# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 00:27:40 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: N-(2,2-dimethylpropyl)-2-[(4S)-1-oxo-7-(thiophen-3-yl)-1,2,3,4-tetrahydropyrrolo[1,2-a]pyrazin-4-yl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)CNC(=O)C[C@H]1CNC(=O)c2cc(cn12)c3cscc3
#
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
 UGX  UGX  N-(2,2-dimethylpropyl)-2-[(4S)-1-oxo-7-(thiophen-3-yl)-1,2,3,4-tetrahydropyrrolo[1,2-a]pyrazin-4-yl]acetamide  ligand  47  24  .  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_UGX
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
 UGX  O13   O  O     0  -0.499   2.9902  -0.8266   1.7746
 UGX  C12   C  C     0   0.554   2.8020  -0.3130   0.6796
 UGX  N14   N  NH1   0  -0.634   3.7851   0.0828  -0.1416
 UGX  C21   C  CH2   0  -0.258   5.1973  -0.0611   0.1286
 UGX  C15   C  CT    0  -0.102   5.8773  -1.2163  -0.6229
 UGX  C24   C  CH3   0  -0.649   5.7057  -1.0368  -2.1317
 UGX  C23   C  CH3   0  -0.640   7.3646  -1.1699  -0.2709
 UGX  C22   C  CH3   0  -0.639   5.2928  -2.5600  -0.1911
 UGX  C11   C  CH2   0  -0.571   1.3997  -0.0818   0.1516
 UGX  C6    C  CH1   0  -0.128   0.4782   0.4770   1.2361
 UGX  N5    N  NR5   0  -0.478  -0.8811   0.5781   0.7358
 UGX  C1    C  CR15  0  -0.062  -1.8192  -0.3881   0.6857
 UGX  C7    C  CH2   0  -0.296   0.8704   1.8698   1.7068
 UGX  N8    N  NH1   0  -0.644   0.6480   2.8420   0.6554
 UGX  C9    C  C     0   0.508  -0.5000   2.8848  -0.0559
 UGX  O10   O  O     0  -0.484  -0.8165   3.8228  -0.7767
 UGX  C4    C  CR5   0   0.228  -1.3321   1.6893   0.0775
 UGX  C2    C  CR15  0  -0.455  -2.5999   1.4229  -0.3870
 UGX  C3    C  CR5   0   0.033  -2.9213   0.1018   0.0018
 UGX  C16   C  CR5   0   0.168  -4.1714  -0.6043  -0.2529
 UGX  C18   C  CR15  0  -0.601  -4.5376  -1.7912   0.3221
 UGX  S20   S  S2    0   0.225  -6.0705  -2.3271  -0.2190
 UGX  C19   C  CR15  0  -0.466  -6.2550  -0.9571  -1.2298
 UGX  C17   C  CR15  0  -0.233  -5.1793  -0.1307  -1.1507
 UGX  H14   H  HNH1  0   0.402   3.5237   0.5158  -1.0120
 UGX  H111  H  HCH2  0   0.266   1.4005   0.5757  -0.7202
 UGX  H112  H  HCH2  0   0.297   1.0087  -1.0476  -0.1811
 UGX  H211  H  HCH2  0   0.246   5.6858   0.8780  -0.1454
 UGX  H212  H  HCH2  0   0.248   5.3289  -0.1899   1.2034
 UGX  H241  H  HCH3  0   0.224   6.1103  -0.0787  -2.4669
 UGX  H242  H  HCH3  0   0.230   6.2295  -1.8252  -2.6758
 UGX  H243  H  HCH3  0   0.224   4.6562  -1.0805  -2.4312
 UGX  H231  H  HCH3  0   0.225   7.5232  -1.2942   0.8026
 UGX  H232  H  HCH3  0   0.229   7.9091  -1.9677  -0.7796
 UGX  H233  H  HCH3  0   0.224   7.8148  -0.2192  -0.5666
 UGX  H221  H  HCH3  0   0.225   4.2330  -2.6414  -0.4382
 UGX  H222  H  HCH3  0   0.225   5.8089  -3.3798  -0.6951
 UGX  H223  H  HCH3  0   0.223   5.3970  -2.7106   0.8850
 UGX  H6    H  HCH1  0   0.295   0.4745  -0.1920   2.0963
 UGX  H71C  H  HCH2  0   0.271   0.2968   2.1218   2.6043
 UGX  H72C  H  HCH2  0   0.279   1.9225   1.8926   1.9831
 UGX  H1    H  HCR5  0   0.290  -1.6471  -1.3549   1.1328
 UGX  H8    H  HNH1  0   0.406   1.2293   3.6664   0.6432
 UGX  H2    H  HCR5  0   0.255  -3.2261   2.1149  -0.9281
 UGX  H18   H  HCR5  0   0.286  -3.9869  -2.3750   1.0444
 UGX  H17   H  HCR5  0   0.260  -5.0997   0.7845  -1.7205
 UGX  H19   H  HCR5  0   0.296  -7.1420  -0.8332  -1.8314

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
 UGX  O13  C12   double    1.224  0.020  1.224
 UGX  C12  N14   single    1.341  0.020  1.341
 UGX  C12  C11   single    1.516  0.020  1.516
 UGX  N14  C21   single    1.445  0.020  1.445
 UGX  C21  C15   single    1.537  0.020  1.537
 UGX  C15  C24   single    1.529  0.020  1.529
 UGX  C15  C23   single    1.529  0.020  1.529
 UGX  C15  C22   single    1.528  0.020  1.528
 UGX  C11  C6    single    1.529  0.020  1.529
 UGX  C6   N5    single    1.452  0.020  1.452
 UGX  C6   C7    single    1.522  0.020  1.522
 UGX  N5   C1    aromatic  1.348  0.020  1.348
 UGX  N5   C4    aromatic  1.368  0.020  1.368
 UGX  C1   C3    aromatic  1.386  0.020  1.386
 UGX  C7   N8    single    1.449  0.020  1.449
 UGX  N8   C9    single    1.351  0.020  1.351
 UGX  C9   O10   double    1.225  0.020  1.225
 UGX  C9   C4    single    1.463  0.020  1.463
 UGX  C4   C2    aromatic  1.376  0.020  1.376
 UGX  C2   C3    aromatic  1.414  0.020  1.414
 UGX  C3   C16   single    1.458  0.020  1.458
 UGX  C16  C18   aromatic  1.369  0.020  1.369
 UGX  C16  C17   aromatic  1.430  0.020  1.430
 UGX  C18  S20   aromatic  1.712  0.020  1.712
 UGX  S20  C19   aromatic  1.712  0.020  1.712
 UGX  C19  C17   aromatic  1.359  0.020  1.359
 UGX  N14  H14   single    0.860  0.020  1.020
 UGX  C11  H111  single    0.970  0.020  1.090
 UGX  C11  H112  single    0.970  0.020  1.090
 UGX  C21  H211  single    0.970  0.020  1.090
 UGX  C21  H212  single    0.970  0.020  1.090
 UGX  C24  H241  single    0.970  0.020  1.090
 UGX  C24  H242  single    0.970  0.020  1.090
 UGX  C24  H243  single    0.970  0.020  1.090
 UGX  C23  H231  single    0.970  0.020  1.090
 UGX  C23  H232  single    0.970  0.020  1.090
 UGX  C23  H233  single    0.970  0.020  1.090
 UGX  C22  H221  single    0.970  0.020  1.090
 UGX  C22  H222  single    0.970  0.020  1.090
 UGX  C22  H223  single    0.970  0.020  1.090
 UGX  C6   H6    single    0.970  0.020  1.090
 UGX  C7   H71C  single    0.970  0.020  1.090
 UGX  C7   H72C  single    0.970  0.020  1.090
 UGX  C1   H1    single    0.930  0.020  1.080
 UGX  N8   H8    single    0.860  0.020  1.020
 UGX  C2   H2    single    0.930  0.020  1.080
 UGX  C18  H18   single    0.930  0.020  1.080
 UGX  C17  H17   single    0.930  0.020  1.080
 UGX  C19  H19   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
 UGX  C11   C12  N14   114.83  3.000
 UGX  C11   C12  O13   121.19  3.000
 UGX  N14   C12  O13   123.99  3.000
 UGX  H14   N14  C21   117.27  3.000
 UGX  H14   N14  C12   117.79  3.000
 UGX  C21   N14  C12   124.94  3.000
 UGX  H212  C21  H211  107.13  3.000
 UGX  H212  C21  C15   109.86  3.000
 UGX  H211  C21  C15   108.99  3.000
 UGX  H212  C21  N14   108.30  3.000
 UGX  H211  C21  N14   107.72  3.000
 UGX  C15   C21  N14   114.57  3.000
 UGX  C22   C15  C23   109.50  3.000
 UGX  C22   C15  C24   109.83  3.000
 UGX  C23   C15  C24   109.43  3.000
 UGX  C22   C15  C21   110.71  3.000
 UGX  C23   C15  C21   107.16  3.000
 UGX  C24   C15  C21   110.16  3.000
 UGX  H243  C24  H242  107.18  3.000
 UGX  H243  C24  H241  107.86  3.000
 UGX  H242  C24  H241  107.62  3.000
 UGX  H243  C24  C15   111.94  3.000
 UGX  H242  C24  C15   110.68  3.000
 UGX  H241  C24  C15   111.36  3.000
 UGX  H233  C23  H232  107.71  3.000
 UGX  H233  C23  H231  107.76  3.000
 UGX  H232  C23  H231  107.60  3.000
 UGX  H233  C23  C15   111.40  3.000
 UGX  H232  C23  C15   110.84  3.000
 UGX  H231  C23  C15   111.35  3.000
 UGX  H223  C22  H222  107.84  3.000
 UGX  H223  C22  H221  107.80  3.000
 UGX  H222  C22  H221  107.36  3.000
 UGX  H223  C22  C15   111.32  3.000
 UGX  H222  C22  C15   110.43  3.000
 UGX  H221  C22  C15   111.91  3.000
 UGX  H112  C11  H111  106.81  3.000
 UGX  H112  C11  C6    108.84  3.000
 UGX  H111  C11  C6    110.28  3.000
 UGX  H112  C11  C12   107.57  3.000
 UGX  H111  C11  C12   111.67  3.000
 UGX  C6    C11  C12   111.48  3.000
 UGX  H6    C6   C7    108.58  3.000
 UGX  H6    C6   N5    108.15  3.000
 UGX  C7    C6   N5    106.51  3.000
 UGX  H6    C6   C11   109.73  3.000
 UGX  C7    C6   C11   113.49  3.000
 UGX  N5    C6   C11   110.20  3.000
 UGX  C4    N5   C1    109.57  3.000
 UGX  C4    N5   C6    122.07  3.000
 UGX  C1    N5   C6    127.92  3.000
 UGX  H1    C1   C3    130.37  3.000
 UGX  H1    C1   N5    121.06  3.000
 UGX  C3    C1   N5    108.56  3.000
 UGX  H72C  C7   H71C  107.08  3.000
 UGX  H72C  C7   N8    108.58  3.000
 UGX  H71C  C7   N8    111.10  3.000
 UGX  H72C  C7   C6    110.30  3.000
 UGX  H71C  C7   C6    109.22  3.000
 UGX  N8    C7   C6    110.49  3.000
 UGX  H8    N8   C9    117.22  3.000
 UGX  H8    N8   C7    117.94  3.000
 UGX  C9    N8   C7    122.25  3.000
 UGX  C4    C9   O10   122.18  3.000
 UGX  C4    C9   N8    114.17  3.000
 UGX  O10   C9   N8    123.62  3.000
 UGX  C2    C4   C9    130.66  3.000
 UGX  C2    C4   N5    107.99  3.000
 UGX  C9    C4   N5    121.34  3.000
 UGX  H2    C2   C3    127.25  3.000
 UGX  H2    C2   C4    125.44  3.000
 UGX  C3    C2   C4    107.30  3.000
 UGX  C16   C3   C2    126.81  3.000
 UGX  C16   C3   C1    126.62  3.000
 UGX  C2    C3   C1    106.56  3.000
 UGX  C17   C16  C18   111.24  3.000
 UGX  C17   C16  C3    123.60  3.000
 UGX  C18   C16  C3    125.16  3.000
 UGX  H18   C18  S20   119.93  3.000
 UGX  H18   C18  C16   127.84  3.000
 UGX  S20   C18  C16   112.23  3.000
 UGX  C19   S20  C18    91.87  3.000
 UGX  H19   C19  C17   127.84  3.000
 UGX  H19   C19  S20   120.64  3.000
 UGX  C17   C19  S20   111.52  3.000
 UGX  H17   C17  C19   122.85  3.000
 UGX  H17   C17  C16   124.00  3.000
 UGX  C19   C17  C16   113.14  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
 UGX  CONST_01  C2    C3   C1   N5     0.00   0.0  0
 UGX  CONST_02  C16   C3   C1   N5   180.00   0.0  0
 UGX  CONST_03  C3    C2   C4   N5     0.00   0.0  0
 UGX  CONST_04  C2    C4   N5   C1     0.00   0.0  0
 UGX  CONST_05  C4    C2   C3   C1     0.00   0.0  0
 UGX  CONST_06  C18   C16  C3   C1     0.00   0.0  0
 UGX  CONST_07  C17   C16  C3   C1   180.00   0.0  0
 UGX  CONST_08  C3    C1   N5   C4     0.00   0.0  0
 UGX  CONST_09  C16   C3   C2   C4   180.00   0.0  0
 UGX  CONST_10  C18   C16  C3   C2   180.00   0.0  0
 UGX  CONST_11  C17   C16  C3   C2     0.00   0.0  0
 UGX  CONST_12  S20   C18  C16  C3   180.00   0.0  0
 UGX  CONST_13  C19   C17  C16  C3   180.00   0.0  0
 UGX  CONST_14  C19   S20  C18  C16    0.00   0.0  0
 UGX  CONST_15  S20   C19  C17  C16    0.00   0.0  0
 UGX  CONST_16  C19   C17  C16  C18    0.00   0.0  0
 UGX  CONST_17  C17   C19  S20  C18    0.00   0.0  0
 UGX  CONST_18  C17   C16  C18  S20    0.00   0.0  0
 UGX  CONST_19  C4    C9   N8   C7     0.00   0.0  0
 UGX  CONST_20  O10   C9   N8   C7   180.00   0.0  0
 UGX  CONST_21  H1    C1   N5   C6     0.00   0.0  0
 UGX  CONST_22  H2    C2   C4   N5   180.00   0.0  0
 UGX  CONST_23  H18   C18  C16  C3     0.00   0.0  0
 UGX  CONST_24  H17   C17  C16  C3     0.00   0.0  0
 UGX  CONST_25  H19   C19  C17  C16  180.00   0.0  0
 UGX  CONST_26  H8    N8   C9   C4   180.00   0.0  0
 UGX  CONST_27  C21   N14  C12  O13    0.00   0.0  0
 UGX  CONST_28  C11   C12  N14  C21  180.00   0.0  0
 UGX  CONST_29  H14   N14  C12  O13  180.00   0.0  0
 UGX  Var_01    C9    N8   C7   C6    47.06  30.0  1
 UGX  Var_02    N8    C9   C4   N5    -7.70  30.0  1
 UGX  Var_03    C6    C11  C12  O13   43.43  30.0  3
 UGX  Var_04    C15   C21  N14  C12  102.70  30.0  3
 UGX  Var_05    C24   C15  C21  N14   58.26  30.0  3
 UGX  Var_06    H241  C24  C15  C21   57.42  30.0  3
 UGX  Var_07    H231  C23  C15  C21   60.50  30.0  3
 UGX  Var_08    H221  C22  C15  C21   62.93  30.0  3

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
 UGX  chir_01  C6  C11  N5  C7  positiv

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
 UGX  plan-1  C3   0.020
 UGX  plan-1  C16  0.020
 UGX  plan-1  C18  0.020
 UGX  plan-1  S20  0.020
 UGX  plan-1  C19  0.020
 UGX  plan-1  C17  0.020
 UGX  plan-1  H18  0.020
 UGX  plan-1  H17  0.020
 UGX  plan-1  H19  0.020
 UGX  plan-2  C6   0.020
 UGX  plan-2  N5   0.020
 UGX  plan-2  C1   0.020
 UGX  plan-2  C9   0.020
 UGX  plan-2  C4   0.020
 UGX  plan-2  C2   0.020
 UGX  plan-2  C3   0.020
 UGX  plan-2  C16  0.020
 UGX  plan-2  H1   0.020
 UGX  plan-2  H2   0.020
 UGX  plan-3  O13  0.020
 UGX  plan-3  C12  0.020
 UGX  plan-3  N14  0.020
 UGX  plan-3  C21  0.020
 UGX  plan-3  C11  0.020
 UGX  plan-3  H14  0.020
 UGX  plan-4  C7   0.020
 UGX  plan-4  N8   0.020
 UGX  plan-4  C9   0.020
 UGX  plan-4  O10  0.020
 UGX  plan-4  C4   0.020
 UGX  plan-4  H8   0.020

