# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 18:37:27 2021
#   Inital geometry file: a 157 line input string
#   Ligand name: methyl (6-cyano-3-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenoxy}-4-methylnaphthalen-1-yl)acetate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)Cc1cc(Oc2ccccc2OCCN3C=CC(=O)NC3=O)c(C)c4cc(ccc14)C#N
#
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
 UMV  UMV  'methyl (6-cyano-3-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenoxy}-4-methylnaphthalen-1-yl)acetate'  ligand  59  36  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UMV
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
 UMV  C1   C  CR16  0  -0.386  845.0257  -24.6983  141.0103
 UMV  O1   O  O2    0  -0.504  843.6543  -25.9209  144.1728
 UMV  C2   C  CR6   0   0.366  844.1391  -25.2877  141.9047
 UMV  N1   N  NR6   0  -0.521  840.8393  -27.5458  140.8903
 UMV  O2   O  O2    0  -0.463  842.9841  -25.8878  141.5705
 UMV  N2   N  NR16  0  -0.731  840.8451  -29.8538  141.0658
 UMV  C3   C  CR6   0   0.236  844.4422  -25.2556  143.2731
 UMV  C4   C  CR16  0  -0.316  845.5889  -24.6350  143.7293
 UMV  C5   C  CR16  0  -0.279  846.4684  -24.0446  142.8293
 UMV  C6   C  CR16  0  -0.246  846.1830  -24.0829  141.4753
 UMV  C7   C  CH2   0  -0.190  842.5951  -25.9249  140.2109
 UMV  C8   C  CH2   0  -0.350  841.1360  -26.3215  140.1595
 UMV  C9   C  CR6   0   0.736  841.1540  -28.7549  140.3090
 UMV  C10  C  CR6   0   0.567  840.2615  -29.8864  142.3240
 UMV  C11  C  CR16  0  -0.513  839.9628  -28.5788  142.8494
 UMV  C12  C  CR16  0   0.123  840.2710  -27.4883  142.1272
 UMV  C13  C  CR6   0   0.376  842.3691  -25.5505  144.4116
 UMV  C14  C  CR6   0  -0.059  841.6008  -26.4077  145.1637
 UMV  C15  C  CR66  0   0.104  840.2560  -26.0254  145.4282
 UMV  C16  C  CR66  0   0.092  839.7268  -24.8009  144.9328
 UMV  C17  C  CR6   0   0.119  840.5727  -23.9417  144.1825
 UMV  C18  C  CR16  0  -0.400  841.8618  -24.3226  143.9404
 UMV  C19  C  CR16  0  -0.324  839.4055  -26.8668  146.1783
 UMV  C20  C  CR6   0   0.015  838.0996  -26.5123  146.4219
 UMV  C21  C  CR16  0  -0.245  837.5717  -25.2987  145.9312
 UMV  C22  C  CR16  0  -0.330  838.3783  -24.4711  145.2054
 UMV  O3   O  O     0  -0.479  841.6630  -28.8399  139.2106
 UMV  O4   O  O     0  -0.465  840.0480  -30.9488  142.8792
 UMV  C23  C  CSP   0   0.053  837.2649  -27.3869  147.1803
 UMV  N3   N  NS    0  -0.249  836.5851  -28.0887  147.7912
 UMV  C24  C  CH3   0  -0.756  842.1362  -27.7093  145.6816
 UMV  C25  C  CH2   0  -0.704  840.0733  -22.6239  143.6649
 UMV  C26  C  C     0   0.601  839.9018  -21.5599  144.7265
 UMV  O5   O  O2    0  -0.440  840.8157  -21.6559  145.6758
 UMV  C27  C  CH3   0  -0.427  840.7910  -20.6800  146.7191
 UMV  O6   O  O     0  -0.450  839.0530  -20.7044  144.6929
 UMV  H1   H  HCR6  0   0.288  844.8339  -24.7174  139.9461
 UMV  H2   H  HNR6  0   0.426  841.0721  -30.7462  140.6443
 UMV  H3   H  HCR6  0   0.273  845.7952  -24.6269  144.7922
 UMV  H4   H  HCR6  0   0.262  847.3672  -23.5640  143.1900
 UMV  H5   H  HCR6  0   0.264  846.8616  -23.6343  140.7621
 UMV  H6   H  HCH2  0   0.249  843.2242  -26.6233  139.6531
 UMV  H7   H  HCH2  0   0.253  842.6819  -24.9411  139.7400
 UMV  H8   H  HCH2  0   0.278  840.5193  -25.5308  140.5842
 UMV  H9   H  HCH2  0   0.294  840.8374  -26.4330  139.1185
 UMV  H10  H  HCR6  0   0.289  839.4928  -28.4850  143.8157
 UMV  H11  H  HCR6  0   0.307  840.0589  -26.4933  142.4931
 UMV  H12  H  HCR6  0   0.286  842.5051  -23.6553  143.3802
 UMV  H13  H  HCR6  0   0.288  839.7764  -27.8034  146.5703
 UMV  H14  H  HCR6  0   0.281  836.5421  -25.0351  146.1281
 UMV  H15  H  HCR6  0   0.264  837.9601  -23.5473  144.8297
 UMV  H16  H  HCH3  0   0.255  842.0470  -27.7722  146.7672
 UMV  H17  H  HCH3  0   0.249  841.5863  -28.5544  145.2620
 UMV  H18  H  HCH3  0   0.271  843.1834  -27.8503  145.4336
 UMV  H19  H  HCH2  0   0.321  840.7880  -22.2259  142.9378
 UMV  H20  H  HCH2  0   0.300  839.1291  -22.7242  143.1279
 UMV  H21  H  HCH3  0   0.254  841.6207  -20.9251  147.3751
 UMV  H22  H  HCH3  0   0.242  840.9264  -19.6731  146.3255
 UMV  H23  H  HCH3  0   0.242  839.8596  -20.7256  147.2824

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
 UMV  O3   C9   double    1.214  0.020  1.214
 UMV  C8   C7   single    1.513  0.020  1.513
 UMV  C8   N1   single    1.456  0.020  1.456
 UMV  C9   N1   single    1.378  0.020  1.378
 UMV  C9   N2   single    1.370  0.020  1.370
 UMV  C7   O2   single    1.415  0.020  1.415
 UMV  N1   C12  single    1.362  0.020  1.362
 UMV  N2   C10  single    1.387  0.020  1.387
 UMV  C12  C11  double    1.344  0.020  1.344
 UMV  O2   C2   single    1.344  0.020  1.344
 UMV  C1   C2   aromatic  1.391  0.020  1.391
 UMV  C1   C6   aromatic  1.391  0.020  1.391
 UMV  C10  C11  single    1.441  0.020  1.441
 UMV  C10  O4   double    1.218  0.020  1.218
 UMV  C2   C3   aromatic  1.402  0.020  1.402
 UMV  C6   C5   aromatic  1.384  0.020  1.384
 UMV  C3   O1   single    1.369  0.020  1.369
 UMV  C3   C4   aromatic  1.381  0.020  1.381
 UMV  C5   C4   aromatic  1.390  0.020  1.390
 UMV  O1   C13  single    1.359  0.020  1.359
 UMV  C18  C13  aromatic  1.410  0.020  1.410
 UMV  C18  C17  aromatic  1.366  0.020  1.366
 UMV  C25  C17  single    1.501  0.020  1.501
 UMV  C25  C26  single    1.513  0.020  1.513
 UMV  C13  C14  aromatic  1.375  0.020  1.375
 UMV  C17  C16  aromatic  1.420  0.020  1.420
 UMV  C14  C24  single    1.500  0.020  1.500
 UMV  C14  C15  aromatic  1.423  0.020  1.423
 UMV  C26  O6   double    1.206  0.020  1.206
 UMV  C26  O5   single    1.321  0.020  1.321
 UMV  C16  C15  aromatic  1.423  0.020  1.423
 UMV  C16  C22  aromatic  1.415  0.020  1.415
 UMV  C15  C19  aromatic  1.412  0.020  1.412
 UMV  O5   C27  single    1.429  0.020  1.429
 UMV  C22  C21  aromatic  1.365  0.020  1.365
 UMV  C19  C20  aromatic  1.375  0.020  1.375
 UMV  C21  C20  aromatic  1.411  0.020  1.411
 UMV  C20  C23  single    1.427  0.020  1.427
 UMV  C23  N3   triple    1.152  0.020  1.152
 UMV  C1   H1   single    0.930  0.020  1.080
 UMV  N2   H2   single    0.860  0.020  1.020
 UMV  C4   H3   single    0.930  0.020  1.080
 UMV  C5   H4   single    0.930  0.020  1.080
 UMV  C6   H5   single    0.930  0.020  1.080
 UMV  C7   H6   single    0.970  0.020  1.090
 UMV  C7   H7   single    0.970  0.020  1.090
 UMV  C8   H8   single    0.970  0.020  1.090
 UMV  C8   H9   single    0.970  0.020  1.090
 UMV  C11  H10  single    0.930  0.020  1.080
 UMV  C12  H11  single    0.930  0.020  1.080
 UMV  C18  H12  single    0.930  0.020  1.080
 UMV  C19  H13  single    0.930  0.020  1.080
 UMV  C21  H14  single    0.930  0.020  1.080
 UMV  C22  H15  single    0.930  0.020  1.080
 UMV  C24  H16  single    0.970  0.020  1.090
 UMV  C24  H17  single    0.970  0.020  1.090
 UMV  C24  H18  single    0.970  0.020  1.090
 UMV  C25  H19  single    0.970  0.020  1.090
 UMV  C25  H20  single    0.970  0.020  1.090
 UMV  C27  H21  single    0.970  0.020  1.090
 UMV  C27  H22  single    0.970  0.020  1.090
 UMV  C27  H23  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
 UMV  H1   C1   C6   118.98  3.000
 UMV  H1   C1   C2   120.82  3.000
 UMV  C6   C1   C2   120.20  3.000
 UMV  C13  O1   C3   121.84  3.000
 UMV  C3   C2   O2   116.02  3.000
 UMV  C3   C2   C1   118.70  3.000
 UMV  O2   C2   C1   125.27  3.000
 UMV  C12  N1   C9   121.01  3.000
 UMV  C12  N1   C8   120.34  3.000
 UMV  C9   N1   C8   118.64  3.000
 UMV  C7   O2   C2   119.14  3.000
 UMV  H2   N2   C10  116.82  3.000
 UMV  H2   N2   C9   115.24  3.000
 UMV  C10  N2   C9   127.94  3.000
 UMV  C4   C3   C2   120.80  3.000
 UMV  C4   C3   O1   118.63  3.000
 UMV  C2   C3   O1   120.41  3.000
 UMV  H3   C4   C5   120.79  3.000
 UMV  H3   C4   C3   119.06  3.000
 UMV  C5   C4   C3   120.15  3.000
 UMV  H4   C5   C6   120.67  3.000
 UMV  H4   C5   C4   119.92  3.000
 UMV  C6   C5   C4   119.41  3.000
 UMV  H5   C6   C5   120.26  3.000
 UMV  H5   C6   C1   119.01  3.000
 UMV  C5   C6   C1   120.72  3.000
 UMV  H7   C7   H6   108.02  3.000
 UMV  H7   C7   C8   107.31  3.000
 UMV  H6   C7   C8   111.73  3.000
 UMV  H7   C7   O2   111.61  3.000
 UMV  H6   C7   O2   110.42  3.000
 UMV  C8   C7   O2   107.74  3.000
 UMV  H9   C8   H8   106.97  3.000
 UMV  H9   C8   C7   108.90  3.000
 UMV  H8   C8   C7   110.03  3.000
 UMV  H9   C8   N1   109.75  3.000
 UMV  H8   C8   N1   107.41  3.000
 UMV  C7   C8   N1   113.57  3.000
 UMV  O3   C9   N2   122.59  3.000
 UMV  N2   C9   N1   114.80  3.000
 UMV  O3   C9   N1   122.62  3.000
 UMV  O4   C10  C11  126.12  3.000
 UMV  O4   C10  N2   120.51  3.000
 UMV  C11  C10  N2   113.37  3.000
 UMV  H10  C11  C12  120.72  3.000
 UMV  H10  C11  C10  119.73  3.000
 UMV  C12  C11  C10  119.55  3.000
 UMV  H11  C12  C11  121.33  3.000
 UMV  H11  C12  N1   115.34  3.000
 UMV  C11  C12  N1   123.32  3.000
 UMV  C18  C13  C14  121.65  3.000
 UMV  C14  C13  O1   117.05  3.000
 UMV  C18  C13  O1   121.28  3.000
 UMV  C24  C14  C15  120.42  3.000
 UMV  C15  C14  C13  117.53  3.000
 UMV  C24  C14  C13  122.04  3.000
 UMV  C19  C15  C16  118.27  3.000
 UMV  C19  C15  C14  120.53  3.000
 UMV  C16  C15  C14  121.20  3.000
 UMV  C22  C16  C17  121.90  3.000
 UMV  C22  C16  C15  119.21  3.000
 UMV  C17  C16  C15  118.88  3.000
 UMV  C25  C17  C18  119.84  3.000
 UMV  C25  C17  C16  121.00  3.000
 UMV  C18  C17  C16  119.15  3.000
 UMV  H12  C18  C17  118.72  3.000
 UMV  H12  C18  C13  119.72  3.000
 UMV  C17  C18  C13  121.56  3.000
 UMV  H13  C19  C20  119.02  3.000
 UMV  H13  C19  C15  120.15  3.000
 UMV  C20  C19  C15  120.83  3.000
 UMV  C23  C20  C21  119.53  3.000
 UMV  C23  C20  C19  119.45  3.000
 UMV  C21  C20  C19  121.02  3.000
 UMV  H14  C21  C22  120.80  3.000
 UMV  H14  C21  C20  120.17  3.000
 UMV  C22  C21  C20  119.03  3.000
 UMV  H15  C22  C21  118.32  3.000
 UMV  H15  C22  C16  120.05  3.000
 UMV  C21  C22  C16  121.63  3.000
 UMV  N3   C23  C20  180.00  3.000
 UMV  H18  C24  H17  107.30  3.000
 UMV  H18  C24  H16  107.38  3.000
 UMV  H17  C24  H16  107.25  3.000
 UMV  H18  C24  C14  112.23  3.000
 UMV  H17  C24  C14  111.05  3.000
 UMV  H16  C24  C14  111.38  3.000
 UMV  H20  C25  H19  105.76  3.000
 UMV  H20  C25  C26  108.18  3.000
 UMV  H19  C25  C26  106.53  3.000
 UMV  H20  C25  C17  112.15  3.000
 UMV  H19  C25  C17  109.33  3.000
 UMV  C26  C25  C17  114.40  3.000
 UMV  O6   C26  O5   123.95  3.000
 UMV  O5   C26  C25  112.01  3.000
 UMV  O6   C26  C25  124.02  3.000
 UMV  C27  O5   C26  117.59  3.000
 UMV  H23  C27  H22  109.37  3.000
 UMV  H23  C27  H21  109.36  3.000
 UMV  H22  C27  H21  109.39  3.000
 UMV  H23  C27  O5   111.33  3.000
 UMV  H22  C27  O5   111.43  3.000
 UMV  H21  C27  O5   105.89  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
 UMV  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 UMV  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 UMV  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 UMV  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 UMV  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 UMV  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 UMV  CONST_07  C16  C17  C18  C13     0.00   0.0  0
 UMV  CONST_08  C16  C15  C14  C13     0.00   0.0  0
 UMV  CONST_09  C19  C15  C14  C13   180.00   0.0  0
 UMV  CONST_10  C17  C18  C13  C14     0.00   0.0  0
 UMV  CONST_11  C17  C16  C15  C14     0.00   0.0  0
 UMV  CONST_12  C22  C16  C15  C14   180.00   0.0  0
 UMV  CONST_13  C20  C19  C15  C14   180.00   0.0  0
 UMV  CONST_14  C18  C13  C14  C15     0.00   0.0  0
 UMV  CONST_15  C18  C17  C16  C15     0.00   0.0  0
 UMV  CONST_16  C21  C22  C16  C15     0.00   0.0  0
 UMV  CONST_17  C21  C20  C19  C15     0.00   0.0  0
 UMV  CONST_18  C20  C19  C15  C16     0.00   0.0  0
 UMV  CONST_19  C20  C21  C22  C16     0.00   0.0  0
 UMV  CONST_20  C19  C15  C16  C17   180.00   0.0  0
 UMV  CONST_21  C21  C22  C16  C17   180.00   0.0  0
 UMV  CONST_22  C22  C16  C17  C18   180.00   0.0  0
 UMV  CONST_23  C22  C16  C15  C19     0.00   0.0  0
 UMV  CONST_24  C22  C21  C20  C19     0.00   0.0  0
 UMV  CONST_25  C10  N2   C9   N1      0.00   0.0  0
 UMV  CONST_26  C12  N1   C9   N2      0.00   0.0  0
 UMV  CONST_27  C11  C10  N2   C9      0.00   0.0  0
 UMV  CONST_28  O1   C3   C2   C1    180.00   0.0  0
 UMV  CONST_29  C5   C4   C3   O1    180.00   0.0  0
 UMV  CONST_30  C17  C18  C13  O1    180.00   0.0  0
 UMV  CONST_31  C15  C14  C13  O1    180.00   0.0  0
 UMV  CONST_32  C6   C1   C2   O2    180.00   0.0  0
 UMV  CONST_33  C4   C3   C2   O2    180.00   0.0  0
 UMV  CONST_34  C25  C17  C18  C13   180.00   0.0  0
 UMV  CONST_35  C25  C17  C16  C15   180.00   0.0  0
 UMV  CONST_36  C23  C20  C19  C15   180.00   0.0  0
 UMV  CONST_37  C24  C14  C15  C16   180.00   0.0  0
 UMV  CONST_38  C24  C14  C13  C18   180.00   0.0  0
 UMV  CONST_39  C24  C14  C15  C19     0.00   0.0  0
 UMV  CONST_40  C25  C17  C16  C22     0.00   0.0  0
 UMV  CONST_41  C23  C20  C21  C22   180.00   0.0  0
 UMV  CONST_42  C8   N1   C9   N2    180.00   0.0  0
 UMV  CONST_43  O4   C10  N2   C9    180.00   0.0  0
 UMV  CONST_44  O3   C9   N2   C10   180.00   0.0  0
 UMV  CONST_45  O3   C9   N1   C12   180.00   0.0  0
 UMV  CONST_46  H4   C5   C6   C1    180.00   0.0  0
 UMV  CONST_47  H5   C6   C1   C2    180.00   0.0  0
 UMV  CONST_48  H3   C4   C3   C2    180.00   0.0  0
 UMV  CONST_49  H1   C1   C2   C3    180.00   0.0  0
 UMV  CONST_50  H12  C18  C13  C14   180.00   0.0  0
 UMV  CONST_51  H13  C19  C15  C14     0.00   0.0  0
 UMV  CONST_52  H15  C22  C16  C15   180.00   0.0  0
 UMV  CONST_53  H14  C21  C22  C16   180.00   0.0  0
 UMV  CONST_54  H2   N2   C9   N1    180.00   0.0  0
 UMV  CONST_55  O3   C9   N1   C8      0.00   0.0  0
 UMV  Var_01    C18  C13  O1   C3    -12.10  30.0  2
 UMV  Var_02    C9   N1   C8   C7    -77.98  30.0  3
 UMV  Var_03    C26  C25  C17  C16    73.21  30.0  2
 UMV  Var_04    H16  C24  C14  C13   123.21  30.0  2
 UMV  Var_05    C8   C7   O2   C2   -165.69  30.0  1
 UMV  Var_06    O2   C7   C8   N1    -52.94  30.0  3
 UMV  Var_07    O6   C26  C25  C17  -147.35  30.0  3
 UMV  Var_08    H21  C27  O5   C26  -179.06  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
 UMV  plan-1  C1   0.020
 UMV  plan-1  O1   0.020
 UMV  plan-1  C2   0.020
 UMV  plan-1  O2   0.020
 UMV  plan-1  C3   0.020
 UMV  plan-1  C4   0.020
 UMV  plan-1  C5   0.020
 UMV  plan-1  C6   0.020
 UMV  plan-1  H1   0.020
 UMV  plan-1  H3   0.020
 UMV  plan-1  H4   0.020
 UMV  plan-1  H5   0.020
 UMV  plan-2  C25  0.020
 UMV  plan-2  C26  0.020
 UMV  plan-2  O5   0.020
 UMV  plan-2  O6   0.020
 UMV  plan-3  N1   0.020
 UMV  plan-3  N2   0.020
 UMV  plan-3  C8   0.020
 UMV  plan-3  C9   0.020
 UMV  plan-3  C10  0.020
 UMV  plan-3  C11  0.020
 UMV  plan-3  C12  0.020
 UMV  plan-3  O3   0.020
 UMV  plan-3  O4   0.020
 UMV  plan-3  H2   0.020
 UMV  plan-3  H10  0.020
 UMV  plan-3  H11  0.020
 UMV  plan-4  O1   0.020
 UMV  plan-4  C13  0.020
 UMV  plan-4  C14  0.020
 UMV  plan-4  C15  0.020
 UMV  plan-4  C16  0.020
 UMV  plan-4  C17  0.020
 UMV  plan-4  C18  0.020
 UMV  plan-4  C19  0.020
 UMV  plan-4  C20  0.020
 UMV  plan-4  C21  0.020
 UMV  plan-4  C22  0.020
 UMV  plan-4  C23  0.020
 UMV  plan-4  N3   0.020
 UMV  plan-4  C24  0.020
 UMV  plan-4  C25  0.020
 UMV  plan-4  H12  0.020
 UMV  plan-4  H13  0.020
 UMV  plan-4  H14  0.020
 UMV  plan-4  H15  0.020

