# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 22:44:35 2020
#   Inital geometry file: a 158 line input string
#   Ligand name: methyl 2-[2-(3,5-dihydro-2~{H}-pyrazin-4-yl)ethoxy]-5-[(5-ethanoyl-2-ethoxy-phenyl)carbamoyl]benzoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOc1ccc(cc1NC(=O)c2ccc(OCCN3CCN=CC3)c(c2)C(=O)OC)C(C)=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
 5QN  5QN  'methyl 2-[2-(3,5-dihydro-2~{H}-pyrazin-4-yl)ethoxy]-5-[(5-ethanoyl-2-ethoxy-phenyl)carbamoyl]benzoate'  ligand  63  34  .  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_5QN
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
 5QN  C17  C  CR16  0  -0.276   0.1060   0.6592  -1.1547
 5QN  C21  C  CH2   0  -0.228  -3.9952   1.3311  -1.7084
 5QN  C22  C  CH2   0  -0.289  -5.5056   1.2539  -1.7221
 5QN  C24  C  C     0  -0.341  -5.8926   2.1423   0.4842
 5QN  C28  C  C     0  -0.316  -7.4857   0.6720  -0.4790
 5QN  C01  C  CH3   0  -0.681   3.2847   4.7131   0.7309
 5QN  C02  C  CH2   0  -0.192   4.4505   3.7561   0.7086
 5QN  C04  C  CR6   0   0.350   4.8022   1.4348   0.2535
 5QN  C05  C  CR16  0  -0.366   6.1726   1.5148   0.4542
 5QN  C06  C  CR16  0  -0.290   6.9641   0.3853   0.3093
 5QN  C07  C  CR6   0  -0.039   6.3988  -0.8325  -0.0453
 5QN  C08  C  C     0   0.364   7.2140  -2.0611  -0.2162
 5QN  C09  C  CH3   0  -0.801   8.6992  -1.9663   0.0091
 5QN  O10  O  O     0  -0.405   6.6935  -3.1140  -0.5291
 5QN  C11  C  CR16  0  -0.331   5.0170  -0.9113  -0.2529
 5QN  C12  C  CR6   0   0.307   4.2103   0.2004  -0.1004
 5QN  N13  N  NH1   0  -0.766   2.8273   0.2139  -0.3033
 5QN  C14  C  C     0   0.551   1.9731  -0.8410  -0.2829
 5QN  O15  O  O     0  -0.463   2.3259  -1.9871  -0.0594
 5QN  C16  C  CR6   0  -0.058   0.5431  -0.5127  -0.5421
 5QN  C18  C  CR16  0  -0.376  -1.2370   0.8900  -1.3860
 5QN  C19  C  CR6   0   0.414  -2.1925  -0.0604  -1.0210
 5QN  O20  O  O2    0  -0.428  -3.4987   0.1064  -1.1876
 5QN  N23  N  NR6   0  -0.411  -6.0845   1.0335  -0.4180
 5QN  C25  C  CR16  0  -0.072  -6.7101   2.0037   1.7318
 5QN  N26  N  N     0  -0.342  -7.6182   1.1570   1.9592
 5QN  C27  C  C     0  -0.316  -7.9491   0.2282   0.8956
 5QN  C29  C  CR6   0  -0.155  -1.7634  -1.2588  -0.4171
 5QN  C30  C  C     0   0.574  -2.7364  -2.3310  -0.0777
 5QN  O31  O  O     0  -0.430  -3.7188  -2.5984  -0.7203
 5QN  O32  O  O2    0  -0.454  -2.3740  -2.9860   1.0177
 5QN  C33  C  CH3   0  -0.423  -3.1730  -4.1035   1.4064
 5QN  C34  C  CR16  0  -0.266  -0.4120  -1.4585  -0.1826
 5QN  H1   H  HCR6  0   0.265   0.8022   1.4163  -1.4933
 5QN  H2   H  HCH2  0   0.254  -3.6411   1.4874  -2.7324
 5QN  H3   H  HCH2  0   0.240  -3.6392   2.1745  -1.1077
 5QN  H4   H  HCH2  0   0.211  -5.8705   2.1821  -2.1948
 5QN  H5   H  HCH2  0   0.250  -5.8085   0.4322  -2.3753
 5QN  H6   H  H     0   0.263  -4.8450   2.2188   0.7913
 5QN  H7   H  H     0   0.224  -6.1442   3.1200   0.0310
 5QN  H8   H  H     0   0.202  -8.1144   1.5071  -0.8345
 5QN  H9   H  H     0   0.246  -7.6152  -0.1471  -1.1888
 5QN  H10  H  HCH3  0   0.238   2.8089   4.7844  -0.2470
 5QN  H11  H  HCH3  0   0.239   2.5353   4.4147   1.4637
 5QN  H12  H  HCH3  0   0.242   3.6431   5.7054   1.0025
 5QN  H13  H  HCH2  0   0.235   5.1978   4.0755  -0.0237
 5QN  H14  H  HCH2  0   0.236   4.9368   3.7119   1.6877
 5QN  H15  H  HCR6  0   0.293   6.6382   2.4511   0.7280
 5QN  H16  H  HCR6  0   0.268   8.0281   0.4826   0.4758
 5QN  H17  H  HCH3  0   0.267   8.9186  -1.6419   1.0273
 5QN  H18  H  HCH3  0   0.269   9.1683  -2.9326  -0.1598
 5QN  H19  H  HCH3  0   0.267   9.1504  -1.2361  -0.6643
 5QN  H20  H  HCR6  0   0.282   4.5869  -1.8562  -0.5416
 5QN  H21  H  HNH1  0   0.415   2.4227   1.1358  -0.3473
 5QN  H22  H  HCR6  0   0.299  -1.5272   1.8140  -1.8645
 5QN  H24  H  HCR6  0   0.248  -6.4767   2.7197   2.5195
 5QN  H25  H  H     0   0.234  -9.0317   0.0833   0.8938
 5QN  H26  H  H     0   0.239  -7.5117  -0.7431   1.1449
 5QN  H27  H  HCH3  0   0.240  -4.1940  -3.8006   1.6362
 5QN  H28  H  HCH3  0   0.240  -3.1908  -4.8700   0.6322
 5QN  H29  H  HCH3  0   0.253  -2.7061  -4.5048   2.3008
 5QN  H30  H  HCR6  0   0.271  -0.0839  -2.3793   0.2794
 5QN  O03  O  O2    0  -0.477   3.9550   2.4641   0.3616

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
 5QN  C01  C02  single    1.508  0.020  1.508
 5QN  C02  O03  single    1.427  0.020  1.427
 5QN  C05  C06  aromatic  1.387  0.020  1.387
 5QN  C05  C04  aromatic  1.387  0.020  1.387
 5QN  O03  C04  single    1.337  0.020  1.337
 5QN  C06  C07  aromatic  1.389  0.020  1.389
 5QN  C04  C12  aromatic  1.414  0.020  1.414
 5QN  O10  C08  double    1.215  0.020  1.215
 5QN  C07  C08  single    1.484  0.020  1.484
 5QN  C07  C11  aromatic  1.400  0.020  1.400
 5QN  C12  C11  aromatic  1.382  0.020  1.382
 5QN  C12  N13  single    1.398  0.020  1.398
 5QN  C08  C09  single    1.505  0.020  1.505
 5QN  N13  C14  single    1.358  0.020  1.358
 5QN  C14  O15  double    1.220  0.020  1.220
 5QN  C14  C16  single    1.490  0.020  1.490
 5QN  C16  C34  aromatic  1.391  0.020  1.391
 5QN  C16  C17  aromatic  1.393  0.020  1.393
 5QN  C34  C29  aromatic  1.386  0.020  1.386
 5QN  C17  C18  aromatic  1.382  0.020  1.382
 5QN  C33  O32  single    1.428  0.020  1.428
 5QN  O32  C30  single    1.327  0.020  1.327
 5QN  C29  C30  single    1.487  0.020  1.487
 5QN  C29  C19  aromatic  1.409  0.020  1.409
 5QN  C30  O31  double    1.204  0.020  1.204
 5QN  C18  C19  aromatic  1.396  0.020  1.396
 5QN  C19  O20  single    1.327  0.020  1.327
 5QN  O20  C21  single    1.420  0.020  1.420
 5QN  C25  C24  single    1.498  0.020  1.498
 5QN  C25  N26  double    1.262  0.020  1.262
 5QN  C24  N23  single    1.442  0.020  1.442
 5QN  C21  C22  single    1.512  0.020  1.512
 5QN  C22  N23  single    1.444  0.020  1.444
 5QN  N26  C27  single    1.450  0.020  1.450
 5QN  N23  C28  single    1.448  0.020  1.448
 5QN  C27  C28  single    1.517  0.020  1.517
 5QN  C17  H1   single    0.930  0.020  1.080
 5QN  C21  H2   single    0.970  0.020  1.090
 5QN  C21  H3   single    0.970  0.020  1.090
 5QN  C22  H4   single    0.970  0.020  1.090
 5QN  C22  H5   single    0.970  0.020  1.090
 5QN  C24  H6   single    0.970  0.020  1.090
 5QN  C24  H7   single    0.970  0.020  1.090
 5QN  C28  H8   single    0.970  0.020  1.090
 5QN  C28  H9   single    0.970  0.020  1.090
 5QN  C01  H10  single    0.970  0.020  1.090
 5QN  C01  H11  single    0.970  0.020  1.090
 5QN  C01  H12  single    0.970  0.020  1.090
 5QN  C02  H13  single    0.970  0.020  1.090
 5QN  C02  H14  single    0.970  0.020  1.090
 5QN  C05  H15  single    0.930  0.020  1.080
 5QN  C06  H16  single    0.930  0.020  1.080
 5QN  C09  H17  single    0.970  0.020  1.090
 5QN  C09  H18  single    0.970  0.020  1.090
 5QN  C09  H19  single    0.970  0.020  1.090
 5QN  C11  H20  single    0.930  0.020  1.080
 5QN  N13  H21  single    0.860  0.020  1.020
 5QN  C18  H22  single    0.930  0.020  1.080
 5QN  C25  H24  single    0.930  0.020  1.080
 5QN  C27  H25  single    0.970  0.020  1.090
 5QN  C27  H26  single    0.970  0.020  1.090
 5QN  C33  H27  single    0.970  0.020  1.090
 5QN  C33  H28  single    0.970  0.020  1.090
 5QN  C33  H29  single    0.970  0.020  1.090
 5QN  C34  H30  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
 5QN  H1   C17  C18  117.10  3.000
 5QN  H1   C17  C16  121.61  3.000
 5QN  C18  C17  C16  121.27  3.000
 5QN  H3   C21  H2   107.35  3.000
 5QN  H3   C21  O20  110.45  3.000
 5QN  H2   C21  O20  110.67  3.000
 5QN  H3   C21  C22  111.65  3.000
 5QN  H2   C21  C22  108.78  3.000
 5QN  O20  C21  C22  107.96  3.000
 5QN  H5   C22  H4   106.55  3.000
 5QN  H5   C22  N23  108.30  3.000
 5QN  H4   C22  N23  112.50  3.000
 5QN  H5   C22  C21  108.70  3.000
 5QN  H4   C22  C21  106.93  3.000
 5QN  N23  C22  C21  113.58  3.000
 5QN  H7   C24  H6   105.71  3.000
 5QN  H7   C24  C25  107.38  3.000
 5QN  H6   C24  C25  107.17  3.000
 5QN  H7   C24  N23  113.13  3.000
 5QN  H6   C24  N23  110.89  3.000
 5QN  C25  C24  N23  112.17  3.000
 5QN  H9   C28  H8   106.90  3.000
 5QN  H9   C28  C27  109.48  3.000
 5QN  H8   C28  C27  109.82  3.000
 5QN  H9   C28  N23  109.23  3.000
 5QN  H8   C28  N23  112.06  3.000
 5QN  C27  C28  N23  109.29  3.000
 5QN  H12  C01  H11  107.94  3.000
 5QN  H12  C01  H10  107.92  3.000
 5QN  H11  C01  H10  108.72  3.000
 5QN  H12  C01  C02  109.10  3.000
 5QN  H11  C01  C02  111.57  3.000
 5QN  H10  C01  C02  111.45  3.000
 5QN  H14  C02  H13  107.89  3.000
 5QN  H14  C02  O03  109.60  3.000
 5QN  H13  C02  O03  109.81  3.000
 5QN  H14  C02  C01  110.85  3.000
 5QN  H13  C02  C01  110.65  3.000
 5QN  O03  C02  C01  108.04  3.000
 5QN  C12  C04  C05  120.00  3.000
 5QN  C12  C04  O03  115.28  3.000
 5QN  C05  C04  O03  124.72  3.000
 5QN  H15  C05  C06  119.09  3.000
 5QN  H15  C05  C04  120.80  3.000
 5QN  C06  C05  C04  120.11  3.000
 5QN  H16  C06  C07  121.25  3.000
 5QN  H16  C06  C05  118.18  3.000
 5QN  C07  C06  C05  120.58  3.000
 5QN  C11  C07  C08  118.59  3.000
 5QN  C11  C07  C06  119.28  3.000
 5QN  C08  C07  C06  122.13  3.000
 5QN  O10  C08  C09  121.04  3.000
 5QN  C09  C08  C07  118.20  3.000
 5QN  O10  C08  C07  120.76  3.000
 5QN  H19  C09  H18  108.70  3.000
 5QN  H19  C09  H17  107.09  3.000
 5QN  H18  C09  H17  108.81  3.000
 5QN  H19  C09  C08  110.97  3.000
 5QN  H18  C09  C08  110.27  3.000
 5QN  H17  C09  C08  110.90  3.000
 5QN  H20  C11  C12  120.13  3.000
 5QN  H20  C11  C07  118.89  3.000
 5QN  C12  C11  C07  120.98  3.000
 5QN  N13  C12  C11  124.70  3.000
 5QN  N13  C12  C04  116.23  3.000
 5QN  C11  C12  C04  119.05  3.000
 5QN  H21  N13  C14  117.31  3.000
 5QN  H21  N13  C12  114.36  3.000
 5QN  C14  N13  C12  127.80  3.000
 5QN  C16  C14  O15  121.10  3.000
 5QN  C16  C14  N13  115.47  3.000
 5QN  O15  C14  N13  123.42  3.000
 5QN  C34  C16  C14  117.65  3.000
 5QN  C34  C16  C17  118.05  3.000
 5QN  C14  C16  C17  124.28  3.000
 5QN  H22  C18  C19  120.94  3.000
 5QN  H22  C18  C17  118.56  3.000
 5QN  C19  C18  C17  120.50  3.000
 5QN  C29  C19  O20  117.41  3.000
 5QN  O20  C19  C18  123.72  3.000
 5QN  C29  C19  C18  118.86  3.000
 5QN  C19  O20  C21  119.89  3.000
 5QN  C28  N23  C24  110.30  3.000
 5QN  C28  N23  C22  112.83  3.000
 5QN  C24  N23  C22  113.22  3.000
 5QN  H24  C25  N26  117.69  3.000
 5QN  H24  C25  C24  115.11  3.000
 5QN  N26  C25  C24  127.20  3.000
 5QN  C27  N26  C25  117.49  3.000
 5QN  H26  C27  H25  106.19  3.000
 5QN  H26  C27  N26  108.08  3.000
 5QN  H25  C27  N26  108.20  3.000
 5QN  H26  C27  C28  110.13  3.000
 5QN  H25  C27  C28  109.88  3.000
 5QN  N26  C27  C28  114.05  3.000
 5QN  C34  C29  C30  119.70  3.000
 5QN  C30  C29  C19  120.79  3.000
 5QN  C34  C29  C19  119.47  3.000
 5QN  O32  C30  O31  123.63  3.000
 5QN  O31  C30  C29  124.91  3.000
 5QN  O32  C30  C29  111.45  3.000
 5QN  C33  O32  C30  117.29  3.000
 5QN  H29  C33  H28  109.41  3.000
 5QN  H29  C33  H27  109.39  3.000
 5QN  H28  C33  H27  109.27  3.000
 5QN  H29  C33  O32  105.84  3.000
 5QN  H28  C33  O32  111.49  3.000
 5QN  H27  C33  O32  111.36  3.000
 5QN  H30  C34  C29  119.39  3.000
 5QN  H30  C34  C16  118.76  3.000
 5QN  C29  C34  C16  121.85  3.000
 5QN  C04  O03  C02  119.78  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
 5QN  CONST_01  C29  C34  C16  C17     0.00   0.0  0
 5QN  CONST_02  C29  C19  C18  C17     0.00   0.0  0
 5QN  CONST_03  C07  C06  C05  C04     0.00   0.0  0
 5QN  CONST_04  C07  C11  C12  C04     0.00   0.0  0
 5QN  CONST_05  C11  C07  C06  C05     0.00   0.0  0
 5QN  CONST_06  C11  C12  C04  C05     0.00   0.0  0
 5QN  CONST_07  C12  C04  C05  C06     0.00   0.0  0
 5QN  CONST_08  C12  C11  C07  C06     0.00   0.0  0
 5QN  CONST_09  C19  C29  C34  C16     0.00   0.0  0
 5QN  CONST_10  C19  C18  C17  C16     0.00   0.0  0
 5QN  CONST_11  C34  C16  C17  C18     0.00   0.0  0
 5QN  CONST_12  C34  C29  C19  C18     0.00   0.0  0
 5QN  CONST_13  O20  C19  C18  C17   180.00   0.0  0
 5QN  CONST_14  C06  C05  C04  O03   180.00   0.0  0
 5QN  CONST_15  C11  C12  C04  O03   180.00   0.0  0
 5QN  CONST_16  C08  C07  C06  C05   180.00   0.0  0
 5QN  CONST_17  N13  C12  C04  C05   180.00   0.0  0
 5QN  CONST_18  N13  C12  C11  C07   180.00   0.0  0
 5QN  CONST_19  C12  C11  C07  C08   180.00   0.0  0
 5QN  CONST_20  C29  C34  C16  C14   180.00   0.0  0
 5QN  CONST_21  C18  C17  C16  C14   180.00   0.0  0
 5QN  CONST_22  C30  C29  C34  C16   180.00   0.0  0
 5QN  CONST_23  C30  C29  C19  C18   180.00   0.0  0
 5QN  CONST_24  C34  C29  C19  O20   180.00   0.0  0
 5QN  CONST_25  H30  C34  C16  C17   180.00   0.0  0
 5QN  CONST_26  H16  C06  C05  C04   180.00   0.0  0
 5QN  CONST_27  H20  C11  C12  C04   180.00   0.0  0
 5QN  CONST_28  H15  C05  C06  C07   180.00   0.0  0
 5QN  CONST_29  H22  C18  C17  C16   180.00   0.0  0
 5QN  CONST_30  H1   C17  C18  C19   180.00   0.0  0
 5QN  CONST_31  C16  C14  N13  C12   180.00   0.0  0
 5QN  CONST_34  H21  N13  C12  C04     0.00   0.0  0
 5QN  CONST_35  O15  C14  N13  C12     0.00   0.0  0
 5QN  Var_01    C27  C28  N23  C24   -61.98  30.0  1
 5QN  Var_02    C25  C24  N23  C28    41.87  30.0  1
 5QN  Var_03    N26  C25  C24  N23    -9.80  30.0  1
 5QN  Var_04    N26  C27  C28  N23    50.69  30.0  1
 5QN  Var_05    N13  C14  C16  C17    19.04  30.0  2
 5QN  Var_06    C29  C19  O20  C21   175.80  30.0  2
 5QN  Var_07    C24  N23  C22  C21    66.53  30.0  3
 5QN  Var_08    C05  C04  O03  C02    -0.11  30.0  2
 5QN  Var_09    O10  C08  C07  C06  -179.89  30.0  2
 5QN  Var_10    O32  C30  C29  C19  -146.90  30.0  2
 5QN  Var_11    N23  C22  C21  O20    59.22  30.0  3
 5QN  Var_12    H13  C02  O03  C04    58.19  30.0  2
 5QN  Var_13    H17  C09  C08  C07    59.99  30.0  3
 5QN  Var_14    H2   C21  O20  C19    63.74  30.0  3
 5QN  Var_15    H10  C01  C02  O03   -61.38  30.0  3
 5QN  Var_16    H27  C33  O32  C30   -62.19  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
 5QN  plan-1  C04  0.020
 5QN  plan-1  C05  0.020
 5QN  plan-1  C06  0.020
 5QN  plan-1  C07  0.020
 5QN  plan-1  C08  0.020
 5QN  plan-1  C11  0.020
 5QN  plan-1  C12  0.020
 5QN  plan-1  N13  0.020
 5QN  plan-1  H15  0.020
 5QN  plan-1  H16  0.020
 5QN  plan-1  H20  0.020
 5QN  plan-1  O03  0.020
 5QN  plan-2  C17  0.020
 5QN  plan-2  C14  0.020
 5QN  plan-2  C16  0.020
 5QN  plan-2  C18  0.020
 5QN  plan-2  C19  0.020
 5QN  plan-2  O20  0.020
 5QN  plan-2  C29  0.020
 5QN  plan-2  C30  0.020
 5QN  plan-2  C34  0.020
 5QN  plan-2  H1   0.020
 5QN  plan-2  H22  0.020
 5QN  plan-2  H30  0.020
 5QN  plan-3  C12  0.020
 5QN  plan-3  N13  0.020
 5QN  plan-3  C14  0.020
 5QN  plan-3  O15  0.020
 5QN  plan-3  C16  0.020
 5QN  plan-3  H21  0.020
 5QN  plan-4  C07  0.020
 5QN  plan-4  C08  0.020
 5QN  plan-4  C09  0.020
 5QN  plan-4  O10  0.020
 5QN  plan-5  C29  0.020
 5QN  plan-5  C30  0.020
 5QN  plan-5  O31  0.020
 5QN  plan-5  O32  0.020

