# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jun  4 07:29:12 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: ({[6-(4-methylphenyl)thieno[2,3-d]pyrimidin-4-yl]amino}methyl)phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cc1)c2sc3ncnc(NC[P](O)(O)=O)c3c2
#
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
 YL3  YL3  '({[6-(4-methylphenyl)thieno[2,3-d]pyrimidin-4-yl]amino}methyl)phosphonic acid'  ligand  36  22  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_YL3
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
 YL3  OAT  O  OH1   0  -0.775  -5.0139  -0.6064   0.5469
 YL3  PAS  P  P     0   1.336  -4.7867   0.9007   0.0911
 YL3  OAU  O  OH1   0  -0.740  -6.1712   1.1710  -0.6788
 YL3  OAV  O  O     0  -0.710  -4.4468   1.8792   1.1524
 YL3  CAR  C  CH2   0  -0.602  -3.5321   0.8099  -1.2403
 YL3  NAJ  N  NH1   0  -0.661  -2.1804   0.6521  -0.7601
 YL3  C4   C  CR6   0   0.603  -1.6869  -0.4779  -0.2452
 YL3  N3   N  N     0  -0.587  -2.5215  -1.4782   0.0501
 YL3  C2   C  CR16  0   0.091  -2.0237  -2.6160   0.5430
 YL3  N1   N  N     0  -0.429  -0.7651  -2.8866   0.7909
 YL3  C6   C  CR56  0  -0.023   0.0677  -1.8814   0.5123
 YL3  SAE  S  S2    0   0.236   1.7736  -1.9703   0.7533
 YL3  C5   C  CR56  0   0.055  -0.3002  -0.6448  -0.0051
 YL3  CAC  C  CR15  0  -0.268   0.8103   0.2212  -0.2141
 YL3  CAD  C  CR5   0  -0.202   1.9926  -0.3478   0.1462
 YL3  CAK  C  CR6   0   0.128   3.3294   0.2362   0.0752
 YL3  CAL  C  CR16  0  -0.305   4.4729  -0.5580  -0.0051
 YL3  CAM  C  CR16  0  -0.283   5.7325   0.0168  -0.0848
 YL3  CAN  C  CR6   0   0.088   5.8971   1.3983  -0.0940
 YL3  CAQ  C  CH3   0  -0.723   7.2554   2.0240  -0.2033
 YL3  CAO  C  CR16  0  -0.271   4.7509   2.1902  -0.0089
 YL3  CAP  C  CR16  0  -0.307   3.4922   1.6248   0.0789
 YL3  H1   H  HOH1  0   0.500  -4.1765  -1.1243   0.3739
 YL3  H2   H  HOH1  0   0.495  -6.4066   2.1062  -0.7314
 YL3  H3   H  HCH2  0   0.296  -3.7974   0.0148  -1.9428
 YL3  H4   H  HCH2  0   0.315  -3.5686   1.7477  -1.7931
 YL3  H5   H  HNH1  0   0.426  -1.5409   1.4048  -0.9513
 YL3  H6   H  HCR6  0   0.275  -2.7496  -3.3897   0.7624
 YL3  H7   H  HCR5  0   0.276   0.7443   1.2167  -0.6313
 YL3  H8   H  HCR6  0   0.254   4.3929  -1.6386  -0.0234
 YL3  H9   H  HCR6  0   0.256   6.6007  -0.6276  -0.1470
 YL3  H10  H  HCH3  0   0.251   7.3823   2.5138  -1.1707
 YL3  H11  H  HCH3  0   0.248   7.4051   2.7864   0.5620
 YL3  H12  H  HCH3  0   0.246   8.0473   1.2835  -0.1010
 YL3  H13  H  HCR6  0   0.254   4.8452   3.2696  -0.0002
 YL3  H14  H  HCR6  0   0.257   2.6295   2.2724   0.1682

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
 YL3  OAV  PAS  double    1.483  0.020  1.483
 YL3  PAS  OAU  single    1.607  0.020  1.607
 YL3  PAS  CAR  single    1.832  0.020  1.832
 YL3  PAS  OAT  single    1.591  0.020  1.591
 YL3  CAR  NAJ  single    1.443  0.020  1.443
 YL3  NAJ  C4   single    1.336  0.020  1.336
 YL3  CAQ  CAN  single    1.500  0.020  1.500
 YL3  CAO  CAN  aromatic  1.396  0.020  1.396
 YL3  CAO  CAP  aromatic  1.383  0.020  1.383
 YL3  CAC  C5   aromatic  1.424  0.020  1.424
 YL3  CAC  CAD  aromatic  1.361  0.020  1.361
 YL3  C4   C5   aromatic  1.417  0.020  1.417
 YL3  C4   N3   aromatic  1.336  0.020  1.336
 YL3  CAN  CAM  aromatic  1.391  0.020  1.391
 YL3  CAP  CAK  aromatic  1.398  0.020  1.398
 YL3  CAM  CAL  aromatic  1.387  0.020  1.387
 YL3  C5   C6   aromatic  1.390  0.020  1.390
 YL3  CAK  CAL  aromatic  1.395  0.020  1.395
 YL3  CAK  CAD  single    1.461  0.020  1.461
 YL3  N3   C2   aromatic  1.336  0.020  1.336
 YL3  CAD  SAE  aromatic  1.746  0.020  1.746
 YL3  C6   SAE  aromatic  1.725  0.020  1.725
 YL3  C6   N1   aromatic  1.335  0.020  1.335
 YL3  C2   N1   aromatic  1.311  0.020  1.311
 YL3  OAT  H1   single    0.850  0.020  0.980
 YL3  OAU  H2   single    0.850  0.020  0.980
 YL3  CAR  H3   single    0.970  0.020  1.090
 YL3  CAR  H4   single    0.970  0.020  1.090
 YL3  NAJ  H5   single    0.860  0.020  1.020
 YL3  C2   H6   single    0.930  0.020  1.080
 YL3  CAC  H7   single    0.930  0.020  1.080
 YL3  CAL  H8   single    0.930  0.020  1.080
 YL3  CAM  H9   single    0.930  0.020  1.080
 YL3  CAQ  H10  single    0.970  0.020  1.090
 YL3  CAQ  H11  single    0.970  0.020  1.090
 YL3  CAQ  H12  single    0.970  0.020  1.090
 YL3  CAO  H13  single    0.930  0.020  1.080
 YL3  CAP  H14  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
 YL3  H1   OAT  PAS  108.76  3.000
 YL3  CAR  PAS  OAV  113.32  3.000
 YL3  CAR  PAS  OAU  104.49  3.000
 YL3  OAV  PAS  OAU  115.42  3.000
 YL3  CAR  PAS  OAT  105.02  3.000
 YL3  OAU  PAS  OAT  100.00  3.000
 YL3  OAV  PAS  OAT  116.92  3.000
 YL3  H2   OAU  PAS  113.51  3.000
 YL3  H4   CAR  H3   106.96  3.000
 YL3  H4   CAR  NAJ  107.12  3.000
 YL3  H3   CAR  NAJ  111.19  3.000
 YL3  H4   CAR  PAS  107.66  3.000
 YL3  H3   CAR  PAS  109.68  3.000
 YL3  NAJ  CAR  PAS  113.90  3.000
 YL3  H5   NAJ  C4   118.11  3.000
 YL3  H5   NAJ  CAR  116.77  3.000
 YL3  C4   NAJ  CAR  124.51  3.000
 YL3  C5   C4   N3   119.06  3.000
 YL3  N3   C4   NAJ  119.19  3.000
 YL3  C5   C4   NAJ  121.75  3.000
 YL3  C2   N3   C4   119.11  3.000
 YL3  H6   C2   N1   117.23  3.000
 YL3  H6   C2   N3   115.67  3.000
 YL3  N1   C2   N3   127.10  3.000
 YL3  C6   N1   C2   113.83  3.000
 YL3  C5   C6   SAE  111.07  3.000
 YL3  SAE  C6   N1   123.30  3.000
 YL3  C5   C6   N1   125.63  3.000
 YL3  CAD  SAE  C6    91.58  3.000
 YL3  CAC  C5   C6   112.91  3.000
 YL3  C6   C5   C4   115.26  3.000
 YL3  CAC  C5   C4   131.82  3.000
 YL3  H7   CAC  CAD  122.69  3.000
 YL3  H7   CAC  C5   124.68  3.000
 YL3  CAD  CAC  C5   112.62  3.000
 YL3  CAK  CAD  CAC  127.97  3.000
 YL3  CAK  CAD  SAE  120.21  3.000
 YL3  CAC  CAD  SAE  111.81  3.000
 YL3  CAP  CAK  CAL  118.06  3.000
 YL3  CAL  CAK  CAD  121.71  3.000
 YL3  CAP  CAK  CAD  120.24  3.000
 YL3  H8   CAL  CAM  118.64  3.000
 YL3  H8   CAL  CAK  120.55  3.000
 YL3  CAM  CAL  CAK  120.80  3.000
 YL3  H9   CAM  CAN  119.71  3.000
 YL3  H9   CAM  CAL  119.00  3.000
 YL3  CAN  CAM  CAL  121.29  3.000
 YL3  CAO  CAN  CAQ  120.77  3.000
 YL3  CAO  CAN  CAM  117.76  3.000
 YL3  CAQ  CAN  CAM  121.47  3.000
 YL3  H12  CAQ  H11  108.04  3.000
 YL3  H12  CAQ  H10  107.69  3.000
 YL3  H11  CAQ  H10  106.99  3.000
 YL3  H12  CAQ  CAN  111.60  3.000
 YL3  H11  CAQ  CAN  111.40  3.000
 YL3  H10  CAQ  CAN  110.92  3.000
 YL3  H13  CAO  CAP  119.08  3.000
 YL3  H13  CAO  CAN  119.62  3.000
 YL3  CAP  CAO  CAN  121.30  3.000
 YL3  H14  CAP  CAO  119.10  3.000
 YL3  H14  CAP  CAK  120.11  3.000
 YL3  CAO  CAP  CAK  120.79  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
 YL3  CONST_01  CAD  CAC  C5   C4   180.00   0.0  0
 YL3  CONST_02  SAE  C6   C5   C4   180.00   0.0  0
 YL3  CONST_03  N1   C6   C5   C4     0.00   0.0  0
 YL3  CONST_04  N1   C2   N3   C4     0.00   0.0  0
 YL3  CONST_05  CAC  C5   C4   N3   180.00   0.0  0
 YL3  CONST_06  C6   C5   C4   N3     0.00   0.0  0
 YL3  CONST_07  C6   N1   C2   N3     0.00   0.0  0
 YL3  CONST_08  C5   C4   N3   C2     0.00   0.0  0
 YL3  CONST_09  C5   C6   N1   C2     0.00   0.0  0
 YL3  CONST_10  SAE  C6   N1   C2   180.00   0.0  0
 YL3  CONST_11  CAC  C5   C6   N1   180.00   0.0  0
 YL3  CONST_12  CAD  SAE  C6   N1   180.00   0.0  0
 YL3  CONST_13  CAD  CAC  C5   C6     0.00   0.0  0
 YL3  CONST_14  CAC  CAD  SAE  C6     0.00   0.0  0
 YL3  CONST_15  CAK  CAD  SAE  C6   180.00   0.0  0
 YL3  CONST_16  C5   CAC  CAD  SAE    0.00   0.0  0
 YL3  CONST_19  CAC  C5   C6   SAE    0.00   0.0  0
 YL3  CONST_20  CAK  CAD  CAC  C5   180.00   0.0  0
 YL3  CONST_21  CAD  SAE  C6   C5     0.00   0.0  0
 YL3  CONST_24  CAO  CAP  CAK  CAD  180.00   0.0  0
 YL3  CONST_25  CAM  CAL  CAK  CAD  180.00   0.0  0
 YL3  CONST_26  CAN  CAO  CAP  CAK    0.00   0.0  0
 YL3  CONST_27  CAN  CAM  CAL  CAK    0.00   0.0  0
 YL3  CONST_28  CAO  CAN  CAM  CAL    0.00   0.0  0
 YL3  CONST_29  CAO  CAP  CAK  CAL    0.00   0.0  0
 YL3  CONST_30  CAP  CAO  CAN  CAM    0.00   0.0  0
 YL3  CONST_31  CAP  CAK  CAL  CAM    0.00   0.0  0
 YL3  CONST_32  CAC  C5   C4   NAJ    0.00   0.0  0
 YL3  CONST_33  C6   C5   C4   NAJ  180.00   0.0  0
 YL3  CONST_34  C2   N3   C4   NAJ  180.00   0.0  0
 YL3  CONST_35  CAQ  CAN  CAM  CAL  180.00   0.0  0
 YL3  CONST_36  CAP  CAO  CAN  CAQ  180.00   0.0  0
 YL3  CONST_37  H7   CAC  C5   C4     0.00   0.0  0
 YL3  CONST_38  H6   C2   N3   C4   180.00   0.0  0
 YL3  CONST_39  H14  CAP  CAK  CAD    0.00   0.0  0
 YL3  CONST_40  H8   CAL  CAK  CAD    0.00   0.0  0
 YL3  CONST_41  H13  CAO  CAP  CAK  180.00   0.0  0
 YL3  CONST_42  H9   CAM  CAL  CAK  180.00   0.0  0
 YL3  CONST_43  C5   C4   NAJ  CAR  180.00   0.0  0
 YL3  CONST_44  N3   C4   NAJ  CAR    0.00   0.0  0
 YL3  CONST_45  H5   NAJ  C4   N3   180.00   0.0  0
 YL3  Var_01    H10  CAQ  CAN  CAM  110.48  30.0  2
 YL3  Var_02    C4   NAJ  CAR  PAS   73.44  30.0  3
 YL3  Var_03    NAJ  CAR  PAS  OAT  -78.89  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
 YL3  plan-1  CAD  0.020
 YL3  plan-1  CAK  0.020
 YL3  plan-1  CAL  0.020
 YL3  plan-1  CAM  0.020
 YL3  plan-1  CAN  0.020
 YL3  plan-1  CAQ  0.020
 YL3  plan-1  CAO  0.020
 YL3  plan-1  CAP  0.020
 YL3  plan-1  H8   0.020
 YL3  plan-1  H9   0.020
 YL3  plan-1  H13  0.020
 YL3  plan-1  H14  0.020
 YL3  plan-2  NAJ  0.020
 YL3  plan-2  C4   0.020
 YL3  plan-2  N3   0.020
 YL3  plan-2  C2   0.020
 YL3  plan-2  N1   0.020
 YL3  plan-2  C6   0.020
 YL3  plan-2  SAE  0.020
 YL3  plan-2  C5   0.020
 YL3  plan-2  CAC  0.020
 YL3  plan-2  CAD  0.020
 YL3  plan-2  CAK  0.020
 YL3  plan-2  H6   0.020
 YL3  plan-2  H7   0.020
 YL3  plan-3  CAR  0.020
 YL3  plan-3  NAJ  0.020
 YL3  plan-3  C4   0.020
 YL3  plan-3  H5   0.020

