# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 04:05:58 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 5'-O-[(R)-{[(3S)-3-aminobutanoyl]oxy}(hydroxy)phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](N)CC(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
#
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
 6L1  6L1  5'-O-[(R)-{[(3S)-3-aminobutanoyl]oxy}(hydroxy)phosphoryl]adenosine  ligand  50  29  .  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_6L1
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
 6L1  C1   C  CR56  0   0.487   4.1715  -0.7364   0.5107
 6L1  C2   C  CR56  0  -0.002   4.3570  -1.7685  -0.3947
 6L1  C3   C  CR6   0   0.459   5.6249  -2.3806  -0.3869
 6L1  C4   C  CR15  0   0.101   2.3729  -1.1026  -0.6746
 6L1  N1   N  N     0  -0.474   6.5341  -1.9257   0.4828
 6L1  N2   N  N     0  -0.458   5.0653  -0.2710   1.3819
 6L1  C5   C  CH3   0  -0.654  -7.3877  -2.4765   2.0739
 6L1  C6   C  CH1   0  -0.107  -7.0196  -1.6568   0.8444
 6L1  N3   N  NH2   0  -0.787  -7.1953  -2.4724  -0.3458
 6L1  C7   C  CH2   0  -0.581  -5.6084  -1.0871   1.0281
 6L1  C8   C  C     0   0.615  -5.1773  -0.1524  -0.0579
 6L1  O1   O  O     0  -0.405  -5.8653   0.3411  -0.9035
 6L1  O2   O  O2    0  -0.579  -3.8444   0.1128   0.0225
 6L1  P1   P  P     0   1.464  -3.1014   1.1425  -1.0042
 6L1  O3   O  O     0  -0.674  -3.5921   2.5265  -1.0171
 6L1  O4   O  OH1   0  -0.729  -3.1604   0.4916  -2.4504
 6L1  O5   O  O2    0  -0.575  -1.6474   0.8861  -0.4135
 6L1  C10  C  CH1   0   0.012   0.4683   1.8861   0.0800
 6L1  O6   O  O2    0  -0.493   0.8728   0.7338   0.8108
 6L1  C11  C  CH1   0  -0.041   1.7618   2.4843  -0.4690
 6L1  O7   O  OH1   0  -0.654   1.6086   3.8568  -0.6840
 6L1  C12  C  CH1   0  -0.045   2.7532   2.1337   0.6464
 6L1  O8   O  OH1   0  -0.662   2.5992   2.9917   1.7417
 6L1  C13  C  CH1   0   0.176   2.2449   0.7565   1.0694
 6L1  N4   N  NR5   0  -0.537   2.8903  -0.3116   0.3148
 6L1  N5   N  N     0  -0.450   3.2192  -1.9823  -1.1260
 6L1  C14  C  CR16  0   0.039   6.2111  -0.9243   1.2973
 6L1  N6   N  NH2   0  -0.816   5.9483  -3.3803  -1.2070
 6L1  H1   H  HCR5  0   0.295   1.3560  -1.0030  -1.0188
 6L1  H3   H  HCH3  0   0.237  -8.3974  -2.8751   1.9796
 6L1  H4   H  HCH3  0   0.220  -6.7030  -3.3186   2.2000
 6L1  H5   H  HCH1  0   0.236  -7.7201  -0.8203   0.7714
 6L1  H6   H  HNH2  0   0.347  -7.0174  -1.9323  -1.1823
 6L1  H7   H  HNH2  0   0.338  -6.5272  -3.2351  -0.3472
 6L1  H9   H  HCH2  0   0.294  -5.5389  -0.5291   1.9694
 6L1  H10  H  HCH2  0   0.281  -4.8769  -1.8967   1.1092
 6L1  H11  H  HOH1  0   0.505  -2.8076  -0.4049  -2.5413
 6L1  H12  H  HCH2  0   0.252  -0.0492   0.8039  -1.7137
 6L1  H13  H  HCH2  0   0.265  -0.7700   2.4118  -1.5584
 6L1  H14  H  HCH1  0   0.261  -0.0149   2.5992   0.7584
 6L1  H15  H  HCH1  0   0.252   2.0549   1.9609  -1.3889
 6L1  H16  H  HOH1  0   0.471   2.2789   4.1503  -1.3094
 6L1  H17  H  HCH1  0   0.266   3.7902   2.0991   0.2927
 6L1  H18  H  HOH1  0   0.454   2.4826   3.8878   1.4027
 6L1  H19  H  HCH1  0   0.288   2.4385   0.5681   2.1289
 6L1  H20  H  HCR6  0   0.253   6.9942  -0.6070   1.9778
 6L1  H21  H  HNH2  0   0.412   5.2800  -3.7588  -1.8546
 6L1  H22  H  HNH2  0   0.404   6.8580  -3.8054  -1.1563
 6L1  C9   C  CH2   0  -0.188  -0.5004   1.5056  -1.0092
 6L1  H2   H  HCH3  0   0.229  -7.3447  -1.8742   2.9817

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
 6L1  C5   C6   single    1.523  0.020  1.523
 6L1  C6   C7   single    1.533  0.020  1.533
 6L1  C6   N3   single    1.453  0.020  1.453
 6L1  C7   C8   single    1.496  0.020  1.496
 6L1  O1   C8   double    1.197  0.020  1.197
 6L1  C8   O2   single    1.361  0.020  1.361
 6L1  O3   P1   double    1.468  0.020  1.468
 6L1  N6   C3   single    1.333  0.020  1.333
 6L1  O2   P1   single    1.633  0.020  1.633
 6L1  C3   C2   aromatic  1.408  0.020  1.408
 6L1  C3   N1   aromatic  1.338  0.020  1.338
 6L1  N5   C2   aromatic  1.369  0.020  1.369
 6L1  N5   C4   aromatic  1.301  0.020  1.301
 6L1  P1   O5   single    1.590  0.020  1.590
 6L1  P1   O4   single    1.587  0.020  1.587
 6L1  C2   C1   aromatic  1.385  0.020  1.385
 6L1  N1   C14  aromatic  1.331  0.020  1.331
 6L1  C4   N4   aromatic  1.368  0.020  1.368
 6L1  O5   C9   single    1.433  0.020  1.433
 6L1  C1   N4   aromatic  1.364  0.020  1.364
 6L1  C1   N2   aromatic  1.332  0.020  1.332
 6L1  C14  N2   aromatic  1.322  0.020  1.322
 6L1  N4   C13  single    1.458  0.020  1.458
 6L1  O6   C13  single    1.396  0.020  1.396
 6L1  O6   C10  single    1.423  0.020  1.423
 6L1  C13  C12  single    1.528  0.020  1.528
 6L1  C9   C10  single    1.506  0.020  1.506
 6L1  C10  C11  single    1.527  0.020  1.527
 6L1  C12  C11  single    1.533  0.020  1.533
 6L1  C12  O8   single    1.400  0.020  1.400
 6L1  C11  O7   single    1.398  0.020  1.398
 6L1  C4   H1   single    0.930  0.020  1.080
 6L1  C5   H2   single    0.970  0.020  1.090
 6L1  C5   H3   single    0.970  0.020  1.090
 6L1  C5   H4   single    0.970  0.020  1.090
 6L1  C6   H5   single    0.970  0.020  1.090
 6L1  N3   H6   single    0.890  0.020  1.040
 6L1  N3   H7   single    0.890  0.020  1.040
 6L1  C7   H9   single    0.970  0.020  1.090
 6L1  C7   H10  single    0.970  0.020  1.090
 6L1  O4   H11  single    0.850  0.020  0.980
 6L1  C9   H12  single    0.970  0.020  1.090
 6L1  C9   H13  single    0.970  0.020  1.090
 6L1  C10  H14  single    0.970  0.020  1.090
 6L1  C11  H15  single    0.970  0.020  1.090
 6L1  O7   H16  single    0.850  0.020  0.980
 6L1  C12  H17  single    0.970  0.020  1.090
 6L1  O8   H18  single    0.850  0.020  0.980
 6L1  C13  H19  single    0.970  0.020  1.090
 6L1  C14  H20  single    0.930  0.020  1.080
 6L1  N6   H21  single    0.860  0.020  1.020
 6L1  N6   H22  single    0.860  0.020  1.020

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
 6L1  N4   C1   N2   127.98  3.000
 6L1  N2   C1   C2   126.71  3.000
 6L1  N4   C1   C2   105.30  3.000
 6L1  N5   C2   C3   133.11  3.000
 6L1  N5   C2   C1   110.73  3.000
 6L1  C3   C2   C1   116.16  3.000
 6L1  N6   C3   N1   119.35  3.000
 6L1  N1   C3   C2   117.89  3.000
 6L1  N6   C3   C2   122.77  3.000
 6L1  H1   C4   N5   124.40  3.000
 6L1  H1   C4   N4   122.28  3.000
 6L1  N5   C4   N4   113.31  3.000
 6L1  C14  N1   C3   119.27  3.000
 6L1  C14  N2   C1   111.54  3.000
 6L1  H4   C5   H3   107.98  3.000
 6L1  H4   C5   H2   107.75  3.000
 6L1  H3   C5   H2   108.10  3.000
 6L1  H4   C5   C6   110.89  3.000
 6L1  H3   C5   C6   110.55  3.000
 6L1  H2   C5   C6   111.43  3.000
 6L1  H5   C6   C7   108.26  3.000
 6L1  H5   C6   N3   107.29  3.000
 6L1  C7   C6   N3   114.71  3.000
 6L1  H5   C6   C5   108.11  3.000
 6L1  N3   C6   C5   109.26  3.000
 6L1  C7   C6   C5   109.01  3.000
 6L1  H7   N3   H6   106.54  3.000
 6L1  H7   N3   C6   110.09  3.000
 6L1  H6   N3   C6   110.88  3.000
 6L1  H10  C7   H9   105.70  3.000
 6L1  H10  C7   C8   108.86  3.000
 6L1  H9   C7   C8   106.68  3.000
 6L1  H10  C7   C6   110.45  3.000
 6L1  H9   C7   C6   110.51  3.000
 6L1  C8   C7   C6   114.23  3.000
 6L1  O2   C8   O1   121.62  3.000
 6L1  O2   C8   C7   111.16  3.000
 6L1  O1   C8   C7   127.22  3.000
 6L1  P1   O2   C8   122.09  3.000
 6L1  O5   P1   O4   107.84  3.000
 6L1  O4   P1   O3   111.48  3.000
 6L1  O5   P1   O3   117.43  3.000
 6L1  O4   P1   O2   107.30  3.000
 6L1  O5   P1   O2    94.63  3.000
 6L1  O3   P1   O2   116.60  3.000
 6L1  H11  O4   P1   116.88  3.000
 6L1  C9   O5   P1   120.51  3.000
 6L1  H14  C10  C11  109.93  3.000
 6L1  H14  C10  O6   109.52  3.000
 6L1  C11  C10  O6   105.13  3.000
 6L1  H14  C10  C9   109.16  3.000
 6L1  C11  C10  C9   112.56  3.000
 6L1  O6   C10  C9   110.46  3.000
 6L1  C13  O6   C10  111.17  3.000
 6L1  H15  C11  C12  109.15  3.000
 6L1  H15  C11  O7   111.61  3.000
 6L1  C12  C11  O7   114.04  3.000
 6L1  H15  C11  C10  109.91  3.000
 6L1  O7   C11  C10  110.31  3.000
 6L1  C12  C11  C10  101.34  3.000
 6L1  H16  O7   C11  108.85  3.000
 6L1  H17  C12  C13  112.07  3.000
 6L1  H17  C12  O8   112.08  3.000
 6L1  C13  C12  O8   107.42  3.000
 6L1  H17  C12  C11  112.59  3.000
 6L1  O8   C12  C11  110.98  3.000
 6L1  C13  C12  C11  101.10  3.000
 6L1  H18  O8   C12  107.92  3.000
 6L1  H19  C13  N4   107.27  3.000
 6L1  H19  C13  C12  111.39  3.000
 6L1  N4   C13  C12  111.70  3.000
 6L1  H19  C13  O6   110.53  3.000
 6L1  C12  C13  O6   106.88  3.000
 6L1  N4   C13  O6   109.09  3.000
 6L1  C13  N4   C4   129.06  3.000
 6L1  C13  N4   C1   124.71  3.000
 6L1  C4   N4   C1   106.20  3.000
 6L1  C4   N5   C2   104.45  3.000
 6L1  H20  C14  N2   116.17  3.000
 6L1  H20  C14  N1   115.39  3.000
 6L1  N2   C14  N1   128.43  3.000
 6L1  H22  N6   H21  118.37  3.000
 6L1  H22  N6   C3   120.38  3.000
 6L1  H21  N6   C3   121.18  3.000
 6L1  H13  C9   H12  108.08  3.000
 6L1  H13  C9   C10  108.20  3.000
 6L1  H12  C9   C10  111.29  3.000
 6L1  H13  C9   O5   111.69  3.000
 6L1  H12  C9   O5   108.72  3.000
 6L1  C10  C9   O5   108.86  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
 6L1  CONST_01  N1   C3   C2  C1     0.00   0.0  0
 6L1  CONST_02  C4   N5   C2  C1     0.00   0.0  0
 6L1  CONST_03  N5   C4   N4  C1     0.00   0.0  0
 6L1  CONST_04  N1   C14  N2  C1     0.00   0.0  0
 6L1  CONST_05  C14  N1   C3  C2     0.00   0.0  0
 6L1  CONST_06  N4   C4   N5  C2     0.00   0.0  0
 6L1  CONST_07  C4   N4   C1  C2     0.00   0.0  0
 6L1  CONST_08  C14  N2   C1  C2     0.00   0.0  0
 6L1  CONST_09  C4   N5   C2  C3   180.00   0.0  0
 6L1  CONST_10  N4   C1   C2  C3   180.00   0.0  0
 6L1  CONST_11  N2   C1   C2  C3     0.00   0.0  0
 6L1  CONST_12  N2   C14  N1  C3     0.00   0.0  0
 6L1  CONST_13  N2   C1   N4  C4   180.00   0.0  0
 6L1  CONST_14  N5   C2   C3  N1   180.00   0.0  0
 6L1  CONST_15  N5   C2   C1  N2   180.00   0.0  0
 6L1  CONST_16  N5   C2   C1  N4     0.00   0.0  0
 6L1  CONST_17  C14  N2   C1  N4   180.00   0.0  0
 6L1  CONST_18  C13  N4   C1  C2   180.00   0.0  0
 6L1  CONST_19  C13  N4   C1  N2     0.00   0.0  0
 6L1  CONST_20  N5   C4   N4  C13  180.00   0.0  0
 6L1  CONST_21  N6   C3   C2  C1   180.00   0.0  0
 6L1  CONST_22  N6   C3   C2  N5     0.00   0.0  0
 6L1  CONST_23  N6   C3   N1  C14  180.00   0.0  0
 6L1  CONST_24  H1   C4   N4  C1   180.00   0.0  0
 6L1  CONST_25  H20  C14  N2  C1   180.00   0.0  0
 6L1  CONST_26  H21  N6   C3  C2     0.00   0.0  0
 6L1  CONST_27  H22  N6   C3  C2   180.00   0.0  0
 6L1  Var_01    C10  C9   O5  P1   143.06  30.0  3
 6L1  Var_02    O1   C8   C7  C6    12.51  30.0  3
 6L1  Var_03    O3   P1   O2  C8    59.73  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
 6L1  chir_01  C6   C5  C7   N3   negativ
 6L1  chir_03  C10  O6  C9   C11  positiv
 6L1  chir_04  C11  O7  C10  C12  positiv
 6L1  chir_05  C12  O8  C11  C13  positiv
 6L1  chir_06  C13  O6  N4   C12  negativ
 6L1  chir_07  P1   O2  O5   O4   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
 6L1  plan-1  C1   0.020
 6L1  plan-1  C2   0.020
 6L1  plan-1  C3   0.020
 6L1  plan-1  C4   0.020
 6L1  plan-1  N1   0.020
 6L1  plan-1  N2   0.020
 6L1  plan-1  C13  0.020
 6L1  plan-1  N4   0.020
 6L1  plan-1  N5   0.020
 6L1  plan-1  C14  0.020
 6L1  plan-1  N6   0.020
 6L1  plan-1  H1   0.020
 6L1  plan-1  H20  0.020
 6L1  plan-2  C3   0.020
 6L1  plan-2  N6   0.020
 6L1  plan-2  H21  0.020
 6L1  plan-2  H22  0.020
 6L1  plan-3  C7   0.020
 6L1  plan-3  C8   0.020
 6L1  plan-3  O1   0.020
 6L1  plan-3  O2   0.020

