# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 11:59:07 2022
#   Inital geometry file: a 119 line input string
#   Ligand name: 4-[(1~{R},3~{S})-3-carboxy-4-oxidanyl-4-oxidanylidene-1-(phenylmethyl)-1,4$l^{5}-azaphosphinan-1-ium-3-yl]butylazanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [NH3+]CCCC[C@]1(C[NH+](CC[P]1(O)=O)Cc2ccccc2)C(O)=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 U9B  U9B  4-[(1~{R},3~{S})-3-carboxy-4-oxidanyl-4-oxidanylidene-1-(phenylmethyl)-1,4$l^{5}-azaphosphinan-1-ium-3-yl]butylazanium  ligand  49  23  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_U9B
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
 U9B  C1   C  CH2    0  -0.330   8.1564  13.2803  25.5355
 U9B  C2   C  CH2    0  -0.453   8.5316  14.1471  24.3501
 U9B  C5   C  CT     0  -0.524  11.7994  15.7766  22.9343
 U9B  C6   C  C      0   0.492  12.2385  16.7058  24.1231
 U9B  C7   C  CH2    0  -0.308  12.7080  14.5486  22.9068
 U9B  C8   C  CH2    0  -0.381  13.0612  12.2589  22.0237
 U9B  C15  C  CH2    0  -0.311  12.8562  14.1768  20.4609
 U9B  C16  C  CH2    0  -0.758  12.0295  15.3957  20.1010
 U9B  N1   N  NT3    1  -0.777   8.1258  14.0569  26.8093
 U9B  C3   C  CH2    0  -0.439   9.9843  14.6096  24.3539
 U9B  C4   C  CH2    0  -0.457  10.3095  15.4074  23.0931
 U9B  O1   O  OC    -1  -0.571  11.7116  17.8279  24.1329
 U9B  O2   O  O      0  -0.561  13.0470  16.2242  24.9300
 U9B  N2   N  NT1    1  -0.545  12.4300  13.6029  21.7741
 U9B  C9   C  CR6    0   0.068  12.3737  11.5493  23.1513
 U9B  C10  C  CR16   0  -0.283  12.9681  11.4493  24.4055
 U9B  C11  C  CR16   0  -0.240  12.2987  10.8283  25.4512
 U9B  C12  C  CR16   0  -0.252  11.0299  10.3029  25.2501
 U9B  C13  C  CR16   0  -0.238  10.4345  10.3903  23.9976
 U9B  C14  C  CR16   0  -0.284  11.1052  11.0070  22.9523
 U9B  P1   P  P      0   1.283  11.9921  16.7027  21.3714
 U9B  O3   O  OH1    0  -0.751  13.5267  17.1899  21.5181
 U9B  O4   O  O      0  -0.697  10.9881  17.7481  21.0322
 U9B  H5   H  HCH2   0   0.303   7.1638  12.8528  25.4157
 U9B  H4   H  HCH2   0   0.293   8.8685  12.4697  25.6801
 U9B  H7   H  HCH2   0   0.255   7.8512  15.0011  24.2835
 U9B  H6   H  HCH2   0   0.263   8.3519  13.5419  23.4584
 U9B  H12  H  HCH2   0   0.314  12.5952  13.9869  23.8298
 U9B  H13  H  HCH2   0   0.316  13.7607  14.8152  22.8206
 U9B  H15  H  HCH2   0   0.319  12.9754  11.6957  21.0949
 U9B  H16  H  HCH2   0   0.318  14.1177  12.4347  22.2236
 U9B  H23  H  HCH2   0   0.315  12.7291  13.4001  19.7088
 U9B  H22  H  HCH2   0   0.305  13.9180  14.4054  20.5471
 U9B  H24  H  HCH2   0   0.320  12.4220  15.8222  19.1748
 U9B  H25  H  HCH2   0   0.300  10.9973  15.1033  19.8919
 U9B  H3   H  HNT3   0   0.477   7.8508  13.4693  27.5968
 U9B  H1   H  HNT3   0   0.473   9.0335  14.4583  27.0452
 U9B  H2   H  HNT3   0   0.470   7.4567  14.8275  26.7658
 U9B  H9   H  HCH2   0   0.235  10.6215  13.7245  24.4353
 U9B  H8   H  HCH2   0   0.243  10.1960  15.2265  25.2316
 U9B  H11  H  HCH2   0   0.271   9.7276  16.3301  23.0951
 U9B  H10  H  HCH2   0   0.241   9.9468  14.8468  22.2226
 U9B  H14  H  HNT1   0   0.466  11.4214  13.4376  21.7221
 U9B  H17  H  HCR6   0   0.272  13.9572  11.8612  24.5683
 U9B  H18  H  HCR6   0   0.264  12.7685  10.7573  26.4232
 U9B  H19  H  HCR6   0   0.266  10.5068   9.8203  26.0656
 U9B  H20  H  HCR6   0   0.265   9.4496   9.9730  23.8336
 U9B  H21  H  HCR6   0   0.268  10.6389  11.0627  21.9747
 U9B  H27  H  HOH1   0   0.488  13.8724  17.6429  20.7364

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
 U9B  C16  C15  single    1.516  0.020  1.516
 U9B  C16  P1   single    1.823  0.020  1.823
 U9B  C15  N2   single    1.495  0.020  1.495
 U9B  O4   P1   double    1.489  0.020  1.489
 U9B  N2   C8   single    1.506  0.020  1.506
 U9B  N2   C7   single    1.501  0.020  1.501
 U9B  C8   C9   single    1.499  0.020  1.499
 U9B  P1   O3   single    1.617  0.020  1.617
 U9B  P1   C5   single    1.827  0.020  1.827
 U9B  C7   C5   single    1.528  0.020  1.528
 U9B  C9   C14  aromatic  1.394  0.020  1.394
 U9B  C9   C10  aromatic  1.392  0.020  1.392
 U9B  C5   C4   single    1.543  0.020  1.543
 U9B  C5   C6   single    1.571  0.020  1.571
 U9B  C14  C13  aromatic  1.387  0.020  1.387
 U9B  C4   C3   single    1.527  0.020  1.527
 U9B  C10  C11  aromatic  1.388  0.020  1.388
 U9B  C6   O2   deloc     1.240  0.020  1.240
 U9B  C6   O1   deloc     1.240  0.020  1.240
 U9B  C13  C12  aromatic  1.390  0.020  1.390
 U9B  C3   C2   single    1.524  0.020  1.524
 U9B  C2   C1   single    1.516  0.020  1.516
 U9B  C11  C12  aromatic  1.388  0.020  1.388
 U9B  C1   N1   single    1.492  0.020  1.492
 U9B  C1   H5   single    0.970  0.020  1.090
 U9B  C1   H4   single    0.970  0.020  1.090
 U9B  C2   H7   single    0.970  0.020  1.090
 U9B  C2   H6   single    0.970  0.020  1.090
 U9B  C7   H12  single    0.970  0.020  1.090
 U9B  C7   H13  single    0.970  0.020  1.090
 U9B  C8   H15  single    0.970  0.020  1.090
 U9B  C8   H16  single    0.970  0.020  1.090
 U9B  C15  H23  single    0.970  0.020  1.090
 U9B  C15  H22  single    0.970  0.020  1.090
 U9B  C16  H24  single    0.970  0.020  1.090
 U9B  C16  H25  single    0.970  0.020  1.090
 U9B  N1   H3   single    0.890  0.020  1.040
 U9B  N1   H1   single    0.890  0.020  1.040
 U9B  N1   H2   single    0.890  0.020  1.040
 U9B  C3   H9   single    0.970  0.020  1.090
 U9B  C3   H8   single    0.970  0.020  1.090
 U9B  C4   H11  single    0.970  0.020  1.090
 U9B  C4   H10  single    0.970  0.020  1.090
 U9B  N2   H14  single    0.890  0.020  1.040
 U9B  C10  H17  single    0.930  0.020  1.080
 U9B  C11  H18  single    0.930  0.020  1.080
 U9B  C12  H19  single    0.930  0.020  1.080
 U9B  C13  H20  single    0.930  0.020  1.080
 U9B  C14  H21  single    0.930  0.020  1.080
 U9B  O3   H27  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
 U9B  H4   C1   H5   108.60  3.000
 U9B  H4   C1   N1   106.72  3.000
 U9B  H5   C1   N1   106.26  3.000
 U9B  H4   C1   C2   111.58  3.000
 U9B  H5   C1   C2   111.39  3.000
 U9B  N1   C1   C2   112.03  3.000
 U9B  H6   C2   H7   106.28  3.000
 U9B  H6   C2   C3   109.08  3.000
 U9B  H7   C2   C3   110.85  3.000
 U9B  H6   C2   C1   106.31  3.000
 U9B  H7   C2   C1   109.88  3.000
 U9B  C3   C2   C1   114.04  3.000
 U9B  P1   C5   C4   108.13  3.000
 U9B  C4   C5   C7   112.56  3.000
 U9B  P1   C5   C7   109.23  3.000
 U9B  C4   C5   C6   109.48  3.000
 U9B  C7   C5   C6   108.82  3.000
 U9B  P1   C5   C6   108.54  3.000
 U9B  O2   C6   O1   128.59  3.000
 U9B  O1   C6   C5   114.99  3.000
 U9B  O2   C6   C5   116.42  3.000
 U9B  H13  C7   H12  107.10  3.000
 U9B  H13  C7   N2   105.87  3.000
 U9B  H12  C7   N2   107.23  3.000
 U9B  H13  C7   C5   112.30  3.000
 U9B  H12  C7   C5   109.79  3.000
 U9B  N2   C7   C5   114.18  3.000
 U9B  H16  C8   H15  108.44  3.000
 U9B  H16  C8   C9   112.52  3.000
 U9B  H15  C8   C9   111.12  3.000
 U9B  H16  C8   N2   107.03  3.000
 U9B  H15  C8   N2   106.68  3.000
 U9B  C9   C8   N2   110.79  3.000
 U9B  H22  C15  H23  108.54  3.000
 U9B  H22  C15  N2   106.79  3.000
 U9B  H23  C15  N2   107.44  3.000
 U9B  H22  C15  C16  112.42  3.000
 U9B  H23  C15  C16  110.24  3.000
 U9B  N2   C15  C16  111.20  3.000
 U9B  H25  C16  H24  106.36  3.000
 U9B  H25  C16  P1   107.80  3.000
 U9B  H24  C16  P1   108.56  3.000
 U9B  H25  C16  C15  110.19  3.000
 U9B  H24  C16  C15  108.61  3.000
 U9B  P1   C16  C15  114.97  3.000
 U9B  H2   N1   H1   107.21  3.000
 U9B  H2   N1   H3   106.90  3.000
 U9B  H1   N1   H3   106.73  3.000
 U9B  H2   N1   C1   111.70  3.000
 U9B  H1   N1   C1   112.58  3.000
 U9B  H3   N1   C1   111.39  3.000
 U9B  H8   C3   H9   106.50  3.000
 U9B  H8   C3   C4   109.07  3.000
 U9B  H9   C3   C4   111.11  3.000
 U9B  H8   C3   C2   110.96  3.000
 U9B  H9   C3   C2   108.05  3.000
 U9B  C4   C3   C2   111.06  3.000
 U9B  H10  C4   H11  104.91  3.000
 U9B  H10  C4   C3   108.53  3.000
 U9B  H11  C4   C3   109.07  3.000
 U9B  H10  C4   C5   111.09  3.000
 U9B  H11  C4   C5   108.23  3.000
 U9B  C3   C4   C5   114.56  3.000
 U9B  H14  N2   C15  107.36  3.000
 U9B  H14  N2   C8   106.10  3.000
 U9B  C15  N2   C8   111.63  3.000
 U9B  H14  N2   C7   108.82  3.000
 U9B  C8   N2   C7   111.07  3.000
 U9B  C15  N2   C7   111.60  3.000
 U9B  C14  C9   C10  119.30  3.000
 U9B  C10  C9   C8   121.07  3.000
 U9B  C14  C9   C8   119.61  3.000
 U9B  H17  C10  C11  119.80  3.000
 U9B  H17  C10  C9   119.86  3.000
 U9B  C11  C10  C9   120.34  3.000
 U9B  H18  C11  C12  120.15  3.000
 U9B  H18  C11  C10  119.78  3.000
 U9B  C12  C11  C10  120.07  3.000
 U9B  H19  C12  C13  120.01  3.000
 U9B  H19  C12  C11  120.09  3.000
 U9B  C13  C12  C11  119.90  3.000
 U9B  H20  C13  C14  119.83  3.000
 U9B  H20  C13  C12  120.16  3.000
 U9B  C14  C13  C12  120.02  3.000
 U9B  H21  C14  C13  119.63  3.000
 U9B  H21  C14  C9   120.00  3.000
 U9B  C13  C14  C9   120.37  3.000
 U9B  O4   P1   O3   116.70  3.000
 U9B  O3   P1   C16  105.06  3.000
 U9B  O4   P1   C16  111.01  3.000
 U9B  O3   P1   C5   100.09  3.000
 U9B  O4   P1   C5   118.67  3.000
 U9B  C16  P1   C5   103.59  3.000
 U9B  H27  O3   P1   114.01  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
 U9B  CONST_01  C12  C13  C14  C9      0.00   0.0  0
 U9B  CONST_02  C12  C11  C10  C9      0.00   0.0  0
 U9B  CONST_03  C13  C14  C9   C10     0.00   0.0  0
 U9B  CONST_04  C13  C12  C11  C10     0.00   0.0  0
 U9B  CONST_05  C14  C9   C10  C11     0.00   0.0  0
 U9B  CONST_06  C14  C13  C12  C11     0.00   0.0  0
 U9B  CONST_07  C13  C14  C9   C8    180.00   0.0  0
 U9B  CONST_08  C11  C10  C9   C8    180.00   0.0  0
 U9B  CONST_09  H20  C13  C14  C9    180.00   0.0  0
 U9B  CONST_10  H18  C11  C10  C9    180.00   0.0  0
 U9B  CONST_11  H21  C14  C9   C10   180.00   0.0  0
 U9B  CONST_12  H19  C12  C11  C10   180.00   0.0  0
 U9B  CONST_13  H17  C10  C11  C12   180.00   0.0  0
 U9B  Var_01    C15  C16  P1   C5    -42.25  30.0  1
 U9B  Var_02    P1   C16  C15  N2     54.11  30.0  1
 U9B  Var_03    C14  C9   C8   N2     73.32  30.0  2
 U9B  Var_04    C5   C4   C3   C2   -173.28  30.0  1
 U9B  Var_05    C4   C3   C2   C1    176.70  30.0  2
 U9B  Var_06    C3   C2   C1   N1     69.73  30.0  1
 U9B  Var_07    H3   N1   C1   C2    178.65  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
 U9B  chir_01  C5  C7  P1  C6   positiv
 U9B  chir_02  N2  C7  C8  C15  positiv
 U9B  chir_03  P1  O4  O3  C5   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
 U9B  plan-1  C8   0.020
 U9B  plan-1  C9   0.020
 U9B  plan-1  C10  0.020
 U9B  plan-1  C11  0.020
 U9B  plan-1  C12  0.020
 U9B  plan-1  C13  0.020
 U9B  plan-1  C14  0.020
 U9B  plan-1  H17  0.020
 U9B  plan-1  H18  0.020
 U9B  plan-1  H19  0.020
 U9B  plan-1  H20  0.020
 U9B  plan-1  H21  0.020
 U9B  plan-2  C5   0.020
 U9B  plan-2  C6   0.020
 U9B  plan-2  O1   0.020
 U9B  plan-2  O2   0.020

