# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 03:20:40 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: (E)-N~6~-{2-hydroxy-3-methyl-6-[(phosphonooxy)methyl]benzylidene}-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(CO[P](O)(O)=O)c(C=NCCCC[C@H](N)C(O)=O)c1O
#
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
 3QN  3QN  (E)-N~6~-{2-hydroxy-3-methyl-6-[(phosphonooxy)methyl]benzylidene}-L-lysine  L-peptide  45  25  .  2022-09-22  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_3QN
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
 3QN  C1   C  C      0   0.404  -7.5155  -1.1995   0.7614
 3QN  N1   N  NH2    0  -0.802  -7.1331  -0.4698  -1.5646
 3QN  O1   O  O      0  -0.607  -8.5065  -0.4427   0.7429
 3QN  P1   P  P      0   1.222   4.6626  -2.6175   0.2190
 3QN  C2   C  CR16   0  -0.274   3.7791   3.0346   0.6481
 3QN  C3   C  CR6    0  -0.021   2.5674   3.6756   0.4686
 3QN  C4   C  CR6    0   0.335   1.4844   2.9036   0.0225
 3QN  O2   O  OH1    0  -0.635   0.3147   3.5195  -0.1470
 3QN  C5   C  CR6    0  -0.121   1.6371   1.5256  -0.2374
 3QN  C6   C  CR6    0  -0.005   2.8899   0.9055  -0.0459
 3QN  C7   C  CR16   0  -0.340   3.9493   1.6739   0.3982
 3QN  C8   C  CH1    0  -0.204  -6.5067  -1.0792  -0.4027
 3QN  C9   C  CH2    0  -0.425  -5.2550  -0.3479   0.1146
 3QN  C10  C  CH2    0  -0.429  -2.8833   0.4337  -0.3428
 3QN  C11  C  CH2    0  -0.278  -1.7490   0.4748  -1.3600
 3QN  C12  C  CH2    0  -0.430  -4.1104  -0.2865  -0.8894
 3QN  N2   N  N      0  -0.469  -0.6511   1.2824  -0.8903
 3QN  O3   O  OP    -1  -0.901   4.0659  -3.3558  -0.9740
 3QN  O4   O  O      0  -0.899   3.9339  -2.8670   1.5342
 3QN  O5   O  OP    -1  -0.892   6.1815  -2.6354   0.3052
 3QN  C14  C  C1     0   0.042   0.4929   0.7541  -0.7059
 3QN  C15  C  CH2    0  -0.174   3.0761  -0.5695  -0.3319
 3QN  OXT  O  OC    -1  -0.622  -7.2271  -2.0228   1.6537
 3QN  H1   H  HNH2   0   0.326  -7.6103   0.3720  -1.2671
 3QN  H2   H  HNH2   0   0.332  -6.4329  -0.1866  -2.2382
 3QN  H3   H  HCR6   0   0.245   4.6288   3.6128   0.9935
 3QN  H4   H  HCR6   0   0.243   4.9175   1.2212   0.5544
 3QN  H5   H  HCH1   0   0.198  -6.1952  -2.0944  -0.6790
 3QN  H6   H  HCH2   0   0.206  -5.5345   0.6698   0.4125
 3QN  H7   H  HCH2   0   0.212  -4.9045  -0.8540   1.0186
 3QN  H8   H  HCH2   0   0.222  -2.5358  -0.0611   0.5692
 3QN  H9   H  HCH2   0   0.209  -1.4235  -0.5452  -1.6012
 3QN  H10  H  HCH2   0   0.235  -2.1205   0.9218  -2.2873
 3QN  H11  H  HCH2   0   0.215  -3.8353  -1.3042  -1.1870
 3QN  H12  H  HCH2   0   0.206  -4.4299   0.2251  -1.8035
 3QN  H14  H  HCH3   0   0.239   2.0689   5.6790  -0.1600
 3QN  H15  H  HCH3   0   0.239   1.6438   5.3292   1.5047
 3QN  H16  H  HCH3   0   0.240   3.3297   5.5861   1.0646
 3QN  H18  H  H      0   0.245   0.6412  -0.3090  -0.9066
 3QN  H19  H  HCH2   0   0.195   2.3812  -1.1363   0.3053
 3QN  H20  H  HCH2   0   0.196   2.7625  -0.7700  -1.3678
 3QN  H22  H  HCH2   0   0.222  -3.1514   1.4569  -0.0635
 3QN  H23  H  HOH1   0   0.464  -0.3442   2.8324  -0.4618
 3QN  C13  C  CH3    0  -0.711   2.3925   5.1409   0.7330
 3QN  O6   O  O2     0  -0.654   4.3903  -0.9593  -0.1194

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
 3QN  C1   O1   deloc     1.247  0.020  1.247
 3QN  C1   OXT  deloc     1.248  0.020  1.248
 3QN  N1   C8   single    1.454  0.020  1.454
 3QN  N1   H1   single    0.890  0.020  1.040
 3QN  N1   H2   single    0.890  0.020  1.040
 3QN  P1   O3   deloc     1.525  0.020  1.525
 3QN  P1   O6   single    1.714  0.020  1.714
 3QN  C2   C3   aromatic  1.383  0.020  1.383
 3QN  C2   H3   single    0.930  0.020  1.080
 3QN  C3   C13  single    1.499  0.020  1.499
 3QN  C4   C3   aromatic  1.403  0.020  1.403
 3QN  C4   O2   single    1.333  0.020  1.333
 3QN  C5   C4   aromatic  1.411  0.020  1.411
 3QN  C6   C5   aromatic  1.411  0.020  1.411
 3QN  C6   C7   aromatic  1.382  0.020  1.382
 3QN  C7   C2   aromatic  1.394  0.020  1.394
 3QN  C7   H4   single    0.930  0.020  1.080
 3QN  C8   C1   single    1.545  0.020  1.545
 3QN  C8   C9   single    1.539  0.020  1.539
 3QN  C8   H5   single    0.970  0.020  1.090
 3QN  C9   H6   single    0.970  0.020  1.090
 3QN  C9   H7   single    0.970  0.020  1.090
 3QN  C10  C12  single    1.524  0.020  1.524
 3QN  C10  H8   single    0.970  0.020  1.090
 3QN  C10  H22  single    0.970  0.020  1.090
 3QN  C11  C10  single    1.524  0.020  1.524
 3QN  C11  N2   single    1.442  0.020  1.442
 3QN  C11  H9   single    0.970  0.020  1.090
 3QN  C11  H10  single    0.970  0.020  1.090
 3QN  C12  C9   single    1.524  0.020  1.524
 3QN  C12  H11  single    0.970  0.020  1.090
 3QN  C12  H12  single    0.970  0.020  1.090
 3QN  C13  H14  single    0.970  0.020  1.090
 3QN  C13  H15  single    0.970  0.020  1.090
 3QN  C13  H16  single    0.970  0.020  1.090
 3QN  O4   P1   deloc     1.524  0.020  1.524
 3QN  O5   P1   deloc     1.521  0.020  1.521
 3QN  C14  C5   single    1.457  0.020  1.457
 3QN  C14  N2   double    1.274  0.020  1.274
 3QN  C14  H18  single    0.930  0.020  1.080
 3QN  O6   C15  single    1.387  0.020  1.387
 3QN  C15  C6   single    1.514  0.020  1.514
 3QN  C15  H19  single    0.970  0.020  1.090
 3QN  C15  H20  single    0.970  0.020  1.090
 3QN  O2   H23  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
 3QN  OXT  C1   C8   116.05  3.000
 3QN  C8   C1   O1   117.41  3.000
 3QN  OXT  C1   O1   126.49  3.000
 3QN  H2   N1   H1   106.80  3.000
 3QN  H2   N1   C8   110.55  3.000
 3QN  H1   N1   C8   108.47  3.000
 3QN  O6   P1   O5   100.44  3.000
 3QN  O5   P1   O4   115.25  3.000
 3QN  O6   P1   O4   104.64  3.000
 3QN  O5   P1   O3   115.43  3.000
 3QN  O4   P1   O3   114.13  3.000
 3QN  O6   P1   O3   104.58  3.000
 3QN  H3   C2   C7   118.82  3.000
 3QN  C7   C2   C3   122.44  3.000
 3QN  H3   C2   C3   118.75  3.000
 3QN  C13  C3   C4   120.26  3.000
 3QN  C4   C3   C2   117.56  3.000
 3QN  C13  C3   C2   122.18  3.000
 3QN  C5   C4   O2   121.54  3.000
 3QN  C5   C4   C3   120.84  3.000
 3QN  O2   C4   C3   117.62  3.000
 3QN  H23  O2   C4   107.46  3.000
 3QN  C14  C5   C6   120.53  3.000
 3QN  C14  C5   C4   119.44  3.000
 3QN  C6   C5   C4   120.03  3.000
 3QN  C15  C6   C7   120.54  3.000
 3QN  C15  C6   C5   120.78  3.000
 3QN  C7   C6   C5   118.68  3.000
 3QN  H4   C7   C6   120.04  3.000
 3QN  H4   C7   C2   119.51  3.000
 3QN  C6   C7   C2   120.45  3.000
 3QN  H5   C8   C9   107.06  3.000
 3QN  H5   C8   N1   107.99  3.000
 3QN  C9   C8   N1   114.82  3.000
 3QN  H5   C8   C1   107.64  3.000
 3QN  C9   C8   C1   108.34  3.000
 3QN  N1   C8   C1   110.70  3.000
 3QN  H7   C9   H6   106.65  3.000
 3QN  H7   C9   C12  108.82  3.000
 3QN  H6   C9   C12  109.45  3.000
 3QN  C12  C9   C8   114.11  3.000
 3QN  H7   C9   C8   108.58  3.000
 3QN  H6   C9   C8   108.96  3.000
 3QN  H22  C10  H8   106.74  3.000
 3QN  H22  C10  C12  109.64  3.000
 3QN  H8   C10  C12  109.93  3.000
 3QN  H22  C10  C11  109.13  3.000
 3QN  H8   C10  C11  109.40  3.000
 3QN  C12  C10  C11  111.87  3.000
 3QN  H10  C11  H9   107.10  3.000
 3QN  H10  C11  N2   107.81  3.000
 3QN  H9   C11  N2   111.50  3.000
 3QN  H10  C11  C10  108.89  3.000
 3QN  H9   C11  C10  110.02  3.000
 3QN  N2   C11  C10  111.37  3.000
 3QN  H12  C12  H11  106.29  3.000
 3QN  H12  C12  C10  108.27  3.000
 3QN  H11  C12  C10  109.52  3.000
 3QN  H12  C12  C9   110.47  3.000
 3QN  H11  C12  C9   109.28  3.000
 3QN  C10  C12  C9   112.80  3.000
 3QN  C14  N2   C11  119.92  3.000
 3QN  H18  C14  N2   119.95  3.000
 3QN  H18  C14  C5   117.90  3.000
 3QN  N2   C14  C5   122.15  3.000
 3QN  H20  C15  H19  105.74  3.000
 3QN  H20  C15  O6   111.28  3.000
 3QN  H19  C15  O6   111.40  3.000
 3QN  H20  C15  C6   108.67  3.000
 3QN  H19  C15  C6   108.35  3.000
 3QN  O6   C15  C6   111.19  3.000
 3QN  H16  C13  H15  107.72  3.000
 3QN  H16  C13  H14  107.61  3.000
 3QN  H15  C13  H14  106.85  3.000
 3QN  H16  C13  C3   110.66  3.000
 3QN  H15  C13  C3   111.92  3.000
 3QN  H14  C13  C3   111.85  3.000
 3QN  C15  O6   P1   116.91  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
 3QN  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 3QN  CONST_02  C5   C6   C7   C2      0.00   0.0  0
 3QN  CONST_03  C6   C7   C2   C3      0.00   0.0  0
 3QN  CONST_04  C6   C5   C4   C3      0.00   0.0  0
 3QN  CONST_05  C7   C2   C3   C4      0.00   0.0  0
 3QN  CONST_06  C7   C6   C5   C4      0.00   0.0  0
 3QN  CONST_07  O2   C4   C3   C2    180.00   0.0  0
 3QN  CONST_08  C15  C6   C7   C2    180.00   0.0  0
 3QN  CONST_09  C14  C5   C4   C3    180.00   0.0  0
 3QN  CONST_10  C15  C6   C5   C4    180.00   0.0  0
 3QN  CONST_11  C6   C5   C4   O2    180.00   0.0  0
 3QN  CONST_12  C13  C3   C4   C5    180.00   0.0  0
 3QN  CONST_13  C14  C5   C6   C7    180.00   0.0  0
 3QN  CONST_14  C13  C3   C2   C7    180.00   0.0  0
 3QN  CONST_15  H4   C7   C2   C3    180.00   0.0  0
 3QN  CONST_16  H3   C2   C3   C4    180.00   0.0  0
 3QN  Var_01    N2   C14  C5   C4     -0.05  30.0  2
 3QN  Var_02    O6   C15  C6   C5    178.01  30.0  1
 3QN  Var_03    H14  C13  C3   C2    120.30  30.0  2
 3QN  Var_04    C6   C15  O6   P1    156.27  30.0  3
 3QN  Var_05    C10  C12  C9   C8   -179.54  30.0  1
 3QN  Var_06    C11  C10  C12  C9    179.62  30.0  2
 3QN  Var_07    N2   C11  C10  C12   173.65  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
 3QN  chir_01  C8  N1  C1  C9  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
 3QN  plan-1  C2   0.020
 3QN  plan-1  C3   0.020
 3QN  plan-1  C4   0.020
 3QN  plan-1  O2   0.020
 3QN  plan-1  C5   0.020
 3QN  plan-1  C6   0.020
 3QN  plan-1  C7   0.020
 3QN  plan-1  C14  0.020
 3QN  plan-1  C15  0.020
 3QN  plan-1  H3   0.020
 3QN  plan-1  H4   0.020
 3QN  plan-1  C13  0.020
 3QN  plan-2  C1   0.020
 3QN  plan-2  O1   0.020
 3QN  plan-2  C8   0.020
 3QN  plan-2  OXT  0.020
 3QN  plan-3  C5   0.020
 3QN  plan-3  C11  0.020
 3QN  plan-3  N2   0.020
 3QN  plan-3  C14  0.020
 3QN  plan-3  H18  0.020

