# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 03:34:26 2022
#   Inital geometry file: a 103 line input string
#   Ligand name: [(1S)-1-(acetylamino)-2-(4-chlorophenyl)ethyl](dihydroxy)(L-serinato-kappaO~3~)borate(1-)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@H](Cc1ccc(Cl)cc1)[B-](O)(O)OC[C@H](N)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
 CLD  CLD  '[(1S)-1-(acetylamino)-2-(4-chlorophenyl)ethyl](dihydroxy)(L-serinato-kappaO~3~)borate(1-)'  D-peptide  41  23  .  2016-05-13  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_CLD
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
 CLD  N     N   NH2    0  -0.803  16.8563   3.6597  27.1595
 CLD  CA    C   CH1    0  -0.252  18.1063   3.2300  26.5495
 CLD  CB    C   CH2    0  -0.073  18.0962   3.5994  25.0703
 CLD  OB3   O   OC2    0  -0.556  17.0149   2.9906  24.4356
 CLD  C     C   C      0   0.395  19.3340   3.8377  27.2674
 CLD  O     O   O      0  -0.615  20.4369   3.6493  26.7115
 CLD  OXT   O   OC    -1  -0.603  19.1395   4.4358  28.3434
 CLD  N9    N   NH1    0  -0.627  15.0200   2.7946  21.2344
 CLD  C8    C   CH1    0  -0.233  15.3136   2.5831  22.6441
 CLD  C7    C   CH2    0  -0.536  14.1586   3.1266  23.5050
 CLD  C1    C   CR6    0   0.174  12.8469   2.4470  23.2504
 CLD  C2    C   CR16   0  -0.321  11.9383   2.9402  22.3166
 CLD  C3    C   CR16   0  -0.200  10.7452   2.2831  22.0461
 CLD  C6    C   CR16   0  -0.321  12.5187   1.2656  23.9140
 CLD  C5    C   CR16   0  -0.197  11.3310   0.5954  23.6646
 CLD  C4    C   CR6    0  -0.062  10.4505   1.1137  22.7273
 CLD  CL4   CL  CL     0  -0.145   8.9531   0.2898  22.4123
 CLD  OB1   O   OB     0  -0.754  16.6659   4.6962  22.6876
 CLD  OB2   O   OB     0  -0.720  17.8718   2.6171  22.2509
 CLD  B     B   B     -1   0.508  16.7799   3.2590  23.0097
 CLD  O10   O   O      0  -0.522  14.3838   0.7044  20.6156
 CLD  C11   C   CH3    0  -0.776  14.3483   2.4187  18.9550
 CLD  H     H   HNH2   0   0.324  16.9033   3.5056  28.1574
 CLD  H2    H   HNH2   0   0.327  16.1044   3.0815  26.8085
 CLD  HA    H   HCH1   0   0.174  18.2392   2.1331  26.6055
 CLD  HB2   H   HCH2   0   0.137  18.0465   4.7000  24.9984
 CLD  HB3   H   HCH2   0   0.152  19.0561   3.3000  24.6313
 CLD  HN9   H   HNH1   0   0.378  15.1631   3.7346  20.8995
 CLD  H8    H   HCH1   0   0.187  15.3727   1.5018  22.7986
 CLD  H71   H   HCH2   0   0.232  14.4334   3.0057  24.5545
 CLD  H72   H   HCH2   0   0.218  14.0549   4.2015  23.3316
 CLD  HC2   H   HCR6   0   0.248  12.1605   3.8600  21.7892
 CLD  H3    H   HCR6   0   0.269  10.0534   2.6847  21.3175
 CLD  H6    H   HCR6   0   0.249  13.2044   0.8567  24.6474
 CLD  H5    H   HCR6   0   0.269  11.0936  -0.3164  24.1967
 CLD  HOB1  H   H      0   0.419  17.5386   5.0953  22.6519
 CLD  HOB2  H   H      0   0.416  17.7041   2.7220  21.3112
 CLD  H111  H   HCH3   0   0.252  14.9607   1.8627  18.2448
 CLD  H112  H   HCH3   0   0.252  13.3065   2.2578  18.6762
 CLD  H113  H   HCH3   0   0.238  14.5714   3.4786  18.8432
 CLD  C10   C   C      0   0.500  14.5807   1.8888  20.3541

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
 CLD  N    CA    single    1.458  0.019  1.458
 CLD  N    H     single    0.860  0.020  0.860
 CLD  N    H2    single    0.890  0.020  1.040
 CLD  CA   CB    single    1.521  0.033  1.521
 CLD  CA   C     single    1.525  0.021  1.525
 CLD  CA   HA    single    0.970  0.020  0.970
 CLD  CB   OB3   single    1.394  0.020  1.394
 CLD  CB   HB2   single    0.970  0.020  1.090
 CLD  CB   HB3   single    0.970  0.020  1.090
 CLD  OB3  B     single    1.470  0.020  1.470
 CLD  C    O     deloc     1.231  0.020  1.231
 CLD  C    OXT   deloc     1.246  0.020  1.246
 CLD  N9   C8    single    1.455  0.020  1.455
 CLD  N9   C10   single    1.337  0.020  1.337
 CLD  N9   HN9   single    0.860  0.020  1.020
 CLD  C8   C7    single    1.540  0.020  1.540
 CLD  C8   B     single    1.655  0.020  1.655
 CLD  C8   H8    single    0.970  0.020  1.090
 CLD  C7   C1    single    1.499  0.020  1.499
 CLD  C7   H71   single    0.970  0.020  1.090
 CLD  C7   H72   single    0.970  0.020  1.090
 CLD  C1   C2    aromatic  1.393  0.020  1.393
 CLD  C1   C6    aromatic  1.394  0.020  1.394
 CLD  C2   C3    aromatic  1.389  0.020  1.389
 CLD  C2   HC2   single    0.930  0.020  1.080
 CLD  C3   C4    aromatic  1.385  0.020  1.385
 CLD  C3   H3    single    0.930  0.020  1.080
 CLD  C6   C5    aromatic  1.386  0.020  1.386
 CLD  C6   H6    single    0.930  0.020  1.080
 CLD  C5   C4    aromatic  1.387  0.020  1.387
 CLD  C5   H5    single    0.930  0.020  1.080
 CLD  C4   CL4   single    1.738  0.020  1.738
 CLD  OB1  B     single    1.477  0.020  1.477
 CLD  OB1  HOB1  single    0.850  0.020  0.980
 CLD  OB2  B     single    1.477  0.020  1.477
 CLD  OB2  HOB2  single    0.850  0.020  0.980
 CLD  C10  O10   double    1.229  0.020  1.229
 CLD  C10  C11   single    1.514  0.020  1.514
 CLD  C11  H111  single    0.970  0.020  1.090
 CLD  C11  H112  single    0.970  0.020  1.090
 CLD  C11  H113  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
 CLD  H2    N    H     106.86  3.000
 CLD  H2    N    CA    108.92  3.000
 CLD  H     N    CA    114.00  3.000
 CLD  HA    CA   C     110.00  3.000
 CLD  HA    CA   CB    109.00  3.000
 CLD  C     CA   CB    110.50  1.500
 CLD  HA    CA   N     110.00  3.000
 CLD  C     CA   N     111.00  2.800
 CLD  CB    CA   N     110.40  1.500
 CLD  HB3   CB   HB2   106.58  3.000
 CLD  HB3   CB   OB3   112.17  3.000
 CLD  HB2   CB   OB3   111.76  3.000
 CLD  HB3   CB   CA    108.44  3.000
 CLD  HB2   CB   CA    107.76  3.000
 CLD  OB3   CB   CA    109.95  3.000
 CLD  B     OB3  CB    119.08  3.000
 CLD  OXT   C    O     126.46  3.000
 CLD  OXT   C    CA    120.80  1.700
 CLD  O     C    CA    120.80  1.700
 CLD  HN9   N9   C10   117.36  3.000
 CLD  HN9   N9   C8    115.38  3.000
 CLD  C10   N9   C8    127.26  3.000
 CLD  H8    C8   B     108.94  3.000
 CLD  H8    C8   C7    108.09  3.000
 CLD  B     C8   C7    113.38  3.000
 CLD  H8    C8   N9    106.94  3.000
 CLD  B     C8   N9    109.47  3.000
 CLD  C7    C8   N9    109.82  3.000
 CLD  H72   C7   H71   106.57  3.000
 CLD  H72   C7   C1    109.61  3.000
 CLD  H71   C7   C1    109.47  3.000
 CLD  H72   C7   C8    109.23  3.000
 CLD  H71   C7   C8    108.04  3.000
 CLD  C1    C7   C8    113.67  3.000
 CLD  C6    C1   C2    117.74  3.000
 CLD  C6    C1   C7    120.62  3.000
 CLD  C2    C1   C7    121.60  3.000
 CLD  HC2   C2   C3    118.90  3.000
 CLD  HC2   C2   C1    119.54  3.000
 CLD  C3    C2   C1    121.56  3.000
 CLD  H3    C3   C4    120.57  3.000
 CLD  H3    C3   C2    120.31  3.000
 CLD  C4    C3   C2    119.11  3.000
 CLD  H6    C6   C5    118.76  3.000
 CLD  H6    C6   C1    119.52  3.000
 CLD  C5    C6   C1    121.72  3.000
 CLD  H5    C5   C4    120.54  3.000
 CLD  H5    C5   C6    120.46  3.000
 CLD  C4    C5   C6    119.01  3.000
 CLD  CL4   C4   C5    119.50  3.000
 CLD  CL4   C4   C3    119.63  3.000
 CLD  C5    C4   C3    120.86  3.000
 CLD  HOB1  OB1  B     110.01  3.000
 CLD  HOB2  OB2  B     109.04  3.000
 CLD  OB2   B    OB1   111.59  3.000
 CLD  OB2   B    C8    111.35  3.000
 CLD  OB1   B    C8    106.30  3.000
 CLD  OB2   B    OB3   107.51  3.000
 CLD  OB1   B    OB3   113.67  3.000
 CLD  C8    B    OB3   106.34  3.000
 CLD  H113  C11  H112  108.25  3.000
 CLD  H113  C11  H111  108.33  3.000
 CLD  H112  C11  H111  107.15  3.000
 CLD  H113  C11  C10   113.84  3.000
 CLD  H112  C11  C10   109.34  3.000
 CLD  H111  C11  C10   109.71  3.000
 CLD  C11   C10  O10   120.63  3.000
 CLD  C11   C10  N9    114.93  3.000
 CLD  O10   C10  N9    124.43  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
 CLD  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 CLD  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 CLD  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 CLD  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 CLD  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 CLD  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 CLD  CONST_07  C3    C2   C1   C7    180.00   0.0  0
 CLD  CONST_08  C5    C6   C1   C7    180.00   0.0  0
 CLD  CONST_09  CL4   C4   C3   C2    180.00   0.0  0
 CLD  CONST_10  CL4   C4   C5   C6    180.00   0.0  0
 CLD  CONST_11  H3    C3   C2   C1    180.00   0.0  0
 CLD  CONST_12  H5    C5   C6   C1    180.00   0.0  0
 CLD  CONST_13  H6    C6   C1   C2    180.00   0.0  0
 CLD  CONST_14  HC2   C2   C1   C6    180.00   0.0  0
 CLD  CONST_15  O10   C10  N9   C8      0.00   0.0  0
 CLD  CONST_16  C11   C10  N9   C8    180.00   0.0  0
 CLD  CONST_17  HN9   N9   C10  O10   180.00   0.0  0
 CLD  Var_01    C2    C1   C7   C8    -92.14  30.0  2
 CLD  Var_02    C8    B    OB3  CB   -171.45  30.0  3
 CLD  Var_03    H111  C11  C10  N9    121.62  30.0  3
 CLD  Var_04    HB2   CB   OB3  B      57.79  30.0  1

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
 CLD  chir_01  CA  N   CB  C  negativ
 CLD  chir_02  C8  N9  C7  B  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
 CLD  plan-1  C7   0.020
 CLD  plan-1  C1   0.020
 CLD  plan-1  C2   0.020
 CLD  plan-1  C3   0.020
 CLD  plan-1  C6   0.020
 CLD  plan-1  C5   0.020
 CLD  plan-1  C4   0.020
 CLD  plan-1  CL4  0.020
 CLD  plan-1  HC2  0.020
 CLD  plan-1  H3   0.020
 CLD  plan-1  H6   0.020
 CLD  plan-1  H5   0.020
 CLD  plan-2  N9   0.020
 CLD  plan-2  C8   0.020
 CLD  plan-2  O10  0.020
 CLD  plan-2  C11  0.020
 CLD  plan-2  HN9  0.020
 CLD  plan-2  C10  0.020
 CLD  plan-3  CA   0.020
 CLD  plan-3  C    0.020
 CLD  plan-3  O    0.020
 CLD  plan-3  OXT  0.020

