# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 03:47:06 2021
#   Inital geometry file: a 130 line input string
#   Ligand name: [[(2R,3S,5R)-5-(3-methoxynaphthalen-2-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc2ccccc2cc1[C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3
#
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
 BMR  BMR  '[[(2R,3S,5R)-5-(3-methoxynaphthalen-2-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate'  ligand  53  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_BMR
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
 BMR  C1    C  CR6   0  -0.067  20.7350  -19.9572   -3.9060
 BMR  C2    C  CR16  0  -0.341  20.0451  -18.8336   -4.2576
 BMR  C3    C  CR66  0   0.100  19.2342  -18.1316   -3.3342
 BMR  C4    C  CR66  0   0.283  19.1577  -18.6010   -2.0015
 BMR  C5    C  CR16  0  -0.469  19.8782  -19.7634   -1.6360
 BMR  C6    C  CR6   0   0.411  20.6388  -20.4298   -2.5625
 BMR  PA    P  P     0   1.423  19.4045  -17.3978   -8.4108
 BMR  PB    P  P     0   1.408  18.7970  -17.2503  -11.3115
 BMR  PC    P  P     0   1.405  18.3582  -14.3824  -11.7478
 BMR  C1'   C  CH1   0  -0.038  21.5853  -20.7258   -4.8900
 BMR  O1A   O  OH1   0  -0.603  20.6608  -16.5143   -8.8102
 BMR  O1B   O  O     0  -0.676  17.8308  -17.9694  -12.1483
 BMR  O1C   O  O     0  -0.696  17.3476  -13.4793  -11.1830
 BMR  C2'   C  CH2   0  -0.516  20.8832  -21.9839   -5.4219
 BMR  C20   C  CR16  0  -0.351  18.3566  -17.8939   -1.0754
 BMR  C21   C  CR16  0  -0.278  17.6626  -16.7778   -1.4628
 BMR  C22   C  CR16  0  -0.250  17.7333  -16.3161   -2.7930
 BMR  C23   C  CR16  0  -0.367  18.5041  -16.9816   -3.7092
 BMR  O2A   O  O     0  -0.692  18.3368  -16.7640   -7.6273
 BMR  O2B   O  OH1   0  -0.670  20.2633  -17.0659  -11.8711
 BMR  O2C   O  OH1   0  -0.707  19.8603  -13.8951  -11.8105
 BMR  C3'   C  CH1   0  -0.010  20.2914  -21.5003   -6.7354
 BMR  O3'   O  OH1   0  -0.566  20.0478  -22.5661   -7.6131
 BMR  O37   O  O2    0  -0.500  21.3404  -21.5490   -2.3081
 BMR  C38   C  CH3   0  -0.425  21.3128  -22.0852   -1.0004
 BMR  O3A   O  O2    0  -0.564  18.9579  -17.9470   -9.8708
 BMR  O3B   O  O2    0  -0.647  18.4043  -15.7606  -10.8636
 BMR  O3C   O  OH1   0  -0.735  18.2109  -14.8860  -13.2432
 BMR  C4'   C  CH1   0   0.004  21.3966  -20.5511   -7.2066
 BMR  O4'   O  O2    0  -0.541  21.8699  -19.9265   -6.0327
 BMR  C5'   C  CH2   0  -0.212  21.0167  -19.5146   -8.2339
 BMR  O5'   O  O2    0  -0.584  19.9290  -18.7270   -7.7349
 BMR  H2    H  HCR6  0   0.276  20.1142  -18.4559   -5.2676
 BMR  H5    H  HCR6  0   0.231  19.8085  -20.1073   -0.6121
 BMR  H2'   H  HCH2  0   0.225  21.6148  -22.7717   -5.6194
 BMR  H5'   H  HCH2  0   0.230  21.8763  -18.8781   -8.4565
 BMR  H1'   H  HCH1  0   0.264  22.5333  -20.9927   -4.4139
 BMR  H2'A  H  HCH2  0   0.253  20.1363  -22.3806   -4.7361
 BMR  H20   H  HCR6  0   0.238  18.2956  -18.2469   -0.0529
 BMR  H21   H  HCR6  0   0.222  17.0499  -16.2472   -0.7455
 BMR  H22   H  HCR6  0   0.260  17.1761  -15.4359   -3.0862
 BMR  H23   H  HCR6  0   0.240  18.5546  -16.6411   -4.7374
 BMR  H3'   H  HCH1  0   0.185  19.3727  -20.9342   -6.5360
 BMR  HO3'  H  HOH1  0   0.455  19.4637  -22.2643   -8.3149
 BMR  H38   H  HCH3  0   0.286  21.9321  -22.9782   -1.0199
 BMR  H4'   H  HCH1  0   0.263  22.1878  -21.1577   -7.6742
 BMR  H5'A  H  HCH2  0   0.235  20.7222  -20.0191   -9.1578
 BMR  H38A  H  HCH3  0   0.251  21.7222  -21.3860   -0.2667
 BMR  H38B  H  HCH3  0   0.245  20.3003  -22.3624   -0.6967
 BMR  H1A   H  HOH1  0   0.508  20.8913  -15.8264   -8.1700
 BMR  H2B   H  HOH1  0   0.557  20.5167  -17.7091  -12.5487
 BMR  H2C   H  HOH1  0   0.525  20.1149  -13.2870  -11.1028
 BMR  H3C   H  HOH1  0   0.523  17.3074  -15.1046  -13.5131

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
 BMR  C1   C2    aromatic  1.365  0.020  1.365
 BMR  C1   C6    aromatic  1.427  0.020  1.427
 BMR  C1   C1'   single    1.511  0.020  1.511
 BMR  C2   C3    aromatic  1.415  0.020  1.415
 BMR  C2   H2    single    0.930  0.020  1.080
 BMR  C3   C4    aromatic  1.415  0.020  1.415
 BMR  C3   C23   aromatic  1.413  0.020  1.413
 BMR  C4   C5    aromatic  1.416  0.020  1.416
 BMR  C4   C20   aromatic  1.414  0.020  1.414
 BMR  C5   C6    aromatic  1.372  0.020  1.372
 BMR  C5   H5    single    0.930  0.020  1.080
 BMR  C6   O37   single    1.345  0.020  1.345
 BMR  PA   O1A   single    1.587  0.020  1.587
 BMR  PA   O2A   double    1.468  0.020  1.468
 BMR  PA   O3A   single    1.623  0.020  1.623
 BMR  PA   O5'   single    1.581  0.020  1.581
 BMR  PB   O1B   double    1.467  0.020  1.467
 BMR  PB   O2B   single    1.580  0.020  1.580
 BMR  PB   O3A   single    1.608  0.020  1.608
 BMR  PB   O3B   single    1.604  0.020  1.604
 BMR  PC   O1C   double    1.468  0.020  1.468
 BMR  PC   O2C   single    1.580  0.020  1.580
 BMR  PC   O3B   single    1.638  0.020  1.638
 BMR  PC   O3C   single    1.585  0.020  1.585
 BMR  C1'  C2'   single    1.536  0.020  1.536
 BMR  C1'  O4'   single    1.423  0.020  1.423
 BMR  C1'  H1'   single    0.970  0.020  1.090
 BMR  C2'  C3'   single    1.520  0.020  1.520
 BMR  C2'  H2'   single    0.970  0.020  1.090
 BMR  C2'  H2'A  single    0.970  0.020  1.090
 BMR  C20  C21   aromatic  1.370  0.020  1.370
 BMR  C20  H20   single    0.930  0.020  1.080
 BMR  C21  C22   aromatic  1.410  0.020  1.410
 BMR  C21  H21   single    0.930  0.020  1.080
 BMR  C22  C23   aromatic  1.370  0.020  1.370
 BMR  C22  H22   single    0.930  0.020  1.080
 BMR  C23  H23   single    0.930  0.020  1.080
 BMR  C3'  O3'   single    1.402  0.020  1.402
 BMR  C3'  C4'   single    1.531  0.020  1.531
 BMR  C3'  H3'   single    0.970  0.020  1.090
 BMR  O3'  HO3'  single    0.850  0.020  0.980
 BMR  O37  C38   single    1.414  0.020  1.414
 BMR  C38  H38   single    0.970  0.020  1.090
 BMR  C38  H38A  single    0.970  0.020  1.090
 BMR  C38  H38B  single    0.970  0.020  1.090
 BMR  C4'  O4'   single    1.411  0.020  1.411
 BMR  C4'  C5'   single    1.508  0.020  1.508
 BMR  C4'  H4'   single    0.970  0.020  1.090
 BMR  C5'  O5'   single    1.433  0.020  1.433
 BMR  C5'  H5'   single    0.970  0.020  1.090
 BMR  C5'  H5'A  single    0.970  0.020  1.090
 BMR  O1A  H1A   single    0.850  0.020  0.980
 BMR  O2B  H2B   single    0.850  0.020  0.980
 BMR  O2C  H2C   single    0.850  0.020  0.980
 BMR  O3C  H3C   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
 BMR  C1'   C1   C6    118.85  3.000
 BMR  C1'   C1   C2    122.39  3.000
 BMR  C6    C1   C2    118.75  3.000
 BMR  H2    C2   C3    118.24  3.000
 BMR  H2    C2   C1    119.76  3.000
 BMR  C3    C2   C1    122.00  3.000
 BMR  C23   C3   C4    119.48  3.000
 BMR  C23   C3   C2    121.78  3.000
 BMR  C4    C3   C2    118.75  3.000
 BMR  C20   C4   C5    122.00  3.000
 BMR  C20   C4   C3    118.79  3.000
 BMR  C5    C4   C3    119.21  3.000
 BMR  H5    C5   C6    121.35  3.000
 BMR  H5    C5   C4    118.19  3.000
 BMR  C6    C5   C4    120.46  3.000
 BMR  O37   C6   C5    124.46  3.000
 BMR  O37   C6   C1    114.72  3.000
 BMR  C5    C6   C1    120.82  3.000
 BMR  O5'   PA   O3A   101.04  3.000
 BMR  O5'   PA   O2A   112.09  3.000
 BMR  O3A   PA   O2A   115.22  3.000
 BMR  O5'   PA   O1A   108.24  3.000
 BMR  O3A   PA   O1A   100.36  3.000
 BMR  O2A   PA   O1A   118.02  3.000
 BMR  O3B   PB   O3A   100.17  3.000
 BMR  O3B   PB   O2B   102.57  3.000
 BMR  O3A   PB   O2B   105.96  3.000
 BMR  O3B   PB   O1B   116.95  3.000
 BMR  O3A   PB   O1B   111.39  3.000
 BMR  O2B   PB   O1B   117.80  3.000
 BMR  O3C   PC   O3B   104.16  3.000
 BMR  O3C   PC   O2C    98.56  3.000
 BMR  O3B   PC   O2C   104.72  3.000
 BMR  O3C   PC   O1C   119.64  3.000
 BMR  O3B   PC   O1C   109.22  3.000
 BMR  O2C   PC   O1C   118.67  3.000
 BMR  H1'   C1'  O4'   108.25  3.000
 BMR  H1'   C1'  C2'   110.30  3.000
 BMR  O4'   C1'  C2'   105.87  3.000
 BMR  H1'   C1'  C1    109.18  3.000
 BMR  O4'   C1'  C1    110.48  3.000
 BMR  C2'   C1'  C1    112.65  3.000
 BMR  H1A   O1A  PA    114.70  3.000
 BMR  H2'A  C2'  H2'   108.08  3.000
 BMR  H2'A  C2'  C3'   113.16  3.000
 BMR  H2'   C2'  C3'   109.50  3.000
 BMR  H2'A  C2'  C1'   113.20  3.000
 BMR  H2'   C2'  C1'   110.30  3.000
 BMR  C3'   C2'  C1'   102.51  3.000
 BMR  H20   C20  C21   120.24  3.000
 BMR  H20   C20  C4    119.15  3.000
 BMR  C21   C20  C4    120.61  3.000
 BMR  H21   C21  C22   119.55  3.000
 BMR  H21   C21  C20   119.92  3.000
 BMR  C22   C21  C20   120.54  3.000
 BMR  H22   C22  C23   120.24  3.000
 BMR  H22   C22  C21   119.74  3.000
 BMR  C23   C22  C21   120.01  3.000
 BMR  H23   C23  C22   120.53  3.000
 BMR  H23   C23  C3    118.90  3.000
 BMR  C22   C23  C3    120.57  3.000
 BMR  H2B   O2B  PB    114.41  3.000
 BMR  H2C   O2C  PC    114.52  3.000
 BMR  H3'   C3'  C4'   109.90  3.000
 BMR  H3'   C3'  O3'   111.12  3.000
 BMR  C4'   C3'  O3'   113.83  3.000
 BMR  H3'   C3'  C2'   109.46  3.000
 BMR  C4'   C3'  C2'   100.50  3.000
 BMR  O3'   C3'  C2'   111.52  3.000
 BMR  HO3'  O3'  C3'   108.90  3.000
 BMR  C38   O37  C6    118.70  3.000
 BMR  H38B  C38  H38A  108.83  3.000
 BMR  H38B  C38  H38   108.93  3.000
 BMR  H38A  C38  H38   108.91  3.000
 BMR  H38B  C38  O37   111.81  3.000
 BMR  H38A  C38  O37   111.78  3.000
 BMR  H38   C38  O37   106.49  3.000
 BMR  PB    O3A  PA    133.39  3.000
 BMR  PC    O3B  PB    129.60  3.000
 BMR  H3C   O3C  PC    114.94  3.000
 BMR  H4'   C4'  C5'   105.69  3.000
 BMR  H4'   C4'  O4'   110.86  3.000
 BMR  C5'   C4'  O4'   110.30  3.000
 BMR  H4'   C4'  C3'   107.92  3.000
 BMR  C5'   C4'  C3'   117.00  3.000
 BMR  O4'   C4'  C3'   105.09  3.000
 BMR  C4'   O4'  C1'   110.62  3.000
 BMR  H5'A  C5'  H5'   107.98  3.000
 BMR  H5'A  C5'  O5'   110.10  3.000
 BMR  H5'   C5'  O5'   110.37  3.000
 BMR  H5'A  C5'  C4'   109.05  3.000
 BMR  H5'   C5'  C4'   109.94  3.000
 BMR  O5'   C5'  C4'   109.38  3.000
 BMR  C5'   O5'  PA    124.42  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
 BMR  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 BMR  CONST_02  C23  C3   C2   C1    180.00   0.0  0
 BMR  CONST_03  C4   C5   C6   C1      0.00   0.0  0
 BMR  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 BMR  CONST_05  C5   C4   C3   C2      0.00   0.0  0
 BMR  CONST_06  C20  C4   C3   C2    180.00   0.0  0
 BMR  CONST_07  C22  C23  C3   C2    180.00   0.0  0
 BMR  CONST_08  C6   C1   C2   C3      0.00   0.0  0
 BMR  CONST_09  C6   C5   C4   C3      0.00   0.0  0
 BMR  CONST_10  C21  C20  C4   C3      0.00   0.0  0
 BMR  CONST_11  C21  C22  C23  C3      0.00   0.0  0
 BMR  CONST_12  C22  C23  C3   C4      0.00   0.0  0
 BMR  CONST_13  C22  C21  C20  C4      0.00   0.0  0
 BMR  CONST_14  C23  C3   C4   C5    180.00   0.0  0
 BMR  CONST_15  C21  C20  C4   C5    180.00   0.0  0
 BMR  CONST_16  C20  C4   C5   C6    180.00   0.0  0
 BMR  CONST_17  C23  C3   C4   C20     0.00   0.0  0
 BMR  CONST_18  C23  C22  C21  C20     0.00   0.0  0
 BMR  CONST_19  C1'  C1   C2   C3    180.00   0.0  0
 BMR  CONST_20  C1'  C1   C6   C5    180.00   0.0  0
 BMR  CONST_21  O37  C6   C1   C2    180.00   0.0  0
 BMR  CONST_22  O37  C6   C5   C4    180.00   0.0  0
 BMR  CONST_23  O37  C6   C1   C1'     0.00   0.0  0
 BMR  CONST_24  H5   C5   C6   C1    180.00   0.0  0
 BMR  CONST_25  H23  C23  C3   C2      0.00   0.0  0
 BMR  CONST_26  H20  C20  C4   C3    180.00   0.0  0
 BMR  CONST_27  H22  C22  C23  C3    180.00   0.0  0
 BMR  CONST_28  H2   C2   C3   C4    180.00   0.0  0
 BMR  CONST_29  H21  C21  C20  C4    180.00   0.0  0
 BMR  Var_01    C4'  C5'  O5'  PA    169.55  30.0  2
 BMR  Var_02    H38  C38  O37  C6    179.62  30.0  3
 BMR  Var_03    O1B  PB   O3A  PA   -154.39  30.0  2
 BMR  Var_04    O1A  PA   O3A  PB    -44.38  30.0  1
 BMR  Var_05    O1C  PC   O3B  PB    151.13  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
 BMR  chir_03  C1'  C1   C2'  O4'  negativ
 BMR  chir_04  C3'  O3'  C4'  C2'  positiv
 BMR  chir_05  C4'  O4'  C3'  C5'  negativ
 BMR  chir_06  PA   O2A  O3A  O5'  both
 BMR  chir_07  PB   O2B  O3A  O3B  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
 BMR  plan-1  C1   0.020
 BMR  plan-1  C2   0.020
 BMR  plan-1  C3   0.020
 BMR  plan-1  C4   0.020
 BMR  plan-1  C5   0.020
 BMR  plan-1  C6   0.020
 BMR  plan-1  C1'  0.020
 BMR  plan-1  C20  0.020
 BMR  plan-1  C21  0.020
 BMR  plan-1  C22  0.020
 BMR  plan-1  C23  0.020
 BMR  plan-1  O37  0.020
 BMR  plan-1  H2   0.020
 BMR  plan-1  H5   0.020
 BMR  plan-1  H20  0.020
 BMR  plan-1  H21  0.020
 BMR  plan-1  H22  0.020
 BMR  plan-1  H23  0.020

