# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 20 19:40:23 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: N-(3-cyclopropyl-1H-pyrazol-5-yl)-2-[4-(thiophen-2-yl)phenyl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Cc1ccc(cc1)c2sccc2)Nc3[nH]nc(c3)C4CC4
#
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
 10K  10K  N-(3-cyclopropyl-1H-pyrazol-5-yl)-2-[4-(thiophen-2-yl)phenyl]acetamide  ligand  40  23  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_10K
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
 10K  O     O  O     0  -0.443   1.1689   0.1439  -0.2415
 10K  S     S  S2    0   0.212  -6.1160  -0.0580  -1.0491
 10K  C1    C  CR15  0  -0.469  -7.3218   0.7102  -0.1076
 10K  N1    N  NH1   0  -0.742   2.6894  -1.5250  -0.0763
 10K  C2    C  CR15  0  -0.172  -6.8727   0.9872   1.1473
 10K  N2    N  NR15  0  -0.513   5.0310  -1.3470   0.1662
 10K  C3    C  CR15  0  -0.247  -5.5302   0.5754   1.3505
 10K  N3    N  N     0  -0.318   6.0359  -0.4657   0.2414
 10K  C4    C  CR5   0  -0.213  -4.9723  -0.0100   0.2462
 10K  C5    C  CR6   0   0.140  -3.6231  -0.5509   0.0893
 10K  C6    C  CR16  0  -0.310  -3.0130  -0.6481  -1.1627
 10K  C7    C  CR16  0  -0.283  -1.7334  -1.1633  -1.2907
 10K  C8    C  CR6   0   0.140  -1.0191  -1.5917  -0.1776
 10K  C9    C  CR16  0  -0.275  -1.6241  -1.4932   1.0717
 10K  C10   C  CR16  0  -0.309  -2.9058  -0.9871   1.2059
 10K  C11   C  CH2   0  -0.706   0.3716  -2.1298  -0.3144
 10K  C12   C  C     0   0.559   1.4236  -1.0411  -0.2042
 10K  C13   C  CR5   0   0.639   3.8323  -0.7553   0.0159
 10K  C14   C  CR5   0   0.332   5.4633   0.7175   0.1385
 10K  C15   C  CR15  0  -0.563   4.0629   0.6043  -0.0073
 10K  C16   C  CH1   0  -0.352   6.2751   1.9450   0.1785
 10K  C17   C  CH2   0  -0.480   5.7034   3.2171   0.7403
 10K  C18   C  CH2   0  -0.479   5.9470   3.1012  -0.7273
 10K  HN1   H  HNH1  0   0.425   2.8072  -2.5272  -0.0456
 10K  H2    H  HCR5  0   0.269  -7.4742   1.4736   1.9017
 10K  H3    H  HCR5  0   0.264  -4.9943   0.7254   2.2776
 10K  H6    H  HCR6  0   0.253  -3.5308  -0.3085  -2.0519
 10K  H7    H  HCR6  0   0.256  -1.2877  -1.2320  -2.2756
 10K  H9    H  HCR6  0   0.255  -1.0936  -1.8279   1.9551
 10K  H10   H  HCR6  0   0.255  -3.3583  -0.9470   2.1885
 10K  H11   H  HCH2  0   0.298   0.5651  -2.8966   0.4399
 10K  H11A  H  HCH2  0   0.310   0.5012  -2.6195  -1.2847
 10K  H15   H  HCR5  0   0.270   3.3426   1.3950  -0.1067
 10K  H16   H  HCH1  0   0.260   7.3276   1.7659   0.3652
 10K  H17   H  HCH2  0   0.252   4.6789   3.1955   1.0920
 10K  H17A  H  HCH2  0   0.259   6.3614   3.8462   1.3255
 10K  H18   H  HCH2  0   0.258   6.7744   3.6499  -1.1581
 10K  H18A  H  HCH2  0   0.252   5.0916   2.9982  -1.3832
 10K  HN2   H  HNR5  0   0.419   5.2253  -2.3346   0.2161
 10K  H1    H  HCR5  0   0.297  -8.2945   0.9126  -0.5285

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
 10K  C12  O     double    1.213  0.020  1.213
 10K  C1   S     aromatic  1.712  0.020  1.712
 10K  C4   S     aromatic  1.729  0.020  1.729
 10K  C2   C1    aromatic  1.361  0.020  1.361
 10K  C1   H1    single    0.930  0.020  1.080
 10K  N1   C13   single    1.381  0.020  1.381
 10K  N1   C12   single    1.361  0.020  1.361
 10K  N1   HN1   single    0.860  0.020  1.020
 10K  C2   C3    aromatic  1.419  0.020  1.419
 10K  C2   H2    single    0.930  0.020  1.080
 10K  N2   C13   aromatic  1.345  0.020  1.345
 10K  N2   N3    aromatic  1.339  0.020  1.339
 10K  C3   C4    aromatic  1.369  0.020  1.369
 10K  C3   H3    single    0.930  0.020  1.080
 10K  N3   C14   aromatic  1.319  0.020  1.319
 10K  C4   C5    single    1.462  0.020  1.462
 10K  C10  C5    aromatic  1.397  0.020  1.397
 10K  C5   C6    aromatic  1.396  0.020  1.396
 10K  C6   C7    aromatic  1.385  0.020  1.385
 10K  C6   H6    single    0.930  0.020  1.080
 10K  C8   C7    aromatic  1.390  0.020  1.390
 10K  C7   H7    single    0.930  0.020  1.080
 10K  C9   C8    aromatic  1.392  0.020  1.392
 10K  C8   C11   single    1.497  0.020  1.497
 10K  C10  C9    aromatic  1.385  0.020  1.385
 10K  C9   H9    single    0.930  0.020  1.080
 10K  C10  H10   single    0.930  0.020  1.080
 10K  C11  C12   single    1.518  0.020  1.518
 10K  C11  H11   single    0.970  0.020  1.090
 10K  C11  H11A  single    0.970  0.020  1.090
 10K  C13  C15   aromatic  1.379  0.020  1.379
 10K  C14  C15   aromatic  1.413  0.020  1.413
 10K  C14  C16   single    1.472  0.020  1.472
 10K  C15  H15   single    0.930  0.020  1.080
 10K  C16  C18   single    1.505  0.020  1.505
 10K  C16  C17   single    1.504  0.020  1.504
 10K  C16  H16   single    0.970  0.020  1.090
 10K  C18  C17   single    1.492  0.020  1.492
 10K  C17  H17   single    0.970  0.020  1.090
 10K  C17  H17A  single    0.970  0.020  1.090
 10K  C18  H18   single    0.970  0.020  1.090
 10K  C18  H18A  single    0.970  0.020  1.090
 10K  N2   HN2   single    0.860  0.020  1.020

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
 10K  C4    S    C1    92.38  3.000
 10K  H1    C1   C2   128.23  3.000
 10K  H1    C1   S    120.31  3.000
 10K  C2    C1   S    111.46  3.000
 10K  HN1   N1   C13  117.05  3.000
 10K  HN1   N1   C12  117.66  3.000
 10K  C13   N1   C12  125.29  3.000
 10K  H2    C2   C3   123.87  3.000
 10K  H2    C2   C1   123.47  3.000
 10K  C3    C2   C1   112.65  3.000
 10K  HN2   N2   C13  127.47  3.000
 10K  HN2   N2   N3   119.84  3.000
 10K  C13   N2   N3   112.68  3.000
 10K  H3    C3   C4   123.30  3.000
 10K  H3    C3   C2   123.47  3.000
 10K  C4    C3   C2   113.22  3.000
 10K  C14   N3   N2   105.09  3.000
 10K  C5    C4   C3   128.39  3.000
 10K  C5    C4   S    121.32  3.000
 10K  C3    C4   S    110.29  3.000
 10K  C10   C5   C6   118.08  3.000
 10K  C6    C5   C4   121.68  3.000
 10K  C10   C5   C4   120.24  3.000
 10K  H6    C6   C7   118.83  3.000
 10K  H6    C6   C5   120.35  3.000
 10K  C7    C6   C5   120.82  3.000
 10K  H7    C7   C8   119.80  3.000
 10K  H7    C7   C6   119.18  3.000
 10K  C8    C7   C6   121.01  3.000
 10K  C11   C8   C9   120.74  3.000
 10K  C11   C8   C7   120.98  3.000
 10K  C9    C8   C7   118.27  3.000
 10K  H9    C9   C10  119.15  3.000
 10K  H9    C9   C8   119.82  3.000
 10K  C10   C9   C8   121.02  3.000
 10K  H10   C10  C9   119.25  3.000
 10K  H10   C10  C5   119.95  3.000
 10K  C9    C10  C5   120.79  3.000
 10K  H11A  C11  H11  106.08  3.000
 10K  H11A  C11  C12  107.66  3.000
 10K  H11   C11  C12  109.29  3.000
 10K  H11A  C11  C8   110.59  3.000
 10K  H11   C11  C8   110.70  3.000
 10K  C12   C11  C8   112.29  3.000
 10K  C11   C12  N1   113.35  3.000
 10K  C11   C12  O    123.57  3.000
 10K  N1    C12  O    123.07  3.000
 10K  C15   C13  N2   106.65  3.000
 10K  C15   C13  N1   133.36  3.000
 10K  N2    C13  N1   119.98  3.000
 10K  C16   C14  C15  128.05  3.000
 10K  C16   C14  N3   120.44  3.000
 10K  C15   C14  N3   111.51  3.000
 10K  H15   C15  C14  127.98  3.000
 10K  H15   C15  C13  127.95  3.000
 10K  C14   C15  C13  104.06  3.000
 10K  H16   C16  C18  116.25  3.000
 10K  H16   C16  C17  116.40  3.000
 10K  C18   C16  C17   59.47  3.000
 10K  H16   C16  C14  113.73  3.000
 10K  C17   C16  C14  120.39  3.000
 10K  C18   C16  C14  120.27  3.000
 10K  H17A  C17  H17  114.27  3.000
 10K  H17A  C17  C18  118.53  3.000
 10K  H17   C17  C18  118.17  3.000
 10K  H17A  C17  C16  117.56  3.000
 10K  H17   C17  C16  117.65  3.000
 10K  C18   C17  C16   60.31  3.000
 10K  H18A  C18  H18  114.27  3.000
 10K  H18A  C18  C17  118.30  3.000
 10K  H18   C18  C17  118.49  3.000
 10K  H18A  C18  C16  117.62  3.000
 10K  H18   C18  C16  117.54  3.000
 10K  C17   C18  C16   60.22  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
 10K  CONST_01  C3   C2   C1   S      0.00   0.0  0
 10K  CONST_02  C2   C3   C4   S      0.00   0.0  0
 10K  CONST_05  C3   C4   S    C1     0.00   0.0  0
 10K  CONST_06  C5   C4   S    C1   180.00   0.0  0
 10K  CONST_07  C4   C3   C2   C1     0.00   0.0  0
 10K  CONST_08  C4   S    C1   C2     0.00   0.0  0
 10K  CONST_09  C5   C4   C3   C2   180.00   0.0  0
 10K  CONST_10  C14  C15  C13  N2     0.00   0.0  0
 10K  CONST_11  C15  C14  N3   N2     0.00   0.0  0
 10K  CONST_14  C15  C13  N2   N3     0.00   0.0  0
 10K  CONST_15  C13  C15  C14  N3     0.00   0.0  0
 10K  CONST_16  C9   C10  C5   C4   180.00   0.0  0
 10K  CONST_17  C7   C6   C5   C4   180.00   0.0  0
 10K  CONST_18  C8   C9   C10  C5     0.00   0.0  0
 10K  CONST_19  C8   C7   C6   C5     0.00   0.0  0
 10K  CONST_20  C9   C10  C5   C6     0.00   0.0  0
 10K  CONST_21  C9   C8   C7   C6     0.00   0.0  0
 10K  CONST_22  C10  C5   C6   C7     0.00   0.0  0
 10K  CONST_23  C10  C9   C8   C7     0.00   0.0  0
 10K  CONST_24  C14  N3   N2   C13    0.00   0.0  0
 10K  CONST_25  C16  C14  N3   N2   180.00   0.0  0
 10K  CONST_26  C16  C14  C15  C13  180.00   0.0  0
 10K  CONST_27  N3   N2   C13  N1   180.00   0.0  0
 10K  CONST_28  C14  C15  C13  N1   180.00   0.0  0
 10K  CONST_29  C11  C8   C7   C6   180.00   0.0  0
 10K  CONST_30  C11  C8   C9   C10  180.00   0.0  0
 10K  CONST_31  H2   C2   C1   S    180.00   0.0  0
 10K  CONST_32  H3   C3   C4   S    180.00   0.0  0
 10K  CONST_33  H15  C15  C13  N2   180.00   0.0  0
 10K  CONST_34  H1   C1   C2   C3   180.00   0.0  0
 10K  CONST_35  H10  C10  C5   C4     0.00   0.0  0
 10K  CONST_36  H6   C6   C5   C4     0.00   0.0  0
 10K  CONST_37  H9   C9   C10  C5   180.00   0.0  0
 10K  CONST_38  H7   C7   C6   C5   180.00   0.0  0
 10K  CONST_39  HN2  N2   N3   C14  180.00   0.0  0
 10K  CONST_40  C12  N1   C13  N2   180.00   0.0  0
 10K  CONST_41  C15  C13  N1   C12    0.00   0.0  0
 10K  CONST_42  HN1  N1   C13  N2     0.00   0.0  0
 10K  CONST_43  C13  N1   C12  O      0.00   0.0  0
 10K  CONST_44  C13  N1   C12  C11  180.00   0.0  0
 10K  Var_01    C18  C16  C14  N3   140.64  30.0  2
 10K  Var_02    C17  C18  C16  C14  109.63  30.0  1
 10K  Var_03    C12  C11  C8   C7    89.85  30.0  2
 10K  Var_04    C8   C11  C12  O    -12.30  30.0  1

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
 10K  chir_01  C16  C14  C18  C17  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
 10K  plan-1  S    0.020
 10K  plan-1  C1   0.020
 10K  plan-1  C2   0.020
 10K  plan-1  C3   0.020
 10K  plan-1  C4   0.020
 10K  plan-1  C5   0.020
 10K  plan-1  H2   0.020
 10K  plan-1  H3   0.020
 10K  plan-1  H1   0.020
 10K  plan-2  N1   0.020
 10K  plan-2  N2   0.020
 10K  plan-2  N3   0.020
 10K  plan-2  C13  0.020
 10K  plan-2  C14  0.020
 10K  plan-2  C15  0.020
 10K  plan-2  C16  0.020
 10K  plan-2  H15  0.020
 10K  plan-2  HN2  0.020
 10K  plan-3  C4   0.020
 10K  plan-3  C5   0.020
 10K  plan-3  C6   0.020
 10K  plan-3  C7   0.020
 10K  plan-3  C8   0.020
 10K  plan-3  C9   0.020
 10K  plan-3  C10  0.020
 10K  plan-3  C11  0.020
 10K  plan-3  H6   0.020
 10K  plan-3  H7   0.020
 10K  plan-3  H9   0.020
 10K  plan-3  H10  0.020
 10K  plan-4  O    0.020
 10K  plan-4  N1   0.020
 10K  plan-4  C11  0.020
 10K  plan-4  C12  0.020
 10K  plan-4  C13  0.020
 10K  plan-4  HN1  0.020

