# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 07:26:43 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: (2~{S})-2-[(2-chlorophenyl)methylcarbamoylamino]-4-methyl-~{N}-oxidanyl-pentanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](NC(=O)NCc1ccccc1Cl)C(=O)NO
#
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
 B1B  B1B  (2~{S})-2-[(2-chlorophenyl)methylcarbamoylamino]-4-methyl-~{N}-oxidanyl-pentanamide  ligand  41  21  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_B1B
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
 B1B  CL1  CL  CL    0  -0.115   1.7480  -1.6771  -0.1118
 B1B  CG1  C   CR6   0  -0.107   3.1725  -0.6896  -0.0658
 B1B  CD1  C   CR16  0  -0.201   4.2475  -1.0500  -0.8633
 B1B  C3   C   CR16  0  -0.276   5.4044  -0.2838  -0.8385
 B1B  C4   C   CR16  0  -0.232   5.4774   0.8320  -0.0187
 B1B  CG2  C   CR16  0  -0.319   4.3890   1.1775   0.7699
 B1B  CB   C   CR6   0   0.185   3.2168   0.4272   0.7670
 B1B  CA   C   CH2   0  -0.354   2.0587   0.8364   1.6408
 B1B  N    N   NH1   0  -0.671   0.9085   1.2339   0.8703
 B1B  C8   C   C     0   0.758  -0.3145   0.6650   1.0057
 B1B  O    O   O     0  -0.537  -0.5910  -0.1512   1.8752
 B1B  N2   N   NH1   0  -0.673  -1.2508   1.1103   0.1121
 B1B  C9   C   CH1   0  -0.221  -2.5075   0.4176   0.0129
 B1B  C10  C   CH2   0  -0.437  -3.4415   1.1551  -0.9480
 B1B  C11  C   CH1   0  -0.227  -3.7951   2.5850  -0.5340
 B1B  C12  C   CH3   0  -0.652  -4.7152   3.2019  -1.5833
 B1B  C13  C   CH3   0  -0.666  -4.4385   2.6407   0.8479
 B1B  C14  C   C     0   0.533  -2.3069  -1.0099  -0.4967
 B1B  O2   O   O     0  -0.465  -1.5070  -1.2896  -1.3681
 B1B  N3   N   NH1   0  -0.374  -3.1172  -1.9041   0.0966
 B1B  O3   O   OH1   0  -0.544  -3.2502  -3.1572  -0.4218
 B1B  H1   H   HCR6  0   0.278   4.1834  -1.9239  -1.4975
 B1B  H2   H   HCR6  0   0.268   6.2433  -0.5652  -1.4611
 B1B  H3   H   HCR6  0   0.262   6.3759   1.4338   0.0074
 B1B  H4   H   HCR6  0   0.263   4.4437   2.0517   1.4073
 B1B  H5   H   HCH2  0   0.269   1.7649   0.0140   2.2921
 B1B  H6   H   HCH2  0   0.261   2.3842   1.6530   2.2902
 B1B  H7   H   HNH1  0   0.393   1.0481   1.9389   0.1646
 B1B  H8   H   HNH1  0   0.388  -0.9153   1.5291  -0.7427
 B1B  H9   H   HCH1  0   0.269  -2.9705   0.3847   1.0019
 B1B  H10  H   HCH2  0   0.243  -2.9904   1.1649  -1.9459
 B1B  H11  H   HCH2  0   0.241  -4.3663   0.5764  -1.0344
 B1B  H12  H   HCH1  0   0.224  -2.8753   3.1783  -0.5070
 B1B  H13  H   HCH3  0   0.228  -4.9639   4.2334  -1.3291
 B1B  H14  H   HCH3  0   0.226  -4.2494   3.2060  -2.5704
 B1B  H15  H   HCH3  0   0.215  -5.6520   2.6445  -1.6617
 B1B  H16  H   HCH3  0   0.229  -3.7490   2.3388   1.6376
 B1B  H17  H   HCH3  0   0.232  -4.7688   3.6542   1.0806
 B1B  H18  H   HCH3  0   0.216  -5.3122   1.9860   0.8997
 B1B  H19  H   HNH1  0   0.413  -3.8457  -1.6334   0.7416
 B1B  H20  H   HOH1  0   0.477  -2.6607  -3.7246   0.0915

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
 B1B  O3   N3   single    1.363  0.020  1.363
 B1B  N3   C14  single    1.345  0.020  1.345
 B1B  O2   C14  double    1.216  0.020  1.216
 B1B  C14  C9   single    1.529  0.020  1.529
 B1B  C12  C11  single    1.526  0.020  1.526
 B1B  C11  C13  single    1.525  0.020  1.525
 B1B  C11  C10  single    1.530  0.020  1.530
 B1B  C9   C10  single    1.530  0.020  1.530
 B1B  C9   N2   single    1.438  0.020  1.438
 B1B  N2   C8   single    1.369  0.020  1.369
 B1B  C8   O    double    1.224  0.020  1.224
 B1B  C8   N    single    1.356  0.020  1.356
 B1B  N    CA   single    1.440  0.020  1.440
 B1B  CA   CB   single    1.507  0.020  1.507
 B1B  CG2  CB   aromatic  1.392  0.020  1.392
 B1B  CG2  C4   aromatic  1.388  0.020  1.388
 B1B  CB   CG1  aromatic  1.394  0.020  1.394
 B1B  C4   C3   aromatic  1.387  0.020  1.387
 B1B  CG1  CL1  single    1.734  0.020  1.734
 B1B  CG1  CD1  aromatic  1.386  0.020  1.386
 B1B  C3   CD1  aromatic  1.388  0.020  1.388
 B1B  CD1  H1   single    0.930  0.020  1.080
 B1B  C3   H2   single    0.930  0.020  1.080
 B1B  C4   H3   single    0.930  0.020  1.080
 B1B  CG2  H4   single    0.930  0.020  1.080
 B1B  CA   H5   single    0.970  0.020  1.090
 B1B  CA   H6   single    0.970  0.020  1.090
 B1B  N    H7   single    0.860  0.020  1.020
 B1B  N2   H8   single    0.890  0.020  1.040
 B1B  C9   H9   single    0.970  0.020  1.090
 B1B  C10  H10  single    0.970  0.020  1.090
 B1B  C10  H11  single    0.970  0.020  1.090
 B1B  C11  H12  single    0.970  0.020  1.090
 B1B  C12  H13  single    0.970  0.020  1.090
 B1B  C12  H14  single    0.970  0.020  1.090
 B1B  C12  H15  single    0.970  0.020  1.090
 B1B  C13  H16  single    0.970  0.020  1.090
 B1B  C13  H17  single    0.970  0.020  1.090
 B1B  C13  H18  single    0.970  0.020  1.090
 B1B  N3   H19  single    0.860  0.020  1.020
 B1B  O3   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
 B1B  CB   CG1  CD1  121.83  3.000
 B1B  CD1  CG1  CL1  118.28  3.000
 B1B  CB   CG1  CL1  119.89  3.000
 B1B  H1   CD1  C3   120.39  3.000
 B1B  H1   CD1  CG1  120.09  3.000
 B1B  C3   CD1  CG1  119.52  3.000
 B1B  H2   C3   C4   120.58  3.000
 B1B  H2   C3   CD1  119.51  3.000
 B1B  C4   C3   CD1  119.92  3.000
 B1B  H3   C4   CG2  119.95  3.000
 B1B  H3   C4   C3   120.38  3.000
 B1B  CG2  C4   C3   119.67  3.000
 B1B  H4   CG2  CB   118.61  3.000
 B1B  H4   CG2  C4   119.71  3.000
 B1B  CB   CG2  C4   121.68  3.000
 B1B  CA   CB   CG2  119.97  3.000
 B1B  CG2  CB   CG1  117.39  3.000
 B1B  CA   CB   CG1  122.65  3.000
 B1B  H6   CA   H5   106.80  3.000
 B1B  H6   CA   N    110.46  3.000
 B1B  H5   CA   N    108.22  3.000
 B1B  H6   CA   CB   108.57  3.000
 B1B  H5   CA   CB   110.41  3.000
 B1B  N    CA   CB   112.23  3.000
 B1B  H7   N    C8   119.25  3.000
 B1B  H7   N    CA   117.21  3.000
 B1B  C8   N    CA   123.45  3.000
 B1B  N2   C8   O    121.74  3.000
 B1B  O    C8   N    123.67  3.000
 B1B  N2   C8   N    114.55  3.000
 B1B  H8   N2   C9   115.58  3.000
 B1B  H8   N2   C8   117.42  3.000
 B1B  C9   N2   C8   119.08  3.000
 B1B  H9   C9   C14  109.22  3.000
 B1B  H9   C9   C10  108.93  3.000
 B1B  C14  C9   C10  108.72  3.000
 B1B  H9   C9   N2   108.80  3.000
 B1B  C10  C9   N2   110.16  3.000
 B1B  C14  C9   N2   110.98  3.000
 B1B  H11  C10  H10  106.31  3.000
 B1B  H11  C10  C11  108.68  3.000
 B1B  H10  C10  C11  109.47  3.000
 B1B  H11  C10  C9   108.10  3.000
 B1B  H10  C10  C9   108.98  3.000
 B1B  C11  C10  C9   114.95  3.000
 B1B  H12  C11  C13  108.20  3.000
 B1B  H12  C11  C12  107.72  3.000
 B1B  C13  C11  C12  110.72  3.000
 B1B  H12  C11  C10  108.60  3.000
 B1B  C13  C11  C10  112.13  3.000
 B1B  C12  C11  C10  109.33  3.000
 B1B  H15  C12  H14  107.63  3.000
 B1B  H15  C12  H13  107.67  3.000
 B1B  H14  C12  H13  107.72  3.000
 B1B  H15  C12  C11  111.10  3.000
 B1B  H14  C12  C11  111.48  3.000
 B1B  H13  C12  C11  111.07  3.000
 B1B  H18  C13  H17  107.72  3.000
 B1B  H18  C13  H16  107.77  3.000
 B1B  H17  C13  H16  107.10  3.000
 B1B  H18  C13  C11  110.99  3.000
 B1B  H17  C13  C11  110.78  3.000
 B1B  H16  C13  C11  112.27  3.000
 B1B  N3   C14  O2   124.05  3.000
 B1B  O2   C14  C9   122.69  3.000
 B1B  N3   C14  C9   113.25  3.000
 B1B  H19  N3   O3   114.78  3.000
 B1B  H19  N3   C14  122.56  3.000
 B1B  O3   N3   C14  120.16  3.000
 B1B  H20  O3   N3   106.17  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
 B1B  CONST_01  C4   CG2  CB   CG1     0.00   0.0  0
 B1B  CONST_02  C4   C3   CD1  CG1     0.00   0.0  0
 B1B  CONST_03  CG2  CB   CG1  CD1     0.00   0.0  0
 B1B  CONST_04  CG2  C4   C3   CD1     0.00   0.0  0
 B1B  CONST_05  CB   CG2  C4   C3      0.00   0.0  0
 B1B  CONST_06  CB   CG1  CD1  C3      0.00   0.0  0
 B1B  CONST_07  CG2  CB   CG1  CL1   180.00   0.0  0
 B1B  CONST_08  C3   CD1  CG1  CL1   180.00   0.0  0
 B1B  CONST_09  CA   CB   CG1  CD1   180.00   0.0  0
 B1B  CONST_10  CA   CB   CG2  C4    180.00   0.0  0
 B1B  CONST_11  H4   CG2  CB   CG1   180.00   0.0  0
 B1B  CONST_12  H2   C3   CD1  CG1   180.00   0.0  0
 B1B  CONST_13  H3   C4   C3   CD1   180.00   0.0  0
 B1B  CONST_14  H1   CD1  C3   C4    180.00   0.0  0
 B1B  CONST_15  O    C8   N    CA      0.00   0.0  0
 B1B  CONST_16  C9   N2   C8   O       0.00   0.0  0
 B1B  CONST_17  O3   N3   C14  C9    180.00   0.0  0
 B1B  CONST_18  O3   N3   C14  O2      0.00   0.0  0
 B1B  CONST_19  N2   C8   N    CA    180.00   0.0  0
 B1B  CONST_20  C9   N2   C8   N     180.00   0.0  0
 B1B  CONST_22  H7   N    C8   O     180.00   0.0  0
 B1B  CONST_23  H19  N3   C14  C9      0.00   0.0  0
 B1B  Var_01    N    CA   CB   CG1   -65.11  30.0  3
 B1B  Var_02    C8   N    CA   CB    123.70  30.0  1
 B1B  Var_03    C12  C11  C10  C9    179.42  30.0  2
 B1B  Var_04    H13  C12  C11  C10  -178.47  30.0  3
 B1B  Var_05    H16  C13  C11  C10    65.78  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
 B1B  chir_01  C9  C14  C10  N2  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
 B1B  plan-1  CL1  0.020
 B1B  plan-1  CG1  0.020
 B1B  plan-1  CD1  0.020
 B1B  plan-1  C3   0.020
 B1B  plan-1  C4   0.020
 B1B  plan-1  CG2  0.020
 B1B  plan-1  CB   0.020
 B1B  plan-1  CA   0.020
 B1B  plan-1  H1   0.020
 B1B  plan-1  H2   0.020
 B1B  plan-1  H3   0.020
 B1B  plan-1  H4   0.020
 B1B  plan-2  CA   0.020
 B1B  plan-2  N    0.020
 B1B  plan-2  C8   0.020
 B1B  plan-2  O    0.020
 B1B  plan-2  N2   0.020
 B1B  plan-2  C9   0.020
 B1B  plan-2  H7   0.020
 B1B  plan-2  H8   0.020
 B1B  plan-3  C9   0.020
 B1B  plan-3  C14  0.020
 B1B  plan-3  O2   0.020
 B1B  plan-3  N3   0.020
 B1B  plan-3  O3   0.020
 B1B  plan-3  H19  0.020

