# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 21:12:04 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: (1R)-1,4-anhydro-2-deoxy-5-O-[(S)-hydroxy(oxido)-lambda~5~-phosphanyl]-1-phenanthren-2-yl-D-erythro-pentitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1C[C@@H](O[C@@H]1CO[PH](O)=O)c2ccc3c(ccc4ccccc34)c2
#
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
 61H  61H  (1R)-1,4-anhydro-2-deoxy-5-O-[(S)-hydroxy(oxido)-lambda~5~-phosphanyl]-1-phenanthren-2-yl-D-erythro-pentitol  ligand  44  25  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_61H
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
 61H  P    P  P     0   1.146   3.6361  -2.1546   0.2699
 61H  O1P  O  O     0  -0.703   2.4030  -2.3613   1.0659
 61H  O2P  O  OH1   0  -0.735   3.6972  -2.8267  -1.1802
 61H  O5'  O  O2    0  -0.587   3.9249  -0.6573  -0.2130
 61H  C5'  C  CH2   0  -0.166   3.7609   0.4518   0.6684
 61H  C4'  C  CR15  0  -0.017   3.3492   1.6535  -0.1589
 61H  O4'  O  O     0  -0.501   2.1546   1.3844  -0.8741
 61H  C1'  C  CR15  0   0.010   1.0732   2.1525  -0.3645
 61H  C1   C  CR6   0   0.115  -0.1751   1.3208  -0.2761
 61H  C2   C  CR16  0  -0.386  -1.3991   1.8834  -0.5490
 61H  C3   C  CR66  0   0.108  -2.5927   1.1492  -0.4271
 61H  C4   C  CR16  0  -0.325  -3.8522   1.7630  -0.7141
 61H  C5   C  CR16  0  -0.326  -5.0051   1.0665  -0.6080
 61H  C6   C  CR66  0   0.078  -5.0038  -0.3068  -0.2071
 61H  C7   C  CR16  0  -0.308  -6.2124  -1.0196  -0.1002
 61H  C8   C  CR16  0  -0.264  -6.2218  -2.3380   0.2836
 61H  C9   C  CR16  0  -0.242  -5.0117  -2.9841   0.5699
 61H  C10  C  CR16  0  -0.354  -3.8198  -2.3056   0.4707
 61H  C11  C  CR66  0   0.127  -3.7805  -0.9526   0.0834
 61H  C12  C  CR66  0   0.107  -2.5458  -0.2041  -0.0282
 61H  C13  C  CR16  0  -0.345  -1.2823  -0.7628   0.2408
 61H  C14  C  CR16  0  -0.308  -0.1296  -0.0261   0.1214
 61H  C3'  C  CR15  0  -0.017   3.0523   2.8567   0.7331
 61H  C2'  C  CH2   0  -0.532   1.5615   2.6726   0.9870
 61H  O3'  O  OH1   0  -0.671   3.3274   4.0218  -0.0095
 61H  H1   H  H     0   0.079   4.7957  -2.5727   0.9371
 61H  H2   H  HOH1  0   0.501   3.5827  -3.7861  -1.1706
 61H  H3   H  HCH2  0   0.231   3.0109   0.2365   1.4349
 61H  H4   H  HCH2  0   0.253   4.7088   0.6602   1.1706
 61H  H5   H  HCR5  0   0.256   4.1485   1.8834  -0.8721
 61H  H6   H  HCR5  0   0.236   0.8810   2.9999  -1.0352
 61H  H7   H  HCR6  0   0.249  -1.4597   2.9183  -0.8691
 61H  H8   H  HCR6  0   0.254  -3.8646   2.8024  -1.0190
 61H  H9   H  HCR6  0   0.255  -5.9545   1.5402  -0.8270
 61H  H10  H  HCR6  0   0.256  -7.1414  -0.5103  -0.3266
 61H  H11  H  HCR6  0   0.259  -7.1566  -2.8767   0.3661
 61H  H12  H  HCR6  0   0.261  -5.0133  -4.0238   0.8700
 61H  H13  H  HCR6  0   0.255  -2.9040  -2.8350   0.6956
 61H  H14  H  HCR6  0   0.250  -1.1956  -1.7966   0.5465
 61H  H15  H  HCR6  0   0.270   0.8178  -0.5041   0.3331
 61H  H16  H  HCR5  0   0.247   3.6369   2.8292   1.6616
 61H  H17  H  HCH2  0   0.276   1.0567   3.5900   1.2919
 61H  H18  H  HCH2  0   0.254   1.3975   1.9288   1.7715
 61H  H19  H  HOH1  0   0.454   3.0406   4.7819   0.5068

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
 61H  O3'  C3'  single    1.409  0.020  1.409
 61H  C2'  C3'  single    1.523  0.020  1.523
 61H  C2'  C1'  single    1.528  0.020  1.528
 61H  C3'  C4'  single    1.527  0.020  1.527
 61H  C14  C13  aromatic  1.373  0.020  1.373
 61H  C14  C1   aromatic  1.405  0.020  1.405
 61H  C13  C12  aromatic  1.407  0.020  1.407
 61H  C10  C9   aromatic  1.375  0.020  1.375
 61H  C10  C11  aromatic  1.408  0.020  1.408
 61H  C9   C8   aromatic  1.401  0.020  1.401
 61H  C1'  C1   single    1.503  0.020  1.503
 61H  C1'  O4'  single    1.421  0.020  1.421
 61H  C1   C2   aromatic  1.375  0.020  1.375
 61H  C12  C11  aromatic  1.448  0.020  1.448
 61H  C12  C3   aromatic  1.412  0.020  1.412
 61H  C11  C6   aromatic  1.413  0.020  1.413
 61H  C8   C7   aromatic  1.373  0.020  1.373
 61H  C2   C3   aromatic  1.407  0.020  1.407
 61H  C4'  O4'  single    1.418  0.020  1.418
 61H  C4'  C5'  single    1.516  0.020  1.516
 61H  C3   C4   aromatic  1.430  0.020  1.430
 61H  C6   C7   aromatic  1.407  0.020  1.407
 61H  C6   C5   aromatic  1.431  0.020  1.431
 61H  C4   C5   aromatic  1.351  0.020  1.351
 61H  C5'  O5'  single    1.426  0.020  1.426
 61H  O2P  P    single    1.599  0.020  1.599
 61H  O5'  P    single    1.600  0.020  1.600
 61H  P    O1P  double    1.482  0.020  1.482
 61H  P    H1   single    1.209  0.020  1.412
 61H  O2P  H2   single    0.850  0.020  0.980
 61H  C5'  H3   single    0.970  0.020  1.090
 61H  C5'  H4   single    0.970  0.020  1.090
 61H  C4'  H5   single    0.970  0.020  1.090
 61H  C1'  H6   single    0.970  0.020  1.090
 61H  C2   H7   single    0.930  0.020  1.080
 61H  C4   H8   single    0.930  0.020  1.080
 61H  C5   H9   single    0.930  0.020  1.080
 61H  C7   H10  single    0.930  0.020  1.080
 61H  C8   H11  single    0.930  0.020  1.080
 61H  C9   H12  single    0.930  0.020  1.080
 61H  C10  H13  single    0.930  0.020  1.080
 61H  C13  H14  single    0.930  0.020  1.080
 61H  C14  H15  single    0.930  0.020  1.080
 61H  C3'  H16  single    0.970  0.020  1.090
 61H  C2'  H17  single    0.970  0.020  1.090
 61H  C2'  H18  single    0.970  0.020  1.090
 61H  O3'  H19  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
 61H  H1   P    O5'  105.88  3.000
 61H  H1   P    O2P  105.94  3.000
 61H  O5'  P    O2P   96.47  3.000
 61H  H1   P    O1P  113.02  3.000
 61H  O5'  P    O1P  116.29  3.000
 61H  O2P  P    O1P  117.39  3.000
 61H  H2   O2P  P    113.81  3.000
 61H  C5'  O5'  P    121.37  3.000
 61H  H4   C5'  H3   108.07  3.000
 61H  H4   C5'  C4'  109.58  3.000
 61H  H3   C5'  C4'  110.63  3.000
 61H  H4   C5'  O5'  109.43  3.000
 61H  H3   C5'  O5'  111.04  3.000
 61H  C4'  C5'  O5'  108.08  3.000
 61H  H5   C4'  C3'  110.90  3.000
 61H  H5   C4'  O4'  109.04  3.000
 61H  C3'  C4'  O4'  106.29  3.000
 61H  H5   C4'  C5'  108.87  3.000
 61H  O4'  C4'  C5'  110.70  3.000
 61H  C3'  C4'  C5'  111.01  3.000
 61H  C1'  O4'  C4'  110.96  3.000
 61H  H6   C1'  C2'  109.48  3.000
 61H  H6   C1'  C1   108.53  3.000
 61H  C2'  C1'  C1   113.69  3.000
 61H  H6   C1'  O4'  109.36  3.000
 61H  C1   C1'  O4'  110.74  3.000
 61H  C2'  C1'  O4'  104.95  3.000
 61H  C14  C1   C2   118.52  3.000
 61H  C2   C1   C1'  120.10  3.000
 61H  C14  C1   C1'  121.35  3.000
 61H  H7   C2   C3   118.43  3.000
 61H  H7   C2   C1   119.92  3.000
 61H  C3   C2   C1   121.65  3.000
 61H  C12  C3   C4   119.83  3.000
 61H  C4   C3   C2   120.39  3.000
 61H  C12  C3   C2   119.78  3.000
 61H  H8   C4   C5   120.46  3.000
 61H  H8   C4   C3   118.58  3.000
 61H  C5   C4   C3   120.96  3.000
 61H  H9   C5   C6   118.51  3.000
 61H  H9   C5   C4   120.42  3.000
 61H  C6   C5   C4   121.07  3.000
 61H  C11  C6   C7   119.75  3.000
 61H  C7   C6   C5   120.45  3.000
 61H  C11  C6   C5   119.80  3.000
 61H  H10  C7   C8   120.26  3.000
 61H  H10  C7   C6   118.84  3.000
 61H  C8   C7   C6   120.89  3.000
 61H  H11  C8   C9   120.06  3.000
 61H  H11  C8   C7   120.34  3.000
 61H  C9   C8   C7   119.60  3.000
 61H  H12  C9   C10  119.69  3.000
 61H  H12  C9   C8   119.89  3.000
 61H  C10  C9   C8   120.41  3.000
 61H  H13  C10  C11  120.26  3.000
 61H  H13  C10  C9   118.53  3.000
 61H  C11  C10  C9   121.22  3.000
 61H  C12  C11  C10  122.80  3.000
 61H  C12  C11  C6   119.07  3.000
 61H  C10  C11  C6   118.13  3.000
 61H  C13  C12  C11  123.06  3.000
 61H  C11  C12  C3   119.27  3.000
 61H  C13  C12  C3   117.67  3.000
 61H  H14  C13  C14  118.04  3.000
 61H  H14  C13  C12  120.36  3.000
 61H  C14  C13  C12  121.60  3.000
 61H  H15  C14  C13  118.74  3.000
 61H  H15  C14  C1   120.48  3.000
 61H  C13  C14  C1   120.78  3.000
 61H  H16  C3'  O3'  111.26  3.000
 61H  H16  C3'  C2'  112.16  3.000
 61H  O3'  C3'  C2'  112.26  3.000
 61H  H16  C3'  C4'  111.77  3.000
 61H  C2'  C3'  C4'  101.09  3.000
 61H  O3'  C3'  C4'  107.80  3.000
 61H  H18  C2'  H17  107.59  3.000
 61H  H18  C2'  C3'  110.40  3.000
 61H  H17  C2'  C3'  113.45  3.000
 61H  H18  C2'  C1'  110.79  3.000
 61H  H17  C2'  C1'  112.68  3.000
 61H  C3'  C2'  C1'  101.91  3.000
 61H  H19  O3'  C3'  108.19  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
 61H  CONST_01  C12  C13  C14  C1      0.00   0.0  0
 61H  CONST_02  C12  C3   C2   C1      0.00   0.0  0
 61H  CONST_03  C4   C3   C2   C1    180.00   0.0  0
 61H  CONST_04  C13  C14  C1   C2      0.00   0.0  0
 61H  CONST_05  C13  C12  C3   C2      0.00   0.0  0
 61H  CONST_06  C11  C12  C3   C2    180.00   0.0  0
 61H  CONST_07  C5   C4   C3   C2    180.00   0.0  0
 61H  CONST_08  C14  C13  C12  C3      0.00   0.0  0
 61H  CONST_09  C10  C11  C12  C3    180.00   0.0  0
 61H  CONST_10  C6   C11  C12  C3      0.00   0.0  0
 61H  CONST_11  C14  C1   C2   C3      0.00   0.0  0
 61H  CONST_12  C6   C5   C4   C3      0.00   0.0  0
 61H  CONST_13  C13  C12  C3   C4    180.00   0.0  0
 61H  CONST_14  C11  C12  C3   C4      0.00   0.0  0
 61H  CONST_15  C11  C6   C5   C4      0.00   0.0  0
 61H  CONST_16  C7   C6   C5   C4    180.00   0.0  0
 61H  CONST_17  C10  C11  C6   C5    180.00   0.0  0
 61H  CONST_18  C12  C11  C6   C5      0.00   0.0  0
 61H  CONST_19  C8   C7   C6   C5    180.00   0.0  0
 61H  CONST_20  C12  C3   C4   C5      0.00   0.0  0
 61H  CONST_21  C9   C10  C11  C6      0.00   0.0  0
 61H  CONST_22  C13  C12  C11  C6    180.00   0.0  0
 61H  CONST_23  C9   C8   C7   C6      0.00   0.0  0
 61H  CONST_24  C10  C9   C8   C7      0.00   0.0  0
 61H  CONST_25  C10  C11  C6   C7      0.00   0.0  0
 61H  CONST_26  C12  C11  C6   C7    180.00   0.0  0
 61H  CONST_27  C11  C10  C9   C8      0.00   0.0  0
 61H  CONST_28  C11  C6   C7   C8      0.00   0.0  0
 61H  CONST_29  C12  C11  C10  C9    180.00   0.0  0
 61H  CONST_30  C13  C12  C11  C10     0.00   0.0  0
 61H  CONST_31  C14  C13  C12  C11   180.00   0.0  0
 61H  CONST_32  C13  C14  C1   C1'   180.00   0.0  0
 61H  CONST_33  C3   C2   C1   C1'   180.00   0.0  0
 61H  CONST_34  H15  C14  C1   C1'     0.00   0.0  0
 61H  CONST_35  H7   C2   C1   C1'     0.00   0.0  0
 61H  CONST_36  H14  C13  C14  C1    180.00   0.0  0
 61H  CONST_37  H8   C4   C3   C2      0.00   0.0  0
 61H  CONST_38  H9   C5   C4   C3    180.00   0.0  0
 61H  CONST_39  H10  C7   C6   C5      0.00   0.0  0
 61H  CONST_40  H13  C10  C11  C6    180.00   0.0  0
 61H  CONST_41  H11  C8   C7   C6    180.00   0.0  0
 61H  CONST_42  H12  C9   C8   C7    180.00   0.0  0
 61H  Var_01    C4'  C5'  O5'  P    -149.07  30.0  2
 61H  Var_02    H1   P    O5'  C5'   -82.34  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
 61H  chir_02  C4'  C3'  O4'  C5'  positiv
 61H  chir_03  C1'  O4'  C2'  C1   positiv
 61H  chir_04  C3'  O3'  C4'  C2'  positiv
 61H  chir_05  P    O2P  O5'  O1P  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
 61H  plan-1  C1'  0.020
 61H  plan-1  C1   0.020
 61H  plan-1  C2   0.020
 61H  plan-1  C3   0.020
 61H  plan-1  C4   0.020
 61H  plan-1  C5   0.020
 61H  plan-1  C6   0.020
 61H  plan-1  C7   0.020
 61H  plan-1  C8   0.020
 61H  plan-1  C9   0.020
 61H  plan-1  C10  0.020
 61H  plan-1  C11  0.020
 61H  plan-1  C12  0.020
 61H  plan-1  C13  0.020
 61H  plan-1  C14  0.020
 61H  plan-1  H7   0.020
 61H  plan-1  H8   0.020
 61H  plan-1  H9   0.020
 61H  plan-1  H10  0.020
 61H  plan-1  H11  0.020
 61H  plan-1  H12  0.020
 61H  plan-1  H13  0.020
 61H  plan-1  H14  0.020
 61H  plan-1  H15  0.020

