  111.32  3.000
 U9K  H23  C18  C17  111.66  3.000
 U9K  H22  C18  N4   106.29  3.000
 U9K  H23  C18  N4   106.58  3.000
 U9K  C17  C18  N4   112.19  3.000
 U9K  O4   C19  O3   126.23  3.000
 U9K  O4   C19  C14  119.25  3.000
 U9K  O3   C19  C14  114.52  3.000
 U9K  H27  C20  H28  107.53  3.000
 U9K  H27  C20  N3   107.04  3.000
 U9K  H28  C20  N3   105.82  3.000
 U9K  H27  C20  C14  109.26  3.000
 U9K  H28  C20  C14  112.07  3.000
 U9K  N3   C20  C14  114.76  3.000
 U9K  H3   C1   H2   108.94  3.000
 U9K  H3   C1   H1   108.43  3.000
 U9K  H2   C1   H1   108.71  3.000
 U9K  H3   C1   N1   111.44  3.000
 U9K  H2   C1   N1   110.40  3.000
 U9K  H1   C1   N1   108.86  3.000
 U9K  H4   C2   N2   126.12  3.000
 U9K  H4   C2   N1   121.68  3.000
 U9K  N2   C2   N1   112.19  3.000
 U9K  C5   C4   C3   131.26  3.000
 U9K  C3   C4   N1   105.28  3.000
 U9K  C5   C4   N1   123.44  3.000
 U9K  C4   C5   C10  122.12  3.000
 U9K  C4   C5   C6   118.35  3.000
 U9K  C10  C5   C6   119.52  3.000
 U9K  H7   C8   C9   121.02  3.000
 U9K  H7   C8   C7   120.92  3.000
 U9K  C9   C8   C7   118.06  3.000
 U9K  H11  N3   C20  109.24  3.000
 U9K  H11  N3   C12  107.38  3.000
 U9K  C20  N3   C12  112.41  3.000
 U9K  H11  N3   C11  106.79  3.000
 U9K  C12  N3   C11  109.42  3.000
 U9K  C20  N3   C11  111.36  3.000
 U9K  O2   P1   O1   117.43  3.000
 U9K  O1   P1   C14  102.51  3.000
 U9K  O2   P1   C14  114.05  3.000
 U9K  O1   P1   C13  103.93  3.000
 U9K  C14  P1   C13  103.38  3.000
 U9K  O2   P1   C13  113.86  3.000
 U9K  H29  O1   P1   104.59  3.000
 U9K  H20  C17  H21  106.22  3.000
 U9K  H20  C17  C18  109.84  3.000
 U9K  H21  C17  C18  106.19  3.000
 U9K  H20  C17  C16  110.61  3.000
 U9K  H21  C17  C16  109.39  3.000
 U9K  C18  C17  C16  114.20  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
 U9K  CONST_03  N2   C3   C4   N1      0.00   0.0  0
 U9K  CONST_04  C3   N2   C2   N1      0.00   0.0  0
 U9K  CONST_05  C5   C4   C3   N2    180.00   0.0  0
 U9K  CONST_06  C4   N1   C2   N2      0.00   0.0  0
 U9K  CONST_09  C2   N1   C4   C3      0.00   0.0  0
 U9K  CONST_10  C9   C8   C7   C6      0.00   0.0  0
 U9K  CONST_11  C9   C10  C5   C6      0.00   0.0  0
 U9K  CONST_12  C10  C9   C8   C7      0.00   0.0  0
 U9K  CONST_13  C10  C5   C6   C7      0.00   0.0  0
 U9K  CONST_14  C4   C5   C6   C7    180.00   0.0  0
 U9K  CONST_15  C4   C5   C10  C9    180.00   0.0  0
 U9K  CONST_16  C5   C4   N1   C2    180.00   0.0  0
 U9K  CONST_17  C4   C3   N2   C2      0.00   0.0  0
 U9K  CONST_18  C8   C9   C10  C5      0.00   0.0  0
 U9K  CONST_19  C8   C7   C6   C5      0.00   0.0  0
 U9K  CONST_20  C1   N1   C2   N2    180.00   0.0  0
 U9K  CONST_21  C1   N1   C4   C3    180.00   0.0  0
 U9K  CONST_22  C11  C10  C5   C6    180.00   0.0  0
 U9K  CONST_23  F1   C7   C8   C9    180.00   0.0  0
 U9K  CONST_24  C8   C9   C10  C11   180.00   0.0  0
 U9K  CONST_25  C4   C5   C10  C11     0.00   0.0  0
 U9K  CONST_26  C5   C4   N1   C1      0.00   0.0  0
 U9K  CONST_27  F1   C7   C6   C5    180.00   0.0  0
 U9K  CONST_28  H5   C3   C4   N1    180.00   0.0  0
 U9K  CONST_29  H4   C2   N2   C3    180.00   0.0  0
 U9K  CONST_30  H7   C8   C7   C6    180.00   0.0  0
 U9K  CONST_31  H8   C9   C8   C7    180.00   0.0  0
 U9K  CONST_32  H6   C6   C5   C10   180.00   0.0  0
 U9K  Var_01    C14  P1   C13  C12   -46.64  30.0  1
 U9K  Var_02    P1   C13  C12  N3     57.46  30.0  1
 U9K  Var_03    N3   C11  C10  C9     71.16  30.0  2
 U9K  Var_04    H1   C1   N1   C2      8.44  30.0  2
 U9K  Var_05    C17  C16  C15  C14  -178.58  30.0  2
 U9K  Var_06    C16  C17  C18  N4     66.91  30.0  3
 U9K  Var_07    C18  C17  C16  C15   173.07  30.0  1
 U9K  Var_08    H24  N4   C18  C17   179.39  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
 U9K  chir_01  C14  P1   C19  C20  positiv
 U9K  chir_02  N3   C12  C11  C20  negativ
 U9K  chir_03  P1   C14  C13  O1   both

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
 U9K  plan-1  N1   0.020
 U9K  plan-1  N2   0.020
 U9K  plan-1  C3   0.020
 U9K  plan-1  C1   0.020
 U9K  plan-1  C2   0.020
 U9K  plan-1  C4   0.020
 U9K  plan-1  C5   0.020
 U9K  plan-1  H5   0.020
 U9K  plan-1  H4   0.020
 U9K  plan-2  C6   0.020
 U9K  plan-2  C7   0.020
 U9K  plan-2  C9   0.020
 U9K  plan-2  C10  0.020
 U9K  plan-2  C11  0.020
 U9K  plan-2  C4   0.020
 U9K  plan-2  C5   0.020
 U9K  plan-2  C8   0.020
 U9K  plan-2  H6   0.020
 U9K  plan-2  H8   0.020
 U9K  plan-2  H7   0.020
 U9K  plan-2  F1   0.020
 U9K  plan-3  C14  0.020
 U9K  plan-3  C19  0.020
 U9K  plan-3  O3   0.020
 U9K  plan-3  O4   0.020

