# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 13:29:51 2021
#   Inital geometry file: a 125 line input string
#   Ligand name: 5'-O-[(S)-hydroxy(4-nitrophenoxy)phosphoryl]thymidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)Oc3ccc(cc3)[N+]([O-])=O)O2)C(=O)NC1=O
#
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
 9RC  9RC  5'-O-[(S)-hydroxy(4-nitrophenoxy)phosphoryl]thymidine  ligand  48  30  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9RC
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
 9RC  OAJ  O  O      0  -0.480  -14.3992  -33.6227  -20.0742
 9RC  CAE  C  CR6    0   0.734  -13.4162  -33.6776  -20.7835
 9RC  NAI  N  NR16   0  -0.737  -13.0631  -34.8228  -21.4475
 9RC  CAL  C  CR6    0   0.563  -11.9918  -35.0223  -22.3004
 9RC  OAS  O  O      0  -0.449  -11.8149  -36.1025  -22.8308
 9RC  CAT  C  CR6    0  -0.189  -11.1462  -33.8579  -22.4818
 9RC  CAU  C  CH3    0  -0.706   -9.9656  -33.9521  -23.3908
 9RC  CAF  C  CR16   0   0.076  -11.4759  -32.7367  -21.8220
 9RC  NAB  N  NR6    0  -0.568  -12.5577  -32.6182  -20.9875
 9RC  CAA  C  CH1    0   0.207  -12.8626  -31.3258  -20.4019
 9RC  OAC  O  O2     0  -0.493  -13.1220  -30.4106  -21.4456
 9RC  CAD  C  CH2    0  -0.549  -11.7372  -30.7065  -19.5871
 9RC  CAH  C  CH1    0  -0.021  -12.0711  -29.2239  -19.6812
 9RC  OAK  O  OH1    0  -0.666  -13.0865  -28.8453  -18.7842
 9RC  CAG  C  CH1    0  -0.006  -12.6461  -29.1169  -21.0984
 9RC  CAR  C  CH2    0  -0.191  -11.6064  -28.6528  -22.0953
 9RC  OAQ  O  O2     0  -0.567  -12.2183  -28.5366  -23.3858
 9RC  PAP  P  P      0   1.473  -11.7402  -29.2917  -24.6888
 9RC  OAO  O  O      0  -0.668  -12.5861  -28.9886  -25.8522
 9RC  OAN  O  OH1    0  -0.729  -11.5175  -30.8299  -24.3442
 9RC  OAM  O  O2     0  -0.619  -10.1991  -28.8092  -24.7742
 9RC  CAV  C  CR6    0   0.390   -9.3522  -29.3003  -25.7324
 9RC  CAW  C  CR16   0  -0.312   -8.3983  -30.2367  -25.3609
 9RC  CAY  C  CR16   0  -0.260   -7.5049  -30.7087  -26.3040
 9RC  CBA  C  CR6    0   0.252   -7.5893  -30.2372  -27.6067
 9RC  NBB  N  N      1   0.331   -6.6512  -30.7325  -28.6006
 9RC  OBD  O  O     -1  -0.377   -6.7392  -30.3052  -29.7273
 9RC  OBC  O  O      0  -0.377   -5.8306  -31.5470  -28.2494
 9RC  CAZ  C  CR16   0  -0.260   -8.5432  -29.3027  -27.9829
 9RC  CAX  C  CR16   0  -0.309   -9.4348  -28.8323  -27.0362
 9RC  H1   H  HNR6   0   0.427  -13.6766  -35.6145  -21.2955
 9RC  H2   H  HCH3   0   0.249   -9.2683  -34.7234  -23.0618
 9RC  H3   H  HCH3   0   0.249  -10.2675  -34.2000  -24.4092
 9RC  H4   H  HCH3   0   0.243   -9.4260  -33.0072  -23.4231
 9RC  H5   H  HCR6   0   0.302  -10.8751  -31.8464  -21.9275
 9RC  H6   H  HCH1   0   0.275  -13.7494  -31.4644  -19.7839
 9RC  H7   H  HCH2   0   0.268  -10.7571  -30.9025  -20.0276
 9RC  H8   H  HCH2   0   0.290  -11.7121  -31.0794  -18.5634
 9RC  H9   H  HCH1   0   0.257  -11.1781  -28.5994  -19.5597
 9RC  H10  H  HOH1   0   0.456  -12.7628  -28.9756  -17.8871
 9RC  H11  H  HCH1   0   0.270  -13.4826  -28.4100  -21.1072
 9RC  H12  H  HCH2   0   0.242  -10.7452  -29.3261  -22.1149
 9RC  H13  H  HCH2   0   0.271  -11.2465  -27.6623  -21.8153
 9RC  H14  H  HOH1   0   0.504  -12.2974  -31.3885  -24.4659
 9RC  H15  H  HCR6   0   0.293   -8.3480  -30.5881  -24.3393
 9RC  H16  H  HCR6   0   0.307   -6.7604  -31.4367  -26.0179
 9RC  H17  H  HCR6   0   0.307   -8.6017  -28.9371  -28.9973
 9RC  H18  H  HCR6   0   0.299  -10.1788  -28.0972  -27.3099

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
 9RC  OBD  NBB  single    1.208  0.020  1.208
 9RC  OBC  NBB  double    1.208  0.020  1.208
 9RC  NBB  CBA  single    1.454  0.020  1.454
 9RC  CAZ  CBA  aromatic  1.387  0.020  1.387
 9RC  CAZ  CAX  aromatic  1.383  0.020  1.383
 9RC  CBA  CAY  aromatic  1.388  0.020  1.388
 9RC  CAX  CAV  aromatic  1.388  0.020  1.388
 9RC  OAO  PAP  double    1.470  0.020  1.470
 9RC  CAY  CAW  aromatic  1.382  0.020  1.382
 9RC  CAV  CAW  aromatic  1.387  0.020  1.387
 9RC  CAV  OAM  single    1.370  0.020  1.370
 9RC  OAN  PAP  single    1.592  0.020  1.592
 9RC  PAP  OAM  single    1.617  0.020  1.617
 9RC  PAP  OAQ  single    1.580  0.020  1.580
 9RC  OAQ  CAR  single    1.433  0.020  1.433
 9RC  CAR  CAG  single    1.513  0.020  1.513
 9RC  OAC  CAG  single    1.421  0.020  1.421
 9RC  OAC  CAA  single    1.412  0.020  1.412
 9RC  CAG  CAH  single    1.533  0.020  1.533
 9RC  CAU  CAT  single    1.493  0.020  1.493
 9RC  CAF  CAT  double    1.342  0.020  1.342
 9RC  CAF  NAB  single    1.371  0.020  1.371
 9RC  CAH  CAD  single    1.523  0.020  1.523
 9RC  CAH  OAK  single    1.407  0.020  1.407
 9RC  CAA  NAB  single    1.451  0.020  1.451
 9RC  CAA  CAD  single    1.521  0.020  1.521
 9RC  CAT  CAL  single    1.450  0.020  1.450
 9RC  NAB  CAE  single    1.379  0.020  1.379
 9RC  CAL  OAS  double    1.216  0.020  1.216
 9RC  CAL  NAI  single    1.384  0.020  1.384
 9RC  CAE  NAI  single    1.370  0.020  1.370
 9RC  CAE  OAJ  double    1.213  0.020  1.213
 9RC  NAI  H1   single    0.860  0.020  1.020
 9RC  CAU  H2   single    0.970  0.020  1.090
 9RC  CAU  H3   single    0.970  0.020  1.090
 9RC  CAU  H4   single    0.970  0.020  1.090
 9RC  CAF  H5   single    0.930  0.020  1.080
 9RC  CAA  H6   single    0.970  0.020  1.090
 9RC  CAD  H7   single    0.970  0.020  1.090
 9RC  CAD  H8   single    0.970  0.020  1.090
 9RC  CAH  H9   single    0.970  0.020  1.090
 9RC  OAK  H10  single    0.850  0.020  0.980
 9RC  CAG  H11  single    0.970  0.020  1.090
 9RC  CAR  H12  single    0.970  0.020  1.090
 9RC  CAR  H13  single    0.970  0.020  1.090
 9RC  OAN  H14  single    0.850  0.020  0.980
 9RC  CAW  H15  single    0.930  0.020  1.080
 9RC  CAY  H16  single    0.930  0.020  1.080
 9RC  CAZ  H17  single    0.930  0.020  1.080
 9RC  CAX  H18  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
 9RC  NAB  CAE  NAI  114.21  3.000
 9RC  NAI  CAE  OAJ  122.00  3.000
 9RC  NAB  CAE  OAJ  123.79  3.000
 9RC  H1   NAI  CAL  116.66  3.000
 9RC  H1   NAI  CAE  115.12  3.000
 9RC  CAL  NAI  CAE  128.22  3.000
 9RC  CAT  CAL  OAS  125.00  3.000
 9RC  OAS  CAL  NAI  120.62  3.000
 9RC  CAT  CAL  NAI  114.38  3.000
 9RC  CAF  CAT  CAU  123.12  3.000
 9RC  CAF  CAT  CAL  117.77  3.000
 9RC  CAU  CAT  CAL  119.11  3.000
 9RC  H4   CAU  H3   107.87  3.000
 9RC  H4   CAU  H2   107.81  3.000
 9RC  H3   CAU  H2   107.34  3.000
 9RC  H4   CAU  CAT  110.81  3.000
 9RC  H3   CAU  CAT  111.34  3.000
 9RC  H2   CAU  CAT  111.50  3.000
 9RC  H5   CAF  NAB  115.30  3.000
 9RC  H5   CAF  CAT  120.28  3.000
 9RC  NAB  CAF  CAT  124.42  3.000
 9RC  CAA  NAB  CAF  119.22  3.000
 9RC  CAA  NAB  CAE  119.59  3.000
 9RC  CAF  NAB  CAE  120.98  3.000
 9RC  H6   CAA  CAD  110.49  3.000
 9RC  H6   CAA  OAC  110.61  3.000
 9RC  CAD  CAA  OAC  105.54  3.000
 9RC  H6   CAA  NAB  106.65  3.000
 9RC  CAD  CAA  NAB  115.04  3.000
 9RC  OAC  CAA  NAB  108.51  3.000
 9RC  CAG  OAC  CAA  110.35  3.000
 9RC  H8   CAD  H7   107.26  3.000
 9RC  H8   CAD  CAH  113.35  3.000
 9RC  H7   CAD  CAH  110.28  3.000
 9RC  H8   CAD  CAA  112.39  3.000
 9RC  H7   CAD  CAA  112.01  3.000
 9RC  CAH  CAD  CAA  101.60  3.000
 9RC  H9   CAH  CAG  111.60  3.000
 9RC  H9   CAH  OAK  111.34  3.000
 9RC  CAG  CAH  OAK  107.45  3.000
 9RC  H9   CAH  CAD  111.66  3.000
 9RC  OAK  CAH  CAD  112.40  3.000
 9RC  CAG  CAH  CAD  101.97  3.000
 9RC  H10  OAK  CAH  108.37  3.000
 9RC  H11  CAG  CAR  108.76  3.000
 9RC  H11  CAG  CAH  109.81  3.000
 9RC  CAR  CAG  CAH  111.88  3.000
 9RC  H11  CAG  OAC  109.26  3.000
 9RC  CAH  CAG  OAC  106.73  3.000
 9RC  CAR  CAG  OAC  110.38  3.000
 9RC  H13  CAR  H12  107.70  3.000
 9RC  H13  CAR  OAQ  107.37  3.000
 9RC  H12  CAR  OAQ  111.72  3.000
 9RC  H13  CAR  CAG  109.65  3.000
 9RC  H12  CAR  CAG  111.35  3.000
 9RC  OAQ  CAR  CAG  108.95  3.000
 9RC  PAP  OAQ  CAR  125.08  3.000
 9RC  OAM  PAP  OAN   99.58  3.000
 9RC  OAM  PAP  OAO  116.43  3.000
 9RC  OAN  PAP  OAO  116.81  3.000
 9RC  OAM  PAP  OAQ  100.91  3.000
 9RC  OAN  PAP  OAQ  109.00  3.000
 9RC  OAO  PAP  OAQ  112.33  3.000
 9RC  H14  OAN  PAP  114.71  3.000
 9RC  CAV  OAM  PAP  121.27  3.000
 9RC  CAX  CAV  CAW  121.34  3.000
 9RC  CAW  CAV  OAM  118.66  3.000
 9RC  CAX  CAV  OAM  119.97  3.000
 9RC  H15  CAW  CAY  120.23  3.000
 9RC  H15  CAW  CAV  120.28  3.000
 9RC  CAY  CAW  CAV  119.48  3.000
 9RC  H16  CAY  CBA  121.30  3.000
 9RC  H16  CAY  CAW  119.67  3.000
 9RC  CBA  CAY  CAW  119.02  3.000
 9RC  CAZ  CBA  NBB  119.20  3.000
 9RC  CAZ  CBA  CAY  121.67  3.000
 9RC  NBB  CBA  CAY  119.13  3.000
 9RC  OBC  NBB  OBD  123.97  3.000
 9RC  OBC  NBB  CBA  117.98  3.000
 9RC  OBD  NBB  CBA  118.04  3.000
 9RC  H17  CAZ  CAX  119.54  3.000
 9RC  H17  CAZ  CBA  121.33  3.000
 9RC  CAX  CAZ  CBA  119.13  3.000
 9RC  H18  CAX  CAZ  120.11  3.000
 9RC  H18  CAX  CAV  120.53  3.000
 9RC  CAZ  CAX  CAV  119.35  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
 9RC  CONST_01  CBA  CAZ  CAX  CAV    0.00   0.0  0
 9RC  CONST_02  CBA  CAY  CAW  CAV    0.00   0.0  0
 9RC  CONST_03  CAZ  CBA  CAY  CAW    0.00   0.0  0
 9RC  CONST_04  CAZ  CAX  CAV  CAW    0.00   0.0  0
 9RC  CONST_05  CAX  CAZ  CBA  CAY    0.00   0.0  0
 9RC  CONST_06  CAX  CAV  CAW  CAY    0.00   0.0  0
 9RC  CONST_07  CAF  NAB  CAE  NAI    0.00   0.0  0
 9RC  CONST_08  CAA  NAB  CAE  NAI  180.00   0.0  0
 9RC  CONST_09  NAB  CAE  NAI  CAL    0.00   0.0  0
 9RC  CONST_10  CAZ  CAX  CAV  OAM  180.00   0.0  0
 9RC  CONST_11  CAY  CAW  CAV  OAM  180.00   0.0  0
 9RC  CONST_12  NBB  CBA  CAY  CAW  180.00   0.0  0
 9RC  CONST_13  CAX  CAZ  CBA  NBB  180.00   0.0  0
 9RC  CONST_14  CAF  NAB  CAE  OAJ  180.00   0.0  0
 9RC  CONST_15  CAA  NAB  CAE  OAJ    0.00   0.0  0
 9RC  CONST_16  CAL  NAI  CAE  OAJ  180.00   0.0  0
 9RC  CONST_17  H17  CAZ  CAX  CAV  180.00   0.0  0
 9RC  CONST_18  H16  CAY  CAW  CAV  180.00   0.0  0
 9RC  CONST_19  H18  CAX  CAV  CAW  180.00   0.0  0
 9RC  CONST_20  H15  CAW  CAY  CBA  180.00   0.0  0
 9RC  CONST_21  H1   NAI  CAE  NAB  180.00   0.0  0
 9RC  CONST_22  OBD  NBB  CBA  CAY  180.00   0.0  0
 9RC  CONST_23  OBC  NBB  CBA  CAY    0.00   0.0  0
 9RC  CONST_24  CAZ  CBA  NBB  OBD    0.00   0.0  0
 9RC  CONST_25  CAZ  CBA  NBB  OBC  180.00   0.0  0
 9RC  Var_01    CAX  CAV  OAM  PAP   77.06  30.0  2
 9RC  Var_02    H2   CAU  CAT  CAL  -59.63  30.0  3
 9RC  Var_03    OAO  PAP  OAQ  CAR  178.84  30.0  2
 9RC  Var_04    H12  CAR  OAQ  PAP    0.77  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
 9RC  chir_01  CAA  OAC  NAB  CAD  negativ
 9RC  chir_02  CAH  OAK  CAG  CAD  positiv
 9RC  chir_03  CAG  OAC  CAH  CAR  negativ
 9RC  chir_04  PAP  OAN  OAM  OAQ  both

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
 9RC  plan-1  OAJ  0.020
 9RC  plan-1  CAE  0.020
 9RC  plan-1  NAI  0.020
 9RC  plan-1  CAL  0.020
 9RC  plan-1  OAS  0.020
 9RC  plan-1  CAT  0.020
 9RC  plan-1  CAU  0.020
 9RC  plan-1  CAF  0.020
 9RC  plan-1  NAB  0.020
 9RC  plan-1  CAA  0.020
 9RC  plan-1  H1   0.020
 9RC  plan-1  H5   0.020
 9RC  plan-2  OAM  0.020
 9RC  plan-2  CAV  0.020
 9RC  plan-2  CAW  0.020
 9RC  plan-2  CAY  0.020
 9RC  plan-2  CBA  0.020
 9RC  plan-2  NBB  0.020
 9RC  plan-2  CAZ  0.020
 9RC  plan-2  CAX  0.020
 9RC  plan-2  H15  0.020
 9RC  plan-2  H16  0.020
 9RC  plan-2  H17  0.020
 9RC  plan-2  H18  0.020
 9RC  plan-3  CBA  0.020
 9RC  plan-3  NBB  0.020
 9RC  plan-3  OBD  0.020
 9RC  plan-3  OBC  0.020

