# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 10:31:35 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: 2-(nitrooxy)ethyl 2-(4-{2-[(3,5-dimethylphenyl)amino]-2-oxoethyl}phenoxy)-2-methylpropanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(C)cc(NC(=O)Cc2ccc(OC(C)(C)C(=O)OCCO[N+]([O-])=O)cc2)c1
#
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
 5JN  5JN  '2-(nitrooxy)ethyl 2-(4-{2-[(3,5-dimethylphenyl)amino]-2-oxoethyl}phenoxy)-2-methylpropanoate'  ligand  57  31  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5JN
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
 5JN  C1   C  CH3    0  -0.725   7.2788   1.5561   3.1169
 5JN  C6   C  CR16   0  -0.372   8.0944   1.8643   0.7597
 5JN  C5   C  CR6    0   0.128   7.1298   1.3805   1.6327
 5JN  C4   C  CR16   0  -0.383   5.9959   0.7427   1.1283
 5JN  C3   C  CR6    0   0.411   5.8347   0.5974  -0.2466
 5JN  C13  C  CR6    0   0.134   1.4018  -1.6139  -0.7797
 5JN  C21  C  CH3    0  -0.663  -4.6307  -2.7988   1.1673
 5JN  C20  C  CT     0   0.073  -3.5934  -2.0278   0.3459
 5JN  C18  C  CR16   0  -0.282   1.1710  -2.7274   0.0249
 5JN  C17  C  CR16   0  -0.340  -0.0896  -3.0032   0.5206
 5JN  O30  O  O      0  -0.370  -8.0896   2.3838  -1.8788
 5JN  C7   C  CR6    0   0.130   7.9463   1.7287  -0.6204
 5JN  C8   C  CR16   0  -0.425   6.8143   1.0978  -1.1101
 5JN  N9   N  NH1    0  -0.750   4.7384  -0.0266  -0.8525
 5JN  C10  C  C      0   0.555   3.6811  -0.6650  -0.2908
 5JN  O11  O  O      0  -0.456   3.4840  -0.7455   0.9062
 5JN  C12  C  CH2    0  -0.697   2.7681  -1.3194  -1.3177
 5JN  C14  C  CR16   0  -0.295   0.3257  -0.7843  -1.0589
 5JN  C15  C  CR16   0  -0.349  -0.9482  -1.0428  -0.5650
 5JN  C16  C  CR6    0   0.380  -1.1650  -2.1621   0.2319
 5JN  O19  O  O2     0  -0.488  -2.3444  -2.5298   0.7865
 5JN  C22  C  CH3    0  -0.674  -3.8329  -2.2798  -1.1406
 5JN  C23  C  C      0   0.583  -3.7145  -0.5623   0.7722
 5JN  O24  O  O      0  -0.428  -3.1033  -0.0777   1.6866
 5JN  O25  O  O2     0  -0.446  -4.6205   0.0848   0.0580
 5JN  C26  C  CH2    0  -0.224  -4.9215   1.4315   0.4278
 5JN  C27  C  CH2    0  -0.215  -5.9466   1.9562  -0.5371
 5JN  O28  O  OC2    0  -0.380  -7.1389   1.1782  -0.3194
 5JN  N29  N  N      1   0.767  -8.1975   1.4927  -1.0881
 5JN  O31  O  O     -1  -0.382  -9.1534   0.8123  -0.8712
 5JN  H1   H  HCH3   0   0.248   6.6063   2.3325   3.4872
 5JN  H2   H  HCH3   0   0.244   7.0342   0.6398   3.6549
 5JN  H3   H  HCH3   0   0.243   8.2933   1.8463   3.3864
 5JN  H4   H  HCR6   0   0.238   8.9771   2.3538   1.1561
 5JN  H5   H  HCR6   0   0.269   5.2513   0.3696   1.8134
 5JN  H6   H  HCH3   0   0.249   9.8473   1.5368  -1.6030
 5JN  H7   H  HCH3   0   0.244   8.6246   2.3495  -2.5700
 5JN  H8   H  HCH3   0   0.244   9.4026   3.1937  -1.2308
 5JN  H9   H  HCH3   0   0.255  -4.4747  -2.6629   2.2375
 5JN  H10  H  HCH3   0   0.247  -5.6385  -2.4690   0.9206
 5JN  H11  H  HCH3   0   0.259  -4.5583  -3.8622   0.9385
 5JN  H12  H  HCR6   0   0.251   1.9844  -3.4046   0.2562
 5JN  H13  H  HCR6   0   0.262  -0.2527  -3.8784   1.1371
 5JN  H14  H  HCR6   0   0.258   6.6868   0.9864  -2.1820
 5JN  H15  H  HNH1   0   0.417   4.7668  -0.0326  -1.8611
 5JN  H16  H  HCH2   0   0.303   3.2605  -2.2454  -1.6332
 5JN  H17  H  HCH2   0   0.286   2.7044  -0.6945  -2.2113
 5JN  H18  H  HCR6   0   0.255   0.4687   0.0892  -1.6838
 5JN  H19  H  HCR6   0   0.271  -1.7392  -0.3557  -0.8300
 5JN  H20  H  HCH3   0   0.257  -4.8660  -2.0597  -1.4011
 5JN  H21  H  HCH3   0   0.253  -3.1940  -1.6946  -1.7985
 5JN  H22  H  HCH3   0   0.254  -3.6579  -3.3354  -1.3500
 5JN  H23  H  HCH2   0   0.269  -5.2830   1.4757   1.4571
 5JN  H24  H  HCH2   0   0.274  -4.0342   2.0627   0.3503
 5JN  H25  H  HCH2   0   0.281  -6.1301   3.0088  -0.3170
 5JN  H26  H  HCH2   0   0.278  -5.6070   1.8566  -1.5691
 5JN  C2   C  CH3    0  -0.724   9.0065   2.2318  -1.5566

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
 5JN  C1   C5   single    1.502  0.020  1.502
 5JN  C12  C13  single    1.498  0.020  1.498
 5JN  C12  C10  single    1.522  0.020  1.522
 5JN  C4   C5   aromatic  1.395  0.020  1.395
 5JN  C4   C3   aromatic  1.392  0.020  1.392
 5JN  N9   C3   single    1.399  0.020  1.399
 5JN  N9   C10  single    1.357  0.020  1.357
 5JN  C5   C6   aromatic  1.388  0.020  1.388
 5JN  C3   C8   aromatic  1.398  0.020  1.398
 5JN  C13  C14  aromatic  1.387  0.020  1.387
 5JN  C13  C18  aromatic  1.393  0.020  1.393
 5JN  C10  O11  double    1.216  0.020  1.216
 5JN  C14  C15  aromatic  1.391  0.020  1.391
 5JN  C18  C17  aromatic  1.382  0.020  1.382
 5JN  C21  C20  single    1.531  0.020  1.531
 5JN  C15  C16  aromatic  1.391  0.020  1.391
 5JN  C6   C7   aromatic  1.395  0.020  1.395
 5JN  C8   C7   aromatic  1.385  0.020  1.385
 5JN  C17  C16  aromatic  1.395  0.020  1.395
 5JN  C16  O19  single    1.354  0.020  1.354
 5JN  C7   C2   single    1.501  0.020  1.501
 5JN  C20  O19  single    1.416  0.020  1.416
 5JN  C20  C23  single    1.531  0.020  1.531
 5JN  C20  C22  single    1.527  0.020  1.527
 5JN  O24  C23  double    1.202  0.020  1.202
 5JN  C23  O25  single    1.323  0.020  1.323
 5JN  O25  C26  single    1.429  0.020  1.429
 5JN  C27  C26  single    1.502  0.020  1.502
 5JN  C27  O28  single    1.440  0.020  1.440
 5JN  O30  N29  double    1.196  0.020  1.196
 5JN  N29  O28  single    1.346  0.020  1.346
 5JN  N29  O31  single    1.193  0.020  1.193
 5JN  C1   H1   single    0.970  0.020  1.090
 5JN  C1   H2   single    0.970  0.020  1.090
 5JN  C1   H3   single    0.970  0.020  1.090
 5JN  C6   H4   single    0.930  0.020  1.080
 5JN  C4   H5   single    0.930  0.020  1.080
 5JN  C2   H6   single    0.970  0.020  1.090
 5JN  C2   H7   single    0.970  0.020  1.090
 5JN  C2   H8   single    0.970  0.020  1.090
 5JN  C21  H9   single    0.970  0.020  1.090
 5JN  C21  H10  single    0.970  0.020  1.090
 5JN  C21  H11  single    0.970  0.020  1.090
 5JN  C18  H12  single    0.930  0.020  1.080
 5JN  C17  H13  single    0.930  0.020  1.080
 5JN  C8   H14  single    0.930  0.020  1.080
 5JN  N9   H15  single    0.860  0.020  1.020
 5JN  C12  H16  single    0.970  0.020  1.090
 5JN  C12  H17  single    0.970  0.020  1.090
 5JN  C14  H18  single    0.930  0.020  1.080
 5JN  C15  H19  single    0.930  0.020  1.080
 5JN  C22  H20  single    0.970  0.020  1.090
 5JN  C22  H21  single    0.970  0.020  1.090
 5JN  C22  H22  single    0.970  0.020  1.090
 5JN  C26  H23  single    0.970  0.020  1.090
 5JN  C26  H24  single    0.970  0.020  1.090
 5JN  C27  H25  single    0.970  0.020  1.090
 5JN  C27  H26  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
 5JN  H3   C1   H2   108.11  3.000
 5JN  H3   C1   H1   107.48  3.000
 5JN  H2   C1   H1   106.98  3.000
 5JN  H3   C1   C5   111.60  3.000
 5JN  H2   C1   C5   111.53  3.000
 5JN  H1   C1   C5   110.93  3.000
 5JN  H4   C6   C7   119.48  3.000
 5JN  H4   C6   C5   119.55  3.000
 5JN  C7   C6   C5   120.98  3.000
 5JN  C4   C5   C6   119.78  3.000
 5JN  C6   C5   C1   120.78  3.000
 5JN  C4   C5   C1   119.43  3.000
 5JN  H5   C4   C3   120.75  3.000
 5JN  H5   C4   C5   119.31  3.000
 5JN  C3   C4   C5   119.93  3.000
 5JN  N9   C3   C8   116.16  3.000
 5JN  C8   C3   C4   119.43  3.000
 5JN  N9   C3   C4   124.40  3.000
 5JN  C14  C13  C12  121.19  3.000
 5JN  C14  C13  C18  117.76  3.000
 5JN  C12  C13  C18  121.06  3.000
 5JN  H11  C21  H10  108.03  3.000
 5JN  H11  C21  H9   108.55  3.000
 5JN  H10  C21  H9   108.50  3.000
 5JN  H11  C21  C20  109.49  3.000
 5JN  H10  C21  C20  110.67  3.000
 5JN  H9   C21  C20  111.52  3.000
 5JN  C23  C20  C22  114.63  3.000
 5JN  C22  C20  O19  112.50  3.000
 5JN  C23  C20  O19  108.81  3.000
 5JN  C22  C20  C21  109.44  3.000
 5JN  C23  C20  C21  106.20  3.000
 5JN  O19  C20  C21  104.60  3.000
 5JN  H12  C18  C17  118.90  3.000
 5JN  H12  C18  C13  119.90  3.000
 5JN  C17  C18  C13  121.18  3.000
 5JN  H13  C17  C16  119.26  3.000
 5JN  H13  C17  C18  120.19  3.000
 5JN  C16  C17  C18  120.55  3.000
 5JN  C8   C7   C2   120.62  3.000
 5JN  C2   C7   C6   120.63  3.000
 5JN  C8   C7   C6   118.74  3.000
 5JN  H14  C8   C7   119.47  3.000
 5JN  H14  C8   C3   119.40  3.000
 5JN  C7   C8   C3   121.14  3.000
 5JN  H15  N9   C10  115.66  3.000
 5JN  H15  N9   C3   114.42  3.000
 5JN  C10  N9   C3   129.86  3.000
 5JN  C12  C10  O11  122.59  3.000
 5JN  O11  C10  N9   124.41  3.000
 5JN  C12  C10  N9   112.98  3.000
 5JN  H17  C12  H16  105.92  3.000
 5JN  H17  C12  C10  109.94  3.000
 5JN  H16  C12  C10  106.75  3.000
 5JN  H17  C12  C13  110.68  3.000
 5JN  H16  C12  C13  110.33  3.000
 5JN  C10  C12  C13  112.92  3.000
 5JN  H18  C14  C15  118.40  3.000
 5JN  H18  C14  C13  119.73  3.000
 5JN  C15  C14  C13  121.87  3.000
 5JN  H19  C15  C16  122.55  3.000
 5JN  H19  C15  C14  117.73  3.000
 5JN  C16  C15  C14  119.72  3.000
 5JN  O19  C16  C15  126.07  3.000
 5JN  O19  C16  C17  115.01  3.000
 5JN  C15  C16  C17  118.91  3.000
 5JN  C16  O19  C20  122.98  3.000
 5JN  H22  C22  H21  108.08  3.000
 5JN  H22  C22  H20  107.60  3.000
 5JN  H21  C22  H20  107.70  3.000
 5JN  H22  C22  C20  108.76  3.000
 5JN  H21  C22  C20  114.07  3.000
 5JN  H20  C22  C20  110.41  3.000
 5JN  O25  C23  O24  124.18  3.000
 5JN  O25  C23  C20  111.85  3.000
 5JN  O24  C23  C20  123.89  3.000
 5JN  C26  O25  C23  117.76  3.000
 5JN  H24  C26  H23  108.21  3.000
 5JN  H24  C26  C27  107.88  3.000
 5JN  H23  C26  C27  111.44  3.000
 5JN  H24  C26  O25  110.82  3.000
 5JN  H23  C26  O25  110.60  3.000
 5JN  C27  C26  O25  107.87  3.000
 5JN  H26  C27  H25  109.35  3.000
 5JN  H26  C27  O28  110.57  3.000
 5JN  H25  C27  O28  110.58  3.000
 5JN  H26  C27  C26  111.30  3.000
 5JN  H25  C27  C26  108.80  3.000
 5JN  O28  C27  C26  106.21  3.000
 5JN  N29  O28  C27  116.02  3.000
 5JN  O31  N29  O28  113.15  3.000
 5JN  O31  N29  O30  128.11  3.000
 5JN  O28  N29  O30  118.74  3.000
 5JN  H8   C2   H7   108.06  3.000
 5JN  H8   C2   H6   107.14  3.000
 5JN  H7   C2   H6   107.41  3.000
 5JN  H8   C2   C7   111.47  3.000
 5JN  H7   C2   C7   111.64  3.000
 5JN  H6   C2   C7   110.92  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
 5JN  CONST_01  C3   C4   C5   C6      0.00   0.0  0
 5JN  CONST_02  C3   C8   C7   C6      0.00   0.0  0
 5JN  CONST_03  C8   C3   C4   C5      0.00   0.0  0
 5JN  CONST_04  C8   C7   C6   C5      0.00   0.0  0
 5JN  CONST_05  C7   C6   C5   C4      0.00   0.0  0
 5JN  CONST_06  C7   C8   C3   C4      0.00   0.0  0
 5JN  CONST_07  C16  C15  C14  C13     0.00   0.0  0
 5JN  CONST_08  C16  C17  C18  C13     0.00   0.0  0
 5JN  CONST_09  C15  C14  C13  C18     0.00   0.0  0
 5JN  CONST_10  C15  C16  C17  C18     0.00   0.0  0
 5JN  CONST_11  C14  C13  C18  C17     0.00   0.0  0
 5JN  CONST_12  C14  C15  C16  C17     0.00   0.0  0
 5JN  CONST_13  C3   C4   C5   C1    180.00   0.0  0
 5JN  CONST_14  C7   C6   C5   C1    180.00   0.0  0
 5JN  CONST_15  N9   C3   C4   C5    180.00   0.0  0
 5JN  CONST_16  C2   C7   C6   C5    180.00   0.0  0
 5JN  CONST_17  C2   C7   C8   C3    180.00   0.0  0
 5JN  CONST_18  O19  C16  C17  C18   180.00   0.0  0
 5JN  CONST_19  C12  C13  C18  C17   180.00   0.0  0
 5JN  CONST_20  N9   C3   C8   C7    180.00   0.0  0
 5JN  CONST_21  C15  C14  C13  C12   180.00   0.0  0
 5JN  CONST_22  O19  C16  C15  C14   180.00   0.0  0
 5JN  CONST_23  H5   C4   C5   C6    180.00   0.0  0
 5JN  CONST_24  H14  C8   C7   C6    180.00   0.0  0
 5JN  CONST_25  H4   C6   C5   C4    180.00   0.0  0
 5JN  CONST_26  H19  C15  C14  C13   180.00   0.0  0
 5JN  CONST_27  H13  C17  C18  C13   180.00   0.0  0
 5JN  CONST_28  H18  C14  C13  C18   180.00   0.0  0
 5JN  CONST_29  H12  C18  C13  C14   180.00   0.0  0
 5JN  CONST_30  C10  N9   C3   C4      0.00   0.0  0
 5JN  CONST_31  C10  N9   C3   C8    180.00   0.0  0
 5JN  CONST_32  H15  N9   C3   C4    180.00   0.0  0
 5JN  CONST_33  C12  C10  N9   C3    180.00   0.0  0
 5JN  CONST_34  O11  C10  N9   C3      0.00   0.0  0
 5JN  Var_01    C15  C16  O19  C20    17.52  30.0  1
 5JN  Var_02    C10  C12  C13  C18   -79.22  30.0  3
 5JN  Var_03    H1   C1   C5   C6    105.22  30.0  2
 5JN  Var_04    H6   C2   C7   C6     78.54  30.0  2
 5JN  Var_05    N9   C10  C12  C13  -160.66  30.0  3
 5JN  Var_06    C23  C20  O19  C16   -71.46  30.0  3
 5JN  Var_07    O24  C23  C20  C21    88.84  30.0  3
 5JN  Var_08    C27  C26  O25  C23   178.88  30.0  3
 5JN  Var_09    O28  C27  C26  O25    65.35  30.0  2
 5JN  Var_10    O31  N29  O28  C27   179.57  30.0  3
 5JN  Var_11    H20  C22  C20  C21    53.23  30.0  3
 5JN  Var_12    H9   C21  C20  O19    57.79  30.0  3

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
 5JN  plan-1  C1   0.020
 5JN  plan-1  C6   0.020
 5JN  plan-1  C5   0.020
 5JN  plan-1  C4   0.020
 5JN  plan-1  C3   0.020
 5JN  plan-1  C7   0.020
 5JN  plan-1  C8   0.020
 5JN  plan-1  N9   0.020
 5JN  plan-1  H4   0.020
 5JN  plan-1  H5   0.020
 5JN  plan-1  H14  0.020
 5JN  plan-1  C2   0.020
 5JN  plan-2  C13  0.020
 5JN  plan-2  C18  0.020
 5JN  plan-2  C17  0.020
 5JN  plan-2  C12  0.020
 5JN  plan-2  C14  0.020
 5JN  plan-2  C15  0.020
 5JN  plan-2  C16  0.020
 5JN  plan-2  O19  0.020
 5JN  plan-2  H12  0.020
 5JN  plan-2  H13  0.020
 5JN  plan-2  H18  0.020
 5JN  plan-2  H19  0.020
 5JN  plan-3  C3   0.020
 5JN  plan-3  N9   0.020
 5JN  plan-3  C10  0.020
 5JN  plan-3  O11  0.020
 5JN  plan-3  C12  0.020
 5JN  plan-3  H15  0.020
 5JN  plan-4  C20  0.020
 5JN  plan-4  C23  0.020
 5JN  plan-4  O24  0.020
 5JN  plan-4  O25  0.020
 5JN  plan-5  O30  0.020
 5JN  plan-5  O28  0.020
 5JN  plan-5  N29  0.020
 5JN  plan-5  O31  0.020

