# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 14 08:51:08 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: 3-hydroxy-2-({4-[4-(pyrimidin-2-yl)piperazine-1-carbonyl]phenyl}methyl)-1-benzofuran-7-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cccc2c(O)c(Cc3ccc(cc3)C(=O)N4CCN(CC4)c5ncccn5)oc12
#
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
 KYP  KYP  3-hydroxy-2-({4-[4-(pyrimidin-2-yl)piperazine-1-carbonyl]phenyl}methyl)-1-benzofuran-7-carboxamide  ligand  57  34  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_KYP
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
 KYP  O2   O  O     0  -0.487  -2.9133  -3.6220   0.4775
 KYP  C13  C  C     0   0.524  -2.3926  -2.6062   0.0338
 KYP  N1   N  NT    0  -0.460  -3.1033  -1.5135  -0.3214
 KYP  C21  C  CH2   0  -0.315  -2.5564  -0.1824  -0.5309
 KYP  C20  C  CH2   0  -0.305  -3.1008   0.7891   0.5113
 KYP  N2   N  NT    0  -0.498  -4.5459   0.7584   0.5418
 KYP  C16  C  CR6   0   0.641  -5.3129   1.8077   0.1582
 KYP  N4   N  N     0  -0.472  -4.6912   2.9552  -0.1432
 KYP  C19  C  CR16  0  -0.008  -5.4537   3.9744  -0.4967
 KYP  C18  C  CR16  0  -0.400  -6.8356   3.8986  -0.5638
 KYP  C17  C  CR16  0  -0.008  -7.3756   2.6664  -0.2320
 KYP  N3   N  N     0  -0.472  -6.6397   1.6287   0.1244
 KYP  C15  C  CH2   0  -0.313  -5.0828  -0.5657   0.7749
 KYP  C14  C  CH2   0  -0.315  -4.5565  -1.5351  -0.2747
 KYP  C12  C  CR6   0  -0.087  -0.9100  -2.5780  -0.1618
 KYP  C11  C  CR16  0  -0.256  -0.0924  -3.0232   0.8743
 KYP  C10  C  CR16  0  -0.279   1.2800  -3.0877   0.7041
 KYP  C22  C  CR16  0  -0.245  -0.3320  -2.2388  -1.3807
 KYP  C23  C  CR16  0  -0.303   1.0422  -2.3267  -1.5531
 KYP  C9   C  CR6   0   0.135   1.8634  -2.7450  -0.5131
 KYP  C8   C  CH2   0  -0.644   3.3631  -2.7976  -0.6802
 KYP  C7   C  CR5   0   0.296   4.0199  -1.6242  -0.0563
 KYP  C6   C  CR5   0   0.194   4.7832  -1.4906   1.0515
 KYP  O1   O  OH1   0  -0.624   5.1321  -2.4906   1.8837
 KYP  O3   O  O     0  -0.445   3.7944  -0.4018  -0.6334
 KYP  C24  C  CR56  0   0.372   4.4396   0.5175   0.1031
 KYP  C1   C  CR6   0  -0.150   4.4619   1.8919  -0.1094
 KYP  C    C  C     0   0.485   3.8036   2.5015  -1.3024
 KYP  O    O  O     0  -0.473   3.7541   1.9102  -2.3706
 KYP  N    N  NH2   0  -0.804   3.2968   3.7284  -1.1139
 KYP  C5   C  CR56  0  -0.040   5.0781  -0.0906   1.1859
 KYP  C4   C  CR16  0  -0.321   5.7881   0.6807   2.1028
 KYP  C3   C  CR16  0  -0.259   5.8327   2.0489   1.9027
 KYP  C2   C  CR16  0  -0.295   5.1795   2.6414   0.8189
 KYP  H1   H  HCH2  0   0.279  -1.4730  -0.1936  -0.4565
 KYP  H2   H  HCH2  0   0.252  -2.8208   0.1650  -1.5343
 KYP  H3   H  HCH2  0   0.246  -2.7153   0.5115   1.4981
 KYP  H4   H  HCH2  0   0.281  -2.7537   1.7930   0.2867
 KYP  H5   H  HCR6  0   0.269  -4.9379   4.8974  -0.7404
 KYP  H6   H  HCR6  0   0.270  -7.4470   4.7388  -0.8551
 KYP  H7   H  HCR6  0   0.269  -8.4486   2.5074  -0.2556
 KYP  H8   H  HCH2  0   0.248  -4.7810  -0.9044   1.7715
 KYP  H9   H  HCH2  0   0.278  -6.1677  -0.5394   0.7434
 KYP  H10  H  HCH2  0   0.254  -4.9413  -1.2500  -1.2589
 KYP  H11  H  HCH2  0   0.272  -4.9015  -2.5422  -0.0582
 KYP  H12  H  HCR6  0   0.261  -0.5273  -3.3136   1.8219
 KYP  H13  H  HCR6  0   0.255   1.9022  -3.4199   1.5270
 KYP  H14  H  HCR6  0   0.269  -0.9491  -1.9149  -2.2101
 KYP  H15  H  HCR6  0   0.256   1.4755  -2.0677  -2.5112
 KYP  H16  H  HCH2  0   0.291   3.7624  -3.6995  -0.2136
 KYP  H17  H  HCH2  0   0.285   3.6201  -2.8524  -1.7418
 KYP  H19  H  HNH2  0   0.414   3.2320   4.1501  -0.2037
 KYP  H20  H  HNH2  0   0.406   2.8557   4.2129  -1.8789
 KYP  H21  H  HCR6  0   0.265   6.2878   0.2285   2.9499
 KYP  H22  H  HCR6  0   0.265   6.3815   2.6756   2.5923
 KYP  H23  H  HCR6  0   0.269   5.2590   3.7136   0.6919
 KYP  H18  H  HOH1  0   0.480   6.0026  -2.3212   2.2601

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
 KYP  O2   C13  double    1.225  0.020  1.225
 KYP  C22  C23  aromatic  1.388  0.020  1.388
 KYP  C22  C12  aromatic  1.391  0.020  1.391
 KYP  C13  C12  single    1.496  0.020  1.496
 KYP  C13  N1   single    1.351  0.020  1.351
 KYP  C23  C9   aromatic  1.390  0.020  1.390
 KYP  C12  C11  aromatic  1.393  0.020  1.393
 KYP  C21  N1   single    1.454  0.020  1.454
 KYP  C21  C20  single    1.525  0.020  1.525
 KYP  N1   C14  single    1.454  0.020  1.454
 KYP  C9   C8   single    1.510  0.020  1.510
 KYP  C9   C10  aromatic  1.393  0.020  1.393
 KYP  O1   C6   single    1.347  0.020  1.347
 KYP  C11  C10  aromatic  1.384  0.020  1.384
 KYP  C8   C7   single    1.482  0.020  1.482
 KYP  C20  N2   single    1.446  0.020  1.446
 KYP  C6   C7   aromatic  1.352  0.020  1.352
 KYP  C6   C5   aromatic  1.437  0.020  1.437
 KYP  C7   O3   aromatic  1.370  0.020  1.370
 KYP  C14  C15  single    1.523  0.020  1.523
 KYP  N2   C15  single    1.448  0.020  1.448
 KYP  N2   C16  single    1.355  0.020  1.355
 KYP  N4   C16  aromatic  1.339  0.020  1.339
 KYP  N4   C19  aromatic  1.321  0.020  1.321
 KYP  C5   C4   aromatic  1.393  0.020  1.393
 KYP  C5   C24  aromatic  1.396  0.020  1.396
 KYP  O3   C24  aromatic  1.343  0.020  1.343
 KYP  C16  N3   aromatic  1.339  0.020  1.339
 KYP  C4   C3   aromatic  1.383  0.020  1.383
 KYP  C19  C18  aromatic  1.386  0.020  1.386
 KYP  C24  C1   aromatic  1.391  0.020  1.391
 KYP  N3   C17  aromatic  1.321  0.020  1.321
 KYP  C3   C2   aromatic  1.397  0.020  1.397
 KYP  C18  C17  aromatic  1.386  0.020  1.386
 KYP  C1   C2   aromatic  1.392  0.020  1.392
 KYP  C1   C    single    1.493  0.020  1.493
 KYP  N    C    single    1.341  0.020  1.341
 KYP  C    O    double    1.222  0.020  1.222
 KYP  C21  H1   single    0.970  0.020  1.090
 KYP  C21  H2   single    0.970  0.020  1.090
 KYP  C20  H3   single    0.970  0.020  1.090
 KYP  C20  H4   single    0.970  0.020  1.090
 KYP  C19  H5   single    0.930  0.020  1.080
 KYP  C18  H6   single    0.930  0.020  1.080
 KYP  C17  H7   single    0.930  0.020  1.080
 KYP  C15  H8   single    0.970  0.020  1.090
 KYP  C15  H9   single    0.970  0.020  1.090
 KYP  C14  H10  single    0.970  0.020  1.090
 KYP  C14  H11  single    0.970  0.020  1.090
 KYP  C11  H12  single    0.930  0.020  1.080
 KYP  C10  H13  single    0.930  0.020  1.080
 KYP  C22  H14  single    0.930  0.020  1.080
 KYP  C23  H15  single    0.930  0.020  1.080
 KYP  C8   H16  single    0.970  0.020  1.090
 KYP  C8   H17  single    0.970  0.020  1.090
 KYP  N    H19  single    0.860  0.020  1.020
 KYP  N    H20  single    0.860  0.020  1.020
 KYP  C4   H21  single    0.930  0.020  1.080
 KYP  C3   H22  single    0.930  0.020  1.080
 KYP  C2   H23  single    0.930  0.020  1.080
 KYP  O1   H18  single    0.850  0.020  0.980

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
 KYP  C12  C13  N1   118.15  3.000
 KYP  N1   C13  O2   122.85  3.000
 KYP  C12  C13  O2   118.97  3.000
 KYP  C14  N1   C21  113.21  3.000
 KYP  C14  N1   C13  120.35  3.000
 KYP  C21  N1   C13  125.48  3.000
 KYP  H2   C21  H1   107.89  3.000
 KYP  H2   C21  C20  109.76  3.000
 KYP  H1   C21  C20  108.41  3.000
 KYP  H2   C21  N1   109.39  3.000
 KYP  H1   C21  N1   110.85  3.000
 KYP  C20  C21  N1   110.51  3.000
 KYP  H4   C20  H3   107.96  3.000
 KYP  H4   C20  N2   110.10  3.000
 KYP  H3   C20  N2   109.11  3.000
 KYP  H4   C20  C21  109.48  3.000
 KYP  H3   C20  C21  109.18  3.000
 KYP  N2   C20  C21  110.95  3.000
 KYP  C15  N2   C16  122.95  3.000
 KYP  C16  N2   C20  122.91  3.000
 KYP  C15  N2   C20  113.17  3.000
 KYP  N3   C16  N4   124.66  3.000
 KYP  N3   C16  N2   117.67  3.000
 KYP  N4   C16  N2   117.67  3.000
 KYP  C19  N4   C16  116.95  3.000
 KYP  H5   C19  C18  120.65  3.000
 KYP  H5   C19  N4   116.23  3.000
 KYP  C18  C19  N4   123.12  3.000
 KYP  H6   C18  C17  122.43  3.000
 KYP  H6   C18  C19  122.38  3.000
 KYP  C17  C18  C19  115.20  3.000
 KYP  H7   C17  N3   116.21  3.000
 KYP  H7   C17  C18  120.70  3.000
 KYP  N3   C17  C18  123.09  3.000
 KYP  C17  N3   C16  116.98  3.000
 KYP  H9   C15  H8   108.02  3.000
 KYP  H9   C15  C14  109.93  3.000
 KYP  H8   C15  C14  109.59  3.000
 KYP  H9   C15  N2   110.10  3.000
 KYP  H8   C15  N2   109.10  3.000
 KYP  C14  C15  N2   110.07  3.000
 KYP  H11  C14  H10  108.00  3.000
 KYP  H11  C14  C15  110.06  3.000
 KYP  H10  C14  C15  109.42  3.000
 KYP  H11  C14  N1   109.73  3.000
 KYP  H10  C14  N1   108.58  3.000
 KYP  C15  C14  N1   110.98  3.000
 KYP  C22  C12  C11  119.07  3.000
 KYP  C11  C12  C13  118.59  3.000
 KYP  C22  C12  C13  122.08  3.000
 KYP  H12  C11  C10  119.57  3.000
 KYP  H12  C11  C12  120.07  3.000
 KYP  C10  C11  C12  120.36  3.000
 KYP  H13  C10  C9   119.90  3.000
 KYP  H13  C10  C11  119.35  3.000
 KYP  C9   C10  C11  120.75  3.000
 KYP  H14  C22  C23  119.20  3.000
 KYP  H14  C22  C12  120.47  3.000
 KYP  C23  C22  C12  120.32  3.000
 KYP  H15  C23  C9   119.84  3.000
 KYP  H15  C23  C22  119.41  3.000
 KYP  C9   C23  C22  120.75  3.000
 KYP  C8   C9   C23  120.98  3.000
 KYP  C8   C9   C10  120.28  3.000
 KYP  C23  C9   C10  118.72  3.000
 KYP  H17  C8   H16  106.72  3.000
 KYP  H17  C8   C7   110.13  3.000
 KYP  H16  C8   C7   108.19  3.000
 KYP  H17  C8   C9   110.03  3.000
 KYP  H16  C8   C9   110.18  3.000
 KYP  C7   C8   C9   111.46  3.000
 KYP  O3   C7   C6   110.48  3.000
 KYP  O3   C7   C8   117.12  3.000
 KYP  C6   C7   C8   132.32  3.000
 KYP  C5   C6   O1   127.76  3.000
 KYP  C5   C6   C7   106.78  3.000
 KYP  O1   C6   C7   125.40  3.000
 KYP  H18  O1   C6   110.18  3.000
 KYP  C24  O3   C7   107.49  3.000
 KYP  C5   C24  C1   122.78  3.000
 KYP  C1   C24  O3   126.89  3.000
 KYP  C5   C24  O3   110.29  3.000
 KYP  C2   C1   C    122.70  3.000
 KYP  C    C1   C24  121.24  3.000
 KYP  C2   C1   C24  116.00  3.000
 KYP  N    C    O    123.40  3.000
 KYP  O    C    C1   121.26  3.000
 KYP  N    C    C1   115.34  3.000
 KYP  H20  N    H19  117.25  3.000
 KYP  H20  N    C    119.92  3.000
 KYP  H19  N    C    122.38  3.000
 KYP  C4   C5   C24  120.16  3.000
 KYP  C24  C5   C6   104.95  3.000
 KYP  C4   C5   C6   134.89  3.000
 KYP  H21  C4   C3   120.76  3.000
 KYP  H21  C4   C5   121.28  3.000
 KYP  C3   C4   C5   117.96  3.000
 KYP  H22  C3   C2   119.09  3.000
 KYP  H22  C3   C4   119.81  3.000
 KYP  C2   C3   C4   121.10  3.000
 KYP  H23  C2   C3   118.47  3.000
 KYP  H23  C2   C1   119.52  3.000
 KYP  C3   C2   C1   121.99  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
 KYP  CONST_01  C18  C19  N4   C16    0.00   0.0  0
 KYP  CONST_02  C18  C17  N3   C16    0.00   0.0  0
 KYP  CONST_03  C17  N3   C16  N4     0.00   0.0  0
 KYP  CONST_04  C17  C18  C19  N4     0.00   0.0  0
 KYP  CONST_05  N3   C16  N4   C19    0.00   0.0  0
 KYP  CONST_06  N3   C17  C18  C19    0.00   0.0  0
 KYP  CONST_07  C9   C23  C22  C12    0.00   0.0  0
 KYP  CONST_08  C9   C10  C11  C12    0.00   0.0  0
 KYP  CONST_09  C23  C22  C12  C11    0.00   0.0  0
 KYP  CONST_10  C23  C9   C10  C11    0.00   0.0  0
 KYP  CONST_11  C22  C23  C9   C10    0.00   0.0  0
 KYP  CONST_12  C22  C12  C11  C10    0.00   0.0  0
 KYP  CONST_13  C4   C5   C6   C7   180.00   0.0  0
 KYP  CONST_14  C24  C5   C6   C7     0.00   0.0  0
 KYP  CONST_15  C5   C24  O3   C7     0.00   0.0  0
 KYP  CONST_16  C1   C24  O3   C7   180.00   0.0  0
 KYP  CONST_17  C24  O3   C7   C6     0.00   0.0  0
 KYP  CONST_18  C3   C4   C5   C6   180.00   0.0  0
 KYP  CONST_19  O3   C24  C5   C6     0.00   0.0  0
 KYP  CONST_20  C1   C24  C5   C6   180.00   0.0  0
 KYP  CONST_21  C5   C6   C7   O3     0.00   0.0  0
 KYP  CONST_22  C4   C5   C24  O3   180.00   0.0  0
 KYP  CONST_23  C2   C1   C24  O3   180.00   0.0  0
 KYP  CONST_24  C3   C4   C5   C24    0.00   0.0  0
 KYP  CONST_25  C3   C2   C1   C24    0.00   0.0  0
 KYP  CONST_26  C4   C5   C24  C1     0.00   0.0  0
 KYP  CONST_27  C4   C3   C2   C1     0.00   0.0  0
 KYP  CONST_28  C2   C3   C4   C5     0.00   0.0  0
 KYP  CONST_29  C2   C1   C24  C5     0.00   0.0  0
 KYP  CONST_30  C19  N4   C16  N2   180.00   0.0  0
 KYP  CONST_31  C17  N3   C16  N2   180.00   0.0  0
 KYP  CONST_32  C23  C22  C12  C13  180.00   0.0  0
 KYP  CONST_33  C10  C11  C12  C13  180.00   0.0  0
 KYP  CONST_34  C8   C9   C10  C11  180.00   0.0  0
 KYP  CONST_35  C8   C9   C23  C22  180.00   0.0  0
 KYP  CONST_36  C5   C6   C7   C8   180.00   0.0  0
 KYP  CONST_37  C24  O3   C7   C8   180.00   0.0  0
 KYP  CONST_38  O3   C7   C6   O1   180.00   0.0  0
 KYP  CONST_39  C4   C5   C6   O1     0.00   0.0  0
 KYP  CONST_40  C24  C5   C6   O1   180.00   0.0  0
 KYP  CONST_41  C    C1   C24  O3     0.00   0.0  0
 KYP  CONST_42  C5   C24  C1   C    180.00   0.0  0
 KYP  CONST_43  C3   C2   C1   C    180.00   0.0  0
 KYP  CONST_45  C12  C13  N1   C14  180.00   0.0  0
 KYP  CONST_46  H5   C19  N4   C16  180.00   0.0  0
 KYP  CONST_47  H7   C17  N3   C16  180.00   0.0  0
 KYP  CONST_48  H6   C18  C19  N4   180.00   0.0  0
 KYP  CONST_49  H15  C23  C22  C12  180.00   0.0  0
 KYP  CONST_50  H13  C10  C11  C12  180.00   0.0  0
 KYP  CONST_51  H14  C22  C12  C11  180.00   0.0  0
 KYP  CONST_52  H12  C11  C12  C22  180.00   0.0  0
 KYP  CONST_53  H21  C4   C5   C6     0.00   0.0  0
 KYP  CONST_54  H23  C2   C1   C24  180.00   0.0  0
 KYP  CONST_55  H22  C3   C2   C1   180.00   0.0  0
 KYP  CONST_57  C14  N1   C13  O2     0.00   0.0  0
 KYP  CONST_58  H19  N    C    C1     0.00   0.0  0
 KYP  CONST_59  H20  N    C    C1   180.00   0.0  0
 KYP  Var_01    N2   C20  C21  N1   -53.22  30.0  1
 KYP  Var_02    N2   C15  C14  N1    54.26  30.0  1
 KYP  Var_03    C15  C14  N1   C21  -54.81  30.0  1
 KYP  Var_04    C15  N2   C20  C21   55.93  30.0  1
 KYP  Var_05    C14  N1   C21  C20   53.90  30.0  1
 KYP  Var_06    C14  C15  N2   C20  -56.11  30.0  1
 KYP  Var_07    N4   C16  N2   C20   -6.22  30.0  2
 KYP  Var_08    C22  C12  C13  N1   -52.04  30.0  2
 KYP  Var_09    C7   C8   C9   C10  -77.65  30.0  2
 KYP  Var_10    C6   C7   C8   C9   108.68  30.0  2
 KYP  Var_11    N    C    C1   C24  147.91  30.0  2

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
 KYP  plan-1  N2   0.020
 KYP  plan-1  C16  0.020
 KYP  plan-1  N4   0.020
 KYP  plan-1  C19  0.020
 KYP  plan-1  C18  0.020
 KYP  plan-1  C17  0.020
 KYP  plan-1  N3   0.020
 KYP  plan-1  H5   0.020
 KYP  plan-1  H6   0.020
 KYP  plan-1  H7   0.020
 KYP  plan-2  C13  0.020
 KYP  plan-2  C12  0.020
 KYP  plan-2  C11  0.020
 KYP  plan-2  C10  0.020
 KYP  plan-2  C22  0.020
 KYP  plan-2  C23  0.020
 KYP  plan-2  C9   0.020
 KYP  plan-2  C8   0.020
 KYP  plan-2  H12  0.020
 KYP  plan-2  H13  0.020
 KYP  plan-2  H14  0.020
 KYP  plan-2  H15  0.020
 KYP  plan-3  C8   0.020
 KYP  plan-3  C7   0.020
 KYP  plan-3  C6   0.020
 KYP  plan-3  O1   0.020
 KYP  plan-3  O3   0.020
 KYP  plan-3  C24  0.020
 KYP  plan-3  C1   0.020
 KYP  plan-3  C    0.020
 KYP  plan-3  C5   0.020
 KYP  plan-3  C4   0.020
 KYP  plan-3  C3   0.020
 KYP  plan-3  C2   0.020
 KYP  plan-3  H21  0.020
 KYP  plan-3  H22  0.020
 KYP  plan-3  H23  0.020
 KYP  plan-4  C1   0.020
 KYP  plan-4  C    0.020
 KYP  plan-4  O    0.020
 KYP  plan-4  N    0.020
 KYP  plan-4  H19  0.020
 KYP  plan-4  H20  0.020
 KYP  plan-5  O2   0.020
 KYP  plan-5  C13  0.020
 KYP  plan-5  N1   0.020
 KYP  plan-5  C21  0.020
 KYP  plan-5  C14  0.020
 KYP  plan-5  C12  0.020

