# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 11:06:55 2021
#   Inital geometry file: a 124 line input string
#   Ligand name: 1-{2-deoxy-5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-5-nitro-1H-indole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)n2ccc3cc(ccc23)[N+]([O-])=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
 N5P  N5P  1-{2-deoxy-5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-5-nitro-1H-indole  ligand  49  32  .  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_N5P
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
 N5P  OR2   O  O      0  -0.193  -11.9734  66.1185  39.8335
 N5P  NRO   N  N      1   0.336  -11.9687  64.9461  39.5291
 N5P  OR1   O  O     -1  -0.496  -10.9567  64.3173  39.3165
 N5P  CZ3   C  CR6    0   0.176  -13.2400  64.2635  39.4126
 N5P  CE3   C  CR16   0  -0.306  -13.2465  62.9245  39.0659
 N5P  CD2   C  CR56   0  -0.035  -14.4780  62.2909  38.9562
 N5P  CH2   C  CR16   0  -0.295  -14.4189  64.9858  39.6558
 N5P  CZ2   C  CR16   0  -0.311  -15.6428  64.3677  39.5482
 N5P  CE2   C  CR56   0   0.347  -15.6675  63.0181  39.1928
 N5P  NE1   N  NR5    0  -0.494  -16.7181  62.1687  38.9994
 N5P  CD1   C  CR15   0  -0.003  -16.2218  60.9248  38.6723
 N5P  CG    C  CR15   0  -0.361  -14.8662  60.9546  38.6306
 N5P  C1'   C  CH1    0   0.202  -18.1044  62.4864  39.2085
 N5P  O4'   O  O2     0  -0.475  -18.5647  61.8608  40.3899
 N5P  C4'   C  CH1    0  -0.079  -19.8381  61.2667  40.1842
 N5P  C3'   C  CH1    0   0.030  -20.3430  61.8123  38.8488
 N5P  O3'   O  OH1    0  -0.627  -21.0039  63.0253  39.1248
 N5P  C2'   C  CH2    0  -0.579  -19.0378  62.0226  38.0976
 N5P  C5'   C  CH2    0  -0.188  -19.6498  59.7583  40.2190
 N5P  O5'   O  O2     0  -0.546  -20.9491  59.1591  40.0937
 N5P  PA    P  P      0   1.479  -21.1302  57.5856  40.1516
 N5P  O1A   O  O      0  -0.638  -20.2895  56.8079  41.0677
 N5P  O2A   O  OH1    0  -0.665  -22.7019  57.5241  40.3119
 N5P  O3A   O  O2     0  -0.688  -20.8603  57.0904  38.6166
 N5P  PB    P  P      0   1.476  -20.9240  57.8735  37.2226
 N5P  O1B   O  O      0  -0.655  -19.8375  58.8254  36.9652
 N5P  O2B   O  OH1    0  -0.685  -22.4134  58.4154  37.2362
 N5P  O3B   O  O2     0  -0.660  -20.8892  56.6347  36.2016
 N5P  PG    P  P      0   1.437  -22.1149  55.8587  35.4637
 N5P  O3G   O  OH1    0  -0.606  -21.3330  54.6840  34.7411
 N5P  O2G   O  OH1    0  -0.728  -22.7739  55.1368  36.7115
 N5P  O1G   O  O      0  -0.741  -22.9583  56.7251  34.6293
 N5P  HE3   H  HCR6   0   0.291  -12.3298  62.3815  38.8850
 N5P  HH2   H  HCR6   0   0.301  -14.3757  66.0296  39.9277
 N5P  HZ2   H  HCR6   0   0.278  -16.5472  64.9291  39.7376
 N5P  HD1   H  HCR5   0   0.264  -16.8827  60.0933  38.4894
 N5P  HG    H  HCR5   0   0.270  -14.2178  60.1274  38.3927
 N5P  H1'   H  HCH1   0   0.219  -18.1644  63.5711  39.3227
 N5P  H4'   H  HCH1   0   0.233  -20.5071  61.5616  40.9989
 N5P  H3'   H  HCH1   0   0.228  -20.9996  61.1047  38.3325
 N5P  HO3'  H  HOH1   0   0.448  -21.2428  63.4386  38.2897
 N5P  H2'1  H  HCH2   0   0.281  -19.1113  62.7537  37.2927
 N5P  H2'2  H  HCH2   0   0.275  -18.7139  61.0812  37.6506
 N5P  H5'1  H  HCH2   0   0.259  -19.0004  59.4187  39.4093
 N5P  H5'2  H  HCH2   0   0.214  -19.1962  59.4688  41.1684
 N5P  HO2A  H  HOH1   0   0.520  -23.0334  56.6895  40.6702
 N5P  HO2B  H  HOH1   0   0.518  -22.6310  59.0607  36.5490
 N5P  HOG3  H  HOH1   0   0.484  -21.0558  54.8843  33.8369
 N5P  HOG2  H  HOH1   0   0.490  -23.6880  54.8536  36.5744

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
 N5P  OR2  NRO   double    1.211  0.020  1.211
 N5P  NRO  CZ3   single    1.448  0.020  1.448
 N5P  NRO  OR1   single    1.210  0.020  1.210
 N5P  CZ3  CH2   aromatic  1.404  0.020  1.404
 N5P  CZ3  CE3   aromatic  1.383  0.020  1.383
 N5P  CE3  CD2   aromatic  1.389  0.020  1.389
 N5P  CE3  HE3   single    0.930  0.020  1.080
 N5P  CD2  CE2   aromatic  1.414  0.020  1.414
 N5P  CD2  CG    aromatic  1.429  0.020  1.429
 N5P  CH2  CZ2   aromatic  1.375  0.020  1.375
 N5P  CH2  HH2   single    0.930  0.020  1.080
 N5P  CZ2  CE2   aromatic  1.396  0.020  1.396
 N5P  CZ2  HZ2   single    0.930  0.020  1.080
 N5P  CE2  NE1   aromatic  1.365  0.020  1.365
 N5P  NE1  C1'   single    1.438  0.020  1.438
 N5P  NE1  CD1   aromatic  1.379  0.020  1.379
 N5P  CD1  CG    aromatic  1.357  0.020  1.357
 N5P  CD1  HD1   single    0.930  0.020  1.080
 N5P  CG   HG    single    0.930  0.020  1.080
 N5P  C1'  C2'   single    1.523  0.020  1.523
 N5P  C1'  O4'   single    1.414  0.020  1.414
 N5P  C1'  H1'   single    0.970  0.020  1.090
 N5P  O4'  C4'   single    1.420  0.020  1.420
 N5P  C4'  C3'   single    1.528  0.020  1.528
 N5P  C4'  C5'   single    1.521  0.020  1.521
 N5P  C4'  H4'   single    0.970  0.020  1.090
 N5P  C3'  C2'   single    1.521  0.020  1.521
 N5P  C3'  O3'   single    1.409  0.020  1.409
 N5P  C3'  H3'   single    0.970  0.020  1.090
 N5P  O3'  HO3'  single    0.850  0.020  0.980
 N5P  C2'  H2'1  single    0.970  0.020  1.090
 N5P  C2'  H2'2  single    0.970  0.020  1.090
 N5P  C5'  O5'   single    1.436  0.020  1.436
 N5P  C5'  H5'1  single    0.970  0.020  1.090
 N5P  C5'  H5'2  single    0.970  0.020  1.090
 N5P  O5'  PA    single    1.585  0.020  1.585
 N5P  PA   O3A   single    1.635  0.020  1.635
 N5P  PA   O1A   double    1.467  0.020  1.467
 N5P  PA   O2A   single    1.581  0.020  1.581
 N5P  O2A  HO2A  single    0.850  0.020  0.980
 N5P  O3A  PB    single    1.600  0.020  1.600
 N5P  PB   O1B   double    1.467  0.020  1.467
 N5P  PB   O3B   single    1.606  0.020  1.606
 N5P  PB   O2B   single    1.585  0.020  1.585
 N5P  O2B  HO2B  single    0.850  0.020  0.980
 N5P  O3B  PG    single    1.628  0.020  1.628
 N5P  PG   O1G   double    1.469  0.020  1.469
 N5P  PG   O3G   single    1.585  0.020  1.585
 N5P  PG   O2G   single    1.585  0.020  1.585
 N5P  O3G  HOG3  single    0.850  0.020  0.980
 N5P  O2G  HOG2  single    0.850  0.020  0.980

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
 N5P  CZ3   NRO  OR1   118.38  3.000
 N5P  OR1   NRO  OR2   123.38  3.000
 N5P  CZ3   NRO  OR2   118.24  3.000
 N5P  CH2   CZ3  CE3   122.52  3.000
 N5P  CE3   CZ3  NRO   118.73  3.000
 N5P  CH2   CZ3  NRO   118.75  3.000
 N5P  HE3   CE3  CD2   120.64  3.000
 N5P  HE3   CE3  CZ3   121.62  3.000
 N5P  CD2   CE3  CZ3   117.74  3.000
 N5P  CG    CD2  CE2   106.89  3.000
 N5P  CG    CD2  CE3   133.25  3.000
 N5P  CE2   CD2  CE3   119.86  3.000
 N5P  HH2   CH2  CZ2   119.33  3.000
 N5P  HH2   CH2  CZ3   120.50  3.000
 N5P  CZ2   CH2  CZ3   120.16  3.000
 N5P  HZ2   CZ2  CE2   122.13  3.000
 N5P  HZ2   CZ2  CH2   119.82  3.000
 N5P  CE2   CZ2  CH2   118.05  3.000
 N5P  NE1   CE2  CZ2   130.66  3.000
 N5P  NE1   CE2  CD2   107.68  3.000
 N5P  CZ2   CE2  CD2   121.66  3.000
 N5P  C1'   NE1  CD1   125.52  3.000
 N5P  CD1   NE1  CE2   108.55  3.000
 N5P  C1'   NE1  CE2   125.75  3.000
 N5P  HD1   CD1  CG    128.64  3.000
 N5P  HD1   CD1  NE1   121.04  3.000
 N5P  CG    CD1  NE1   110.31  3.000
 N5P  HG    CG   CD1   126.24  3.000
 N5P  HG    CG   CD2   127.20  3.000
 N5P  CD1   CG   CD2   106.56  3.000
 N5P  H1'   C1'  C2'   110.17  3.000
 N5P  H1'   C1'  O4'   109.52  3.000
 N5P  C2'   C1'  O4'   105.97  3.000
 N5P  H1'   C1'  NE1   106.71  3.000
 N5P  O4'   C1'  NE1   109.74  3.000
 N5P  C2'   C1'  NE1   114.68  3.000
 N5P  C4'   O4'  C1'   110.85  3.000
 N5P  H4'   C4'  C5'   109.02  3.000
 N5P  H4'   C4'  C3'   110.62  3.000
 N5P  C5'   C4'  C3'   114.52  3.000
 N5P  H4'   C4'  O4'   109.12  3.000
 N5P  C5'   C4'  O4'   107.49  3.000
 N5P  C3'   C4'  O4'   105.87  3.000
 N5P  H3'   C3'  C2'   111.79  3.000
 N5P  H3'   C3'  O3'   111.57  3.000
 N5P  C2'   C3'  O3'   112.35  3.000
 N5P  H3'   C3'  C4'   112.31  3.000
 N5P  O3'   C3'  C4'   106.93  3.000
 N5P  C2'   C3'  C4'   101.39  3.000
 N5P  HO3'  O3'  C3'   108.45  3.000
 N5P  H2'2  C2'  H2'1  107.22  3.000
 N5P  H2'2  C2'  C3'   109.74  3.000
 N5P  H2'1  C2'  C3'   113.57  3.000
 N5P  H2'2  C2'  C1'   112.30  3.000
 N5P  H2'1  C2'  C1'   112.07  3.000
 N5P  C3'   C2'  C1'   101.99  3.000
 N5P  H5'2  C5'  H5'1  108.39  3.000
 N5P  H5'2  C5'  O5'   109.95  3.000
 N5P  H5'1  C5'  O5'   110.09  3.000
 N5P  H5'2  C5'  C4'   109.55  3.000
 N5P  H5'1  C5'  C4'   111.42  3.000
 N5P  O5'   C5'  C4'   107.44  3.000
 N5P  PA    O5'  C5'   120.95  3.000
 N5P  O3A   PA   O2A   104.33  3.000
 N5P  O2A   PA   O1A   119.07  3.000
 N5P  O3A   PA   O1A   109.34  3.000
 N5P  O2A   PA   O5'    98.97  3.000
 N5P  O1A   PA   O5'   118.93  3.000
 N5P  O3A   PA   O5'   104.33  3.000
 N5P  HO2A  O2A  PA    114.33  3.000
 N5P  PB    O3A  PA    131.52  3.000
 N5P  O3B   PB   O2B   106.83  3.000
 N5P  O2B   PB   O1B   118.39  3.000
 N5P  O3B   PB   O1B   111.90  3.000
 N5P  O2B   PB   O3A   101.38  3.000
 N5P  O3B   PB   O3A   100.11  3.000
 N5P  O1B   PB   O3A   116.16  3.000
 N5P  HO2B  O2B  PB    115.68  3.000
 N5P  PG    O3B  PB    129.78  3.000
 N5P  O1G   PG   O2G   118.49  3.000
 N5P  O2G   PG   O3G   103.08  3.000
 N5P  O1G   PG   O3G   117.47  3.000
 N5P  O2G   PG   O3B    99.98  3.000
 N5P  O3G   PG   O3B   100.86  3.000
 N5P  O1G   PG   O3B   114.12  3.000
 N5P  HOG3  O3G  PG    114.47  3.000
 N5P  HOG2  O2G  PG    114.51  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
 N5P  CONST_01  CE2   CZ2  CH2  CZ3    0.00   0.0  0
 N5P  CONST_02  CE2   CD2  CE3  CZ3    0.00   0.0  0
 N5P  CONST_03  CG    CD2  CE3  CZ3  180.00   0.0  0
 N5P  CONST_04  CZ2   CH2  CZ3  CE3    0.00   0.0  0
 N5P  CONST_05  CZ2   CE2  CD2  CE3    0.00   0.0  0
 N5P  CONST_06  NE1   CE2  CD2  CE3  180.00   0.0  0
 N5P  CONST_07  CD1   CG   CD2  CE3  180.00   0.0  0
 N5P  CONST_08  CH2   CZ3  CE3  CD2    0.00   0.0  0
 N5P  CONST_09  CH2   CZ2  CE2  CD2    0.00   0.0  0
 N5P  CONST_10  CD1   NE1  CE2  CD2    0.00   0.0  0
 N5P  CONST_11  NE1   CD1  CG   CD2    0.00   0.0  0
 N5P  CONST_12  NE1   CE2  CZ2  CH2  180.00   0.0  0
 N5P  CONST_13  CG    CD2  CE2  CZ2  180.00   0.0  0
 N5P  CONST_14  CD1   NE1  CE2  CZ2  180.00   0.0  0
 N5P  CONST_15  CD1   CG   CD2  CE2    0.00   0.0  0
 N5P  CONST_16  CG    CD1  NE1  CE2    0.00   0.0  0
 N5P  CONST_17  CG    CD2  CE2  NE1    0.00   0.0  0
 N5P  CONST_18  C1'   NE1  CE2  CD2  180.00   0.0  0
 N5P  CONST_19  C1'   NE1  CE2  CZ2    0.00   0.0  0
 N5P  CONST_20  C1'   NE1  CD1  CG   180.00   0.0  0
 N5P  CONST_21  CZ2   CH2  CZ3  NRO  180.00   0.0  0
 N5P  CONST_22  CD2   CE3  CZ3  NRO  180.00   0.0  0
 N5P  CONST_23  HZ2   CZ2  CH2  CZ3  180.00   0.0  0
 N5P  CONST_24  HH2   CH2  CZ3  CE3  180.00   0.0  0
 N5P  CONST_25  HG    CG   CD2  CE3    0.00   0.0  0
 N5P  CONST_26  HD1   CD1  CG   CD2  180.00   0.0  0
 N5P  CONST_27  HE3   CE3  CZ3  CH2  180.00   0.0  0
 N5P  CONST_28  CH2   CZ3  NRO  OR2    0.00   0.0  0
 N5P  CONST_29  CE3   CZ3  NRO  OR2  180.00   0.0  0
 N5P  CONST_30  CH2   CZ3  NRO  OR1  180.00   0.0  0
 N5P  CONST_31  CE3   CZ3  NRO  OR1    0.00   0.0  0
 N5P  Var_01    O3A   PA   O5'  C5'  -85.28  30.0  3
 N5P  Var_02    O1B   PB   O3A  PA    72.52  30.0  3
 N5P  Var_03    O1G   PG   O3B  PB    58.38  30.0  3
 N5P  Var_04    H5'1  C5'  O5'  PA    61.00  30.0  1

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
 N5P  chir_01  C1'  NE1  C2'  O4'  negativ
 N5P  chir_02  C4'  O4'  C3'  C5'  negativ
 N5P  chir_03  C3'  O3'  C4'  C2'  positiv
 N5P  chir_04  PA   O3A  O1A  O2A  both
 N5P  chir_05  PB   O1B  O3B  O2B  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
 N5P  plan-1  NRO  0.020
 N5P  plan-1  CZ3  0.020
 N5P  plan-1  CE3  0.020
 N5P  plan-1  CD2  0.020
 N5P  plan-1  CH2  0.020
 N5P  plan-1  CZ2  0.020
 N5P  plan-1  CE2  0.020
 N5P  plan-1  NE1  0.020
 N5P  plan-1  CD1  0.020
 N5P  plan-1  CG   0.020
 N5P  plan-1  C1'  0.020
 N5P  plan-1  HE3  0.020
 N5P  plan-1  HH2  0.020
 N5P  plan-1  HZ2  0.020
 N5P  plan-1  HD1  0.020
 N5P  plan-1  HG   0.020
 N5P  plan-2  OR2  0.020
 N5P  plan-2  NRO  0.020
 N5P  plan-2  OR1  0.020
 N5P  plan-2  CZ3  0.020

