# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 04:16:17 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: [(5R)-5-amino-5-carboxy-8-hydroxyoctyl](trihydroxy)borate(1-)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@](CCCO)(CCCC[B-](O)(O)O)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
 1EC  1EC  '[(5R)-5-amino-5-carboxy-8-hydroxyoctyl](trihydroxy)borate(1-)'  ligand  38  17  .  2021-08-03  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_1EC
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
 1EC  O3   O  OH1    0  -0.579  -1.8765  -2.3901   0.8353
 1EC  C1   C  C      0   0.560  -1.7901  -1.4953  -0.1363
 1EC  O2   O  O      0  -0.453  -1.8101  -1.7982  -1.3059
 1EC  C5   C  CT     0  -0.052  -1.6697  -0.0512   0.3393
 1EC  N16  N  NH2    0  -0.788  -1.6707   0.0179   1.7895
 1EC  C15  C  CH2    0  -0.407  -2.8048   0.7610  -0.3229
 1EC  C19  C  CH2    0  -0.475  -4.2162   0.3325   0.0604
 1EC  C20  C  CH2    0  -0.134  -5.2536   1.2513  -0.5561
 1EC  O21  O  OH1    0  -0.675  -6.5403   0.8177  -0.1700
 1EC  C6   C  CH2    0  -0.404  -0.3242   0.4908  -0.1778
 1EC  C7   C  CH2    0  -0.404   0.9204  -0.1983   0.3675
 1EC  C8   C  CH2    0  -0.430   2.2125   0.4003  -0.1807
 1EC  C9   C  CH2    0  -0.639   3.4823  -0.2560   0.3562
 1EC  B10  B  B     -1   0.429   4.9021   0.3847  -0.1772
 1EC  O23  O  OB     0  -0.747   6.0630  -0.3960   0.3070
 1EC  O13  O  OB     0  -0.753   5.0395   0.3163  -1.6487
 1EC  O11  O  OB     0  -0.751   4.9426   1.7859   0.3141
 1EC  H1   H  HOH1   0   0.477  -1.9555  -3.2758   0.4486
 1EC  H2   H  HNH2   0   0.347  -1.5166   0.9796   2.0689
 1EC  H3   H  HNH2   0   0.349  -2.5706  -0.2426   2.1738
 1EC  H5   H  HCH2   0   0.232  -2.6535   1.8069  -0.0365
 1EC  H6   H  HCH2   0   0.228  -2.6943   0.7237  -1.4098
 1EC  H7   H  HCH2   0   0.230  -4.4084  -0.6928  -0.2714
 1EC  H8   H  HCH2   0   0.218  -4.3378   0.3484   1.1472
 1EC  H9   H  HCH2   0   0.192  -5.0628   2.2812  -0.2258
 1EC  H10  H  HCH2   0   0.190  -5.1398   1.2453  -1.6487
 1EC  H11  H  HOH1   0   0.453  -7.1842   1.4333  -0.5305
 1EC  H12  H  HCH2   0   0.227  -0.3256   0.4396  -1.2696
 1EC  H13  H  HCH2   0   0.227  -0.2842   1.5574   0.0711
 1EC  H14  H  HCH2   0   0.208   0.9295  -0.1348   1.4586
 1EC  H15  H  HCH2   0   0.201   0.8982  -1.2682   0.1290
 1EC  H16  H  HCH2   0   0.177   2.1880   0.3278  -1.2763
 1EC  H17  H  HCH2   0   0.192   2.2270   1.4733   0.0408
 1EC  H18  H  HCH2   0   0.151   3.4374  -0.2232   1.4561
 1EC  H19  H  HCH2   0   0.153   3.4367  -1.3275   0.1099
 1EC  H20  H  H      0   0.417   5.9443  -0.5642   1.2440
 1EC  H21  H  H      0   0.417   4.2509   0.6859  -2.0513
 1EC  H22  H  H      0   0.417   5.7615   2.1928   0.0166

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
 1EC  O2   C1   double  1.208  0.020  1.208
 1EC  C20  O21  single  1.412  0.020  1.412
 1EC  C20  C19  single  1.517  0.020  1.517
 1EC  C15  C19  single  1.524  0.020  1.524
 1EC  C15  C5   single  1.545  0.020  1.545
 1EC  O23  B10  single  1.480  0.020  1.480
 1EC  C6   C5   single  1.540  0.020  1.540
 1EC  C6   C7   single  1.524  0.020  1.524
 1EC  C1   C5   single  1.525  0.020  1.525
 1EC  C1   O3   single  1.324  0.020  1.324
 1EC  C8   C7   single  1.526  0.020  1.526
 1EC  C8   C9   single  1.527  0.020  1.527
 1EC  C5   N16  single  1.452  0.020  1.452
 1EC  C9   B10  single  1.646  0.020  1.646
 1EC  B10  O11  single  1.485  0.020  1.485
 1EC  B10  O13  single  1.479  0.020  1.479
 1EC  O3   H1   single  0.850  0.020  0.980
 1EC  N16  H2   single  0.890  0.020  1.040
 1EC  N16  H3   single  0.890  0.020  1.040
 1EC  C15  H5   single  0.970  0.020  1.090
 1EC  C15  H6   single  0.970  0.020  1.090
 1EC  C19  H7   single  0.970  0.020  1.090
 1EC  C19  H8   single  0.970  0.020  1.090
 1EC  C20  H9   single  0.970  0.020  1.090
 1EC  C20  H10  single  0.970  0.020  1.090
 1EC  O21  H11  single  0.850  0.020  0.980
 1EC  C6   H12  single  0.970  0.020  1.090
 1EC  C6   H13  single  0.970  0.020  1.090
 1EC  C7   H14  single  0.970  0.020  1.090
 1EC  C7   H15  single  0.970  0.020  1.090
 1EC  C8   H16  single  0.970  0.020  1.090
 1EC  C8   H17  single  0.970  0.020  1.090
 1EC  C9   H18  single  0.970  0.020  1.090
 1EC  C9   H19  single  0.970  0.020  1.090
 1EC  O23  H20  single  0.850  0.020  0.980
 1EC  O13  H21  single  0.850  0.020  0.980
 1EC  O11  H22  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
 1EC  H1   O3   C1   109.27  3.000
 1EC  C5   C1   O2   122.72  3.000
 1EC  C5   C1   O3   114.60  3.000
 1EC  O2   C1   O3   122.68  3.000
 1EC  C6   C5   C15  108.24  3.000
 1EC  C6   C5   N16  108.62  3.000
 1EC  C15  C5   N16  113.75  3.000
 1EC  N16  C5   C1   110.88  3.000
 1EC  C6   C5   C1   107.31  3.000
 1EC  C15  C5   C1   107.82  3.000
 1EC  H3   N16  H2   105.95  3.000
 1EC  H3   N16  C5   111.56  3.000
 1EC  H2   N16  C5   108.69  3.000
 1EC  H6   C15  H5   106.18  3.000
 1EC  H6   C15  C19  109.52  3.000
 1EC  H5   C15  C19  109.32  3.000
 1EC  H6   C15  C5   109.51  3.000
 1EC  H5   C15  C5   106.77  3.000
 1EC  C19  C15  C5   115.14  3.000
 1EC  H8   C19  H7   107.18  3.000
 1EC  H8   C19  C20  108.60  3.000
 1EC  H7   C19  C20  108.91  3.000
 1EC  H8   C19  C15  110.42  3.000
 1EC  H7   C19  C15  110.47  3.000
 1EC  C20  C19  C15  111.15  3.000
 1EC  H10  C20  H9   106.63  3.000
 1EC  H10  C20  O21  111.39  3.000
 1EC  H9   C20  O21  111.35  3.000
 1EC  H10  C20  C19  109.28  3.000
 1EC  H9   C20  C19  109.09  3.000
 1EC  O21  C20  C19  109.04  3.000
 1EC  H11  O21  C20  108.14  3.000
 1EC  H13  C6   H12  105.82  3.000
 1EC  H13  C6   C7   109.21  3.000
 1EC  H12  C6   C7   109.71  3.000
 1EC  H13  C6   C5   107.35  3.000
 1EC  H12  C6   C5   108.53  3.000
 1EC  C7   C6   C5   115.74  3.000
 1EC  H15  C7   H14  105.90  3.000
 1EC  H15  C7   C8   108.78  3.000
 1EC  H14  C7   C8   109.20  3.000
 1EC  H15  C7   C6   110.30  3.000
 1EC  H14  C7   C6   109.74  3.000
 1EC  C8   C7   C6   112.69  3.000
 1EC  H17  C8   H16  105.46  3.000
 1EC  H17  C8   C9   109.81  3.000
 1EC  H16  C8   C9   109.93  3.000
 1EC  H17  C8   C7   108.83  3.000
 1EC  H16  C8   C7   108.27  3.000
 1EC  C9   C8   C7   114.16  3.000
 1EC  H19  C9   H18  104.53  3.000
 1EC  H19  C9   B10  110.01  3.000
 1EC  H18  C9   B10  110.31  3.000
 1EC  H19  C9   C8   107.78  3.000
 1EC  H18  C9   C8   107.73  3.000
 1EC  B10  C9   C8   115.85  3.000
 1EC  O11  B10  O13  111.72  3.000
 1EC  O13  B10  O23  103.18  3.000
 1EC  O11  B10  O23  111.59  3.000
 1EC  O13  B10  C9   112.60  3.000
 1EC  O11  B10  C9   106.47  3.000
 1EC  O23  B10  C9   111.41  3.000
 1EC  H20  O23  B10  108.35  3.000
 1EC  H21  O13  B10  108.85  3.000
 1EC  H22  O11  B10  108.67  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
 1EC  CONST_01  H1   O3   C1   O2      0.00   0.0  0
 1EC  Var_01    C20  C19  C15  C5    175.75  30.0  3
 1EC  Var_02    C8   C7   C6   C5   -179.52  30.0  3
 1EC  Var_03    O21  C20  C19  C15  -179.81  30.0  1
 1EC  Var_04    C9   C8   C7   C6    179.37  30.0  1
 1EC  Var_05    B10  C9   C8   C7   -178.41  30.0  3
 1EC  Var_06    O23  B10  C9   C8   -175.00  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
 1EC  chir_01  C5  C6  C1  N16  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
 1EC  plan-1  O3  0.020
 1EC  plan-1  C1  0.020
 1EC  plan-1  O2  0.020
 1EC  plan-1  C5  0.020
 1EC  plan-1  H1  0.020

