# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 03:56:19 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: 5-[2-(2,5-dimethoxyphenyl)ethyl]thieno[2,3-d]pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(OC)c(CCc2csc3nc(N)nc(N)c23)c1
#
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
 MCV  MCV  5-[2-(2,5-dimethoxyphenyl)ethyl]thieno[2,3-d]pyrimidine-2,4-diamine  ligand  41  23  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_MCV
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
 MCV  N1    N  N     0  -0.509   3.7148  -1.7230   0.2476
 MCV  C2    C  CR6   0   0.531   4.7761  -0.9173   0.3540
 MCV  N3    N  N     0  -0.499   4.7804   0.4040   0.1988
 MCV  C4    C  CR56  0   0.002   3.5908   0.9109  -0.0945
 MCV  C5    C  CR56  0  -0.048   2.3947   0.2056  -0.2385
 MCV  C6    C  CR6   0   0.444   2.5308  -1.1972  -0.0441
 MCV  CAA   C  CH3   0  -0.434  -6.9074   1.4228   0.2677
 MCV  CAB   C  CH3   0  -0.433  -1.9754  -3.4780  -0.6001
 MCV  NAC   N  NH2   0  -0.823   5.9622  -1.5143   0.6116
 MCV  NAD   N  NH2   0  -0.857   1.5107  -2.0586  -0.1597
 MCV  CAE   C  CR16  0  -0.384  -5.0046  -0.6147  -0.0929
 MCV  CAF   C  CR16  0  -0.368  -4.0119  -1.5786  -0.2666
 MCV  CAG   C  CR15  0  -0.570   1.6682   2.3527  -0.6764
 MCV  CAH   C  CR16  0  -0.398  -3.3136   0.9714   0.5115
 MCV  CAI   C  CH2   0  -0.521  -0.8787   0.4064   0.5529
 MCV  SAO   S  S2    0   0.185   3.3553   2.6049  -0.3652
 MCV  CAP   C  CR6   0   0.377  -4.6606   0.6701   0.2969
 MCV  CAR   C  CR6   0   0.063  -2.3176   0.0262   0.3448
 MCV  CAT   C  CR5   0   0.257   1.2829   1.0584  -0.5807
 MCV  CAU   C  CR6   0   0.342  -2.6781  -1.2712  -0.0533
 MCV  HAA   H  HCH3  0   0.257  -7.4362   2.3507   0.4726
 MCV  HAAA  H  HCH3  0   0.225  -7.1044   1.1270  -0.7665
 MCV  HAAB  H  HCH3  0   0.225  -7.2937   0.6458   0.9332
 MCV  HAB   H  HCH3  0   0.255  -1.0343  -4.0199  -0.6559
 MCV  HABA  H  HCH3  0   0.231  -2.6250  -3.9760   0.1240
 MCV  HABB  H  HCH3  0   0.230  -2.4540  -3.5048  -1.5823
 MCV  HNAC  H  HNH2  0   0.391   5.9493  -2.4560   0.9637
 MCV  HNAA  H  HNH2  0   0.391   6.7211  -0.9342   0.9255
 MCV  HNAD  H  HNH2  0   0.398   1.6814  -3.0241   0.0657
 MCV  HNAB  H  HNH2  0   0.431   0.5512  -1.7696  -0.2329
 MCV  HAE   H  HCR6  0   0.279  -6.0320  -0.9017  -0.2700
 MCV  HAF   H  HCR6  0   0.282  -4.3184  -2.5699  -0.5712
 MCV  HAG   H  HCR5  0   0.291   1.0404   3.1975  -0.9168
 MCV  HAH   H  HCR6  0   0.256  -3.0414   1.9752   0.8186
 MCV  HAI   H  HCH2  0   0.250  -0.3639  -0.3465   1.1559
 MCV  HAIA  H  HCH2  0   0.265  -0.8338   1.3308   1.1316
 MCV  HAJ   H  HCH2  0   0.254  -0.2001  -0.2466  -1.4144
 MCV  HAJA  H  HCH2  0   0.272  -0.6651   1.4272  -1.3236
 MCV  CAJ   C  CH2   0  -0.567  -0.1425   0.6393  -0.7776
 MCV  OAM   O  O2    0  -0.478  -5.5377   1.6799   0.4920
 MCV  OAN   O  O2    0  -0.493  -1.6623  -2.1581  -0.2040

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
 MCV  C2   N1    aromatic  1.337  0.020  1.337
 MCV  N1   C6    aromatic  1.328  0.020  1.328
 MCV  N3   C2    aromatic  1.330  0.020  1.330
 MCV  NAC  C2    single    1.353  0.020  1.353
 MCV  N3   C4    aromatic  1.326  0.020  1.326
 MCV  SAO  C4    aromatic  1.732  0.020  1.732
 MCV  C4   C5    aromatic  1.396  0.020  1.396
 MCV  C5   CAT   aromatic  1.442  0.020  1.442
 MCV  C5   C6    aromatic  1.423  0.020  1.423
 MCV  C6   NAD   single    1.340  0.020  1.340
 MCV  CAA  OAM   single    1.412  0.020  1.412
 MCV  CAA  HAA   single    0.970  0.020  1.090
 MCV  CAA  HAAA  single    0.970  0.020  1.090
 MCV  CAA  HAAB  single    0.970  0.020  1.090
 MCV  CAB  OAN   single    1.413  0.020  1.413
 MCV  CAB  HAB   single    0.970  0.020  1.090
 MCV  CAB  HABA  single    0.970  0.020  1.090
 MCV  CAB  HABB  single    0.970  0.020  1.090
 MCV  NAC  HNAC  single    0.890  0.020  1.040
 MCV  NAC  HNAA  single    0.890  0.020  1.040
 MCV  NAD  HNAD  single    0.860  0.020  1.020
 MCV  NAD  HNAB  single    0.860  0.020  1.020
 MCV  CAE  CAP   aromatic  1.386  0.020  1.386
 MCV  CAE  CAF   aromatic  1.395  0.020  1.395
 MCV  CAE  HAE   single    0.930  0.020  1.080
 MCV  CAF  CAU   aromatic  1.385  0.020  1.385
 MCV  CAF  HAF   single    0.930  0.020  1.080
 MCV  SAO  CAG   aromatic  1.734  0.020  1.734
 MCV  CAG  CAT   aromatic  1.354  0.020  1.354
 MCV  CAG  HAG   single    0.930  0.020  1.080
 MCV  CAP  CAH   aromatic  1.397  0.020  1.397
 MCV  CAH  CAR   aromatic  1.383  0.020  1.383
 MCV  CAH  HAH   single    0.930  0.020  1.080
 MCV  CAR  CAI   single    1.503  0.020  1.503
 MCV  CAJ  CAI   single    1.538  0.020  1.538
 MCV  CAI  HAI   single    0.970  0.020  1.090
 MCV  CAI  HAIA  single    0.970  0.020  1.090
 MCV  CAT  CAJ   single    1.499  0.020  1.499
 MCV  CAJ  HAJ   single    0.970  0.020  1.090
 MCV  CAJ  HAJA  single    0.970  0.020  1.090
 MCV  OAM  CAP   single    1.352  0.020  1.352
 MCV  CAU  OAN   single    1.357  0.020  1.357
 MCV  CAU  CAR   aromatic  1.404  0.020  1.404

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
 MCV  C6    N1   C2    119.12  3.000
 MCV  NAC   C2   N3    117.24  3.000
 MCV  NAC   C2   N1    116.44  3.000
 MCV  N3    C2   N1    126.30  3.000
 MCV  C4    N3   C2    113.74  3.000
 MCV  SAO   C4   C5    111.20  3.000
 MCV  C5    C4   N3    126.75  3.000
 MCV  SAO   C4   N3    122.05  3.000
 MCV  CAT   C5   C6    133.56  3.000
 MCV  C6    C5   C4    113.71  3.000
 MCV  CAT   C5   C4    112.72  3.000
 MCV  NAD   C6   C5    123.31  3.000
 MCV  NAD   C6   N1    116.31  3.000
 MCV  C5    C6   N1    120.38  3.000
 MCV  HAAB  CAA  HAAA  108.65  3.000
 MCV  HAAB  CAA  HAA   108.65  3.000
 MCV  HAAA  CAA  HAA   108.74  3.000
 MCV  HAAB  CAA  OAM   112.06  3.000
 MCV  HAAA  CAA  OAM   111.98  3.000
 MCV  HAA   CAA  OAM   106.65  3.000
 MCV  HABB  CAB  HABA  108.91  3.000
 MCV  HABB  CAB  HAB   108.70  3.000
 MCV  HABA  CAB  HAB   108.75  3.000
 MCV  HABB  CAB  OAN   111.83  3.000
 MCV  HABA  CAB  OAN   111.81  3.000
 MCV  HAB   CAB  OAN   106.74  3.000
 MCV  HNAA  NAC  HNAC  116.15  3.000
 MCV  HNAA  NAC  C2    117.82  3.000
 MCV  HNAC  NAC  C2    117.96  3.000
 MCV  HNAB  NAD  HNAD  117.03  3.000
 MCV  HNAB  NAD  C6    123.25  3.000
 MCV  HNAD  NAD  C6    117.93  3.000
 MCV  HAE   CAE  CAP   121.86  3.000
 MCV  HAE   CAE  CAF   118.20  3.000
 MCV  CAP   CAE  CAF   119.94  3.000
 MCV  HAF   CAF  CAU   121.31  3.000
 MCV  HAF   CAF  CAE   117.84  3.000
 MCV  CAU   CAF  CAE   120.85  3.000
 MCV  HAG   CAG  CAT   126.75  3.000
 MCV  HAG   CAG  SAO   119.47  3.000
 MCV  CAT   CAG  SAO   113.78  3.000
 MCV  HAH   CAH  CAR   119.07  3.000
 MCV  HAH   CAH  CAP   119.03  3.000
 MCV  CAR   CAH  CAP   121.90  3.000
 MCV  HAIA  CAI  HAI   105.74  3.000
 MCV  HAIA  CAI  CAR   109.09  3.000
 MCV  HAI   CAI  CAR   110.67  3.000
 MCV  HAIA  CAI  CAJ   108.10  3.000
 MCV  HAI   CAI  CAJ   110.85  3.000
 MCV  CAR   CAI  CAJ   112.13  3.000
 MCV  CAG   SAO  C4     91.04  3.000
 MCV  OAM   CAP  CAH   116.26  3.000
 MCV  OAM   CAP  CAE   124.89  3.000
 MCV  CAH   CAP  CAE   118.85  3.000
 MCV  CAU   CAR  CAI   121.26  3.000
 MCV  CAU   CAR  CAH   118.73  3.000
 MCV  CAI   CAR  CAH   119.99  3.000
 MCV  CAJ   CAT  CAG   121.92  3.000
 MCV  CAJ   CAT  C5    126.79  3.000
 MCV  CAG   CAT  C5    111.26  3.000
 MCV  CAR   CAU  OAN   116.31  3.000
 MCV  CAR   CAU  CAF   119.73  3.000
 MCV  OAN   CAU  CAF   123.96  3.000
 MCV  HAJA  CAJ  HAJ   105.57  3.000
 MCV  HAJA  CAJ  CAT   108.61  3.000
 MCV  HAJ   CAJ  CAT   110.70  3.000
 MCV  HAJA  CAJ  CAI   108.22  3.000
 MCV  HAJ   CAJ  CAI   110.86  3.000
 MCV  CAT   CAJ  CAI   112.57  3.000
 MCV  CAP   OAM  CAA   118.08  3.000
 MCV  CAU   OAN  CAB   118.41  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
 MCV  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 MCV  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 MCV  CONST_03  CAT   C5   C6   N1    180.00   0.0  0
 MCV  CONST_04  C5    C6   N1   C2      0.00   0.0  0
 MCV  CONST_05  SAO   C4   N3   C2    180.00   0.0  0
 MCV  CONST_06  C5    C4   N3   C2      0.00   0.0  0
 MCV  CONST_07  C6    N1   C2   N3      0.00   0.0  0
 MCV  CONST_08  CAG   SAO  C4   N3    180.00   0.0  0
 MCV  CONST_09  CAT   C5   C4   N3    180.00   0.0  0
 MCV  CONST_10  C6    C5   C4   N3      0.00   0.0  0
 MCV  CONST_11  CAT   CAG  SAO  C4      0.00   0.0  0
 MCV  CONST_12  CAG   CAT  C5   C4      0.00   0.0  0
 MCV  CONST_13  CAG   SAO  C4   C5      0.00   0.0  0
 MCV  CONST_14  SAO   CAG  CAT  C5      0.00   0.0  0
 MCV  CONST_15  SAO   C4   C5   C6    180.00   0.0  0
 MCV  CONST_16  CAG   CAT  C5   C6    180.00   0.0  0
 MCV  CONST_17  CAR   CAH  CAP  CAE     0.00   0.0  0
 MCV  CONST_18  CAR   CAU  CAF  CAE     0.00   0.0  0
 MCV  CONST_19  CAH   CAP  CAE  CAF     0.00   0.0  0
 MCV  CONST_20  CAH   CAR  CAU  CAF     0.00   0.0  0
 MCV  CONST_21  CAT   C5   C4   SAO     0.00   0.0  0
 MCV  CONST_22  CAU   CAF  CAE  CAP     0.00   0.0  0
 MCV  CONST_23  CAU   CAR  CAH  CAP     0.00   0.0  0
 MCV  CONST_24  NAD   C6   N1   C2    180.00   0.0  0
 MCV  CONST_25  NAC   C2   N3   C4    180.00   0.0  0
 MCV  CONST_26  CAJ   CAT  C5   C4    180.00   0.0  0
 MCV  CONST_27  NAD   C6   C5   C4    180.00   0.0  0
 MCV  CONST_28  NAC   C2   N1   C6    180.00   0.0  0
 MCV  CONST_29  CAJ   CAT  C5   C6      0.00   0.0  0
 MCV  CONST_30  CAT   C5   C6   NAD     0.00   0.0  0
 MCV  CONST_31  OAN   CAU  CAF  CAE   180.00   0.0  0
 MCV  CONST_32  OAM   CAP  CAE  CAF   180.00   0.0  0
 MCV  CONST_33  CAI   CAR  CAU  CAF   180.00   0.0  0
 MCV  CONST_34  OAN   CAU  CAR  CAH   180.00   0.0  0
 MCV  CONST_35  CAP   CAH  CAR  CAI   180.00   0.0  0
 MCV  CONST_36  SAO   CAG  CAT  CAJ   180.00   0.0  0
 MCV  CONST_37  CAR   CAH  CAP  OAM   180.00   0.0  0
 MCV  CONST_38  HAG   CAG  SAO  C4    180.00   0.0  0
 MCV  CONST_39  HAH   CAH  CAP  CAE   180.00   0.0  0
 MCV  CONST_40  HAE   CAE  CAP  CAH   180.00   0.0  0
 MCV  CONST_41  HAF   CAF  CAE  CAP   180.00   0.0  0
 MCV  CONST_44  HNAD  NAD  C6   N1      0.00   0.0  0
 MCV  CONST_45  HNAB  NAD  C6   N1    180.00   0.0  0
 MCV  Var_01    CAI   CAJ  CAT  C5     77.84  30.0  2
 MCV  Var_02    CAE   CAP  OAM  CAA    -0.88  30.0  2
 MCV  Var_03    CAF   CAU  OAN  CAB    -0.10  30.0  2
 MCV  Var_04    CAJ   CAI  CAR  CAH  -101.29  30.0  2
 MCV  Var_05    CAT   CAJ  CAI  CAR   178.32  30.0  2
 MCV  Var_06    HAA   CAA  OAM  CAP  -179.75  30.0  3
 MCV  Var_07    HAB   CAB  OAN  CAU  -179.68  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
 MCV  plan-1  CAE   0.020
 MCV  plan-1  CAF   0.020
 MCV  plan-1  CAH   0.020
 MCV  plan-1  CAI   0.020
 MCV  plan-1  CAP   0.020
 MCV  plan-1  CAR   0.020
 MCV  plan-1  CAU   0.020
 MCV  plan-1  HAE   0.020
 MCV  plan-1  HAF   0.020
 MCV  plan-1  HAH   0.020
 MCV  plan-1  OAM   0.020
 MCV  plan-1  OAN   0.020
 MCV  plan-2  N1    0.020
 MCV  plan-2  C2    0.020
 MCV  plan-2  N3    0.020
 MCV  plan-2  C4    0.020
 MCV  plan-2  C5    0.020
 MCV  plan-2  C6    0.020
 MCV  plan-2  NAC   0.020
 MCV  plan-2  NAD   0.020
 MCV  plan-2  CAG   0.020
 MCV  plan-2  SAO   0.020
 MCV  plan-2  CAT   0.020
 MCV  plan-2  HAG   0.020
 MCV  plan-2  CAJ   0.020
 MCV  plan-3  C2    0.020
 MCV  plan-3  NAC   0.020
 MCV  plan-3  HNAC  0.020
 MCV  plan-3  HNAA  0.020
 MCV  plan-4  C6    0.020
 MCV  plan-4  NAD   0.020
 MCV  plan-4  HNAD  0.020
 MCV  plan-4  HNAB  0.020

