# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 22:57:41 2022
#   Inital geometry file: a 91 line input string
#   Ligand name: (2~{S})-2-[2-(6-aminopurin-9-yl)ethylamino]-3-phosphono-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(CCN[C@H](C[P](O)(O)=O)C(O)=O)cnc12
#
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
 1IH  1IH  "(S)-2-((2-(6-amino-9H-purin-9-yl)ethyl)amino)-3-phosphonopropanoic acid"  ligand  34  22  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1IH
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
 1IH  C02  C  CR6    0   0.445  -6.8040  -49.4198  131.6547
 1IH  C04  C  CR16   0   0.034  -4.9123  -50.7280  131.7125
 1IH  C06  C  CR56   0   0.481  -4.7072  -48.7557  130.7685
 1IH  C07  C  CR56   0  -0.002  -6.0387  -48.4422  130.9949
 1IH  C09  C  CR15   0   0.113  -5.1975  -46.7675  130.0251
 1IH  C12  C  CH2    0  -0.300  -2.4048  -46.1815  129.2104
 1IH  C14  C  CH1    0  -0.149  -2.7408  -44.6323  127.3941
 1IH  C15  C  CH2    0  -0.742  -3.5529  -44.4538  126.1067
 1IH  C20  C  C      0   0.387  -1.2807  -44.1800  127.1501
 1IH  N01  N  NH2    0  -0.818  -8.1005  -49.2543  131.9357
 1IH  N03  N  N      0  -0.473  -6.2021  -50.5635  131.9993
 1IH  N05  N  N      0  -0.459  -4.0910  -49.8878  131.1091
 1IH  N08  N  N      0  -0.462  -6.3274  -47.1911  130.5187
 1IH  N10  N  NR5    0  -0.501  -4.1751  -47.6657  130.1488
 1IH  N13  N  NH1    0  -0.637  -2.8462  -46.0050  127.8515
 1IH  O17  O  OP    -1  -0.901  -5.8676  -43.8041  127.3707
 1IH  O18  O  OP    -1  -0.884  -5.5126  -46.2555  126.6738
 1IH  O19  O  O      0  -0.892  -5.9601  -44.4645  124.8787
 1IH  O21  O  O      0  -0.613  -0.4483  -45.0330  126.7792
 1IH  O22  O  OC    -1  -0.627  -1.0657  -42.9556  127.2967
 1IH  P16  P  P      0   1.183  -5.3907  -44.7660  126.2698
 1IH  H1   H  HCR6   0   0.245  -4.4862  -51.6785  132.0171
 1IH  H2   H  HCR5   0   0.278  -5.0677  -45.8056  129.5532
 1IH  H3   H  HCH2   0   0.254  -2.5243  -48.3194  129.0640
 1IH  H4   H  HCH2   0   0.260  -2.1803  -47.7211  130.6826
 1IH  H5   H  HCH2   0   0.232  -1.3130  -46.1194  129.2483
 1IH  H6   H  HCH2   0   0.184  -2.7633  -45.3935  129.8978
 1IH  H7   H  HCH1   0   0.140  -3.1650  -43.9399  128.1430
 1IH  H8   H  HCH2   0   0.177  -3.1347  -45.1099  125.3330
 1IH  H9   H  HCH2   0   0.186  -3.4096  -43.4289  125.7494
 1IH  H10  H  HNH2   0   0.399  -8.5834  -49.9375  132.4935
 1IH  H11  H  HNH2   0   0.407  -8.5493  -48.3687  131.7804
 1IH  H12  H  HNH1   0   0.356  -3.8078  -46.3109  127.7008
 1IH  C11  C  CH2    0  -0.301  -2.7692  -47.5362  129.7835

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
 1IH  O19  P16  deloc     1.533  0.020  1.533
 1IH  P16  C15  single    1.871  0.020  1.871
 1IH  P16  O18  deloc     1.548  0.020  1.548
 1IH  P16  O17  deloc     1.538  0.020  1.538
 1IH  C15  C14  single    1.533  0.020  1.533
 1IH  O21  C20  deloc     1.248  0.020  1.248
 1IH  C20  C14  single    1.548  0.020  1.548
 1IH  C20  O22  deloc     1.252  0.020  1.252
 1IH  C14  N13  single    1.451  0.020  1.451
 1IH  N13  C12  single    1.440  0.020  1.440
 1IH  C12  C11  single    1.515  0.020  1.515
 1IH  C11  N10  single    1.458  0.020  1.458
 1IH  N10  C09  aromatic  1.367  0.020  1.367
 1IH  N10  C06  aromatic  1.362  0.020  1.362
 1IH  C09  N08  aromatic  1.304  0.020  1.304
 1IH  N05  C06  aromatic  1.333  0.020  1.333
 1IH  N05  C04  aromatic  1.321  0.020  1.321
 1IH  C06  C07  aromatic  1.387  0.020  1.387
 1IH  C04  N03  aromatic  1.331  0.020  1.331
 1IH  N08  C07  aromatic  1.369  0.020  1.369
 1IH  C07  C02  aromatic  1.406  0.020  1.406
 1IH  N03  C02  aromatic  1.337  0.020  1.337
 1IH  C02  N01  single    1.337  0.020  1.337
 1IH  C04  H1   single    0.930  0.020  1.080
 1IH  C09  H2   single    0.930  0.020  1.080
 1IH  C11  H3   single    0.970  0.020  1.090
 1IH  C11  H4   single    0.970  0.020  1.090
 1IH  C12  H5   single    0.970  0.020  1.090
 1IH  C12  H6   single    0.970  0.020  1.090
 1IH  C14  H7   single    0.970  0.020  1.090
 1IH  C15  H8   single    0.970  0.020  1.090
 1IH  C15  H9   single    0.970  0.020  1.090
 1IH  N01  H10  single    0.860  0.020  1.020
 1IH  N01  H11  single    0.860  0.020  1.020
 1IH  N13  H12  single    0.890  0.020  1.040

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
 1IH  N03  C02  N01  119.22  3.000
 1IH  N01  C02  C07  122.71  3.000
 1IH  N03  C02  C07  118.07  3.000
 1IH  H1   C04  N05  116.18  3.000
 1IH  H1   C04  N03  115.35  3.000
 1IH  N05  C04  N03  128.47  3.000
 1IH  N10  C06  N05  127.97  3.000
 1IH  N05  C06  C07  126.45  3.000
 1IH  N10  C06  C07  105.57  3.000
 1IH  N08  C07  C06  110.62  3.000
 1IH  N08  C07  C02  133.14  3.000
 1IH  C06  C07  C02  116.24  3.000
 1IH  H2   C09  N10  122.38  3.000
 1IH  H2   C09  N08  124.01  3.000
 1IH  N10  C09  N08  113.61  3.000
 1IH  H6   C12  H5   105.16  3.000
 1IH  H6   C12  N13  113.59  3.000
 1IH  H5   C12  N13  109.37  3.000
 1IH  H6   C12  C11  108.91  3.000
 1IH  H5   C12  C11  106.12  3.000
 1IH  N13  C12  C11  113.13  3.000
 1IH  H7   C14  N13  110.58  3.000
 1IH  H7   C14  C20  106.61  3.000
 1IH  N13  C14  C20  113.25  3.000
 1IH  H7   C14  C15  107.03  3.000
 1IH  N13  C14  C15  109.67  3.000
 1IH  C20  C14  C15  109.48  3.000
 1IH  H9   C15  H8   106.25  3.000
 1IH  H9   C15  P16  108.25  3.000
 1IH  H8   C15  P16  109.63  3.000
 1IH  H9   C15  C14  108.29  3.000
 1IH  H8   C15  C14  108.71  3.000
 1IH  P16  C15  C14  115.32  3.000
 1IH  O22  C20  O21  126.07  3.000
 1IH  O22  C20  C14  115.43  3.000
 1IH  O21  C20  C14  118.43  3.000
 1IH  H11  N01  H10  118.03  3.000
 1IH  H11  N01  C02  120.65  3.000
 1IH  H10  N01  C02  119.88  3.000
 1IH  C04  N03  C02  119.08  3.000
 1IH  C06  N05  C04  111.68  3.000
 1IH  C09  N08  C07  104.23  3.000
 1IH  C11  N10  C09  129.81  3.000
 1IH  C09  N10  C06  105.96  3.000
 1IH  C11  N10  C06  124.17  3.000
 1IH  H12  N13  C14  107.79  3.000
 1IH  H12  N13  C12  113.05  3.000
 1IH  C14  N13  C12  113.04  3.000
 1IH  O19  P16  O18  113.38  3.000
 1IH  O18  P16  O17  112.99  3.000
 1IH  O19  P16  O17  114.29  3.000
 1IH  O17  P16  C15  105.22  3.000
 1IH  O18  P16  C15  105.11  3.000
 1IH  O19  P16  C15  104.65  3.000
 1IH  H4   C11  H3   107.50  3.000
 1IH  H4   C11  N10  107.40  3.000
 1IH  H3   C11  N10  108.53  3.000
 1IH  H4   C11  C12  109.48  3.000
 1IH  H3   C11  C12  109.77  3.000
 1IH  N10  C11  C12  113.95  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
 1IH  CONST_01  N10  C06  C07  C02   180.00   0.0  0
 1IH  CONST_02  N05  C06  C07  C02     0.00   0.0  0
 1IH  CONST_03  C09  N08  C07  C02   180.00   0.0  0
 1IH  CONST_04  N05  C04  N03  C02     0.00   0.0  0
 1IH  CONST_05  N10  C06  N05  C04   180.00   0.0  0
 1IH  CONST_06  C07  C06  N05  C04     0.00   0.0  0
 1IH  CONST_07  C07  C02  N03  C04     0.00   0.0  0
 1IH  CONST_08  N08  C09  N10  C06     0.00   0.0  0
 1IH  CONST_09  N03  C04  N05  C06     0.00   0.0  0
 1IH  CONST_10  C09  N08  C07  C06     0.00   0.0  0
 1IH  CONST_11  N03  C02  C07  C06     0.00   0.0  0
 1IH  CONST_12  C09  N10  C06  C07     0.00   0.0  0
 1IH  CONST_13  N10  C09  N08  C07     0.00   0.0  0
 1IH  CONST_14  N05  C06  N10  C09   180.00   0.0  0
 1IH  CONST_15  N08  C07  C02  N03   180.00   0.0  0
 1IH  CONST_16  N08  C07  C06  N05   180.00   0.0  0
 1IH  CONST_17  N10  C06  C07  N08     0.00   0.0  0
 1IH  CONST_18  N01  C02  N03  C04   180.00   0.0  0
 1IH  CONST_19  N01  C02  C07  C06   180.00   0.0  0
 1IH  CONST_20  C11  N10  C06  C07   180.00   0.0  0
 1IH  CONST_21  N08  C09  N10  C11   180.00   0.0  0
 1IH  CONST_22  N05  C06  N10  C11     0.00   0.0  0
 1IH  CONST_23  N08  C07  C02  N01     0.00   0.0  0
 1IH  CONST_24  H1   C04  N03  C02   180.00   0.0  0
 1IH  CONST_25  H2   C09  N10  C06   180.00   0.0  0
 1IH  CONST_26  H1   C04  N05  C06   180.00   0.0  0
 1IH  CONST_27  H2   C09  N08  C07   180.00   0.0  0
 1IH  CONST_28  H10  N01  C02  C07   180.00   0.0  0
 1IH  CONST_29  H11  N01  C02  C07     0.00   0.0  0
 1IH  CONST_30  H10  N01  C02  N03     0.00   0.0  0
 1IH  CONST_31  H11  N01  C02  N03   180.00   0.0  0
 1IH  Var_01    C12  C11  N10  C06  -175.11  30.0  3
 1IH  Var_02    C12  C11  N10  C09     1.50  30.0  3
 1IH  Var_03    H3   C11  N10  C06    62.26  30.0  3
 1IH  Var_04    H4   C11  N10  C06   -53.67  30.0  3
 1IH  Var_05    H3   C11  N10  C09  -121.13  30.0  3
 1IH  Var_06    H4   C11  N10  C09   122.94  30.0  3
 1IH  Var_07    N13  C12  C11  N10   -75.69  30.0  1
 1IH  Var_08    H5   C12  C11  N10   164.39  30.0  1
 1IH  Var_09    H6   C12  C11  N10    51.63  30.0  1
 1IH  Var_10    C14  N13  C12  C11   168.35  30.0  1
 1IH  Var_11    O19  P16  C15  C14   177.67  30.0  3
 1IH  Var_12    O18  P16  C15  C14   -62.64  30.0  3
 1IH  Var_13    O17  P16  C15  C14    56.89  30.0  3
 1IH  Var_14    H12  N13  C12  C11    45.54  30.0  1
 1IH  Var_15    H5   C12  N13  C14   -73.60  30.0  3
 1IH  Var_16    H6   C12  N13  C14    43.53  30.0  3
 1IH  Var_17    H3   C11  C12  N13    46.25  30.0  3
 1IH  Var_18    H4   C11  C12  N13   164.03  30.0  3
 1IH  Var_19    H8   C15  P16  O17   179.95  30.0  3
 1IH  Var_20    H9   C15  P16  O17   -64.56  30.0  3
 1IH  Var_21    H8   C15  P16  O18    60.42  30.0  3
 1IH  Var_22    H9   C15  P16  O18   175.92  30.0  3
 1IH  Var_23    H8   C15  P16  O19   -59.27  30.0  3
 1IH  Var_24    H9   C15  P16  O19    56.22  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
 1IH  chir_01  C14  C15  C20  N13  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
 1IH  plan-1  C02  0.020
 1IH  plan-1  C04  0.020
 1IH  plan-1  C06  0.020
 1IH  plan-1  C07  0.020
 1IH  plan-1  C09  0.020
 1IH  plan-1  N01  0.020
 1IH  plan-1  N03  0.020
 1IH  plan-1  N05  0.020
 1IH  plan-1  N08  0.020
 1IH  plan-1  N10  0.020
 1IH  plan-1  H1   0.020
 1IH  plan-1  H2   0.020
 1IH  plan-1  C11  0.020
 1IH  plan-2  C02  0.020
 1IH  plan-2  N01  0.020
 1IH  plan-2  H10  0.020
 1IH  plan-2  H11  0.020
 1IH  plan-3  C14  0.020
 1IH  plan-3  C20  0.020
 1IH  plan-3  O21  0.020
 1IH  plan-3  O22  0.020

