# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 01:06:35 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: N-benzyl-N-(carboxymethyl)glycyl-L-histidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CN(CC(=O)N[C@@H](Cc1[nH]cnc1)C(O)=O)Cc2ccccc2
#
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
 33K  33K  N-benzyl-N-(carboxymethyl)glycyl-L-histidine  ligand  44  26  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_33K
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
 33K  N12  N  NH1    0  -0.605  -1.7411   1.4428   0.6234
 33K  C13  C  C      0   0.533  -0.5627   1.0418   0.1316
 33K  C15  C  CH2    0  -0.393   0.5229   0.8063   1.1699
 33K  C21  C  CR6    0   0.059   3.4555   0.1721   0.7640
 33K  C22  C  CR16   0  -0.278   3.3208   0.2780  -0.6187
 33K  C24  C  CR16   0  -0.273   5.4151   1.4621  -0.7625
 33K  C26  C  CR16   0  -0.317   4.5784   0.7275   1.3712
 33K  O    O  O      0  -0.598   1.3729  -3.1238   0.1062
 33K  C03  C  C      0   0.421  -3.5046   3.1461   0.2997
 33K  O04  O  OC    -1  -0.606  -4.3821   3.6139  -0.4480
 33K  C05  C  CH1    0  -0.226  -2.8786   1.8124  -0.1800
 33K  C06  C  CH2    0  -0.517  -3.9744   0.7272  -0.1736
 33K  C07  C  CR5    0   0.322  -3.4916  -0.6721  -0.3299
 33K  N08  N  NR15   0  -0.611  -2.5809  -1.0902  -1.2593
 33K  C09  C  CR15   0   0.081  -2.4167  -2.4217  -1.1135
 33K  N10  N  N      0  -0.439  -3.1813  -2.8995  -0.1674
 33K  C11  C  CR15   0  -0.280  -3.8520  -1.8166   0.3300
 33K  O14  O  O      0  -0.504  -0.3404   0.8828  -1.0641
 33K  N16  N  NT     0  -0.399   1.1055  -0.5040   1.0164
 33K  C18  C  C      0   0.399   0.5709  -2.9776   1.0449
 33K  O19  O  OC    -1  -0.627  -0.0303  -3.8793   1.6639
 33K  C23  C  CR16   0  -0.244   4.2917   0.9198  -1.3754
 33K  C25  C  CR16   0  -0.244   5.5549   1.3644   0.6156
 33K  H1   H  HNH1   0   0.383  -1.8166   1.6194   1.6128
 33K  H2   H  HCH2   0   0.265   1.2894   1.5664   0.9922
 33K  H3   H  HCH2   0   0.217   0.1424   0.9862   2.1899
 33K  H4   H  HCH2   0   0.185   0.1468  -1.5324   2.6035
 33K  H5   H  HCH2   0   0.254  -0.7866  -1.3470   1.1374
 33K  H6   H  HCH2   0   0.255   2.7296  -1.6256   1.6075
 33K  H7   H  HCH2   0   0.202   2.4693  -0.2238   2.6268
 33K  H8   H  HCR6   0   0.254   2.4342  -0.1310  -1.0850
 33K  H9   H  HCR6   0   0.249   6.1722   1.9627  -1.3525
 33K  H10  H  HCR6   0   0.241   4.6921   0.6647   2.4479
 33K  H12  H  HCH1   0   0.247  -2.5245   1.9460  -1.2040
 33K  H13  H  HCH2   0   0.246  -4.5289   0.7690   0.7679
 33K  H14  H  HCH2   0   0.255  -4.6916   0.9744  -0.9599
 33K  H15  H  HNR5   0   0.407  -2.0235  -0.4924  -1.8513
 33K  H16  H  HCR5   0   0.265  -1.7228  -2.9852  -1.7176
 33K  H18  H  HCR5   0   0.242  -4.5650  -1.9039   1.1369
 33K  H21  H  HCR6   0   0.247   4.1713   0.9985  -2.4489
 33K  H22  H  HCR6   0   0.250   6.4213   1.7910   1.1049
 33K  O02  O  O      0  -0.592  -3.1072   3.6061   1.3849
 33K  C17  C  CH2    0  -0.426   0.2279  -1.5454   1.5027
 33K  C20  C  CH2    0  -0.302   2.4325  -0.5758   1.5811

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
 33K  C23  C22  aromatic  1.388  0.020  1.388
 33K  C23  C24  aromatic  1.390  0.020  1.390
 33K  C22  C21  aromatic  1.393  0.020  1.393
 33K  O14  C13  double    1.227  0.020  1.227
 33K  C09  N08  aromatic  1.349  0.020  1.349
 33K  C09  N10  aromatic  1.307  0.020  1.307
 33K  C24  C25  aromatic  1.389  0.020  1.389
 33K  C21  C20  single    1.508  0.020  1.508
 33K  C21  C26  aromatic  1.392  0.020  1.392
 33K  C20  N16  single    1.444  0.020  1.444
 33K  N08  C07  aromatic  1.367  0.020  1.367
 33K  C25  C26  aromatic  1.389  0.020  1.389
 33K  O02  C03  deloc     1.244  0.020  1.244
 33K  C13  C15  single    1.520  0.020  1.520
 33K  C13  N12  single    1.338  0.020  1.338
 33K  N10  C11  aromatic  1.367  0.020  1.367
 33K  C15  N16  single    1.442  0.020  1.442
 33K  N16  C17  single    1.446  0.020  1.446
 33K  C05  C03  single    1.549  0.020  1.549
 33K  C05  N12  single    1.441  0.020  1.441
 33K  C05  C06  single    1.542  0.020  1.542
 33K  C07  C11  aromatic  1.369  0.020  1.369
 33K  C07  C06  single    1.488  0.020  1.488
 33K  C03  O04  deloc     1.244  0.020  1.244
 33K  C17  C18  single    1.542  0.020  1.542
 33K  C18  O    deloc     1.243  0.020  1.243
 33K  C18  O19  deloc     1.248  0.020  1.248
 33K  N12  H1   single    0.860  0.020  1.020
 33K  C15  H2   single    0.970  0.020  1.090
 33K  C15  H3   single    0.970  0.020  1.090
 33K  C17  H4   single    0.970  0.020  1.090
 33K  C17  H5   single    0.970  0.020  1.090
 33K  C20  H6   single    0.970  0.020  1.090
 33K  C20  H7   single    0.970  0.020  1.090
 33K  C22  H8   single    0.930  0.020  1.080
 33K  C24  H9   single    0.930  0.020  1.080
 33K  C26  H10  single    0.930  0.020  1.080
 33K  C05  H12  single    0.970  0.020  1.090
 33K  C06  H13  single    0.970  0.020  1.090
 33K  C06  H14  single    0.970  0.020  1.090
 33K  N08  H15  single    0.860  0.020  1.020
 33K  C09  H16  single    0.930  0.020  1.080
 33K  C11  H18  single    0.930  0.020  1.080
 33K  C23  H21  single    0.930  0.020  1.080
 33K  C25  H22  single    0.930  0.020  1.080

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
 33K  H1   N12  C05  116.31  3.000
 33K  H1   N12  C13  118.63  3.000
 33K  C05  N12  C13  124.55  3.000
 33K  O14  C13  C15  121.08  3.000
 33K  C15  C13  N12  115.10  3.000
 33K  O14  C13  N12  123.82  3.000
 33K  H3   C15  H2   106.17  3.000
 33K  H3   C15  N16  112.69  3.000
 33K  H2   C15  N16  109.33  3.000
 33K  H3   C15  C13  111.09  3.000
 33K  H2   C15  C13  106.37  3.000
 33K  N16  C15  C13  110.88  3.000
 33K  C26  C21  C22  118.72  3.000
 33K  C26  C21  C20  120.58  3.000
 33K  C22  C21  C20  120.66  3.000
 33K  H8   C22  C23  120.85  3.000
 33K  H8   C22  C21  118.56  3.000
 33K  C23  C22  C21  120.57  3.000
 33K  H9   C24  C25  120.20  3.000
 33K  H9   C24  C23  120.36  3.000
 33K  C25  C24  C23  119.44  3.000
 33K  H10  C26  C25  119.53  3.000
 33K  H10  C26  C21  119.63  3.000
 33K  C25  C26  C21  120.84  3.000
 33K  C05  C03  O04  114.99  3.000
 33K  O04  C03  O02  127.64  3.000
 33K  C05  C03  O02  117.34  3.000
 33K  H12  C05  C06  108.69  3.000
 33K  H12  C05  C03  108.43  3.000
 33K  C06  C05  C03  108.50  3.000
 33K  H12  C05  N12  107.35  3.000
 33K  C06  C05  N12  112.22  3.000
 33K  C03  C05  N12  111.54  3.000
 33K  H14  C06  H13  106.15  3.000
 33K  H14  C06  C07  110.49  3.000
 33K  H13  C06  C07  106.90  3.000
 33K  H14  C06  C05  107.71  3.000
 33K  H13  C06  C05  109.70  3.000
 33K  C07  C06  C05  115.51  3.000
 33K  C11  C07  N08  104.32  3.000
 33K  C11  C07  C06  130.52  3.000
 33K  N08  C07  C06  125.11  3.000
 33K  H15  N08  C09  125.49  3.000
 33K  H15  N08  C07  125.85  3.000
 33K  C09  N08  C07  108.03  3.000
 33K  H16  C09  N10  126.20  3.000
 33K  H16  C09  N08  122.22  3.000
 33K  N10  C09  N08  111.58  3.000
 33K  C11  N10  C09  105.11  3.000
 33K  H18  C11  N10  122.09  3.000
 33K  H18  C11  C07  126.96  3.000
 33K  N10  C11  C07  110.95  3.000
 33K  C20  N16  C17  112.98  3.000
 33K  C17  N16  C15  111.93  3.000
 33K  C20  N16  C15  112.01  3.000
 33K  O19  C18  O    126.89  3.000
 33K  O19  C18  C17  114.62  3.000
 33K  O    C18  C17  118.47  3.000
 33K  H21  C23  C24  119.90  3.000
 33K  H21  C23  C22  119.75  3.000
 33K  C24  C23  C22  120.35  3.000
 33K  H22  C25  C26  119.82  3.000
 33K  H22  C25  C24  120.09  3.000
 33K  C26  C25  C24  120.09  3.000
 33K  H5   C17  H4   105.19  3.000
 33K  H5   C17  C18  105.96  3.000
 33K  H4   C17  C18  108.86  3.000
 33K  H5   C17  N16  108.62  3.000
 33K  H4   C17  N16  111.81  3.000
 33K  C18  C17  N16  115.73  3.000
 33K  H7   C20  H6   105.94  3.000
 33K  H7   C20  N16  112.65  3.000
 33K  H6   C20  N16  107.91  3.000
 33K  H7   C20  C21  109.42  3.000
 33K  H6   C20  C21  107.80  3.000
 33K  N16  C20  C21  112.76  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
 33K  CONST_01  C24  C23  C22  C21    0.00   0.0  0
 33K  CONST_02  C24  C25  C26  C21    0.00   0.0  0
 33K  CONST_03  C25  C24  C23  C22    0.00   0.0  0
 33K  CONST_04  C25  C26  C21  C22    0.00   0.0  0
 33K  CONST_05  C23  C22  C21  C26    0.00   0.0  0
 33K  CONST_06  C23  C24  C25  C26    0.00   0.0  0
 33K  CONST_07  N10  C09  N08  C07    0.00   0.0  0
 33K  CONST_08  C09  N10  C11  C07    0.00   0.0  0
 33K  CONST_09  C11  N10  C09  N08    0.00   0.0  0
 33K  CONST_10  N10  C11  C07  N08    0.00   0.0  0
 33K  CONST_11  C11  C07  N08  C09    0.00   0.0  0
 33K  CONST_12  C23  C22  C21  C20  180.00   0.0  0
 33K  CONST_13  C25  C26  C21  C20  180.00   0.0  0
 33K  CONST_14  C09  N08  C07  C06  180.00   0.0  0
 33K  CONST_15  N10  C11  C07  C06  180.00   0.0  0
 33K  CONST_16  H21  C23  C22  C21  180.00   0.0  0
 33K  CONST_17  H22  C25  C26  C21  180.00   0.0  0
 33K  CONST_18  H9   C24  C23  C22  180.00   0.0  0
 33K  CONST_19  H10  C26  C21  C22  180.00   0.0  0
 33K  CONST_20  H8   C22  C23  C24  180.00   0.0  0
 33K  CONST_21  H16  C09  N08  C07  180.00   0.0  0
 33K  CONST_22  H18  C11  C07  N08  180.00   0.0  0
 33K  CONST_23  H15  N08  C09  N10  180.00   0.0  0
 33K  CONST_24  C05  N12  C13  C15  180.00   0.0  0
 33K  CONST_25  O14  C13  N12  C05    0.00   0.0  0
 33K  CONST_26  H1   N12  C13  C15    0.00   0.0  0
 33K  Var_01    N16  C20  C21  C22  -31.27  30.0  2
 33K  Var_02    N08  C07  C06  C05  -46.45  30.0  2
 33K  Var_03    C21  C20  N16  C15  -72.01  30.0  1
 33K  Var_04    N16  C15  C13  N12  127.56  30.0  3
 33K  Var_05    C20  N16  C15  C13  156.99  30.0  3
 33K  Var_06    C18  C17  N16  C15  163.94  30.0  3
 33K  Var_07    N16  C17  C18  O    -14.23  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
 33K  chir_01  C05  C03  N12  C06  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
 33K  plan-1  C06  0.020
 33K  plan-1  C07  0.020
 33K  plan-1  N08  0.020
 33K  plan-1  C09  0.020
 33K  plan-1  N10  0.020
 33K  plan-1  C11  0.020
 33K  plan-1  H15  0.020
 33K  plan-1  H16  0.020
 33K  plan-1  H18  0.020
 33K  plan-2  C21  0.020
 33K  plan-2  C22  0.020
 33K  plan-2  C24  0.020
 33K  plan-2  C26  0.020
 33K  plan-2  C23  0.020
 33K  plan-2  C25  0.020
 33K  plan-2  H8   0.020
 33K  plan-2  H9   0.020
 33K  plan-2  H10  0.020
 33K  plan-2  H21  0.020
 33K  plan-2  H22  0.020
 33K  plan-2  C20  0.020
 33K  plan-3  N12  0.020
 33K  plan-3  C13  0.020
 33K  plan-3  C15  0.020
 33K  plan-3  C05  0.020
 33K  plan-3  O14  0.020
 33K  plan-3  H1   0.020
 33K  plan-4  C03  0.020
 33K  plan-4  O04  0.020
 33K  plan-4  C05  0.020
 33K  plan-4  O02  0.020
 33K  plan-5  O    0.020
 33K  plan-5  C18  0.020
 33K  plan-5  O19  0.020
 33K  plan-5  C17  0.020

