# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 05:42:38 2022
#   Inital geometry file: a 80 line input string
#   Ligand name: {3-[(2S,3R)-2-carboxypiperidin-3-yl]propyl}(trihydroxy)borate(1-)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H]1NCCC[C@H]1CCC[B-](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
 XFP  XFP  "3-[(2~{S},3~{R})-2-carboxypiperidin-3-yl]propyl-$l^{3}-oxidanyl-bis(oxidanyl)boranuide"
  ligand  34  16  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XFP
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
 XFP  O3   O  OC    -1  -0.610  18.1377  7.0545  24.6285
 XFP  C8   C  C      0   0.403  17.1266  7.7418  24.3777
 XFP  O4   O  O      0  -0.600  17.1122  8.9230  23.9774
 XFP  C    C  CH1    0  -0.202  15.7609  7.0740  24.6576
 XFP  C1   C  CH1    0  -0.206  15.6512  5.6271  24.1587
 XFP  C2   C  CH2    0  -0.438  14.3041  5.0661  24.6348
 XFP  C3   C  CH2    0  -0.426  13.1338  5.9515  24.2169
 XFP  C4   C  CH2    0  -0.283  13.3817  7.3935  24.6400
 XFP  N    N  NH1    0  -0.595  14.6554  7.8451  24.1211
 XFP  C5   C  CH2    0  -0.395  15.8607  5.5074  22.6462
 XFP  C6   C  CH2    0  -0.427  15.8447  4.0775  22.1094
 XFP  C7   C  CH2    0  -0.672  16.2129  3.9476  20.6317
 XFP  B    B  B     -1   0.484  16.1767  2.4053  20.0246
 XFP  O2   O  OB     0  -0.750  17.0950  1.5322  20.8147
 XFP  O1   O  OB     0  -0.740  16.5159  2.4069  18.5821
 XFP  O    O  OB     0  -0.742  14.8296  1.8085  20.0709
 XFP  H2   H  HCH1   0   0.180  15.6911  7.0214  25.7658
 XFP  H3   H  HCH1   0   0.196  16.4434  5.0505  24.6464
 XFP  H4   H  HCH2   0   0.223  14.1544  4.0434  24.2800
 XFP  H5   H  HCH2   0   0.206  14.3239  5.0060  25.7292
 XFP  H6   H  HCH2   0   0.216  12.2047  5.5889  24.6639
 XFP  H7   H  HCH2   0   0.210  12.9980  5.9104  23.1322
 XFP  H8   H  HCH2   0   0.167  13.3338  7.4460  25.7434
 XFP  H9   H  HCH2   0   0.216  12.5876  8.0415  24.2604
 XFP  H10  H  HNH1   0   0.331  14.8041  8.8238  24.3240
 XFP  H12  H  HCH2   0   0.198  16.8316  5.9495  22.3982
 XFP  H13  H  HCH2   0   0.191  15.1178  6.1049  22.1103
 XFP  H14  H  HCH2   0   0.180  14.8503  3.6451  22.2722
 XFP  H15  H  HCH2   0   0.173  16.5290  3.4708  22.7156
 XFP  H16  H  HCH2   0   0.143  17.2095  4.4005  20.4929
 XFP  H17  H  HCH2   0   0.148  15.5351  4.5924  20.0528
 XFP  H18  H  H      0   0.405  17.7964  2.0720  21.1841
 XFP  H19  H  H      0   0.406  17.2476  3.0112  18.4436
 XFP  H20  H  H      0   0.409  14.5536  1.7623  20.9881

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
 XFP  O1  B    single  1.482  0.020  1.482
 XFP  O   B    single  1.474  0.020  1.474
 XFP  B   O2   single  1.493  0.020  1.493
 XFP  B   C7   single  1.658  0.020  1.658
 XFP  C7  C6   single  1.528  0.020  1.528
 XFP  C6  C5   single  1.527  0.020  1.527
 XFP  C5  C1   single  1.532  0.020  1.532
 XFP  O4  C8   deloc   1.247  0.020  1.247
 XFP  C8  O3   deloc   1.248  0.020  1.248
 XFP  C8  C    single  1.546  0.020  1.546
 XFP  N   C    single  1.451  0.020  1.451
 XFP  N   C4   single  1.448  0.020  1.448
 XFP  C1  C    single  1.534  0.020  1.534
 XFP  C1  C2   single  1.535  0.020  1.535
 XFP  C3  C4   single  1.523  0.020  1.523
 XFP  C3  C2   single  1.526  0.020  1.526
 XFP  C   H2   single  0.970  0.020  1.090
 XFP  C1  H3   single  0.970  0.020  1.090
 XFP  C2  H4   single  0.970  0.020  1.090
 XFP  C2  H5   single  0.970  0.020  1.090
 XFP  C3  H6   single  0.970  0.020  1.090
 XFP  C3  H7   single  0.970  0.020  1.090
 XFP  C4  H8   single  0.970  0.020  1.090
 XFP  C4  H9   single  0.970  0.020  1.090
 XFP  N   H10  single  0.890  0.020  1.040
 XFP  C5  H12  single  0.970  0.020  1.090
 XFP  C5  H13  single  0.970  0.020  1.090
 XFP  C6  H14  single  0.970  0.020  1.090
 XFP  C6  H15  single  0.970  0.020  1.090
 XFP  C7  H16  single  0.970  0.020  1.090
 XFP  C7  H17  single  0.970  0.020  1.090
 XFP  O2  H18  single  0.850  0.020  0.980
 XFP  O1  H19  single  0.850  0.020  0.980
 XFP  O   H20  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
 XFP  C    C8  O4   117.20  3.000
 XFP  C    C8  O3   116.20  3.000
 XFP  O4   C8  O3   126.53  3.000
 XFP  H2   C   N    110.24  3.000
 XFP  H2   C   C1   105.97  3.000
 XFP  N    C   C1   109.05  3.000
 XFP  H2   C   C8   104.86  3.000
 XFP  C1   C   C8   114.31  3.000
 XFP  N    C   C8   112.12  3.000
 XFP  H3   C1  C5   107.45  3.000
 XFP  H3   C1  C2   107.73  3.000
 XFP  C5   C1  C2   113.44  3.000
 XFP  H3   C1  C    107.47  3.000
 XFP  C2   C1  C    107.85  3.000
 XFP  C5   C1  C    112.64  3.000
 XFP  H5   C2  H4   105.98  3.000
 XFP  H5   C2  C3   108.61  3.000
 XFP  H4   C2  C3   110.43  3.000
 XFP  H5   C2  C1   108.29  3.000
 XFP  H4   C2  C1   111.20  3.000
 XFP  C3   C2  C1   112.09  3.000
 XFP  H7   C3  H6   106.71  3.000
 XFP  H7   C3  C4   109.34  3.000
 XFP  H6   C3  C4   109.81  3.000
 XFP  H7   C3  C2   110.18  3.000
 XFP  H6   C3  C2   110.33  3.000
 XFP  C4   C3  C2   110.39  3.000
 XFP  H9   C4  H8   106.67  3.000
 XFP  H9   C4  N    109.26  3.000
 XFP  H8   C4  N    112.40  3.000
 XFP  H9   C4  C3   110.28  3.000
 XFP  H8   C4  C3   108.37  3.000
 XFP  N    C4  C3   109.82  3.000
 XFP  H10  N   C4   111.08  3.000
 XFP  H10  N   C    109.17  3.000
 XFP  C4   N   C    111.84  3.000
 XFP  H13  C5  H12  105.71  3.000
 XFP  H13  C5  C6   109.39  3.000
 XFP  H12  C5  C6   107.91  3.000
 XFP  H13  C5  C1   110.38  3.000
 XFP  H12  C5  C1   108.26  3.000
 XFP  C6   C5  C1   114.76  3.000
 XFP  H15  C6  H14  105.40  3.000
 XFP  H15  C6  C7   109.69  3.000
 XFP  H14  C6  C7   109.18  3.000
 XFP  H15  C6  C5   108.48  3.000
 XFP  H14  C6  C5   109.06  3.000
 XFP  C7   C6  C5   114.63  3.000
 XFP  H17  C7  H16  104.46  3.000
 XFP  H17  C7  B    109.82  3.000
 XFP  H16  C7  B    110.83  3.000
 XFP  H17  C7  C6   108.09  3.000
 XFP  H16  C7  C6   107.71  3.000
 XFP  B    C7  C6   115.33  3.000
 XFP  O    B   O1   103.90  3.000
 XFP  O    B   O2   107.98  3.000
 XFP  O1   B   O2   112.02  3.000
 XFP  O2   B   C7   109.68  3.000
 XFP  O    B   C7   112.65  3.000
 XFP  O1   B   C7   110.51  3.000
 XFP  H18  O2  B    108.94  3.000
 XFP  H19  O1  B    108.42  3.000
 XFP  H20  O   B    108.21  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
 XFP  Var_01  C3   C4  N   C    -62.55  30.0  1
 XFP  Var_02  C4   C3  C2  C1   -52.08  30.0  1
 XFP  Var_03  N    C4  C3  C2    54.37  30.0  1
 XFP  Var_04  H8   C4  N   C     58.17  30.0  1
 XFP  Var_05  H9   C4  N   C    176.38  30.0  1
 XFP  Var_06  H6   C3  C2  C1  -173.63  30.0  1
 XFP  Var_07  H7   C3  C2  C1    68.79  30.0  1
 XFP  Var_08  H8   C4  C3  C2   -68.76  30.0  1
 XFP  Var_09  H9   C4  C3  C2   174.82  30.0  1
 XFP  Var_10  H10  N   C4  C3   175.19  30.0  1
 XFP  Var_11  H4   C2  C3  C4  -176.66  30.0  1
 XFP  Var_12  H5   C2  C3  C4    67.53  30.0  1
 XFP  Var_13  H6   C3  C4  N    176.23  30.0  1
 XFP  Var_14  H7   C3  C4  N    -67.00  30.0  1
 XFP  Var_15  C7   C6  C5  C1  -173.29  30.0  1
 XFP  Var_16  H14  C6  C5  C1    63.98  30.0  1
 XFP  Var_17  H15  C6  C5  C1   -50.33  30.0  1
 XFP  Var_18  B    C7  C6  C5  -179.03  30.0  1
 XFP  Var_19  O1   B   C7  C6   178.56  30.0  2
 XFP  Var_20  O    B   C7  C6    62.84  30.0  2
 XFP  Var_21  O2   B   C7  C6   -57.46  30.0  2
 XFP  Var_22  H16  C7  C6  C5    56.62  30.0  1
 XFP  Var_23  H17  C7  C6  C5   -55.72  30.0  1
 XFP  Var_24  H12  C5  C6  C7   -52.51  30.0  3
 XFP  Var_25  H13  C5  C6  C7    62.03  30.0  3
 XFP  Var_26  H14  C6  C7  B    -56.37  30.0  3
 XFP  Var_27  H15  C6  C7  B     58.66  30.0  3
 XFP  Var_28  H16  C7  B   O2    65.23  30.0  3
 XFP  Var_29  H17  C7  B   O2  -179.86  30.0  3
 XFP  Var_30  H16  C7  B   O1   -58.75  30.0  3
 XFP  Var_31  H17  C7  B   O1    56.16  30.0  3
 XFP  Var_32  H16  C7  B   O   -174.47  30.0  3
 XFP  Var_33  H17  C7  B   O    -59.56  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
 XFP  chir_01  C   C8  N  C1  negativ
 XFP  chir_02  C1  C5  C  C2  negativ

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
 XFP  plan-1  O3  0.020
 XFP  plan-1  C8  0.020
 XFP  plan-1  O4  0.020
 XFP  plan-1  C   0.020

