# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 19:53:39 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 2-(4-hydroxy-3,5-dimethylphenyl)-7-methyl-5,6,7,8-tetrahydropyrido[4',3':4,5]thieno[2,3-d]pyrimidin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCc2c(C1)sc3N=C(NC(=O)c23)c4cc(C)c(O)c(C)c4
#
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
 4V1  4V1  2-(4-hydroxy-3,5-dimethylphenyl)-7-methyl-5,6,7,8-tetrahydropyrido[4',3':4,5]thieno[2,3-d]pyrimidin-4(3H)-one  ligand  43  24  .  2021-08-04  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_4V1
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
 4V1  N1   N  N     0  -0.462   0.3541  -0.8149   0.1300
 4V1  N3   N  NR16  0  -0.727   0.5809   1.4555  -0.3102
 4V1  C4   C  CR6   0   0.522  -0.7737   1.7707  -0.3448
 4V1  C5   C  CR56  0  -0.080  -1.6036   0.6195  -0.1210
 4V1  C6   C  CR56  0  -0.043  -0.9711  -0.5922   0.0897
 4V1  CAB  C  CR6   0   0.031   4.4974  -1.3788  -0.2055
 4V1  CAC  C  CR16  0  -0.335   3.1289  -1.1825  -0.2183
 4V1  CAW  C  CR6   0   0.292   5.3267  -0.2684   0.0017
 4V1  OAX  O  OH1   0  -0.607   6.6496  -0.5017   0.0053
 4V1  CAU  C  CR6   0   0.017   4.7963   1.0116   0.1979
 4V1  CAV  C  CH3   0  -0.774   5.7020   2.1854   0.4343
 4V1  CAT  C  CR16  0  -0.365   3.4185   1.1651   0.1726
 4V1  CAD  C  CR6   0   0.023   2.5672   0.0827  -0.0395
 4V1  C2   C  CR6   0   0.515   1.1082   0.2253  -0.0689
 4V1  SAH  S  S2    0   0.230  -2.1158  -1.8611   0.3290
 4V1  CAI  C  CR5   0  -0.299  -3.4360  -0.7532   0.1412
 4V1  CAJ  C  CH2   0  -0.297  -4.8630  -1.1816   0.2368
 4V1  NAK  N  NT    0  -0.418  -5.7059  -0.0210   0.4459
 4V1  CAL  C  CH3   0  -0.522  -7.1010  -0.4006   0.4336
 4V1  CAM  C  CH2   0  -0.297  -5.4151   1.0206  -0.5243
 4V1  CAN  C  CH2   0  -0.498  -4.0304   1.6130  -0.2934
 4V1  CAO  C  CR5   0   0.218  -3.0297   0.5190  -0.0969
 4V1  O4   O  O     0  -0.462  -1.1388   2.9150  -0.5568
 4V1  H1   H  HNR6  0   0.433   1.2079   2.2239  -0.5113
 4V1  H2   H  HCH3  0   0.246   5.6948  -3.0501   0.4445
 4V1  H3   H  HCH3  0   0.246   4.3083  -3.4831  -0.5510
 4V1  H4   H  HCH3  0   0.246   5.7403  -2.7701  -1.2873
 4V1  H5   H  HCR6  0   0.256   2.4786  -2.0328  -0.3782
 4V1  H6   H  HOH1  0   0.486   7.1521   0.3042   0.1688
 4V1  H7   H  HCH3  0   0.258   6.3722   2.3625  -0.4106
 4V1  H8   H  HCH3  0   0.270   5.1242   3.0963   0.5778
 4V1  H9   H  HCH3  0   0.257   6.3215   2.0556   1.3252
 4V1  H10  H  HCR6  0   0.253   3.0265   2.1589   0.3549
 4V1  H11  H  HCH2  0   0.222  -5.1427  -1.7343  -0.6779
 4V1  H12  H  HCH2  0   0.260  -5.0005  -1.8758   1.0707
 4V1  H14  H  HCH3  0   0.236  -7.2870  -1.1607   1.1943
 4V1  H15  H  HCH3  0   0.239  -7.7241   0.4636   0.6665
 4V1  H16  H  HCH3  0   0.197  -7.4316  -0.8071  -0.5343
 4V1  H17  H  HCH2  0   0.202  -5.4877   0.6399  -1.5576
 4V1  H18  H  HCH2  0   0.245  -6.1649   1.8071  -0.4253
 4V1  H19  H  HCH2  0   0.249  -3.7567   2.2396  -1.1430
 4V1  H20  H  HCH2  0   0.247  -4.0406   2.2666   0.5831
 4V1  CAA  C  CH3   0  -0.711   5.0914  -2.7401  -0.4104

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
 4V1  SAH  CAI  aromatic  1.734  0.020  1.734
 4V1  SAH  C6   aromatic  1.726  0.020  1.726
 4V1  CAJ  CAI  single    1.493  0.020  1.493
 4V1  CAJ  NAK  single    1.450  0.020  1.450
 4V1  N1   C6   single    1.344  0.020  1.344
 4V1  N1   C2   double    1.300  0.020  1.300
 4V1  CAI  CAO  aromatic  1.357  0.020  1.357
 4V1  C6   C5   aromatic  1.383  0.020  1.383
 4V1  CAL  NAK  single    1.446  0.020  1.446
 4V1  NAK  CAM  single    1.453  0.020  1.453
 4V1  CAA  CAB  single    1.499  0.020  1.499
 4V1  CAC  CAB  aromatic  1.383  0.020  1.383
 4V1  CAC  CAD  aromatic  1.396  0.020  1.396
 4V1  C2   CAD  single    1.466  0.020  1.466
 4V1  C2   N3   single    1.360  0.020  1.360
 4V1  CAB  CAW  aromatic  1.401  0.020  1.401
 4V1  CAD  CAT  aromatic  1.393  0.020  1.393
 4V1  CAO  C5   aromatic  1.430  0.020  1.430
 4V1  CAO  CAN  single    1.496  0.020  1.496
 4V1  C5   C4   single    1.437  0.020  1.437
 4V1  CAW  OAX  single    1.343  0.020  1.343
 4V1  CAW  CAU  aromatic  1.399  0.020  1.399
 4V1  CAT  CAU  aromatic  1.387  0.020  1.387
 4V1  CAU  CAV  single    1.501  0.020  1.501
 4V1  CAM  CAN  single    1.524  0.020  1.524
 4V1  N3   C4   single    1.391  0.020  1.391
 4V1  C4   O4   double    1.220  0.020  1.220
 4V1  N3   H1   single    0.860  0.020  1.020
 4V1  CAA  H2   single    0.970  0.020  1.090
 4V1  CAA  H3   single    0.970  0.020  1.090
 4V1  CAA  H4   single    0.970  0.020  1.090
 4V1  CAC  H5   single    0.930  0.020  1.080
 4V1  OAX  H6   single    0.850  0.020  0.980
 4V1  CAV  H7   single    0.970  0.020  1.090
 4V1  CAV  H8   single    0.970  0.020  1.090
 4V1  CAV  H9   single    0.970  0.020  1.090
 4V1  CAT  H10  single    0.930  0.020  1.080
 4V1  CAJ  H11  single    0.970  0.020  1.090
 4V1  CAJ  H12  single    0.970  0.020  1.090
 4V1  CAL  H14  single    0.970  0.020  1.090
 4V1  CAL  H15  single    0.970  0.020  1.090
 4V1  CAL  H16  single    0.970  0.020  1.090
 4V1  CAM  H17  single    0.970  0.020  1.090
 4V1  CAM  H18  single    0.970  0.020  1.090
 4V1  CAN  H19  single    0.970  0.020  1.090
 4V1  CAN  H20  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
 4V1  C2   N1   C6   115.76  3.000
 4V1  H1   N3   C2   118.81  3.000
 4V1  H1   N3   C4   115.23  3.000
 4V1  C2   N3   C4   125.94  3.000
 4V1  O4   C4   C5   127.29  3.000
 4V1  O4   C4   N3   120.56  3.000
 4V1  C5   C4   N3   112.15  3.000
 4V1  CAO  C5   C6   113.08  3.000
 4V1  CAO  C5   C4   129.43  3.000
 4V1  C6   C5   C4   117.49  3.000
 4V1  SAH  C6   C5   111.22  3.000
 4V1  C5   C6   N1   126.91  3.000
 4V1  SAH  C6   N1   121.87  3.000
 4V1  CAW  CAB  CAC  118.34  3.000
 4V1  CAW  CAB  CAA  120.35  3.000
 4V1  CAC  CAB  CAA  121.32  3.000
 4V1  H5   CAC  CAD  119.29  3.000
 4V1  H5   CAC  CAB  118.99  3.000
 4V1  CAD  CAC  CAB  121.72  3.000
 4V1  CAU  CAW  OAX  122.13  3.000
 4V1  CAU  CAW  CAB  121.42  3.000
 4V1  OAX  CAW  CAB  116.46  3.000
 4V1  H6   OAX  CAW  111.63  3.000
 4V1  CAT  CAU  CAV  121.05  3.000
 4V1  CAV  CAU  CAW  120.57  3.000
 4V1  CAT  CAU  CAW  118.38  3.000
 4V1  H9   CAV  H8   107.03  3.000
 4V1  H9   CAV  H7   107.57  3.000
 4V1  H8   CAV  H7   106.97  3.000
 4V1  H9   CAV  CAU  112.18  3.000
 4V1  H8   CAV  CAU  110.79  3.000
 4V1  H7   CAV  CAU  112.02  3.000
 4V1  H10  CAT  CAD  121.13  3.000
 4V1  H10  CAT  CAU  117.25  3.000
 4V1  CAD  CAT  CAU  121.60  3.000
 4V1  C2   CAD  CAT  122.38  3.000
 4V1  CAT  CAD  CAC  118.54  3.000
 4V1  C2   CAD  CAC  119.08  3.000
 4V1  CAD  C2   N3   118.51  3.000
 4V1  N3   C2   N1   121.73  3.000
 4V1  CAD  C2   N1   119.75  3.000
 4V1  CAI  SAH  C6    91.16  3.000
 4V1  CAO  CAI  CAJ  124.51  3.000
 4V1  CAO  CAI  SAH  112.97  3.000
 4V1  CAJ  CAI  SAH  122.52  3.000
 4V1  H12  CAJ  H11  106.38  3.000
 4V1  H12  CAJ  NAK  108.97  3.000
 4V1  H11  CAJ  NAK  111.89  3.000
 4V1  H12  CAJ  CAI  110.56  3.000
 4V1  H11  CAJ  CAI  109.42  3.000
 4V1  NAK  CAJ  CAI  109.59  3.000
 4V1  CAM  NAK  CAL  112.07  3.000
 4V1  CAM  NAK  CAJ  111.18  3.000
 4V1  CAL  NAK  CAJ  110.47  3.000
 4V1  H16  CAL  H15  107.99  3.000
 4V1  H16  CAL  H14  107.73  3.000
 4V1  H15  CAL  H14  107.81  3.000
 4V1  H16  CAL  NAK  113.22  3.000
 4V1  H15  CAL  NAK  109.97  3.000
 4V1  H14  CAL  NAK  109.96  3.000
 4V1  H18  CAM  H17  106.76  3.000
 4V1  H18  CAM  CAN  109.30  3.000
 4V1  H17  CAM  CAN  109.61  3.000
 4V1  H18  CAM  NAK  108.58  3.000
 4V1  H17  CAM  NAK  111.40  3.000
 4V1  CAN  CAM  NAK  111.07  3.000
 4V1  H20  CAN  H19  106.46  3.000
 4V1  H20  CAN  CAO  109.76  3.000
 4V1  H19  CAN  CAO  110.77  3.000
 4V1  H20  CAN  CAM  110.21  3.000
 4V1  H19  CAN  CAM  109.48  3.000
 4V1  CAO  CAN  CAM  110.09  3.000
 4V1  CAN  CAO  CAI  120.57  3.000
 4V1  CAN  CAO  C5   127.86  3.000
 4V1  CAI  CAO  C5   111.57  3.000
 4V1  H4   CAA  H3   107.77  3.000
 4V1  H4   CAA  H2   107.04  3.000
 4V1  H3   CAA  H2   107.76  3.000
 4V1  H4   CAA  CAB  111.73  3.000
 4V1  H3   CAA  CAB  110.63  3.000
 4V1  H2   CAA  CAB  111.71  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
 4V1  CONST_01  CAI  SAH  C6   C5      0.00   0.0  0
 4V1  CONST_02  SAH  CAI  CAO  C5      0.00   0.0  0
 4V1  CONST_03  CAO  CAI  SAH  C6      0.00   0.0  0
 4V1  CONST_04  CAI  CAO  C5   C6      0.00   0.0  0
 4V1  CONST_05  CAT  CAD  CAC  CAB     0.00   0.0  0
 4V1  CONST_06  CAT  CAU  CAW  CAB     0.00   0.0  0
 4V1  CONST_07  CAU  CAW  CAB  CAC     0.00   0.0  0
 4V1  CONST_08  CAU  CAT  CAD  CAC     0.00   0.0  0
 4V1  CONST_09  CAD  CAC  CAB  CAW     0.00   0.0  0
 4V1  CONST_10  CAD  CAT  CAU  CAW     0.00   0.0  0
 4V1  CONST_11  CAO  C5   C6   SAH     0.00   0.0  0
 4V1  CONST_12  C2   CAD  CAC  CAB   180.00   0.0  0
 4V1  CONST_13  C2   CAD  CAT  CAU   180.00   0.0  0
 4V1  CONST_14  C4   N3   C2   N1      0.00   0.0  0
 4V1  CONST_15  C6   N1   C2   N3      0.00   0.0  0
 4V1  CONST_16  CAD  C2   N3   C4    180.00   0.0  0
 4V1  CONST_17  C2   N3   C4   C5      0.00   0.0  0
 4V1  CONST_18  CAD  C2   N1   C6    180.00   0.0  0
 4V1  CONST_19  CAD  CAC  CAB  CAA   180.00   0.0  0
 4V1  CONST_20  CAU  CAW  CAB  CAA   180.00   0.0  0
 4V1  CONST_21  CAV  CAU  CAW  CAB   180.00   0.0  0
 4V1  CONST_22  OAX  CAW  CAB  CAC   180.00   0.0  0
 4V1  CONST_23  CAT  CAU  CAW  OAX   180.00   0.0  0
 4V1  CONST_24  CAD  CAT  CAU  CAV   180.00   0.0  0
 4V1  CONST_25  O4   C4   N3   C2    180.00   0.0  0
 4V1  CONST_26  H10  CAT  CAD  CAC   180.00   0.0  0
 4V1  CONST_27  H5   CAC  CAB  CAW   180.00   0.0  0
 4V1  CONST_28  H1   N3   C2   N1    180.00   0.0  0
 4V1  Var_01    CAC  CAD  C2   N1     19.90  30.0  2
 4V1  Var_02    CAM  CAN  CAO  C5    166.29  30.0  1
 4V1  Var_03    NAK  CAJ  CAI  SAH   162.73  30.0  1
 4V1  Var_04    CAM  NAK  CAJ  CAI    50.32  30.0  1
 4V1  Var_05    CAN  CAM  NAK  CAJ   -68.05  30.0  1
 4V1  Var_06    CAO  CAN  CAM  NAK    46.64  30.0  1
 4V1  Var_07    H2   CAA  CAB  CAC  -120.48  30.0  2
 4V1  Var_08    H7   CAV  CAU  CAW    61.31  30.0  2
 4V1  Var_09    H14  CAL  NAK  CAJ    57.17  30.0  3

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
 4V1  plan-1  CAB  0.020
 4V1  plan-1  CAC  0.020
 4V1  plan-1  CAW  0.020
 4V1  plan-1  OAX  0.020
 4V1  plan-1  CAU  0.020
 4V1  plan-1  CAV  0.020
 4V1  plan-1  CAT  0.020
 4V1  plan-1  CAD  0.020
 4V1  plan-1  C2   0.020
 4V1  plan-1  H5   0.020
 4V1  plan-1  H10  0.020
 4V1  plan-1  CAA  0.020
 4V1  plan-2  N1   0.020
 4V1  plan-2  N3   0.020
 4V1  plan-2  C4   0.020
 4V1  plan-2  C5   0.020
 4V1  plan-2  C6   0.020
 4V1  plan-2  CAD  0.020
 4V1  plan-2  C2   0.020
 4V1  plan-2  SAH  0.020
 4V1  plan-2  CAI  0.020
 4V1  plan-2  CAJ  0.020
 4V1  plan-2  CAN  0.020
 4V1  plan-2  CAO  0.020
 4V1  plan-2  O4   0.020
 4V1  plan-2  H1   0.020

