# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 20:47:26 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  48  25  .  2022-09-22  2022-11-17
;
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   0.546  -7.4609  -1.2476   0.7557
 3QN  N1   N  NH2   0  -0.786  -7.1476  -0.4378  -1.4945
 3QN  O1   O  O     0  -0.441  -8.4828  -0.6219   0.8838
 3QN  P1   P  P     0   1.465   4.6007  -2.6106   0.2112
 3QN  C2   C  CR16  0  -0.276   3.7792   2.9898   0.7026
 3QN  C3   C  CR6   0  -0.015   2.5946   3.6584   0.4639
 3QN  C4   C  CR6   0   0.342   1.4994   2.9049   0.0130
 3QN  O2   O  OH1   0  -0.630   0.3562   3.5486  -0.2059
 3QN  C5   C  CR6   0  -0.107   1.6158   1.5163  -0.1996
 3QN  C6   C  CR6   0  -0.007   2.8436   0.8724   0.0551
 3QN  C7   C  CR16  0  -0.329   3.9154   1.6153   0.5074
 3QN  C8   C  CH1   0  -0.215  -6.4745  -1.0694  -0.3799
 3QN  C9   C  CH2   0  -0.436  -5.2277  -0.3330   0.1510
 3QN  C10  C  CH2   0  -0.432  -2.8864   0.4827  -0.3523
 3QN  C11  C  CH2   0  -0.282  -1.7667   0.5331  -1.3856
 3QN  C12  C  CH2   0  -0.432  -4.1194  -0.2343  -0.8887
 3QN  N2   N  N     0  -0.466  -0.6578   1.3220  -0.9091
 3QN  O3   O  OH1   0  -0.743   4.5978  -3.1288  -1.2995
 3QN  O4   O  O     0  -0.707   3.7045  -3.4505   1.0258
 3QN  O5   O  OH1   0  -0.729   6.1149  -2.4605   0.6793
 3QN  C14  C  C1    0   0.043   0.4649   0.7653  -0.6874
 3QN  O6   O  O2    0  -0.591   4.2686  -1.0478   0.1651
 3QN  C15  C  CH2   0  -0.209   2.9594  -0.6122  -0.1791
 3QN  OXT  O  OH1   0  -0.594  -7.0516  -2.1611   1.6290
 3QN  H1   H  HNH2  0   0.344  -7.3614   0.5278  -1.2753
 3QN  H2   H  HNH2  0   0.357  -6.5295  -0.4179  -2.2946
 3QN  H3   H  HCR6  0   0.254   4.6360   3.5526   1.0539
 3QN  H4   H  HCR6  0   0.255   4.8678   1.1499   0.7145
 3QN  H5   H  HCH1  0   0.268  -6.1604  -2.0676  -0.7020
 3QN  H6   H  HCH2  0   0.231  -5.5189   0.6704   0.4797
 3QN  H7   H  HCH2  0   0.236  -4.8414  -0.8525   1.0318
 3QN  H8   H  HCH2  0   0.227  -2.5239  -0.0237   0.5473
 3QN  H9   H  HCH2  0   0.212  -1.4522  -0.4852  -1.6463
 3QN  H10  H  HCH2  0   0.240  -2.1432   1.0006  -2.2999
 3QN  H11  H  HCH2  0   0.225  -3.8441  -1.2418  -1.2179
 3QN  H12  H  HCH2  0   0.218  -4.4767   0.2959  -1.7767
 3QN  H13  H  HOH1  0   0.497   5.2009  -2.6740  -1.9029
 3QN  H14  H  HCH3  0   0.243   2.1645   5.6491  -0.2437
 3QN  H15  H  HCH3  0   0.243   1.6979   5.3686   1.4231
 3QN  H16  H  HCH3  0   0.243   3.3988   5.5664   1.0094
 3QN  H17  H  HOH1  0   0.506   6.5353  -3.2960   0.9237
 3QN  H18  H  H     0   0.249   0.5875  -0.3044  -0.8718
 3QN  H19  H  HCH2  0   0.258   2.2196  -1.1493   0.4220
 3QN  H20  H  HCH2  0   0.260   2.7619  -0.8443  -1.2304
 3QN  HXT  H  HOH1  0   0.481  -7.6773  -2.2205   2.3662
 3QN  H22  H  HCH2  0   0.228  -3.1511   1.5021  -0.0578
 3QN  H23  H  HOH1  0   0.467  -0.3184   2.8732  -0.5131
 3QN  C13  C  CH3   0  -0.711   2.4566   5.1356   0.6739

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   double    1.205  0.020  1.205
 3QN  C1   OXT  single    1.328  0.020  1.328
 3QN  N1   C8   single    1.447  0.020  1.447
 3QN  N1   H1   single    0.890  0.020  1.040
 3QN  N1   H2   single    0.890  0.020  1.040
 3QN  P1   O3   single    1.597  0.020  1.597
 3QN  P1   O6   single    1.598  0.020  1.598
 3QN  C2   C3   aromatic  1.381  0.020  1.381
 3QN  C2   H3   single    0.930  0.020  1.080
 3QN  C3   C13  single    1.498  0.020  1.498
 3QN  C4   C3   aromatic  1.404  0.020  1.404
 3QN  C4   O2   single    1.330  0.020  1.330
 3QN  C5   C4   aromatic  1.410  0.020  1.410
 3QN  C6   C5   aromatic  1.410  0.020  1.410
 3QN  C6   C7   aromatic  1.380  0.020  1.380
 3QN  C7   C2   aromatic  1.395  0.020  1.395
 3QN  C7   H4   single    0.930  0.020  1.080
 3QN  C8   C1   single    1.515  0.020  1.515
 3QN  C8   C9   single    1.542  0.020  1.542
 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    1.523  0.020  1.523
 3QN  C12  H11  single    0.970  0.020  1.090
 3QN  C12  H12  single    0.970  0.020  1.090
 3QN  O3   H13  single    0.850  0.020  0.980
 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   double    1.474  0.020  1.474
 3QN  O5   P1   single    1.592  0.020  1.592
 3QN  O5   H17  single    0.850  0.020  0.980
 3QN  C14  C5   single    1.458  0.020  1.458
 3QN  C14  N2   double    1.273  0.020  1.273
 3QN  C14  H18  single    0.930  0.020  1.080
 3QN  O6   C15  single    1.422  0.020  1.422
 3QN  C15  C6   single    1.507  0.020  1.507
 3QN  C15  H19  single    0.970  0.020  1.090
 3QN  C15  H20  single    0.970  0.020  1.090
 3QN  OXT  HXT  single    0.850  0.020  0.980
 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   111.91  3.000
 3QN  C8   C1   O1   124.81  3.000
 3QN  OXT  C1   O1   123.26  3.000
 3QN  H2   N1   H1   106.35  3.000
 3QN  H2   N1   C8   109.49  3.000
 3QN  H1   N1   C8   110.34  3.000
 3QN  O6   P1   O5    96.54  3.000
 3QN  O5   P1   O4   118.01  3.000
 3QN  O6   P1   O4   116.54  3.000
 3QN  O5   P1   O3   108.09  3.000
 3QN  O4   P1   O3   109.68  3.000
 3QN  O6   P1   O3   106.83  3.000
 3QN  H3   C2   C7   118.68  3.000
 3QN  C7   C2   C3   122.45  3.000
 3QN  H3   C2   C3   118.87  3.000
 3QN  C13  C3   C4   120.15  3.000
 3QN  C4   C3   C2   117.70  3.000
 3QN  C13  C3   C2   122.15  3.000
 3QN  C5   C4   O2   121.52  3.000
 3QN  C5   C4   C3   120.85  3.000
 3QN  O2   C4   C3   117.62  3.000
 3QN  H23  O2   C4   107.62  3.000
 3QN  C14  C5   C6   120.84  3.000
 3QN  C14  C5   C4   119.51  3.000
 3QN  C6   C5   C4   119.64  3.000
 3QN  C15  C6   C7   121.42  3.000
 3QN  C15  C6   C5   119.25  3.000
 3QN  C7   C6   C5   119.32  3.000
 3QN  H4   C7   C6   121.04  3.000
 3QN  H4   C7   C2   118.94  3.000
 3QN  C6   C7   C2   120.02  3.000
 3QN  H5   C8   C9   107.74  3.000
 3QN  H5   C8   N1   107.74  3.000
 3QN  C9   C8   N1   115.64  3.000
 3QN  H5   C8   C1   107.47  3.000
 3QN  C9   C8   C1   108.94  3.000
 3QN  N1   C8   C1   109.02  3.000
 3QN  H7   C9   H6   106.71  3.000
 3QN  H7   C9   C12  108.89  3.000
 3QN  H6   C9   C12  109.81  3.000
 3QN  C12  C9   C8   112.60  3.000
 3QN  H7   C9   C8   109.64  3.000
 3QN  H6   C9   C8   109.01  3.000
 3QN  H22  C10  H8   106.87  3.000
 3QN  H22  C10  C12  109.72  3.000
 3QN  H8   C10  C12  109.86  3.000
 3QN  H22  C10  C11  109.24  3.000
 3QN  H8   C10  C11  109.22  3.000
 3QN  C12  C10  C11  111.79  3.000
 3QN  H10  C11  H9   107.26  3.000
 3QN  H10  C11  N2   107.89  3.000
 3QN  H9   C11  N2   111.46  3.000
 3QN  H10  C11  C10  109.14  3.000
 3QN  H9   C11  C10  109.93  3.000
 3QN  N2   C11  C10  111.04  3.000
 3QN  H12  C12  H11  106.50  3.000
 3QN  H12  C12  C10  108.77  3.000
 3QN  H11  C12  C10  109.59  3.000
 3QN  H12  C12  C9   110.35  3.000
 3QN  H11  C12  C9   109.18  3.000
 3QN  C10  C12  C9   112.28  3.000
 3QN  C14  N2   C11  119.79  3.000
 3QN  H13  O3   P1   115.89  3.000
 3QN  H17  O5   P1   113.98  3.000
 3QN  H18  C14  N2   119.86  3.000
 3QN  H18  C14  C5   118.18  3.000
 3QN  N2   C14  C5   121.96  3.000
 3QN  C15  O6   P1   119.85  3.000
 3QN  H20  C15  H19  107.54  3.000
 3QN  H20  C15  O6   109.49  3.000
 3QN  H19  C15  O6   109.83  3.000
 3QN  H20  C15  C6   110.13  3.000
 3QN  H19  C15  C6   110.26  3.000
 3QN  O6   C15  C6   109.56  3.000
 3QN  HXT  OXT  C1   110.08  3.000
 3QN  H16  C13  H15  107.79  3.000
 3QN  H16  C13  H14  107.73  3.000
 3QN  H15  C13  H14  106.90  3.000
 3QN  H16  C13  C3   110.70  3.000
 3QN  H15  C13  C3   111.76  3.000
 3QN  H14  C13  C3   111.76  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
 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  CONST_17  HXT  OXT  C1   O1      0.00   0.0  0
 3QN  Var_01    N2   C14  C5   C4     -1.18  30.0  1
 3QN  Var_02    O6   C15  C6   C5   -178.90  30.0  2
 3QN  Var_03    H14  C13  C3   C2    121.04  30.0  2
 3QN  Var_04    C6   C15  O6   P1    171.27  30.0  3
 3QN  Var_05    C10  C12  C9   C8   -179.45  30.0  1
 3QN  Var_06    C11  C10  C12  C9    178.04  30.0  1
 3QN  Var_07    N2   C11  C10  C12   174.58  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
 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-2  HXT  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

