# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 14:49:43 2020
#   Inital geometry file: a 153 line input string
#   Ligand name: (2R)-2-[5-cyclopropyl-6-(hydroxysulfanyl)-4-(naphthalen-1-ylmethyl)-2-oxopyridin-1(2H)-yl]-3-phenylpropanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OSC1=C(C2CC2)C(=CC(=O)N1[C@H](Cc3ccccc3)C(O)=O)Cc4cccc5ccccc45
#
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
 EC5  EC5  '(2R)-2-[5-cyclopropyl-6-(hydroxysulfanyl)-4-(naphthalen-1-ylmethyl)-2-oxopyridin-1(2H)-yl]-3-phenylpropanoic acid'  ligand  58  34  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_EC5
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
 EC5  O26   O  O      0  -0.516   1.0862  -2.7983   1.4212
 EC5  C26   C  CR6    0   0.577   0.7563  -1.7096   0.9544
 EC5  N27   N  NR6    0  -0.523   1.4050  -1.1940  -0.1545
 EC5  C28   C  CH1    0  -0.279   2.7200  -1.7752  -0.4721
 EC5  C29   C  CH2    0  -0.525   3.7054  -1.5556   0.6790
 EC5  C6    C  CR6    0   0.134   3.7063  -0.1035   1.0713
 EC5  C5    C  CR16   0  -0.303   3.0575   0.3323   2.2224
 EC5  C4    C  CR16   0  -0.234   2.9651   1.6863   2.5202
 EC5  C3    C  CR16   0  -0.269   3.5282   2.6276   1.6704
 EC5  C2    C  CR16   0  -0.238   4.1898   2.2049   0.5237
 EC5  C1    C  CR16   0  -0.304   4.2733   0.8522   0.2283
 EC5  C21   C  C      0   0.510   2.6074  -3.2066  -1.0235
 EC5  O23   O  OC    -1  -0.546   3.3550  -4.0791  -0.5842
 EC5  O22   O  O      0  -0.619   1.7816  -3.3391  -1.9718
 EC5  C25   C  CR16   0  -0.549  -0.2668  -0.8715   1.5065
 EC5  C24   C  CR6    0   0.323  -0.6224   0.3261   0.9699
 EC5  C23   C  CR6    0   0.011   0.0215   0.7686  -0.2289
 EC5  C18   C  CH1    0  -0.319  -0.2865   2.0847  -0.8517
 EC5  C20   C  CH2    0  -0.483   0.8231   2.9756  -1.3270
 EC5  C19   C  CH2    0  -0.486   0.0635   3.3390  -0.0964
 EC5  C22   C  CR6    0   0.056   0.9565  -0.0581  -0.7841
 EC5  S30   S  S2     0   0.330   1.4903   0.1489  -2.4659
 EC5  O56   O  OH1    0  -0.788   0.8438  -1.2363  -3.0928
 EC5  C17   C  CH2    0  -0.666  -1.7169   1.1347   1.6293
 EC5  C16   C  CR6    0   0.146  -2.9835   1.2763   0.8124
 EC5  C7    C  CR16   0  -0.334  -3.3190   2.4984   0.2859
 EC5  C8    C  CR16   0  -0.244  -4.4704   2.6818  -0.5041
 EC5  C9    C  CR16   0  -0.334  -5.2969   1.6274  -0.7653
 EC5  C10   C  CR66   0   0.109  -5.0179   0.3540  -0.2176
 EC5  C15   C  CR66   0   0.079  -3.8617   0.1721   0.5923
 EC5  C11   C  CR16   0  -0.309  -5.8866  -0.7385  -0.4500
 EC5  C12   C  CR16   0  -0.263  -5.6439  -1.9622   0.1096
 EC5  C13   C  CR16   0  -0.249  -4.5195  -2.1401   0.9389
 EC5  C14   C  CR16   0  -0.317  -3.6549  -1.1042   1.1702
 EC5  H25   H  HCR6   0   0.267  -0.7425  -1.2329   2.4096
 EC5  H291  H  HCH2   0   0.257   3.4783  -2.1924   1.5317
 EC5  H292  H  HCH2   0   0.259   4.6910  -1.8495   0.3133
 EC5  HA    H  HCR6   0   0.244   2.6108  -0.3936   2.8919
 EC5  HB    H  HCR6   0   0.246   4.7821   0.5352  -0.6754
 EC5  HC    H  HCR6   0   0.248   2.4516   2.0055   3.4183
 EC5  HD    H  HCR6   0   0.249   3.4543   3.6830   1.8996
 EC5  HE    H  HCR6   0   0.251   4.6386   2.9302  -0.1431
 EC5  H171  H  HCH2   0   0.281  -1.9471   0.6758   2.5936
 EC5  H172  H  HCH2   0   0.291  -1.3350   2.1326   1.8505
 EC5  H18   H  HCH1   0   0.276  -1.2041   2.1334  -1.4300
 EC5  H201  H  HCH2   0   0.249   1.8471   2.6470  -1.1895
 EC5  H202  H  HCH2   0   0.254   0.6543   3.5431  -2.2326
 EC5  H191  H  HCH2   0   0.255  -0.6286   4.1704  -0.1365
 EC5  H192  H  HCH2   0   0.253   0.5742   3.2281   0.8527
 EC5  H56   H  HOH1   0   0.472   1.2657  -2.0624  -2.6678
 EC5  H7    H  HCR6   0   0.256  -2.6756   3.3491   0.4698
 EC5  H8    H  HCR6   0   0.257  -4.6884   3.6629  -0.9055
 EC5  H9    H  HCR6   0   0.254  -6.1788   1.7550  -1.3816
 EC5  H11   H  HCR6   0   0.254  -6.7564  -0.5861  -1.0779
 EC5  H14   H  HCR6   0   0.242  -2.8104  -1.2705   1.8209
 EC5  H12   H  HCR6   0   0.258  -6.3165  -2.7901  -0.0731
 EC5  H13   H  HCR6   0   0.258  -4.3397  -3.1026   1.4003
 EC5  H28   H  HCH1   0   0.290   3.1075  -1.1837  -1.3031

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
 EC5  O26  C26   double    1.230  0.020  1.230
 EC5  C26  N27   single    1.384  0.020  1.384
 EC5  C26  C25   single    1.433  0.020  1.433
 EC5  N27  C28   single    1.472  0.020  1.472
 EC5  N27  C22   single    1.374  0.020  1.374
 EC5  C28  C29   single    1.531  0.020  1.531
 EC5  C28  C21   single    1.538  0.020  1.538
 EC5  C29  C6    single    1.504  0.020  1.504
 EC5  C6   C5    aromatic  1.391  0.020  1.391
 EC5  C6   C1    aromatic  1.395  0.020  1.395
 EC5  C5   C4    aromatic  1.389  0.020  1.389
 EC5  C4   C3    aromatic  1.388  0.020  1.388
 EC5  C3   C2    aromatic  1.390  0.020  1.390
 EC5  C2   C1    aromatic  1.387  0.020  1.387
 EC5  C21  O23   deloc     1.230  0.020  1.230
 EC5  C21  O22   deloc     1.264  0.020  1.264
 EC5  C25  C24   double    1.360  0.020  1.360
 EC5  C24  C23   single    1.431  0.020  1.431
 EC5  C24  C17   single    1.512  0.020  1.512
 EC5  C23  C18   single    1.488  0.020  1.488
 EC5  C23  C22   double    1.366  0.020  1.366
 EC5  C18  C20   single    1.500  0.020  1.500
 EC5  C18  C19   single    1.505  0.020  1.505
 EC5  C20  C19   single    1.491  0.020  1.491
 EC5  C22  S30   single    1.777  0.020  1.777
 EC5  S30  O56   single    1.652  0.020  1.652
 EC5  C17  C16   single    1.514  0.020  1.514
 EC5  C16  C7    aromatic  1.372  0.020  1.372
 EC5  C16  C15   aromatic  1.428  0.020  1.428
 EC5  C7   C8    aromatic  1.408  0.020  1.408
 EC5  C8   C9    aromatic  1.365  0.020  1.365
 EC5  C9   C10   aromatic  1.414  0.020  1.414
 EC5  C10  C15   aromatic  1.423  0.020  1.423
 EC5  C10  C11   aromatic  1.415  0.020  1.415
 EC5  C15  C14   aromatic  1.416  0.020  1.416
 EC5  C11  C12   aromatic  1.367  0.020  1.367
 EC5  C12  C13   aromatic  1.408  0.020  1.408
 EC5  C13  C14   aromatic  1.369  0.020  1.369
 EC5  C25  H25   single    0.930  0.020  1.080
 EC5  C29  H291  single    0.970  0.020  1.090
 EC5  C29  H292  single    0.970  0.020  1.090
 EC5  C5   HA    single    0.930  0.020  1.080
 EC5  C1   HB    single    0.930  0.020  1.080
 EC5  C4   HC    single    0.930  0.020  1.080
 EC5  C3   HD    single    0.930  0.020  1.080
 EC5  C2   HE    single    0.930  0.020  1.080
 EC5  C17  H171  single    0.970  0.020  1.090
 EC5  C17  H172  single    0.970  0.020  1.090
 EC5  C18  H18   single    0.970  0.020  1.090
 EC5  C20  H201  single    0.970  0.020  1.090
 EC5  C20  H202  single    0.970  0.020  1.090
 EC5  C19  H191  single    0.970  0.020  1.090
 EC5  C19  H192  single    0.970  0.020  1.090
 EC5  O56  H56   single    0.850  0.020  0.980
 EC5  C7   H7    single    0.930  0.020  1.080
 EC5  C8   H8    single    0.930  0.020  1.080
 EC5  C9   H9    single    0.930  0.020  1.080
 EC5  C11  H11   single    0.930  0.020  1.080
 EC5  C14  H14   single    0.930  0.020  1.080
 EC5  C12  H12   single    0.930  0.020  1.080
 EC5  C13  H13   single    0.930  0.020  1.080
 EC5  C28  H28   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
 EC5  C25   C26  N27   115.17  3.000
 EC5  C25   C26  O26   124.27  3.000
 EC5  N27   C26  O26   120.54  3.000
 EC5  C22   N27  C28   121.27  3.000
 EC5  C22   N27  C26   121.47  3.000
 EC5  C28   N27  C26   116.38  3.000
 EC5  H28   C28  C21   104.92  3.000
 EC5  H28   C28  C29   105.44  3.000
 EC5  C21   C28  C29   116.75  3.000
 EC5  H28   C28  N27   105.51  3.000
 EC5  C21   C28  N27   112.29  3.000
 EC5  C29   C28  N27   110.86  3.000
 EC5  H292  C29  H291  107.06  3.000
 EC5  H292  C29  C6    110.29  3.000
 EC5  H291  C29  C6    111.14  3.000
 EC5  H292  C29  C28   106.90  3.000
 EC5  H291  C29  C28   111.77  3.000
 EC5  C6    C29  C28   109.57  3.000
 EC5  C1    C6   C5    118.35  3.000
 EC5  C1    C6   C29   120.27  3.000
 EC5  C5    C6   C29   121.19  3.000
 EC5  HA    C5   C4    119.53  3.000
 EC5  HA    C5   C6    119.57  3.000
 EC5  C4    C5   C6    120.90  3.000
 EC5  HC    C4   C3    120.04  3.000
 EC5  HC    C4   C5    119.77  3.000
 EC5  C3    C4   C5    120.19  3.000
 EC5  HD    C3   C2    120.25  3.000
 EC5  HD    C3   C4    120.26  3.000
 EC5  C2    C3   C4    119.49  3.000
 EC5  HE    C2   C1    119.82  3.000
 EC5  HE    C2   C3    120.11  3.000
 EC5  C1    C2   C3    120.07  3.000
 EC5  HB    C1   C2    119.39  3.000
 EC5  HB    C1   C6    119.61  3.000
 EC5  C2    C1   C6    121.00  3.000
 EC5  O22   C21  O23   126.19  3.000
 EC5  O22   C21  C28   114.47  3.000
 EC5  O23   C21  C28   119.18  3.000
 EC5  H25   C25  C24   120.55  3.000
 EC5  H25   C25  C26   116.08  3.000
 EC5  C24   C25  C26   123.35  3.000
 EC5  C17   C24  C23   121.72  3.000
 EC5  C17   C24  C25   119.22  3.000
 EC5  C23   C24  C25   119.03  3.000
 EC5  C22   C23  C18   120.45  3.000
 EC5  C22   C23  C24   117.48  3.000
 EC5  C18   C23  C24   122.06  3.000
 EC5  H18   C18  C19   115.24  3.000
 EC5  H18   C18  C20   115.45  3.000
 EC5  C19   C18  C20    59.48  3.000
 EC5  H18   C18  C23   115.94  3.000
 EC5  C19   C18  C23   118.61  3.000
 EC5  C20   C18  C23   120.31  3.000
 EC5  H202  C20  H201  114.36  3.000
 EC5  H202  C20  C19   118.91  3.000
 EC5  H201  C20  C19   116.77  3.000
 EC5  H202  C20  C18   117.47  3.000
 EC5  H201  C20  C18   118.58  3.000
 EC5  C19   C20  C18    60.43  3.000
 EC5  H192  C19  H191  114.36  3.000
 EC5  H192  C19  C20   117.25  3.000
 EC5  H191  C19  C20   118.84  3.000
 EC5  H192  C19  C18   117.63  3.000
 EC5  H191  C19  C18   118.21  3.000
 EC5  C20   C19  C18    60.09  3.000
 EC5  S30   C22  C23   121.33  3.000
 EC5  S30   C22  N27   115.60  3.000
 EC5  C23   C22  N27   122.51  3.000
 EC5  O56   S30  C22    98.28  3.000
 EC5  H56   O56  S30   111.03  3.000
 EC5  H172  C17  H171  106.20  3.000
 EC5  H172  C17  C16   108.46  3.000
 EC5  H171  C17  C16   109.84  3.000
 EC5  H172  C17  C24   108.91  3.000
 EC5  H171  C17  C24   108.23  3.000
 EC5  C16   C17  C24   114.85  3.000
 EC5  C15   C16  C7    118.63  3.000
 EC5  C15   C16  C17   121.69  3.000
 EC5  C7    C16  C17   119.66  3.000
 EC5  H7    C7   C8    118.62  3.000
 EC5  H7    C7   C16   119.30  3.000
 EC5  C8    C7   C16   122.08  3.000
 EC5  H8    C8   C9    120.49  3.000
 EC5  H8    C8   C7    119.39  3.000
 EC5  C9    C8   C7    120.12  3.000
 EC5  H9    C9   C10   119.15  3.000
 EC5  H9    C9   C8    120.71  3.000
 EC5  C10   C9   C8    120.14  3.000
 EC5  C11   C10  C15   119.57  3.000
 EC5  C11   C10  C9    120.70  3.000
 EC5  C15   C10  C9    119.72  3.000
 EC5  C14   C15  C10   117.77  3.000
 EC5  C14   C15  C16   122.97  3.000
 EC5  C10   C15  C16   119.24  3.000
 EC5  H11   C11  C12   120.37  3.000
 EC5  H11   C11  C10   118.65  3.000
 EC5  C12   C11  C10   120.99  3.000
 EC5  H12   C12  C13   119.93  3.000
 EC5  H12   C12  C11   120.35  3.000
 EC5  C13   C12  C11   119.72  3.000
 EC5  H13   C13  C14   119.73  3.000
 EC5  H13   C13  C12   119.73  3.000
 EC5  C14   C13  C12   120.54  3.000
 EC5  H14   C14  C13   118.65  3.000
 EC5  H14   C14  C15   119.95  3.000
 EC5  C13   C14  C15   121.39  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
 EC5  CONST_01  C3   C4   C5   C6      0.00   0.0  0
 EC5  CONST_02  C3   C2   C1   C6      0.00   0.0  0
 EC5  CONST_03  C2   C1   C6   C5      0.00   0.0  0
 EC5  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 EC5  CONST_05  C1   C6   C5   C4      0.00   0.0  0
 EC5  CONST_06  C1   C2   C3   C4      0.00   0.0  0
 EC5  CONST_07  C9   C8   C7   C16     0.00   0.0  0
 EC5  CONST_08  C9   C10  C15  C16     0.00   0.0  0
 EC5  CONST_09  C11  C10  C15  C16   180.00   0.0  0
 EC5  CONST_10  C13  C14  C15  C16   180.00   0.0  0
 EC5  CONST_11  C10  C15  C16  C7      0.00   0.0  0
 EC5  CONST_12  C14  C15  C16  C7    180.00   0.0  0
 EC5  CONST_13  C10  C9   C8   C7      0.00   0.0  0
 EC5  CONST_14  C15  C16  C7   C8      0.00   0.0  0
 EC5  CONST_15  C15  C10  C9   C8      0.00   0.0  0
 EC5  CONST_16  C11  C10  C9   C8    180.00   0.0  0
 EC5  CONST_17  C14  C15  C10  C9    180.00   0.0  0
 EC5  CONST_18  C12  C11  C10  C9    180.00   0.0  0
 EC5  CONST_19  C13  C14  C15  C10     0.00   0.0  0
 EC5  CONST_20  C13  C12  C11  C10     0.00   0.0  0
 EC5  CONST_21  C12  C11  C10  C15     0.00   0.0  0
 EC5  CONST_22  C12  C13  C14  C15     0.00   0.0  0
 EC5  CONST_23  C14  C15  C10  C11     0.00   0.0  0
 EC5  CONST_24  C14  C13  C12  C11     0.00   0.0  0
 EC5  CONST_25  C22  N27  C26  C25     0.00   0.0  0
 EC5  CONST_26  C4   C5   C6   C29   180.00   0.0  0
 EC5  CONST_27  C2   C1   C6   C29   180.00   0.0  0
 EC5  CONST_28  C8   C7   C16  C17   180.00   0.0  0
 EC5  CONST_29  C10  C15  C16  C17   180.00   0.0  0
 EC5  CONST_30  C14  C15  C16  C17     0.00   0.0  0
 EC5  CONST_31  C22  N27  C26  O26   180.00   0.0  0
 EC5  CONST_33  HC   C4   C5   C6    180.00   0.0  0
 EC5  CONST_34  HE   C2   C1   C6    180.00   0.0  0
 EC5  CONST_35  HB   C1   C6   C5    180.00   0.0  0
 EC5  CONST_36  HD   C3   C4   C5    180.00   0.0  0
 EC5  CONST_37  HA   C5   C4   C3    180.00   0.0  0
 EC5  CONST_38  H8   C8   C7   C16   180.00   0.0  0
 EC5  CONST_39  H14  C14  C15  C16     0.00   0.0  0
 EC5  CONST_40  H9   C9   C8   C7    180.00   0.0  0
 EC5  CONST_41  H7   C7   C8   C9    180.00   0.0  0
 EC5  CONST_42  H11  C11  C10  C9      0.00   0.0  0
 EC5  CONST_43  H12  C12  C11  C10   180.00   0.0  0
 EC5  CONST_44  H13  C13  C14  C15   180.00   0.0  0
 EC5  Var_01    C20  C18  C23  C24   134.63  30.0  3
 EC5  Var_02    C19  C20  C18  C23  -107.41  30.0  1
 EC5  Var_03    C16  C17  C24  C25  -112.97  30.0  3
 EC5  Var_04    C7   C16  C17  C24  -110.63  30.0  2
 EC5  Var_05    C5   C6   C29  C28   103.88  30.0  2

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
 EC5  chir_01  C28  N27  C29  C21  negativ
 EC5  chir_02  C18  C23  C20  C19  both

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
 EC5  plan-1  O26  0.020
 EC5  plan-1  C26  0.020
 EC5  plan-1  N27  0.020
 EC5  plan-1  C28  0.020
 EC5  plan-1  C25  0.020
 EC5  plan-1  C24  0.020
 EC5  plan-1  C23  0.020
 EC5  plan-1  C18  0.020
 EC5  plan-1  C22  0.020
 EC5  plan-1  S30  0.020
 EC5  plan-1  C17  0.020
 EC5  plan-1  H25  0.020
 EC5  plan-2  C29  0.020
 EC5  plan-2  C6   0.020
 EC5  plan-2  C5   0.020
 EC5  plan-2  C4   0.020
 EC5  plan-2  C3   0.020
 EC5  plan-2  C2   0.020
 EC5  plan-2  C1   0.020
 EC5  plan-2  HA   0.020
 EC5  plan-2  HB   0.020
 EC5  plan-2  HC   0.020
 EC5  plan-2  HD   0.020
 EC5  plan-2  HE   0.020
 EC5  plan-3  C17  0.020
 EC5  plan-3  C16  0.020
 EC5  plan-3  C7   0.020
 EC5  plan-3  C8   0.020
 EC5  plan-3  C9   0.020
 EC5  plan-3  C10  0.020
 EC5  plan-3  C15  0.020
 EC5  plan-3  C11  0.020
 EC5  plan-3  C12  0.020
 EC5  plan-3  C13  0.020
 EC5  plan-3  C14  0.020
 EC5  plan-3  H7   0.020
 EC5  plan-3  H8   0.020
 EC5  plan-3  H9   0.020
 EC5  plan-3  H11  0.020
 EC5  plan-3  H14  0.020
 EC5  plan-3  H12  0.020
 EC5  plan-3  H13  0.020
 EC5  plan-4  C28  0.020
 EC5  plan-4  C21  0.020
 EC5  plan-4  O23  0.020
 EC5  plan-4  O22  0.020

