# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 17:36:48 2022
#   Inital geometry file: a 95 line input string
#   Ligand name: (2~{S})-2-azanyl-6-(6-bromanylhexanoylamino)hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCNC(=O)CCCCCBr)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
 9MN  9MN  '(2~{S})-2-azanyl-6-(6-bromanylhexanoylamino)hexanoic acid'  L-peptide  40  18  .  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_9MN
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
 9MN  CB    C   CH2    0  -0.386   1.6895  -2.2536  -47.2945
 9MN  C6    C   CH2    0  -0.426   1.5480  -3.0554  -46.0060
 9MN  C14   C   CH2    0  -0.420   5.2572  -7.4525  -41.7145
 9MN  C15   C   CH2    0  -0.433   5.7093  -6.9953  -40.3313
 9MN  C16   C   CH2    0  -0.499   7.0701  -7.4797  -39.8684
 9MN  CA    C   CH1    0  -0.221   0.5091  -1.3286  -47.5732
 9MN  N     N   NH2    0  -0.816  -0.7286  -2.0927  -47.6671
 9MN  C     C   C      0   0.414   0.7198  -0.4699  -48.8496
 9MN  O     O   O      0  -0.604  -0.2923  -0.2349  -49.5416
 9MN  CD    C   CH2    0  -0.422   2.7781  -3.9030  -45.7102
 9MN  CE    C   CH2    0  -0.279   2.6407  -4.6991  -44.4174
 9MN  NZ    N   NH1    0  -0.626   3.8258  -5.4630  -44.0911
 9MN  C10   C   C      0   0.516   4.0725  -6.6998  -44.5578
 9MN  O11   O   O      0  -0.499   3.2623  -7.3269  -45.2286
 9MN  C12   C   CH2    0  -0.550   5.4439  -7.2715  -44.2433
 9MN  C13   C   CH2    0  -0.461   6.0646  -6.9208  -42.8930
 9MN  O1    O   OC    -1  -0.605   1.8740  -0.0471  -49.0563
 9MN  H51   H   HCH2   0   0.194   1.8137  -2.9451  -48.1359
 9MN  H52   H   HCH2   0   0.202   2.6020  -1.6565  -47.2437
 9MN  H62   H   HCH2   0   0.204   1.3700  -2.3693  -45.1691
 9MN  H61   H   HCH2   0   0.210   0.6679  -3.7035  -46.0641
 9MN  H142  H   HCH2   0   0.230   4.2126  -7.1487  -41.8267
 9MN  H141  H   HCH2   0   0.224   5.2578  -8.5467  -41.7474
 9MN  H152  H   HCH2   0   0.244   5.6383  -5.9088  -40.2397
 9MN  H151  H   HCH2   0   0.256   4.9977  -7.3978  -39.6033
 9MN  H161  H   HCH2   0   0.295   7.1473  -7.4543  -38.7832
 9MN  H162  H   HCH2   0   0.285   7.2799  -8.4933  -40.2097
 9MN  HA    H   HCH1   0   0.188   0.4709  -0.6003  -46.7415
 9MN  H2    H   HNH2   0   0.329  -1.1085  -2.2567  -46.7444
 9MN  H3    H   HNH2   0   0.332  -1.4029  -1.5261  -48.1649
 9MN  H72   H   HCH2   0   0.218   2.9593  -4.5932  -46.5398
 9MN  H71   H   HCH2   0   0.214   3.6601  -3.2587  -45.6417
 9MN  H82   H   HCH2   0   0.239   2.4449  -4.0215  -43.5843
 9MN  H81   H   HCH2   0   0.236   1.7884  -5.3761  -44.4802
 9MN  H91   H   HNH1   0   0.398   4.5648  -4.9722  -43.6149
 9MN  H121  H   HCH2   0   0.249   5.3682  -8.3559  -44.3422
 9MN  H122  H   HCH2   0   0.271   6.1132  -6.9402  -45.0441
 9MN  H131  H   HCH2   0   0.245   7.0688  -7.3467  -42.8795
 9MN  H132  H   HCH2   0   0.221   6.2124  -5.8407  -42.7957
 9MN  BR1   BR  BR     0  -0.167   8.5769  -6.3607  -40.4980

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
 9MN  O    C     deloc   1.231  0.020  1.231
 9MN  N    CA    single  1.458  0.019  1.458
 9MN  C    CA    single  1.525  0.021  1.525
 9MN  CA   CB    single  1.521  0.033  1.521
 9MN  CB   C6    single  1.524  0.020  1.524
 9MN  C6   CD    single  1.523  0.020  1.523
 9MN  CD   CE    single  1.524  0.020  1.524
 9MN  O11  C10   double  1.225  0.020  1.225
 9MN  C12  C10   single  1.519  0.020  1.519
 9MN  C12  C13   single  1.527  0.020  1.527
 9MN  C10  NZ    single  1.345  0.020  1.345
 9MN  NZ   CE    single  1.447  0.020  1.447
 9MN  C13  C14   single  1.524  0.020  1.524
 9MN  C14  C15   single  1.525  0.020  1.525
 9MN  C16  C15   single  1.517  0.020  1.517
 9MN  C    O1    deloc   1.246  0.020  1.246
 9MN  CB   H51   single  0.970  0.020  1.090
 9MN  CB   H52   single  0.970  0.020  1.090
 9MN  C6   H62   single  0.970  0.020  1.090
 9MN  C6   H61   single  0.970  0.020  1.090
 9MN  C14  H142  single  0.970  0.020  1.090
 9MN  C14  H141  single  0.970  0.020  1.090
 9MN  C15  H152  single  0.970  0.020  1.090
 9MN  C15  H151  single  0.970  0.020  1.090
 9MN  C16  H161  single  0.970  0.020  1.090
 9MN  C16  H162  single  0.970  0.020  1.090
 9MN  CA   HA    single  0.970  0.020  0.970
 9MN  N    H2    single  0.890  0.020  1.040
 9MN  N    H3    single  0.890  0.020  1.040
 9MN  CD   H72   single  0.970  0.020  1.090
 9MN  CD   H71   single  0.970  0.020  1.090
 9MN  CE   H82   single  0.970  0.020  1.090
 9MN  CE   H81   single  0.970  0.020  1.090
 9MN  NZ   H91   single  0.860  0.020  1.020
 9MN  C12  H121  single  0.970  0.020  1.090
 9MN  C12  H122  single  0.970  0.020  1.090
 9MN  C13  H131  single  0.970  0.020  1.090
 9MN  C13  H132  single  0.970  0.020  1.090
 9MN  C16  BR1   single  1.980  0.020  1.980

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
 9MN  H52   CB   H51   106.62  3.000
 9MN  H52   CB   CA    108.89  3.000
 9MN  H51   CB   CA    109.27  3.000
 9MN  H52   CB   C6    109.02  3.000
 9MN  H51   CB   C6    109.12  3.000
 9MN  CA    CB   C6    113.68  3.000
 9MN  H61   C6   H62   106.28  3.000
 9MN  H61   C6   CD    109.28  3.000
 9MN  H62   C6   CD    109.34  3.000
 9MN  H61   C6   CB    109.95  3.000
 9MN  H62   C6   CB    109.34  3.000
 9MN  CD    C6   CB    112.46  3.000
 9MN  H141  C14  H142  105.97  3.000
 9MN  H141  C14  C13   108.97  3.000
 9MN  H142  C14  C13   109.25  3.000
 9MN  H141  C14  C15   109.06  3.000
 9MN  H142  C14  C15   107.03  3.000
 9MN  C13   C14  C15   116.07  3.000
 9MN  H151  C15  H152  105.52  3.000
 9MN  H151  C15  C16   105.24  3.000
 9MN  H152  C15  C16   110.50  3.000
 9MN  H151  C15  C14   107.47  3.000
 9MN  H152  C15  C14   110.78  3.000
 9MN  C16   C15  C14   116.55  3.000
 9MN  BR1   C16  H162  106.24  3.000
 9MN  BR1   C16  H161  104.48  3.000
 9MN  H162  C16  H161  108.68  3.000
 9MN  BR1   C16  C15   113.91  3.000
 9MN  H162  C16  C15   111.97  3.000
 9MN  H161  C16  C15   111.13  3.000
 9MN  HA    CA   C     110.00  3.000
 9MN  HA    CA   N     110.00  3.000
 9MN  C     CA   N     111.00  2.800
 9MN  HA    CA   CB    109.00  3.000
 9MN  C     CA   CB    110.50  1.500
 9MN  N     CA   CB    110.40  1.500
 9MN  H3    N    H2    106.82  3.000
 9MN  H3    N    CA    107.70  3.000
 9MN  H2    N    CA    110.20  3.000
 9MN  O1    C    O     126.50  3.000
 9MN  O1    C    CA    116.72  3.000
 9MN  O     C    CA    120.80  1.700
 9MN  H71   CD   H72   106.58  3.000
 9MN  H71   CD   CE    109.09  3.000
 9MN  H72   CD   CE    109.18  3.000
 9MN  H71   CD   C6    109.60  3.000
 9MN  H72   CD   C6    109.73  3.000
 9MN  CE    CD   C6    112.50  3.000
 9MN  H81   CE   H82   106.81  3.000
 9MN  H81   CE   NZ    108.99  3.000
 9MN  H82   CE   NZ    107.61  3.000
 9MN  H81   CE   CD    110.23  3.000
 9MN  H82   CE   CD    109.83  3.000
 9MN  NZ    CE   CD    113.15  3.000
 9MN  H91   NZ   C10   118.54  3.000
 9MN  H91   NZ   CE    116.77  3.000
 9MN  C10   NZ   CE    123.88  3.000
 9MN  C12   C10  O11   121.20  3.000
 9MN  C12   C10  NZ    116.11  3.000
 9MN  O11   C10  NZ    122.66  3.000
 9MN  H122  C12  H121  106.06  3.000
 9MN  H122  C12  C13   109.19  3.000
 9MN  H121  C12  C13   109.66  3.000
 9MN  H122  C12  C10   106.66  3.000
 9MN  H121  C12  C10   107.02  3.000
 9MN  C13   C12  C10   117.63  3.000
 9MN  H132  C13  H131  105.06  3.000
 9MN  H132  C13  C12   111.11  3.000
 9MN  H131  C13  C12   107.19  3.000
 9MN  H132  C13  C14   110.31  3.000
 9MN  H131  C13  C14   109.99  3.000
 9MN  C12   C13  C14   112.85  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
 9MN  CONST_01  O11  C10  NZ   CE      0.00   0.0  0
 9MN  CONST_02  C12  C10  NZ   CE    180.00   0.0  0
 9MN  CONST_03  H91  NZ   C10  O11   180.00   0.0  0
 9MN  Var_01    CE   CD   C6   CB    179.67  30.0  3
 9MN  Var_02    NZ   CE   CD   C6   -177.36  30.0  3
 9MN  Var_03    C10  C12  C13  C14    63.29  30.0  1
 9MN  Var_04    BR1  C16  C15  C14    84.77  30.0  2
 9MN  Var_05    C12  C13  C14  C15  -172.45  30.0  1
 9MN  Var_06    C13  C14  C15  C16   -66.19  30.0  1
 9MN  Var_07    CD   C6   CB   CA   -176.42  30.0  3
 9MN  Var_08    C10  NZ   CE   CD    -86.27  30.0  1
 9MN  Var_09    C13  C12  C10  NZ     35.51  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
 9MN  chir_01  CA  N  C  CB  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
 9MN  plan-1  CE   0.020
 9MN  plan-1  NZ   0.020
 9MN  plan-1  C10  0.020
 9MN  plan-1  O11  0.020
 9MN  plan-1  C12  0.020
 9MN  plan-1  H91  0.020
 9MN  plan-2  CA   0.020
 9MN  plan-2  C    0.020
 9MN  plan-2  O    0.020
 9MN  plan-2  O1   0.020

