# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 20:17:44 2022
#   Inital geometry file: a 105 line input string
#   Ligand name: (2S,10R)-2,10-diamino-11-(dimethylamino)-11-oxoundecanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)C(=O)[C@H](N)CCCCCCC[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
 B8R  B8R  '(2S,10R)-2,10-diamino-11-(dimethylamino)-11-oxoundecanoic acid'  L-peptide  45  19  .  2019-03-22  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_B8R
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
 B8R  C    C  C      0   0.385  -0.9321  -7.5242  -21.5666
 B8R  O    O  O      0  -0.606  -0.3454  -7.6080  -20.4698
 B8R  N4   N  NH2    0  -0.792   2.9608  -2.6152  -27.1379
 B8R  C16  C  CH1    0  -0.214   3.7374  -2.1441  -26.0023
 B8R  C17  C  C      0   0.541   4.3940  -0.7663  -26.1594
 B8R  O5   O  O      0  -0.512   5.4066  -0.5559  -25.4967
 B8R  N5   N  NT     0  -0.440   3.9192   0.1653  -27.0110
 B8R  C18  C  CH3    0  -0.526   4.7124   1.3605  -27.2312
 B8R  C19  C  CH3    0  -0.517   2.6011   0.1874  -27.6158
 B8R  C20  C  CH2    0  -0.431   3.0529  -2.2609  -24.6302
 B8R  C21  C  CH2    0  -0.463   1.8318  -1.3715  -24.4335
 B8R  C22  C  CH2    0  -0.414   1.1952  -1.5096  -23.0503
 B8R  C23  C  CH2    0  -0.438   0.7519  -2.9214  -22.6691
 B8R  CG   C  CH2    0  -0.425  -0.2449  -3.5426  -23.6405
 B8R  CD   C  CH2    0  -0.422  -0.6573  -4.9674  -23.2802
 B8R  CB   C  CH2    0  -0.429  -1.4150  -5.0781  -21.9623
 B8R  CA   C  CH1    0  -0.154  -2.0404  -6.4508  -21.7007
 B8R  N    N  NH2    0  -0.807  -2.8515  -6.3594  -20.4893
 B8R  OXT  O  OC    -1  -0.615  -0.6979  -8.2001  -22.5907
 B8R  H5   H  HCH1   0   0.268   4.6116  -2.7987  -25.9569
 B8R  H6   H  HCH3   0   0.248   5.7746   1.1392  -27.1796
 B8R  H7   H  HCH3   0   0.241   4.4934   1.7504  -28.2241
 B8R  H8   H  HCH3   0   0.233   4.4867   2.1430  -26.5020
 B8R  H9   H  HCH3   0   0.240   1.8648  -0.3423  -27.0215
 B8R  H10  H  HCH3   0   0.249   2.2648   1.2227  -27.6632
 B8R  H11  H  HCH3   0   0.240   2.6001  -0.2186  -28.6276
 B8R  H12  H  HCH2   0   0.236   2.7761  -3.3112  -24.5010
 B8R  H13  H  HCH2   0   0.223   3.7872  -2.0429  -23.8496
 B8R  H14  H  HCH2   0   0.233   2.1133  -0.3227  -24.5739
 B8R  H15  H  HCH2   0   0.215   1.0785  -1.5848  -25.1984
 B8R  H16  H  HCH2   0   0.217   1.9040  -1.1483  -22.2988
 B8R  H17  H  HCH2   0   0.217   0.3307  -0.8406  -22.9984
 B8R  H18  H  HCH2   0   0.227   0.3136  -2.8802  -21.6683
 B8R  H19  H  HCH2   0   0.209   1.6229  -3.5789  -22.5809
 B8R  H20  H  HCH2   0   0.219   0.1855  -3.5538  -24.6465
 B8R  H21  H  HCH2   0   0.203  -1.1367  -2.9081  -23.6992
 B8R  H22  H  HCH2   0   0.209  -1.2844  -5.3650  -24.0846
 B8R  H23  H  HCH2   0   0.209   0.2352  -5.5999  -23.2579
 B8R  H24  H  HCH2   0   0.208  -0.7622  -4.8300  -21.1203
 B8R  H25  H  HCH2   0   0.203  -2.2169  -4.3284  -21.9576
 B8R  H26  H  HCH1   0   0.166  -2.6439  -6.7114  -22.5839
 B8R  H2   H  HNH2   0   0.328  -3.6229  -5.7260  -20.6643
 B8R  H    H  HNH2   0   0.331  -3.2799  -7.2566  -20.2970
 B8R  H27  H  HNH2   0   0.357   3.0259  -3.6243  -27.1697
 B8R  H3   H  HNH2   0   0.347   1.9757  -2.4122  -27.0300

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
 B8R  C18  N5   single  1.451  0.020  1.451
 B8R  C19  N5   single  1.450  0.020  1.450
 B8R  N5   C17  single  1.348  0.020  1.348
 B8R  N4   C16  single  1.454  0.020  1.454
 B8R  C17  O5   double  1.228  0.020  1.228
 B8R  C17  C16  single  1.534  0.020  1.534
 B8R  C16  C20  single  1.538  0.020  1.538
 B8R  C20  C21  single  1.523  0.020  1.523
 B8R  C21  C22  single  1.529  0.020  1.529
 B8R  CG   CD   single  1.526  0.020  1.526
 B8R  CG   C23  single  1.524  0.020  1.524
 B8R  CD   CB   single  1.524  0.020  1.524
 B8R  C22  C23  single  1.528  0.020  1.528
 B8R  C    CA   single  1.525  0.021  1.525
 B8R  C    O    deloc   1.231  0.020  1.231
 B8R  CA   CB   single  1.521  0.033  1.521
 B8R  CA   N    single  1.458  0.019  1.458
 B8R  C    OXT  deloc   1.249  0.020  1.249
 B8R  N4   H27  single  0.890  0.020  1.040
 B8R  N4   H3   single  0.890  0.020  1.040
 B8R  C16  H5   single  0.970  0.020  1.090
 B8R  C18  H6   single  0.970  0.020  1.090
 B8R  C18  H7   single  0.970  0.020  1.090
 B8R  C18  H8   single  0.970  0.020  1.090
 B8R  C19  H9   single  0.970  0.020  1.090
 B8R  C19  H10  single  0.970  0.020  1.090
 B8R  C19  H11  single  0.970  0.020  1.090
 B8R  C20  H12  single  0.970  0.020  1.090
 B8R  C20  H13  single  0.970  0.020  1.090
 B8R  C21  H14  single  0.970  0.020  1.090
 B8R  C21  H15  single  0.970  0.020  1.090
 B8R  C22  H16  single  0.970  0.020  1.090
 B8R  C22  H17  single  0.970  0.020  1.090
 B8R  C23  H18  single  0.970  0.020  1.090
 B8R  C23  H19  single  0.970  0.020  1.090
 B8R  CG   H20  single  0.970  0.020  1.090
 B8R  CG   H21  single  0.970  0.020  1.090
 B8R  CD   H22  single  0.970  0.020  1.090
 B8R  CD   H23  single  0.970  0.020  1.090
 B8R  CB   H24  single  0.970  0.020  1.090
 B8R  CB   H25  single  0.970  0.020  1.090
 B8R  CA   H26  single  0.970  0.020  1.090
 B8R  N    H2   single  0.890  0.020  1.040
 B8R  N    H    single  0.860  0.020  0.860

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
 B8R  OXT  C    CA   120.80  1.700
 B8R  OXT  C    O    126.63  3.000
 B8R  CA   C    O    120.80  1.700
 B8R  H3   N4   H27  105.45  3.000
 B8R  H3   N4   C16  111.82  3.000
 B8R  H27  N4   C16  108.26  3.000
 B8R  H5   C16  C20  105.87  3.000
 B8R  H5   C16  C17  101.52  3.000
 B8R  C20  C16  C17  110.49  3.000
 B8R  H5   C16  N4   105.40  3.000
 B8R  C20  C16  N4   115.75  3.000
 B8R  C17  C16  N4   116.07  3.000
 B8R  N5   C17  O5   120.84  3.000
 B8R  O5   C17  C16  116.83  3.000
 B8R  N5   C17  C16  122.30  3.000
 B8R  C19  N5   C18  114.89  3.000
 B8R  C19  N5   C17  126.43  3.000
 B8R  C18  N5   C17  118.19  3.000
 B8R  H8   C18  H7   108.09  3.000
 B8R  H8   C18  H6   108.43  3.000
 B8R  H7   C18  H6   108.23  3.000
 B8R  H8   C18  N5   112.05  3.000
 B8R  H7   C18  N5   108.86  3.000
 B8R  H6   C18  N5   111.07  3.000
 B8R  H11  C19  H10  108.25  3.000
 B8R  H11  C19  H9   109.03  3.000
 B8R  H10  C19  H9   106.17  3.000
 B8R  H11  C19  N5   112.47  3.000
 B8R  H10  C19  N5   108.25  3.000
 B8R  H9   C19  N5   112.40  3.000
 B8R  H13  C20  H12  106.08  3.000
 B8R  H13  C20  C21  109.25  3.000
 B8R  H12  C20  C21  110.03  3.000
 B8R  H13  C20  C16  108.83  3.000
 B8R  H12  C20  C16  106.92  3.000
 B8R  C21  C20  C16  115.32  3.000
 B8R  H15  C21  H14  105.91  3.000
 B8R  H15  C21  C22  109.15  3.000
 B8R  H14  C21  C22  108.03  3.000
 B8R  H15  C21  C20  110.34  3.000
 B8R  H14  C21  C20  109.67  3.000
 B8R  C22  C21  C20  113.44  3.000
 B8R  H17  C22  H16  106.09  3.000
 B8R  H17  C22  C23  108.89  3.000
 B8R  H16  C22  C23  108.75  3.000
 B8R  H17  C22  C21  108.46  3.000
 B8R  H16  C22  C21  108.77  3.000
 B8R  C23  C22  C21  115.47  3.000
 B8R  H19  C23  H18  105.53  3.000
 B8R  H19  C23  CG   109.08  3.000
 B8R  H18  C23  CG   109.67  3.000
 B8R  H19  C23  C22  110.13  3.000
 B8R  H18  C23  C22  108.05  3.000
 B8R  CG   C23  C22  114.04  3.000
 B8R  H21  CG   H20  106.06  3.000
 B8R  H21  CG   CD   109.46  3.000
 B8R  H20  CG   CD   108.28  3.000
 B8R  H21  CG   C23  109.29  3.000
 B8R  H20  CG   C23  109.44  3.000
 B8R  CD   CG   C23  114.00  3.000
 B8R  H23  CD   H22  105.80  3.000
 B8R  H23  CD   CB   110.23  3.000
 B8R  H22  CD   CB   108.92  3.000
 B8R  H23  CD   CG   108.91  3.000
 B8R  H22  CD   CG   108.68  3.000
 B8R  CB   CD   CG   113.96  3.000
 B8R  H25  CB   H24  106.13  3.000
 B8R  H25  CB   CA   108.25  3.000
 B8R  H24  CB   CA   108.40  3.000
 B8R  H25  CB   CD   108.50  3.000
 B8R  H24  CB   CD   110.63  3.000
 B8R  CA   CB   CD   114.57  3.000
 B8R  H26  CA   N    112.07  3.000
 B8R  H26  CA   CB   107.40  3.000
 B8R  N    CA   CB   110.40  1.500
 B8R  H26  CA   C    107.32  3.000
 B8R  N    CA   C    111.00  2.800
 B8R  CB   CA   C    110.50  1.500
 B8R  H    N    H2   105.34  3.000
 B8R  H    N    CA   114.00  3.000
 B8R  H2   N    CA   108.57  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
 B8R  CONST_01  C18  N5   C17  C16   180.00   0.0  0
 B8R  CONST_03  C18  N5   C17  O5      0.00   0.0  0
 B8R  Var_01    C22  C21  C20  C16  -179.33  30.0  3
 B8R  Var_02    C23  C22  C21  C20   -57.45  30.0  3
 B8R  Var_03    CG   C23  C22  C21   -57.54  30.0  3
 B8R  Var_04    CD   CG   C23  C22   178.38  30.0  2
 B8R  Var_05    CB   CD   CG   C23    64.34  30.0  3
 B8R  Var_06    CA   CB   CD   CG    170.12  30.0  3
 B8R  Var_07    H6   C18  N5   C17    33.63  30.0  3
 B8R  Var_08    H9   C19  N5   C17    25.61  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
 B8R  chir_01  C16  N4  C17  C20  negativ
 B8R  chir_02  CA   C   CB   N    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
 B8R  plan-1  C16  0.020
 B8R  plan-1  C17  0.020
 B8R  plan-1  O5   0.020
 B8R  plan-1  N5   0.020
 B8R  plan-1  C18  0.020
 B8R  plan-1  C19  0.020
 B8R  plan-2  C    0.020
 B8R  plan-2  O    0.020
 B8R  plan-2  CA   0.020
 B8R  plan-2  OXT  0.020

