# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 23:25:58 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: (1S)-1,4-anhydro-1-(4-oxo-4,5-dihydro-3H-pyrrolo[3,2-d]pyrimidin-7-yl)-2,3-O-[(1S)-2-phosphonoethylidene]-D-ribitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H]([C@@H]2O[C@H](C[P](O)(O)=O)O[C@H]12)c3c[nH]c4C(=O)NC=Nc34
#
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
 P1D  P1D  (1S)-1,4-anhydro-1-(4-oxo-4,5-dihydro-3H-pyrrolo[3,2-d]pyrimidin-7-yl)-2,3-O-[(1S)-2-phosphonoethylidene]-D-ribitol  ligand  39  25  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_P1D
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
 P1D  O3    O  OP    -1  -0.882   3.7758  -0.1970   1.0884
 P1D  P     P  P      0   1.186   3.1006  -1.5601   0.8835
 P1D  O4    O  OP    -1  -0.914   4.0018  -2.7387   1.2877
 P1D  O2    O  O      0  -0.872   1.6872  -1.6551   1.4692
 P1D  C1P   C  CH2    0  -0.767   2.9541  -1.8246  -0.9706
 P1D  C1    C  CH1    0   0.320   2.0938  -0.9300  -1.8359
 P1D  O3'   O  O2     0  -0.509   2.4896   0.4231  -1.7831
 P1D  O2'   O  O2     0  -0.503   0.7356  -0.9829  -1.4695
 P1D  C2'   C  CH1    0  -0.018   0.2005   0.3035  -1.3424
 P1D  C3'   C  CH1    0  -0.018   1.3975   1.2457  -1.4836
 P1D  C4'   C  CH1    0  -0.023   1.5002   1.9363  -0.1179
 P1D  C5'   C  CH2    0  -0.172   1.9072   3.3831  -0.2359
 P1D  O5'   O  OH1    0  -0.672   2.0185   3.9520   1.0471
 P1D  O4'   O  O2     0  -0.516   0.1950   1.8514   0.4273
 P1D  C1'   C  CH1    0  -0.036  -0.3474   0.5910   0.0740
 P1D  C9    C  C      0  -0.070  -1.8300   0.6846   0.1502
 P1D  C8    C  C1     0  -0.056  -2.5927   1.8312   0.1009
 P1D  N7    N  NC1    0  -0.651  -3.9088   1.5113   0.1656
 P1D  C5    C  CR6    0   0.149  -4.0307   0.1626   0.2564
 P1D  C4    C  CR6    0   0.134  -2.7503  -0.3866   0.2506
 P1D  N3    N  N      0  -0.428  -2.5156  -1.7308   0.3308
 P1D  C2    C  CR16   0   0.117  -3.5735  -2.4565   0.4159
 P1D  N1    N  NR16   0  -0.660  -4.8488  -1.9796   0.4271
 P1D  C6    C  CR6    0   0.518  -5.2039  -0.6402   0.3499
 P1D  O6    O  OC     0  -0.485  -6.3699  -0.2708   0.3644
 P1D  H1P1  H  HCH2   0   0.197   2.6059  -2.8498  -1.1427
 P1D  H1P2  H  HCH2   0   0.198   3.9637  -1.7991  -1.3970
 P1D  H1    H  HCH1   0   0.175   2.1779  -1.2597  -2.8863
 P1D  H2'   H  HCH1   0   0.235  -0.5645   0.4759  -2.1078
 P1D  H3'   H  HCH1   0   0.233   1.2511   1.9781  -2.2869
 P1D  H4'   H  HCH1   0   0.261   2.2264   1.3783   0.4907
 P1D  H5'1  H  HCH2   0   0.189   1.1710   3.9153  -0.8558
 P1D  H5'2  H  HCH2   0   0.198   2.8614   3.4143  -0.7794
 P1D  H5'   H  HOH1   0   0.454   2.3152   4.8606   0.9449
 P1D  H1'   H  HCH1   0   0.266   0.0405  -0.2060   0.7239
 P1D  H8    H  H      0   0.287  -2.2835   2.8608   0.0283
 P1D  HN7   H  HNC1   0   0.418  -4.6680   2.1724   0.1584
 P1D  H2    H  HCR6   0   0.289  -3.4909  -3.5337   0.4854
 P1D  HN1   H  HNR6   0   0.429  -5.6015  -2.6512   0.4985

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
 P1D  O3   P     deloc     1.535  0.020  1.535
 P1D  P    O4    deloc     1.538  0.020  1.538
 P1D  P    O2    deloc     1.533  0.020  1.533
 P1D  P    C1P   single    1.879  0.020  1.879
 P1D  C1P  C1    single    1.513  0.020  1.513
 P1D  C1P  H1P1  single    0.970  0.020  1.090
 P1D  C1P  H1P2  single    0.970  0.020  1.090
 P1D  C1   O3'   single    1.411  0.020  1.411
 P1D  C1   O2'   single    1.408  0.020  1.408
 P1D  C1   H1    single    0.970  0.020  1.090
 P1D  O3'  C3'   single    1.400  0.020  1.400
 P1D  O2'  C2'   single    1.399  0.020  1.399
 P1D  C2'  C3'   single    1.530  0.020  1.530
 P1D  C2'  C1'   single    1.546  0.020  1.546
 P1D  C2'  H2'   single    0.970  0.020  1.090
 P1D  C3'  C4'   single    1.534  0.020  1.534
 P1D  C3'  H3'   single    0.970  0.020  1.090
 P1D  C4'  C5'   single    1.508  0.020  1.508
 P1D  C4'  O4'   single    1.417  0.020  1.417
 P1D  C4'  H4'   single    0.970  0.020  1.090
 P1D  C5'  O5'   single    1.408  0.020  1.408
 P1D  C5'  H5'1  single    0.970  0.020  1.090
 P1D  C5'  H5'2  single    0.970  0.020  1.090
 P1D  O5'  H5'   single    0.850  0.020  0.980
 P1D  O4'  C1'   single    1.417  0.020  1.417
 P1D  C1'  C9    single    1.487  0.020  1.487
 P1D  C1'  H1'   single    0.970  0.020  1.090
 P1D  C9   C8    aromatic  1.378  0.020  1.378
 P1D  C9   C4    aromatic  1.416  0.020  1.416
 P1D  C8   N7    aromatic  1.356  0.020  1.356
 P1D  C8   H8    single    0.930  0.020  1.080
 P1D  N7   C5    aromatic  1.357  0.020  1.357
 P1D  N7   HN7   single    0.860  0.020  1.020
 P1D  C5   C4    aromatic  1.393  0.020  1.393
 P1D  C5   C6    aromatic  1.425  0.020  1.425
 P1D  C4   N3    aromatic  1.367  0.020  1.367
 P1D  N3   C2    aromatic  1.286  0.020  1.286
 P1D  C2   N1    aromatic  1.362  0.020  1.362
 P1D  C2   H2    single    0.930  0.020  1.080
 P1D  N1   C6    aromatic  1.388  0.020  1.388
 P1D  N1   HN1   single    0.860  0.020  1.020
 P1D  C6   O6    double    1.223  0.020  1.223

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
 P1D  C1P   P    O2    107.24  3.000
 P1D  C1P   P    O4    101.38  3.000
 P1D  O2    P    O4    113.11  3.000
 P1D  C1P   P    O3    106.92  3.000
 P1D  O2    P    O3    114.18  3.000
 P1D  O4    P    O3    112.82  3.000
 P1D  H1P2  C1P  H1P1  104.67  3.000
 P1D  H1P2  C1P  C1    106.71  3.000
 P1D  H1P1  C1P  C1    106.41  3.000
 P1D  H1P2  C1P  P     107.99  3.000
 P1D  H1P1  C1P  P     108.14  3.000
 P1D  C1    C1P  P     121.71  3.000
 P1D  H1    C1   O2'   108.05  3.000
 P1D  H1    C1   O3'   107.50  3.000
 P1D  O2'   C1   O3'   107.27  3.000
 P1D  H1    C1   C1P   108.92  3.000
 P1D  O2'   C1   C1P   112.18  3.000
 P1D  O3'   C1   C1P   112.71  3.000
 P1D  C3'   O3'  C1    110.66  3.000
 P1D  C2'   O2'  C1    110.99  3.000
 P1D  H2'   C2'  C1'   111.31  3.000
 P1D  H2'   C2'  C3'   112.64  3.000
 P1D  C1'   C2'  C3'   104.32  3.000
 P1D  H2'   C2'  O2'   110.38  3.000
 P1D  C1'   C2'  O2'   112.94  3.000
 P1D  C3'   C2'  O2'   104.99  3.000
 P1D  H3'   C3'  C4'   111.13  3.000
 P1D  H3'   C3'  C2'   111.99  3.000
 P1D  C4'   C3'  C2'   104.33  3.000
 P1D  H3'   C3'  O3'   109.86  3.000
 P1D  C4'   C3'  O3'   113.76  3.000
 P1D  C2'   C3'  O3'   105.56  3.000
 P1D  H4'   C4'  O4'   111.41  3.000
 P1D  H4'   C4'  C5'   110.61  3.000
 P1D  O4'   C4'  C5'   109.65  3.000
 P1D  H4'   C4'  C3'   107.97  3.000
 P1D  O4'   C4'  C3'   104.71  3.000
 P1D  C5'   C4'  C3'   112.36  3.000
 P1D  H5'2  C5'  H5'1  106.79  3.000
 P1D  H5'2  C5'  O5'   111.76  3.000
 P1D  H5'1  C5'  O5'   111.78  3.000
 P1D  H5'2  C5'  C4'   107.49  3.000
 P1D  H5'1  C5'  C4'   109.14  3.000
 P1D  O5'   C5'  C4'   109.74  3.000
 P1D  H5'   O5'  C5'   108.03  3.000
 P1D  C1'   O4'  C4'   108.06  3.000
 P1D  H1'   C1'  C9    111.53  3.000
 P1D  H1'   C1'  O4'   111.25  3.000
 P1D  C9    C1'  O4'   108.23  3.000
 P1D  H1'   C1'  C2'   106.37  3.000
 P1D  C9    C1'  C2'   114.33  3.000
 P1D  O4'   C1'  C2'   104.97  3.000
 P1D  C4    C9   C8    105.80  3.000
 P1D  C4    C9   C1'   127.15  3.000
 P1D  C8    C9   C1'   127.02  3.000
 P1D  H8    C8   N7    120.47  3.000
 P1D  H8    C8   C9    129.70  3.000
 P1D  N7    C8   C9    109.83  3.000
 P1D  HN7   N7   C5    125.82  3.000
 P1D  HN7   N7   C8    125.22  3.000
 P1D  C5    N7   C8    108.96  3.000
 P1D  C6    C5   C4    122.34  3.000
 P1D  C6    C5   N7    129.67  3.000
 P1D  C4    C5   N7    107.99  3.000
 P1D  N3    C4   C5    123.04  3.000
 P1D  N3    C4   C9    129.54  3.000
 P1D  C5    C4   C9    107.42  3.000
 P1D  C2    N3   C4    114.68  3.000
 P1D  H2    C2   N1    114.80  3.000
 P1D  H2    C2   N3    120.21  3.000
 P1D  N1    C2   N3    125.00  3.000
 P1D  HN1   N1   C6    117.04  3.000
 P1D  HN1   N1   C2    117.71  3.000
 P1D  C6    N1   C2    125.25  3.000
 P1D  O6    C6   N1    122.32  3.000
 P1D  O6    C6   C5    128.00  3.000
 P1D  N1    C6   C5    109.68  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
 P1D  CONST_01  C5   N7   C8  C9     0.00   0.0  0
 P1D  CONST_02  N7   C5   C4  C9     0.00   0.0  0
 P1D  CONST_03  C6   C5   C4  C9   180.00   0.0  0
 P1D  CONST_04  C2   N3   C4  C9   180.00   0.0  0
 P1D  CONST_05  C5   C4   C9  C8     0.00   0.0  0
 P1D  CONST_06  N3   C4   C9  C8   180.00   0.0  0
 P1D  CONST_07  C4   C5   N7  C8     0.00   0.0  0
 P1D  CONST_08  C6   C5   N7  C8   180.00   0.0  0
 P1D  CONST_09  C4   C9   C8  N7     0.00   0.0  0
 P1D  CONST_10  N3   C4   C5  N7   180.00   0.0  0
 P1D  CONST_11  N1   C6   C5  N7   180.00   0.0  0
 P1D  CONST_12  C2   N3   C4  C5     0.00   0.0  0
 P1D  CONST_13  C2   N1   C6  C5     0.00   0.0  0
 P1D  CONST_14  N1   C6   C5  C4     0.00   0.0  0
 P1D  CONST_15  N1   C2   N3  C4     0.00   0.0  0
 P1D  CONST_16  C6   C5   C4  N3     0.00   0.0  0
 P1D  CONST_17  C6   N1   C2  N3     0.00   0.0  0
 P1D  CONST_18  N7   C8   C9  C1'  180.00   0.0  0
 P1D  CONST_19  C5   C4   C9  C1'  180.00   0.0  0
 P1D  CONST_20  N3   C4   C9  C1'    0.00   0.0  0
 P1D  CONST_21  O6   C6   C5  N7     0.00   0.0  0
 P1D  CONST_22  O6   C6   C5  C4   180.00   0.0  0
 P1D  CONST_23  O6   C6   N1  C2   180.00   0.0  0
 P1D  CONST_24  H8   C8   C9  C1'    0.00   0.0  0
 P1D  CONST_25  HN7  N7   C8  C9   180.00   0.0  0
 P1D  CONST_26  HN1  N1   C6  C5   180.00   0.0  0
 P1D  CONST_27  H2   C2   N3  C4   180.00   0.0  0
 P1D  Var_01    C1   C1P  P   O3   -64.41  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
 P1D  chir_01  C1   C1P  O3'  O2'  positiv
 P1D  chir_02  C2'  O2'  C3'  C1'  positiv
 P1D  chir_03  C3'  O3'  C4'  C2'  positiv
 P1D  chir_04  C4'  O4'  C5'  C3'  positiv
 P1D  chir_05  C1'  O4'  C2'  C9   positiv

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
 P1D  plan-1  C1'  0.020
 P1D  plan-1  C9   0.020
 P1D  plan-1  C8   0.020
 P1D  plan-1  N7   0.020
 P1D  plan-1  C5   0.020
 P1D  plan-1  C4   0.020
 P1D  plan-1  N3   0.020
 P1D  plan-1  C2   0.020
 P1D  plan-1  N1   0.020
 P1D  plan-1  C6   0.020
 P1D  plan-1  O6   0.020
 P1D  plan-1  H8   0.020
 P1D  plan-1  HN7  0.020
 P1D  plan-1  H2   0.020
 P1D  plan-1  HN1  0.020

