# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 19:46:15 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: ethyl (3S)-1,4-dihydroxy-2-oxo-3,4-dihydro-1,8-naphthyridine-3-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)[C@H]1[C@@H](O)c2cccnc2N(O)C1=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
 LP7  LP7  'ethyl (3S)-1,4-dihydroxy-2-oxo-3,4-dihydro-1,8-naphthyridine-3-carboxylate'  ligand  30  18  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LP7
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
 LP7  C     C  CR16  0  -0.326  -3.9459   1.0954   0.9832
 LP7  N     N  N     0  -0.422  -3.1323  -1.0455   0.2945
 LP7  O     O  OH1   0  -0.643  -0.3811   1.4835  -1.7500
 LP7  C1    C  CR16  0  -0.068  -4.0984  -0.2616   0.7711
 LP7  C2    C  CR16  0  -0.215  -2.7242   1.6763   0.6556
 LP7  C3    C  CR6   0  -0.037  -1.7148   0.8891   0.1432
 LP7  C4    C  CR6   0   0.517  -1.9842  -0.4768   0.0028
 LP7  N5    N  NT    0  -0.275  -0.9602  -1.2883  -0.4783
 LP7  C6    C  C     0   0.572   0.3477  -0.9422  -0.5527
 LP7  C7    C  CH1   0  -0.584   0.6659   0.4026   0.0726
 LP7  C8    C  CH1   0  -0.027  -0.3912   1.4122  -0.3457
 LP7  O9    O  OH1   0  -0.535  -1.3311  -2.5226  -0.9293
 LP7  O10   O  O     0  -0.450   1.1613  -1.6936  -1.0559
 LP7  C11   C  C     0   0.641   2.0905   0.8184  -0.2354
 LP7  O12   O  O     0  -0.426   2.4006   1.7146  -0.9743
 LP7  O13   O  O2    0  -0.447   2.9439   0.0844   0.4504
 LP7  C14   C  CH2   0  -0.184   4.3495   0.3209   0.2551
 LP7  C15   C  CH3   0  -0.690   5.1060  -0.6423   1.1358
 LP7  H     H  HCR6  0   0.276  -4.7595   1.6827   1.3839
 LP7  H1    H  HCR6  0   0.274  -5.0382  -0.7505   0.9986
 LP7  H2    H  HCR6  0   0.280  -2.5634   2.7392   0.7890
 LP7  H7    H  HCH1  0   0.359   0.5874   0.2725   1.1599
 LP7  HO9   H  HOH1  0   0.479  -0.5029  -2.9092  -1.2617
 LP7  H14   H  HCH2  0   0.240   4.5995   0.1687  -0.7964
 LP7  H14A  H  HCH2  0   0.240   4.5844   1.3548   0.5138
 LP7  H15   H  HCH3  0   0.238   4.8825  -0.4843   2.1907
 LP7  H15A  H  HCH3  0   0.238   4.8824  -1.6783   0.8825
 LP7  H15B  H  HCH3  0   0.241   6.1752  -0.4873   0.9942
 LP7  H11   H  HOH1  0   0.462  -1.0651   2.1002  -2.0313
 LP7  H12   H  HCH1  0   0.271  -0.1809   2.3812   0.1216

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
 LP7  C    C1    aromatic  1.382  0.020  1.382
 LP7  C    C2    aromatic  1.392  0.020  1.392
 LP7  C    H     single    0.930  0.020  1.080
 LP7  N    C4    aromatic  1.314  0.020  1.314
 LP7  O    C8    single    1.406  0.020  1.406
 LP7  C1   N     aromatic  1.332  0.020  1.332
 LP7  C1   H1    single    0.930  0.020  1.080
 LP7  C2   C3    aromatic  1.379  0.020  1.379
 LP7  C2   H2    single    0.930  0.020  1.080
 LP7  C3   C4    aromatic  1.399  0.020  1.399
 LP7  C3   C8    single    1.505  0.020  1.505
 LP7  C4   N5    single    1.392  0.020  1.392
 LP7  N5   O9    single    1.365  0.020  1.365
 LP7  N5   C6    single    1.355  0.020  1.355
 LP7  C6   O10   double    1.217  0.020  1.217
 LP7  C7   C6    single    1.517  0.020  1.517
 LP7  C7   C11   single    1.516  0.020  1.516
 LP7  C7   H7    single    0.970  0.020  1.090
 LP7  C8   C7    single    1.520  0.020  1.520
 LP7  O9   HO9   single    0.850  0.020  0.980
 LP7  C11  O12   double    1.202  0.020  1.202
 LP7  C11  O13   single    1.318  0.020  1.318
 LP7  O13  C14   single    1.439  0.020  1.439
 LP7  C14  C15   single    1.509  0.020  1.509
 LP7  C14  H14   single    0.970  0.020  1.090
 LP7  C14  H14A  single    0.970  0.020  1.090
 LP7  C15  H15   single    0.970  0.020  1.090
 LP7  C15  H15A  single    0.970  0.020  1.090
 LP7  C15  H15B  single    0.970  0.020  1.090
 LP7  O    H11   single    0.850  0.020  0.980
 LP7  C8   H12   single    0.970  0.020  1.090

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
 LP7  H     C    C2    121.42  3.000
 LP7  H     C    C1    120.51  3.000
 LP7  C2    C    C1    118.07  3.000
 LP7  C4    N    C1    117.28  3.000
 LP7  H11   O    C8    108.61  3.000
 LP7  H1    C1   N     116.01  3.000
 LP7  H1    C1   C     120.44  3.000
 LP7  N     C1   C     123.56  3.000
 LP7  H2    C2   C3    119.82  3.000
 LP7  H2    C2   C     120.72  3.000
 LP7  C3    C2   C     119.46  3.000
 LP7  C8    C3   C4    118.43  3.000
 LP7  C8    C3   C2    124.48  3.000
 LP7  C4    C3   C2    116.98  3.000
 LP7  N5    C4   C3    117.52  3.000
 LP7  N5    C4   N     117.84  3.000
 LP7  C3    C4   N     124.64  3.000
 LP7  O9    N5   C6    118.36  3.000
 LP7  C6    N5   C4    125.45  3.000
 LP7  O9    N5   C4    116.18  3.000
 LP7  O10   C6   C7    125.30  3.000
 LP7  C7    C6   N5    113.98  3.000
 LP7  O10   C6   N5    120.70  3.000
 LP7  H7    C7   C11   107.51  3.000
 LP7  H7    C7   C8    107.55  3.000
 LP7  C11   C7   C8    114.55  3.000
 LP7  C8    C7   C6    109.24  3.000
 LP7  H7    C7   C6    106.75  3.000
 LP7  C11   C7   C6    110.89  3.000
 LP7  H12   C8   C7    109.65  3.000
 LP7  H12   C8   C3    109.73  3.000
 LP7  C7    C8   C3    106.94  3.000
 LP7  H12   C8   O     112.31  3.000
 LP7  C7    C8   O     107.66  3.000
 LP7  C3    C8   O     110.39  3.000
 LP7  HO9   O9   N5    103.94  3.000
 LP7  O13   C11  O12   124.61  3.000
 LP7  O13   C11  C7    110.49  3.000
 LP7  O12   C11  C7    124.87  3.000
 LP7  C14   O13  C11   118.06  3.000
 LP7  H14A  C14  H14   108.13  3.000
 LP7  H14A  C14  C15   111.02  3.000
 LP7  H14   C14  C15   111.01  3.000
 LP7  H14A  C14  O13   109.50  3.000
 LP7  H14   C14  O13   109.37  3.000
 LP7  C15   C14  O13   107.80  3.000
 LP7  H15B  C15  H15A  107.84  3.000
 LP7  H15B  C15  H15   107.84  3.000
 LP7  H15A  C15  H15   108.71  3.000
 LP7  H15B  C15  C14   108.99  3.000
 LP7  H15A  C15  C14   111.62  3.000
 LP7  H15   C15  C14   111.69  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
 LP7  CONST_01  C4   N    C1   C       0.00   0.0  0
 LP7  CONST_02  C4   C3   C2   C       0.00   0.0  0
 LP7  CONST_03  C2   C3   C4   N       0.00   0.0  0
 LP7  CONST_04  C2   C    C1   N       0.00   0.0  0
 LP7  CONST_05  C3   C2   C    C1      0.00   0.0  0
 LP7  CONST_06  C3   C4   N    C1      0.00   0.0  0
 LP7  CONST_07  C7   C6   N5   C4      0.00   0.0  0
 LP7  CONST_08  O10  C6   N5   C4    180.00   0.0  0
 LP7  CONST_09  O9   N5   C6   C7    180.00   0.0  0
 LP7  CONST_10  H    C    C1   N     180.00   0.0  0
 LP7  CONST_11  H2   C2   C    C1    180.00   0.0  0
 LP7  CONST_12  H1   C1   C    C2    180.00   0.0  0
 LP7  CONST_13  O10  C6   N5   O9      0.00   0.0  0
 LP7  Var_01    C6   N5   C4   N    -164.84  30.0  1
 LP7  Var_02    C15  C14  O13  C11  -179.59  30.0  3
 LP7  Var_03    H15  C15  C14  O13   -61.59  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
 LP7  chir_01  C7  C6  C11  C8  negativ
 LP7  chir_02  C8  O   C7   C3  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
 LP7  plan-1  C4   0.020
 LP7  plan-1  N5   0.020
 LP7  plan-1  C6   0.020
 LP7  plan-1  C7   0.020
 LP7  plan-1  O9   0.020
 LP7  plan-1  O10  0.020
 LP7  plan-2  C    0.020
 LP7  plan-2  N    0.020
 LP7  plan-2  C1   0.020
 LP7  plan-2  C2   0.020
 LP7  plan-2  C3   0.020
 LP7  plan-2  C4   0.020
 LP7  plan-2  N5   0.020
 LP7  plan-2  C8   0.020
 LP7  plan-2  H    0.020
 LP7  plan-2  H1   0.020
 LP7  plan-2  H2   0.020
 LP7  plan-3  C7   0.020
 LP7  plan-3  C11  0.020
 LP7  plan-3  O12  0.020
 LP7  plan-3  O13  0.020

