# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 03:40:21 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: 5'-O-[(S)-{[(2S)-2-amino-3-carboxypropanoyl]oxy}(hydroxy)phosphoryl]-2'-deoxyadenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC(O)=O)C(=O)O[P@](O)(=O)OC[C@H]1O[C@H](C[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
 AMD  AMD  5'-O-[(S)-{[(2S)-2-amino-3-carboxypropanoyl]oxy}(hydroxy)phosphoryl]-2'-deoxyadenosine  ligand  49  30  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AMD
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
 AMD  P     P  P     0   1.475   2.6052   2.0665   0.9230
 AMD  O1P   O  O     0  -0.679   2.5470   1.9278   2.3836
 AMD  O2P   O  OH1   0  -0.722   3.3160   3.4127   0.4822
 AMD  O3P   O  O2    0  -0.579   3.3487   0.8540   0.1127
 AMD  O5'   O  O2    0  -0.579   1.2383   1.9562   0.1215
 AMD  C5'   C  CH2   0  -0.174   0.0320   2.4998   0.6761
 AMD  C4'   C  CH1   0  -0.002  -1.0197   2.5069  -0.4014
 AMD  O4'   O  O2    0  -0.491  -1.2800   1.1808  -0.8370
 AMD  C1'   C  CH1   0   0.175  -2.6444   1.0009  -1.1124
 AMD  N9    N  NR5   0  -0.526  -3.1518  -0.0577  -0.2523
 AMD  C4    C  CR56  0   0.488  -4.0943  -0.9786  -0.6048
 AMD  N3    N  N     0  -0.459  -4.7097  -1.1190  -1.7776
 AMD  C2    C  CR16  0   0.043  -5.5609  -2.1297  -1.7632
 AMD  N1    N  N     0  -0.474  -5.8447  -2.9582  -0.7615
 AMD  C6    C  CR6   0   0.458  -5.2204  -2.8024   0.4116
 AMD  N6    N  NH2   0  -0.816  -5.5049  -3.6302   1.4172
 AMD  C5    C  CR56  0  -0.007  -4.2852  -1.7568   0.5262
 AMD  N7    N  N     0  -0.449  -3.4828  -1.3293   1.5509
 AMD  C8    C  CR15  0   0.108  -2.8300  -0.3213   1.0506
 AMD  C2'   C  CH2   0  -0.543  -3.3182   2.3495  -0.8813
 AMD  C3'   C  CH1   0   0.014  -2.3644   3.0452   0.0852
 AMD  O3'   O  OH1   0  -0.658  -2.3583   4.4419   0.0316
 AMD  N     N  NH2   0  -0.782   6.4575  -0.8961  -0.3542
 AMD  CA    C  CH1   0  -0.234   5.0262  -0.7347  -0.4079
 AMD  CB    C  CH2   0  -0.602   4.2035  -1.9117   0.1404
 AMD  CG    C  C     0   0.563   4.3782  -3.1634  -0.6780
 AMD  OD1   O  O     0  -0.440   4.8886  -3.2134  -1.7693
 AMD  OD2   O  OH1   0  -0.589   3.8675  -4.2203  -0.0617
 AMD  C     C  C     0   0.622   4.6421   0.5185   0.3493
 AMD  O     O  O     0  -0.389   5.3451   1.1514   1.0771
 AMD  HOP2  H  HOH1  0   0.506   3.3065   3.6229  -0.4624
 AMD  H5'1  H  HCH2  0   0.251  -0.2844   1.8945   1.5289
 AMD  H5'2  H  HCH2  0   0.261   0.1840   3.5257   1.0208
 AMD  H4'   H  HCH1  0   0.255  -0.6765   3.1178  -1.2473
 AMD  H1'   H  HCH1  0   0.276  -2.7872   0.6465  -2.1350
 AMD  H2    H  HCR6  0   0.252  -6.1025  -2.3119  -2.6852
 AMD  H61   H  HNH2  0   0.412  -5.0389  -3.5517   2.3037
 AMD  H62   H  HNH2  0   0.404  -6.1582  -4.3827   1.2854
 AMD  H8    H  HCR5  0   0.289  -2.0920   0.2546   1.5873
 AMD  H2'1  H  HCH2  0   0.271  -3.3439   2.9060  -1.8206
 AMD  H2'2  H  HCH2  0   0.285  -4.3384   2.2524  -0.5130
 AMD  H3'   H  HCH1  0   0.224  -2.5512   2.6927   1.1104
 AMD  HO'3  H  HOH1  0   0.464  -3.1537   4.7695   0.4623
 AMD  HN2   H  HNH2  0   0.363   6.7395  -1.6146  -1.0063
 AMD  HA    H  HCH1  0   0.298   4.7402  -0.5700  -1.4511
 AMD  HB1   H  HCH2  0   0.295   4.4811  -2.1158   1.1781
 AMD  HB2   H  HCH2  0   0.306   3.1326  -1.6877   0.1492
 AMD  HD2   H  HOH1  0   0.483   3.9615  -5.0086  -0.6176
 AMD  H     H  HNH2  0   0.352   6.7529  -1.2015   0.5650

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
 AMD  P    O1P   double    1.468  0.020  1.468
 AMD  P    O2P   single    1.585  0.020  1.585
 AMD  P    O3P   single    1.637  0.020  1.637
 AMD  P    O5'   single    1.588  0.020  1.588
 AMD  O2P  HOP2  single    0.850  0.020  0.980
 AMD  O3P  C     single    1.357  0.020  1.357
 AMD  O5'  C5'   single    1.435  0.020  1.435
 AMD  C5'  C4'   single    1.506  0.020  1.506
 AMD  C5'  H5'1  single    0.970  0.020  1.090
 AMD  C5'  H5'2  single    0.970  0.020  1.090
 AMD  C4'  O4'   single    1.420  0.020  1.420
 AMD  C4'  C3'   single    1.528  0.020  1.528
 AMD  C4'  H4'   single    0.970  0.020  1.090
 AMD  O4'  C1'   single    1.403  0.020  1.403
 AMD  C1'  N9    single    1.455  0.020  1.455
 AMD  C1'  C2'   single    1.525  0.020  1.525
 AMD  C1'  H1'   single    0.970  0.020  1.090
 AMD  N9   C4    aromatic  1.364  0.020  1.364
 AMD  N9   C8    aromatic  1.368  0.020  1.368
 AMD  C4   N3    aromatic  1.332  0.020  1.332
 AMD  C4   C5    aromatic  1.386  0.020  1.386
 AMD  N3   C2    aromatic  1.321  0.020  1.321
 AMD  C2   N1    aromatic  1.331  0.020  1.331
 AMD  C2   H2    single    0.930  0.020  1.080
 AMD  N1   C6    aromatic  1.338  0.020  1.338
 AMD  C6   N6    single    1.333  0.020  1.333
 AMD  C6   C5    aromatic  1.408  0.020  1.408
 AMD  N6   H61   single    0.860  0.020  1.020
 AMD  N6   H62   single    0.860  0.020  1.020
 AMD  C5   N7    aromatic  1.370  0.020  1.370
 AMD  N7   C8    aromatic  1.301  0.020  1.301
 AMD  C8   H8    single    0.930  0.020  1.080
 AMD  C2'  C3'   single    1.526  0.020  1.526
 AMD  C2'  H2'1  single    0.970  0.020  1.090
 AMD  C2'  H2'2  single    0.970  0.020  1.090
 AMD  C3'  O3'   single    1.398  0.020  1.398
 AMD  C3'  H3'   single    0.970  0.020  1.090
 AMD  O3'  HO'3  single    0.850  0.020  0.980
 AMD  N    CA    single    1.441  0.020  1.441
 AMD  N    H     single    0.860  0.020  1.020
 AMD  N    HN2   single    0.890  0.020  1.040
 AMD  CA   CB    single    1.537  0.020  1.537
 AMD  CA   C     single    1.514  0.020  1.514
 AMD  CA   HA    single    0.970  0.020  1.090
 AMD  CB   CG    single    1.506  0.020  1.506
 AMD  CB   HB1   single    0.970  0.020  1.090
 AMD  CB   HB2   single    0.970  0.020  1.090
 AMD  CG   OD1   double    1.206  0.020  1.206
 AMD  CG   OD2   single    1.326  0.020  1.326
 AMD  OD2  HD2   single    0.850  0.020  0.980
 AMD  C    O     double    1.194  0.020  1.194

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
 AMD  O5'   P    O3P    95.15  3.000
 AMD  O5'   P    O2P   107.73  3.000
 AMD  O3P   P    O2P   106.72  3.000
 AMD  O5'   P    O1P   117.47  3.000
 AMD  O3P   P    O1P   116.13  3.000
 AMD  O2P   P    O1P   112.00  3.000
 AMD  HOP2  O2P  P     116.84  3.000
 AMD  C     O3P  P     121.99  3.000
 AMD  C5'   O5'  P     120.15  3.000
 AMD  H5'2  C5'  H5'1  108.30  3.000
 AMD  H5'2  C5'  C4'   108.57  3.000
 AMD  H5'1  C5'  C4'   111.03  3.000
 AMD  H5'2  C5'  O5'   111.14  3.000
 AMD  H5'1  C5'  O5'   109.59  3.000
 AMD  C4'   C5'  O5'   108.21  3.000
 AMD  H4'   C4'  C3'   108.92  3.000
 AMD  H4'   C4'  O4'   109.91  3.000
 AMD  C3'   C4'  O4'   105.39  3.000
 AMD  H4'   C4'  C5'   109.60  3.000
 AMD  C3'   C4'  C5'   112.86  3.000
 AMD  O4'   C4'  C5'   110.07  3.000
 AMD  C1'   O4'  C4'   110.99  3.000
 AMD  H1'   C1'  C2'   111.79  3.000
 AMD  H1'   C1'  N9    105.77  3.000
 AMD  C2'   C1'  N9    113.55  3.000
 AMD  H1'   C1'  O4'   110.65  3.000
 AMD  C2'   C1'  O4'   106.64  3.000
 AMD  N9    C1'  O4'   108.43  3.000
 AMD  C8    N9   C4    106.17  3.000
 AMD  C8    N9   C1'   128.40  3.000
 AMD  C4    N9   C1'   125.40  3.000
 AMD  C5    C4   N3    126.56  3.000
 AMD  C5    C4   N9    105.27  3.000
 AMD  N3    C4   N9    128.17  3.000
 AMD  C2    N3   C4    111.63  3.000
 AMD  H2    C2   N1    115.39  3.000
 AMD  H2    C2   N3    116.15  3.000
 AMD  N1    C2   N3    128.45  3.000
 AMD  C6    N1   C2    119.21  3.000
 AMD  C5    C6   N6    122.79  3.000
 AMD  C5    C6   N1    117.90  3.000
 AMD  N6    C6   N1    119.31  3.000
 AMD  H62   N6   H61   118.40  3.000
 AMD  H62   N6   C6    120.30  3.000
 AMD  H61   N6   C6    121.21  3.000
 AMD  N7    C5   C6    133.00  3.000
 AMD  N7    C5   C4    110.76  3.000
 AMD  C6    C5   C4    116.24  3.000
 AMD  C8    N7   C5    104.36  3.000
 AMD  H8    C8   N7    124.43  3.000
 AMD  H8    C8   N9    122.13  3.000
 AMD  N7    C8   N9    113.43  3.000
 AMD  H2'2  C2'  H2'1  108.32  3.000
 AMD  H2'2  C2'  C3'   114.34  3.000
 AMD  H2'1  C2'  C3'   109.10  3.000
 AMD  H2'2  C2'  C1'   112.72  3.000
 AMD  H2'1  C2'  C1'   109.31  3.000
 AMD  C3'   C2'  C1'   102.89  3.000
 AMD  H3'   C3'  O3'   110.90  3.000
 AMD  H3'   C3'  C2'   109.76  3.000
 AMD  O3'   C3'  C2'   115.72  3.000
 AMD  H3'   C3'  C4'   109.47  3.000
 AMD  O3'   C3'  C4'   109.63  3.000
 AMD  C2'   C3'  C4'   100.82  3.000
 AMD  HO'3  O3'  C3'   108.64  3.000
 AMD  HN2   N    H     106.86  3.000
 AMD  HN2   N    CA    109.44  3.000
 AMD  H     N    CA    110.93  3.000
 AMD  HA    CA   C     106.62  3.000
 AMD  HA    CA   CB    108.39  3.000
 AMD  C     CA   CB    108.65  3.000
 AMD  HA    CA   N     108.17  3.000
 AMD  C     CA   N     109.03  3.000
 AMD  CB    CA   N     115.62  3.000
 AMD  HB2   CB   HB1   106.21  3.000
 AMD  HB2   CB   CG    106.74  3.000
 AMD  HB1   CB   CG    109.34  3.000
 AMD  HB2   CB   CA    111.71  3.000
 AMD  HB1   CB   CA    110.22  3.000
 AMD  CG    CB   CA    112.37  3.000
 AMD  OD2   CG   OD1   123.42  3.000
 AMD  OD2   CG   CB    111.43  3.000
 AMD  OD1   CG   CB    125.13  3.000
 AMD  HD2   OD2  CG    110.15  3.000
 AMD  O     C    CA    126.49  3.000
 AMD  O     C    O3P   122.45  3.000
 AMD  CA    C    O3P   111.06  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
 AMD  CONST_01  C2   N3   C4   N9   180.00   0.0  0
 AMD  CONST_02  C6   C5   C4   N9   180.00   0.0  0
 AMD  CONST_03  N7   C5   C4   N9     0.00   0.0  0
 AMD  CONST_04  C5   N7   C8   N9     0.00   0.0  0
 AMD  CONST_05  N7   C8   N9   C4     0.00   0.0  0
 AMD  CONST_06  N1   C2   N3   C4     0.00   0.0  0
 AMD  CONST_07  N1   C6   C5   C4     0.00   0.0  0
 AMD  CONST_08  C8   N7   C5   C4     0.00   0.0  0
 AMD  CONST_09  C8   N9   C4   N3   180.00   0.0  0
 AMD  CONST_10  C6   C5   C4   N3     0.00   0.0  0
 AMD  CONST_11  N7   C5   C4   N3   180.00   0.0  0
 AMD  CONST_12  C6   N1   C2   N3     0.00   0.0  0
 AMD  CONST_13  C5   C4   N3   C2     0.00   0.0  0
 AMD  CONST_14  C5   C6   N1   C2     0.00   0.0  0
 AMD  CONST_15  N7   C5   C6   N1   180.00   0.0  0
 AMD  CONST_16  C8   N7   C5   C6   180.00   0.0  0
 AMD  CONST_17  C8   N9   C4   C5     0.00   0.0  0
 AMD  CONST_18  N3   C4   N9   C1'    0.00   0.0  0
 AMD  CONST_19  C5   C4   N9   C1'  180.00   0.0  0
 AMD  CONST_20  N7   C8   N9   C1'  180.00   0.0  0
 AMD  CONST_21  N6   C6   C5   C4   180.00   0.0  0
 AMD  CONST_22  N6   C6   N1   C2   180.00   0.0  0
 AMD  CONST_23  N7   C5   C6   N6     0.00   0.0  0
 AMD  CONST_24  H8   C8   N9   C1'    0.00   0.0  0
 AMD  CONST_25  H2   C2   N3   C4   180.00   0.0  0
 AMD  CONST_26  H61  N6   C6   N1   180.00   0.0  0
 AMD  CONST_27  H62  N6   C6   N1     0.00   0.0  0
 AMD  CONST_28  HD2  OD2  CG   CB   180.00   0.0  0
 AMD  Var_01    C4'  C5'  O5'  P    168.49  30.0  3
 AMD  Var_02    CA   C    O3P  P    173.08  30.0  3
 AMD  Var_03    OD1  CG   CB   CA   -13.08  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
 AMD  chir_02  C4'  C5'  O4'  C3'  negativ
 AMD  chir_03  C1'  O4'  N9   C2'  negativ
 AMD  chir_04  C3'  O3'  C4'  C2'  positiv
 AMD  chir_05  CA   N    CB   C    negativ
 AMD  chir_06  P    O2P  O3P  O5'  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
 AMD  plan-1  C1'  0.020
 AMD  plan-1  N9   0.020
 AMD  plan-1  C4   0.020
 AMD  plan-1  N3   0.020
 AMD  plan-1  C2   0.020
 AMD  plan-1  N1   0.020
 AMD  plan-1  C6   0.020
 AMD  plan-1  N6   0.020
 AMD  plan-1  C5   0.020
 AMD  plan-1  N7   0.020
 AMD  plan-1  C8   0.020
 AMD  plan-1  H2   0.020
 AMD  plan-1  H8   0.020
 AMD  plan-2  C6   0.020
 AMD  plan-2  N6   0.020
 AMD  plan-2  H61  0.020
 AMD  plan-2  H62  0.020
 AMD  plan-3  CB   0.020
 AMD  plan-3  CG   0.020
 AMD  plan-3  OD1  0.020
 AMD  plan-3  OD2  0.020
 AMD  plan-3  HD2  0.020
 AMD  plan-4  O3P  0.020
 AMD  plan-4  CA   0.020
 AMD  plan-4  C    0.020
 AMD  plan-4  O    0.020

