# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 02:57:04 2022
#   Inital geometry file: a 103 line input string
#   Ligand name: [(1R)-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
 CLB  CLB  '[(1R)-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_CLB
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
 CLB  N     N   NH2    0  -0.803  17.3551   2.7654  26.9444
 CLB  CA    C   CH1    0  -0.251  18.5434   2.8496  26.1072
 CLB  CB    C   CH2    0  -0.063  18.2983   3.8401  24.9731
 CLB  OB3   O   OC2    0  -0.572  17.1953   3.4292  24.2244
 CLB  C     C   C      0   0.397  19.7979   3.2168  26.9358
 CLB  O     O   O      0  -0.614  20.8230   3.5012  26.2811
 CLB  OXT   O   OC    -1  -0.604  19.7052   3.1638  28.1783
 CLB  N9    N   NH1    0  -0.629  16.0662   1.7370  22.2741
 CLB  C8    C   CH1    0  -0.262  15.6380   3.1275  22.3196
 CLB  C7    C   CH2    0  -0.524  14.3437   3.2572  23.1427
 CLB  C1    C   CR6    0   0.174  13.2276   2.3799  22.6623
 CLB  C2    C   CR16   0  -0.321  12.3481   2.8070  21.6685
 CLB  C3    C   CR16   0  -0.198  11.3416   1.9846  21.1847
 CLB  C6    C   CR16   0  -0.322  13.0625   1.0904  23.1644
 CLB  C5    C   CR16   0  -0.200  12.0654   0.2481  22.6925
 CLB  C4    C   CR6    0  -0.063  11.2111   0.7051  21.7026
 CLB  CL4   CL  CL     0  -0.145   9.9538  -0.3370  21.1078
 CLB  OB1   O   OB     0  -0.722  16.4989   5.4478  23.1432
 CLB  OB2   O   OB     0  -0.727  18.0202   4.0312  21.9808
 CLB  B     B   B     -1   0.525  16.8864   4.0525  22.9238
 CLB  O10   O   O      0  -0.521  15.3568   1.1350  20.2034
 CLB  C11   C   CH3    0  -0.776  16.4151  -0.5300  21.5478
 CLB  H     H   HNH2   0   0.324  17.5617   2.1974  27.7542
 CLB  H2    H   HNH2   0   0.324  16.6225   2.2927  26.4321
 CLB  HA    H   HCH1   0   0.174  18.7814   1.8794  25.6298
 CLB  HB2   H   HCH2   0   0.138  18.1399   4.8387  25.4154
 CLB  HB3   H   HCH2   0   0.152  19.2074   3.9072  24.3655
 CLB  HN9   H   HNH1   0   0.376  16.5358   1.4089  23.1038
 CLB  H8    H   HCH1   0   0.189  15.4145   3.4269  21.2905
 CLB  H71   H   HCH2   0   0.220  14.5612   3.0245  24.1887
 CLB  H72   H   HCH2   0   0.222  14.0320   4.3036  23.1147
 CLB  HC2   H   HCR6   0   0.248  12.4489   3.8060  21.2601
 CLB  H3    H   HCR6   0   0.269  10.6678   2.3384  20.4155
 CLB  H6    H   HCR6   0   0.248  13.7188   0.7319  23.9481
 CLB  H5    H   HCR6   0   0.269  11.9538  -0.7488  23.0980
 CLB  HOB1  H   H      0   0.418  16.3275   5.8642  22.2957
 CLB  HOB2  H   H      0   0.412  18.1494   3.1321  21.6687
 CLB  H111  H   HCH3   0   0.253  15.5856  -1.2374  21.5143
 CLB  H112  H   HCH3   0   0.252  17.1167  -0.8192  20.7653
 CLB  H113  H   HCH3   0   0.239  16.9113  -0.6332  22.5116
 CLB  C10   C   C      0   0.498  15.8895   0.8639  21.2768

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
 CLB  N    CA    single    1.458  0.019  1.458
 CLB  N    H     single    0.860  0.020  0.860
 CLB  N    H2    single    0.890  0.020  1.040
 CLB  CA   CB    single    1.521  0.033  1.521
 CLB  CA   C     single    1.525  0.021  1.525
 CLB  CA   HA    single    0.970  0.020  0.970
 CLB  CB   OB3   single    1.395  0.020  1.395
 CLB  CB   HB2   single    0.970  0.020  1.090
 CLB  CB   HB3   single    0.970  0.020  1.090
 CLB  OB3  B     single    1.475  0.020  1.475
 CLB  C    O     deloc     1.231  0.020  1.231
 CLB  C    OXT   deloc     1.247  0.020  1.247
 CLB  N9   C8    single    1.456  0.020  1.456
 CLB  N9   C10   single    1.337  0.020  1.337
 CLB  N9   HN9   single    0.860  0.020  1.020
 CLB  C8   C7    single    1.539  0.020  1.539
 CLB  C8   B     single    1.667  0.020  1.667
 CLB  C8   H8    single    0.970  0.020  1.090
 CLB  C7   C1    single    1.499  0.020  1.499
 CLB  C7   H71   single    0.970  0.020  1.090
 CLB  C7   H72   single    0.970  0.020  1.090
 CLB  C1   C2    aromatic  1.394  0.020  1.394
 CLB  C1   C6    aromatic  1.394  0.020  1.394
 CLB  C2   C3    aromatic  1.387  0.020  1.387
 CLB  C2   HC2   single    0.930  0.020  1.080
 CLB  C3   C4    aromatic  1.387  0.020  1.387
 CLB  C3   H3    single    0.930  0.020  1.080
 CLB  C6   C5    aromatic  1.388  0.020  1.388
 CLB  C6   H6    single    0.930  0.020  1.080
 CLB  C5   C4    aromatic  1.385  0.020  1.385
 CLB  C5   H5    single    0.930  0.020  1.080
 CLB  C4   CL4   single    1.738  0.020  1.738
 CLB  OB1  B     single    1.465  0.020  1.465
 CLB  OB1  HOB1  single    0.850  0.020  0.980
 CLB  OB2  B     single    1.475  0.020  1.475
 CLB  OB2  HOB2  single    0.850  0.020  0.980
 CLB  C10  O10   double    1.229  0.020  1.229
 CLB  C10  C11   single    1.514  0.020  1.514
 CLB  C11  H111  single    0.970  0.020  1.090
 CLB  C11  H112  single    0.970  0.020  1.090
 CLB  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
 CLB  H2    N    H     106.94  3.000
 CLB  H2    N    CA    109.09  3.000
 CLB  H     N    CA    114.00  3.000
 CLB  HA    CA   C     110.00  3.000
 CLB  HA    CA   CB    109.00  3.000
 CLB  C     CA   CB    110.50  1.500
 CLB  HA    CA   N     110.00  3.000
 CLB  C     CA   N     111.00  2.800
 CLB  CB    CA   N     110.40  1.500
 CLB  HB3   CB   HB2   106.62  3.000
 CLB  HB3   CB   OB3   112.12  3.000
 CLB  HB2   CB   OB3   111.60  3.000
 CLB  HB3   CB   CA    108.59  3.000
 CLB  HB2   CB   CA    108.21  3.000
 CLB  OB3   CB   CA    109.56  3.000
 CLB  B     OB3  CB    120.96  3.000
 CLB  OXT   C    O     126.37  3.000
 CLB  OXT   C    CA    120.80  1.700
 CLB  O     C    CA    120.80  1.700
 CLB  HN9   N9   C10   117.57  3.000
 CLB  HN9   N9   C8    114.97  3.000
 CLB  C10   N9   C8    127.46  3.000
 CLB  H8    C8   B     109.98  3.000
 CLB  H8    C8   C7    107.93  3.000
 CLB  B     C8   C7    112.90  3.000
 CLB  H8    C8   N9    106.97  3.000
 CLB  B     C8   N9    108.73  3.000
 CLB  C7    C8   N9    110.16  3.000
 CLB  H72   C7   H71   106.57  3.000
 CLB  H72   C7   C1    109.88  3.000
 CLB  H71   C7   C1    109.28  3.000
 CLB  H72   C7   C8    107.88  3.000
 CLB  H71   C7   C8    109.04  3.000
 CLB  C1    C7   C8    113.92  3.000
 CLB  C6    C1   C2    117.75  3.000
 CLB  C6    C1   C7    120.96  3.000
 CLB  C2    C1   C7    121.26  3.000
 CLB  HC2   C2   C3    118.85  3.000
 CLB  HC2   C2   C1    119.49  3.000
 CLB  C3    C2   C1    121.66  3.000
 CLB  H3    C3   C4    120.58  3.000
 CLB  H3    C3   C2    120.40  3.000
 CLB  C4    C3   C2    119.02  3.000
 CLB  H6    C6   C5    118.71  3.000
 CLB  H6    C6   C1    119.68  3.000
 CLB  C5    C6   C1    121.61  3.000
 CLB  H5    C5   C4    120.55  3.000
 CLB  H5    C5   C6    120.38  3.000
 CLB  C4    C5   C6    119.07  3.000
 CLB  CL4   C4   C5    119.53  3.000
 CLB  CL4   C4   C3    119.57  3.000
 CLB  C5    C4   C3    120.89  3.000
 CLB  HOB1  OB1  B     109.16  3.000
 CLB  HOB2  OB2  B     108.95  3.000
 CLB  OB2   B    OB1   108.24  3.000
 CLB  OB2   B    C8    109.63  3.000
 CLB  OB1   B    C8    112.63  3.000
 CLB  OB2   B    OB3   113.37  3.000
 CLB  OB1   B    OB3   109.02  3.000
 CLB  C8    B    OB3   104.00  3.000
 CLB  H113  C11  H112  108.47  3.000
 CLB  H113  C11  H111  108.20  3.000
 CLB  H112  C11  H111  107.18  3.000
 CLB  H113  C11  C10   113.82  3.000
 CLB  H112  C11  C10   109.83  3.000
 CLB  H111  C11  C10   109.12  3.000
 CLB  C11   C10  O10   120.66  3.000
 CLB  C11   C10  N9    114.94  3.000
 CLB  O10   C10  N9    124.39  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
 CLB  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 CLB  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 CLB  CONST_03  C5    C6   C1   C2     0.00   0.0  0
 CLB  CONST_04  C5    C4   C3   C2     0.00   0.0  0
 CLB  CONST_05  C6    C1   C2   C3     0.00   0.0  0
 CLB  CONST_06  C6    C5   C4   C3     0.00   0.0  0
 CLB  CONST_07  C3    C2   C1   C7   180.00   0.0  0
 CLB  CONST_08  C5    C6   C1   C7   180.00   0.0  0
 CLB  CONST_09  CL4   C4   C3   C2   180.00   0.0  0
 CLB  CONST_10  CL4   C4   C5   C6   180.00   0.0  0
 CLB  CONST_11  H3    C3   C2   C1   180.00   0.0  0
 CLB  CONST_12  H5    C5   C6   C1   180.00   0.0  0
 CLB  CONST_13  H6    C6   C1   C2   180.00   0.0  0
 CLB  CONST_14  HC2   C2   C1   C6   180.00   0.0  0
 CLB  CONST_15  O10   C10  N9   C8     0.00   0.0  0
 CLB  CONST_16  C11   C10  N9   C8   180.00   0.0  0
 CLB  CONST_17  HN9   N9   C10  O10  180.00   0.0  0
 CLB  Var_01    C2    C1   C7   C8   -87.41  30.0  2
 CLB  Var_02    C8    B    OB3  CB   172.85  30.0  3
 CLB  Var_03    H111  C11  C10  N9   118.50  30.0  3
 CLB  Var_04    HB2   CB   OB3  B     71.85  30.0  2

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

