# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 15:46:51 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: ethyl 4-{[(8R)-3,8-dimethyl-4-oxo-4,6,7,8,9,10-hexahydrothieno[2',3':4,5]pyrimido[1,2-a]azepin-2-yl]carbamoyl}piperazine-1-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)N1CCN(CC1)C(=O)Nc2sc3N=C4CC[C@@H](C)CCN4C(=O)c3c2C
#
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
 UX4  UX4  'ethyl 4-{[(8R)-3,8-dimethyl-4-oxo-4,6,7,8,9,10-hexahydrothieno[2',3':4,5]pyrimido[1,2-a]azepin-2-yl]carbamoyl}piperazine-1-carboxylate'  ligand  60  31  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UX4
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
 UX4  O29  O  O     0  -0.526   7.4172  -1.8701  -0.3425
 UX4  C27  C  C     0   0.765   7.0526  -0.7205  -0.4990
 UX4  O28  O  O2    0  -0.480   7.8453   0.3322  -0.3023
 UX4  C30  C  CH2   0  -0.166   9.1956   0.0739   0.1003
 UX4  C31  C  CH3   0  -0.688   9.8750   1.4065   0.3021
 UX4  N23  N  NT    0  -0.494   5.8150  -0.3605  -0.9076
 UX4  C22  C  CH2   0  -0.307   4.7725  -1.3493  -1.0687
 UX4  C26  C  CH2   0  -0.317   3.6742  -1.1577  -0.0299
 UX4  C24  C  CH2   0  -0.320   5.3158   0.9987  -0.9901
 UX4  C25  C  CH2   0  -0.296   4.2345   1.2203   0.0541
 UX4  N20  N  NT    0  -0.519   3.1920   0.2124  -0.0544
 UX4  C19  C  C     0   0.770   1.8921   0.5921   0.0124
 UX4  O21  O  O     0  -0.521   1.5262   1.7555  -0.1129
 UX4  N18  N  NH1   0  -0.775   0.9689  -0.3991   0.2267
 UX4  C7   C  CR5   0   0.067  -0.3993  -0.1904   0.2348
 UX4  C6   C  CR5   0   0.059  -1.3392  -1.1777   0.3172
 UX4  C15  C  CH3   0  -0.715  -1.0373  -2.6435   0.3494
 UX4  C2   C  CR56  0  -0.026  -2.6549  -0.6122   0.3696
 UX4  C1   C  CR6   0   0.561  -3.9183  -1.2866   0.4780
 UX4  O16  O  O     0  -0.475  -4.0703  -2.4967   0.5465
 UX4  S8   S  S2    0   0.238  -1.0747   1.4192   0.1864
 UX4  C9   C  CR56  0  -0.067  -2.6651   0.7596   0.2982
 UX4  N3   N  N     0  -0.457  -3.7573   1.5461   0.2844
 UX4  C4   C  CR6   0   0.491  -4.9002   0.9408   0.3870
 UX4  N5   N  NR6   0  -0.543  -5.0192  -0.4145   0.5138
 UX4  C11  C  CH2   0  -0.556  -6.1390   1.7765   0.3094
 UX4  C12  C  CH2   0  -0.423  -6.9748   1.5193  -0.9510
 UX4  C13  C  CH1   0  -0.239  -7.9121   0.3185  -0.8668
 UX4  C17  C  CH3   0  -0.655  -8.7576   0.2135  -2.1307
 UX4  C14  C  CH2   0  -0.420  -7.1877  -0.9975  -0.5974
 UX4  C10  C  CH2   0  -0.344  -6.3472  -1.0154   0.6737
 UX4  H1   H  HCH2  0   0.230   9.2039  -0.5078   1.0240
 UX4  H2   H  HCH2  0   0.230   9.7078  -0.5090  -0.6681
 UX4  H3   H  HCH3  0   0.238  10.9092   1.2385   0.6012
 UX4  H4   H  HCH3  0   0.235   9.8843   1.9958  -0.6149
 UX4  H5   H  HCH3  0   0.235   9.3915   1.9895   1.0862
 UX4  H6   H  HCH2  0   0.254   4.3419  -1.2508  -2.0695
 UX4  H7   H  HCH2  0   0.279   5.1831  -2.3512  -0.9795
 UX4  H8   H  HCH2  0   0.259   2.8794  -1.8577  -0.2782
 UX4  H9   H  HCH2  0   0.255   4.0516  -1.4125   0.9660
 UX4  H10  H  HCH2  0   0.281   6.1134   1.7201  -0.8444
 UX4  H11  H  HCH2  0   0.252   4.9021   1.1603  -1.9899
 UX4  H12  H  HCH2  0   0.246   4.6821   1.1750   1.0535
 UX4  H13  H  HCH2  0   0.276   3.8019   2.2082  -0.0739
 UX4  H14  H  HNH1  0   0.427   1.2687  -1.2937   0.5786
 UX4  H15  H  HCH3  0   0.251  -1.2559  -3.0786   1.3252
 UX4  H16  H  HCH3  0   0.255  -1.6360  -3.1806  -0.3839
 UX4  H17  H  HCH3  0   0.225   0.0072  -2.8520   0.1216
 UX4  H20  H  HCH2  0   0.265  -6.7601   1.6468   1.2006
 UX4  H21  H  HCH2  0   0.281  -5.7989   2.8104   0.3149
 UX4  H22  H  HCH2  0   0.248  -7.5770   2.4130  -1.1311
 UX4  H23  H  HCH2  0   0.231  -6.3122   1.4186  -1.8170
 UX4  H24  H  HCH1  0   0.222  -8.5892   0.4924  -0.0205
 UX4  H25  H  HCH3  0   0.217  -8.1294   0.0741  -3.0136
 UX4  H26  H  HCH3  0   0.229  -9.4457  -0.6313  -2.0761
 UX4  H27  H  HCH3  0   0.229  -9.3499   1.1169  -2.2855
 UX4  H28  H  HCH2  0   0.245  -7.9360  -1.7883  -0.4999
 UX4  H29  H  HCH2  0   0.233  -6.5614  -1.2741  -1.4519
 UX4  H30  H  HCH2  0   0.286  -6.1905  -2.0397   0.9942
 UX4  H31  H  HCH2  0   0.267  -6.8625  -0.5089   1.4911

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
 UX4  C14  C10  single    1.524  0.020  1.524
 UX4  C14  C13  single    1.526  0.020  1.526
 UX4  O16  C1   double    1.222  0.020  1.222
 UX4  C10  N5   single    1.466  0.020  1.466
 UX4  C13  C12  single    1.526  0.020  1.526
 UX4  C13  C17  single    1.524  0.020  1.524
 UX4  C1   N5   single    1.405  0.020  1.405
 UX4  C1   C2   single    1.436  0.020  1.436
 UX4  N5   C4   single    1.366  0.020  1.366
 UX4  C12  C11  single    1.534  0.020  1.534
 UX4  C15  C6   single    1.497  0.020  1.497
 UX4  C2   C6   aromatic  1.433  0.020  1.433
 UX4  C2   C9   aromatic  1.374  0.020  1.374
 UX4  C6   C7   aromatic  1.366  0.020  1.366
 UX4  C11  C4   single    1.496  0.020  1.496
 UX4  C4   N3   double    1.297  0.020  1.297
 UX4  C9   N3   single    1.346  0.020  1.346
 UX4  C9   S8   aromatic  1.725  0.020  1.725
 UX4  C7   N18  single    1.384  0.020  1.384
 UX4  C7   S8   aromatic  1.746  0.020  1.746
 UX4  N18  C19  single    1.371  0.020  1.371
 UX4  C25  C24  single    1.519  0.020  1.519
 UX4  C25  N20  single    1.454  0.020  1.454
 UX4  C19  N20  single    1.356  0.020  1.356
 UX4  C19  O21  double    1.226  0.020  1.226
 UX4  C24  N23  single    1.450  0.020  1.450
 UX4  N20  C26  single    1.453  0.020  1.453
 UX4  O28  C30  single    1.433  0.020  1.433
 UX4  O28  C27  single    1.332  0.020  1.332
 UX4  N23  C22  single    1.446  0.020  1.446
 UX4  N23  C27  single    1.352  0.020  1.352
 UX4  C26  C22  single    1.524  0.020  1.524
 UX4  C30  C31  single    1.509  0.020  1.509
 UX4  C27  O29  double    1.216  0.020  1.216
 UX4  C30  H1   single    0.970  0.020  1.090
 UX4  C30  H2   single    0.970  0.020  1.090
 UX4  C31  H3   single    0.970  0.020  1.090
 UX4  C31  H4   single    0.970  0.020  1.090
 UX4  C31  H5   single    0.970  0.020  1.090
 UX4  C22  H6   single    0.970  0.020  1.090
 UX4  C22  H7   single    0.970  0.020  1.090
 UX4  C26  H8   single    0.970  0.020  1.090
 UX4  C26  H9   single    0.970  0.020  1.090
 UX4  C24  H10  single    0.970  0.020  1.090
 UX4  C24  H11  single    0.970  0.020  1.090
 UX4  C25  H12  single    0.970  0.020  1.090
 UX4  C25  H13  single    0.970  0.020  1.090
 UX4  N18  H14  single    0.860  0.020  1.020
 UX4  C15  H15  single    0.970  0.020  1.090
 UX4  C15  H16  single    0.970  0.020  1.090
 UX4  C15  H17  single    0.970  0.020  1.090
 UX4  C11  H20  single    0.970  0.020  1.090
 UX4  C11  H21  single    0.970  0.020  1.090
 UX4  C12  H22  single    0.970  0.020  1.090
 UX4  C12  H23  single    0.970  0.020  1.090
 UX4  C13  H24  single    0.970  0.020  1.090
 UX4  C17  H25  single    0.970  0.020  1.090
 UX4  C17  H26  single    0.970  0.020  1.090
 UX4  C17  H27  single    0.970  0.020  1.090
 UX4  C14  H28  single    0.970  0.020  1.090
 UX4  C14  H29  single    0.970  0.020  1.090
 UX4  C10  H30  single    0.970  0.020  1.090
 UX4  C10  H31  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
 UX4  N23  C27  O28  112.26  3.000
 UX4  N23  C27  O29  124.40  3.000
 UX4  O28  C27  O29  123.34  3.000
 UX4  C30  O28  C27  117.37  3.000
 UX4  H2   C30  H1   107.91  3.000
 UX4  H2   C30  C31  110.74  3.000
 UX4  H1   C30  C31  110.73  3.000
 UX4  H2   C30  O28  109.91  3.000
 UX4  H1   C30  O28  109.95  3.000
 UX4  C31  C30  O28  107.61  3.000
 UX4  H5   C31  H4   108.65  3.000
 UX4  H5   C31  H3   107.81  3.000
 UX4  H4   C31  H3   107.83  3.000
 UX4  H5   C31  C30  111.63  3.000
 UX4  H4   C31  C30  111.64  3.000
 UX4  H3   C31  C30  109.13  3.000
 UX4  C24  N23  C22  112.73  3.000
 UX4  C22  N23  C27  120.77  3.000
 UX4  C24  N23  C27  125.58  3.000
 UX4  H7   C22  H6   107.88  3.000
 UX4  H7   C22  C26  109.41  3.000
 UX4  H6   C22  C26  109.18  3.000
 UX4  H7   C22  N23  110.43  3.000
 UX4  H6   C22  N23  108.91  3.000
 UX4  C26  C22  N23  110.96  3.000
 UX4  H9   C26  H8   108.04  3.000
 UX4  H9   C26  N20  110.43  3.000
 UX4  H8   C26  N20  111.14  3.000
 UX4  H9   C26  C22  110.01  3.000
 UX4  H8   C26  C22  106.87  3.000
 UX4  N20  C26  C22  110.26  3.000
 UX4  H11  C24  H10  107.61  3.000
 UX4  H11  C24  C25  109.72  3.000
 UX4  H10  C24  C25  109.50  3.000
 UX4  H11  C24  N23  108.70  3.000
 UX4  H10  C24  N23  111.24  3.000
 UX4  C25  C24  N23  110.03  3.000
 UX4  H13  C25  H12  107.92  3.000
 UX4  H13  C25  N20  109.64  3.000
 UX4  H12  C25  N20  109.40  3.000
 UX4  H13  C25  C24  109.58  3.000
 UX4  H12  C25  C24  109.27  3.000
 UX4  N20  C25  C24  110.97  3.000
 UX4  C19  N20  C25  119.31  3.000
 UX4  C19  N20  C26  125.55  3.000
 UX4  C25  N20  C26  114.49  3.000
 UX4  N18  C19  O21  120.06  3.000
 UX4  O21  C19  N20  123.15  3.000
 UX4  N18  C19  N20  116.79  3.000
 UX4  H14  N18  C7   115.23  3.000
 UX4  H14  N18  C19  119.76  3.000
 UX4  C7   N18  C19  123.87  3.000
 UX4  S8   C7   C6   113.70  3.000
 UX4  S8   C7   N18  121.41  3.000
 UX4  C6   C7   N18  124.86  3.000
 UX4  C2   C6   C15  124.80  3.000
 UX4  C2   C6   C7   110.41  3.000
 UX4  C15  C6   C7   124.78  3.000
 UX4  H17  C15  H16  106.99  3.000
 UX4  H17  C15  H15  107.64  3.000
 UX4  H16  C15  H15  107.20  3.000
 UX4  H17  C15  C6   112.11  3.000
 UX4  H16  C15  C6   110.96  3.000
 UX4  H15  C15  C6   111.68  3.000
 UX4  C9   C2   C1   117.80  3.000
 UX4  C9   C2   C6   113.51  3.000
 UX4  C1   C2   C6   128.69  3.000
 UX4  N5   C1   O16  121.06  3.000
 UX4  N5   C1   C2   113.57  3.000
 UX4  O16  C1   C2   125.37  3.000
 UX4  C9   S8   C7    90.13  3.000
 UX4  N3   C9   S8   121.60  3.000
 UX4  S8   C9   C2   112.23  3.000
 UX4  N3   C9   C2   126.16  3.000
 UX4  C4   N3   C9   116.20  3.000
 UX4  C11  C4   N5   119.12  3.000
 UX4  C11  C4   N3   117.69  3.000
 UX4  N5   C4   N3   123.15  3.000
 UX4  C10  N5   C4   119.70  3.000
 UX4  C4   N5   C1   123.03  3.000
 UX4  C10  N5   C1   117.26  3.000
 UX4  H21  C11  H20  106.62  3.000
 UX4  H21  C11  C12  109.49  3.000
 UX4  H20  C11  C12  109.88  3.000
 UX4  H21  C11  C4   105.76  3.000
 UX4  H20  C11  C4   111.19  3.000
 UX4  C12  C11  C4   113.58  3.000
 UX4  H23  C12  H22  106.17  3.000
 UX4  H23  C12  C13  110.06  3.000
 UX4  H22  C12  C13  108.32  3.000
 UX4  H23  C12  C11  109.60  3.000
 UX4  H22  C12  C11  107.37  3.000
 UX4  C13  C12  C11  114.92  3.000
 UX4  H24  C13  C14  107.05  3.000
 UX4  H24  C13  C17  107.94  3.000
 UX4  C14  C13  C17  110.50  3.000
 UX4  H24  C13  C12  107.27  3.000
 UX4  C17  C13  C12  110.44  3.000
 UX4  C14  C13  C12  113.38  3.000
 UX4  H27  C17  H26  107.80  3.000
 UX4  H27  C17  H25  107.65  3.000
 UX4  H26  C17  H25  107.72  3.000
 UX4  H27  C17  C13  111.20  3.000
 UX4  H26  C17  C13  111.21  3.000
 UX4  H25  C17  C13  111.10  3.000
 UX4  H29  C14  H28  106.16  3.000
 UX4  H29  C14  C10  109.42  3.000
 UX4  H28  C14  C10  107.14  3.000
 UX4  H29  C14  C13  110.58  3.000
 UX4  H28  C14  C13  108.34  3.000
 UX4  C10  C14  C13  114.78  3.000
 UX4  H31  C10  H30  106.57  3.000
 UX4  H31  C10  C14  111.04  3.000
 UX4  H30  C10  C14  109.71  3.000
 UX4  H31  C10  N5   108.61  3.000
 UX4  H30  C10  N5   106.77  3.000
 UX4  C14  C10  N5   113.81  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
 UX4  CONST_01  C9   C2   C6   C7      0.00   0.0  0
 UX4  CONST_02  C2   C9   S8   C7      0.00   0.0  0
 UX4  CONST_03  S8   C9   C2   C6      0.00   0.0  0
 UX4  CONST_04  C9   S8   C7   C6      0.00   0.0  0
 UX4  CONST_05  S8   C7   C6   C2      0.00   0.0  0
 UX4  CONST_06  C2   C6   C7   N18   180.00   0.0  0
 UX4  CONST_07  C9   S8   C7   N18   180.00   0.0  0
 UX4  CONST_08  C1   C2   C6   C15     0.00   0.0  0
 UX4  CONST_09  C9   C2   C6   C15   180.00   0.0  0
 UX4  CONST_10  S8   C7   C6   C15   180.00   0.0  0
 UX4  CONST_11  O21  C19  N20  C26   180.00   0.0  0
 UX4  CONST_13  C7   N18  C19  N20   180.00   0.0  0
 UX4  CONST_14  C6   C7   N18  C19   180.00   0.0  0
 UX4  CONST_15  S8   C7   N18  C19     0.00   0.0  0
 UX4  CONST_16  N18  C19  N20  C26     0.00   0.0  0
 UX4  CONST_19  C7   N18  C19  O21     0.00   0.0  0
 UX4  Var_01    N20  C25  C24  N23   -53.56  30.0  1
 UX4  Var_02    N20  C26  C22  N23    52.95  30.0  1
 UX4  Var_03    C25  C24  N23  C22    57.22  30.0  1
 UX4  Var_04    C25  N20  C26  C22   -52.28  30.0  1
 UX4  Var_05    C24  C25  N20  C26    53.08  30.0  1
 UX4  Var_06    C24  N23  C22  C26   -57.29  30.0  1
 UX4  Var_07    H15  C15  C6   C7    110.69  30.0  2
 UX4  Var_08    N23  C27  O28  C30  -178.44  30.0  3
 UX4  Var_09    C31  C30  O28  C27  -178.19  30.0  3
 UX4  Var_10    H3   C31  C30  O28  -179.51  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
 UX4  chir_01  C13  C14  C12  C17  negativ

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
 UX4  plan-1  O29  0.020
 UX4  plan-1  C27  0.020
 UX4  plan-1  O28  0.020
 UX4  plan-1  N23  0.020
 UX4  plan-2  C26  0.020
 UX4  plan-2  C25  0.020
 UX4  plan-2  N20  0.020
 UX4  plan-2  C19  0.020
 UX4  plan-2  O21  0.020
 UX4  plan-2  N18  0.020
 UX4  plan-2  C7   0.020
 UX4  plan-2  H14  0.020
 UX4  plan-3  N18  0.020
 UX4  plan-3  C7   0.020
 UX4  plan-3  C6   0.020
 UX4  plan-3  C15  0.020
 UX4  plan-3  C2   0.020
 UX4  plan-3  C1   0.020
 UX4  plan-3  O16  0.020
 UX4  plan-3  S8   0.020
 UX4  plan-3  C9   0.020
 UX4  plan-3  N3   0.020
 UX4  plan-3  C4   0.020
 UX4  plan-3  N5   0.020
 UX4  plan-3  C11  0.020
 UX4  plan-3  C10  0.020

