# By using this file you agree to the legally binding terms of use found at
# https://github.com/google-deepmind/alphafold3/blob/main/OUTPUT_TERMS_OF_USE.md.
# To request access to the AlphaFold 3 model parameters, follow the process set
# out at https://github.com/google-deepmind/alphafold3. You may only use these if
# received directly from Google. Use is subject to terms of use available at
# https://github.com/google-deepmind/alphafold3/blob/main/WEIGHTS_TERMS_OF_USE.md.
data_basic-sub-ligands-test
#
_entry.id basic-sub-ligands-test
#
loop_
_atom_type.symbol
C 
N 
O 
P 
#
loop_
_audit_author.name
_audit_author.pdbx_ordinal
"Google DeepMind" 1 
"Isomorphic Labs" 2 
#
_audit_conform.dict_location https://raw.githubusercontent.com/ihmwg/ModelCIF/master/dist/mmcif_ma.dic
_audit_conform.dict_name     mmcif_ma.dic
_audit_conform.dict_version  1.4.5
#
_chem_comp.formula        "C10 H14 N5 O7 P"
_chem_comp.formula_weight 347.221
_chem_comp.id             AMP
_chem_comp.mon_nstd_flag  .
_chem_comp.name           "ADENOSINE MONOPHOSPHATE"
_chem_comp.pdbx_smiles    c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N
_chem_comp.pdbx_synonyms  ?
_chem_comp.type           NON-POLYMER
#
_citation.book_publisher          ?
_citation.country                 UK
_citation.id                      primary
_citation.journal_full            Nature
_citation.journal_id_ASTM         NATUAS
_citation.journal_id_CSD          0006
_citation.journal_id_ISSN         0028-0836
_citation.journal_volume          630
_citation.page_first              493
_citation.page_last               500
_citation.pdbx_database_id_DOI    10.1038/s41586-024-07487-w
_citation.pdbx_database_id_PubMed 38718835
_citation.title                   "Accurate structure prediction of biomolecular interactions with AlphaFold 3"
_citation.year                    2024
#
loop_
_citation_author.citation_id
_citation_author.name
_citation_author.ordinal
primary "Google DeepMind" 1 
primary "Isomorphic Labs" 2 
#
loop_
_entity.id
_entity.pdbx_description
_entity.type
1 . non-polymer 
2 . non-polymer 
#
_ma_data.content_type "model coordinates"
_ma_data.id           1
_ma_data.name         Model
#
_ma_model_list.data_id          1
_ma_model_list.model_group_id   1
_ma_model_list.model_group_name "AlphaFold-beta-20231127 (3.0.1 @ 2025-04-17 12:45:15)"
_ma_model_list.model_id         1
_ma_model_list.model_name       "Top ranked model"
_ma_model_list.model_type       "Ab initio model"
_ma_model_list.ordinal_id       1
#
loop_
_ma_protocol_step.method_type
_ma_protocol_step.ordinal_id
_ma_protocol_step.protocol_id
_ma_protocol_step.step_id
"coevolution MSA" 1 1 1 
"template search" 2 1 2 
modeling          3 1 3 
#
loop_
_ma_qa_metric.id
_ma_qa_metric.mode
_ma_qa_metric.name
_ma_qa_metric.software_group_id
_ma_qa_metric.type
1 global pLDDT 1 pLDDT 
2 local  pLDDT 1 pLDDT 
#
_ma_qa_metric_global.metric_id    1
_ma_qa_metric_global.metric_value 60.61
_ma_qa_metric_global.model_id     1
_ma_qa_metric_global.ordinal_id   1
#
loop_
_ma_qa_metric_local.label_asym_id
_ma_qa_metric_local.label_comp_id
_ma_qa_metric_local.label_seq_id
_ma_qa_metric_local.metric_id
_ma_qa_metric_local.metric_value
_ma_qa_metric_local.model_id
_ma_qa_metric_local.ordinal_id
A AMP . 2 59.37 1 1 
B AMP . 2 61.85 1 2 
#
_ma_software_group.group_id    1
_ma_software_group.ordinal_id  1
_ma_software_group.software_id 1
#
loop_
_ma_target_entity.data_id
_ma_target_entity.entity_id
_ma_target_entity.origin
1 1 . 
1 2 . 
#
loop_
_ma_target_entity_instance.asym_id
_ma_target_entity_instance.details
_ma_target_entity_instance.entity_id
A . 1 
B . 2 
#
loop_
_pdbx_data_usage.details
_pdbx_data_usage.id
_pdbx_data_usage.type
_pdbx_data_usage.url
;Non-commercial use only, by using this file you agree to the terms of use found
at https://github.com/google-deepmind/alphafold3/blob/main/OUTPUT_TERMS_OF_USE.md.
To request access to the AlphaFold 3 model parameters, follow the process set
out at https://github.com/google-deepmind/alphafold3. You may only use these if
received directly from Google. Use is subject to terms of use available at
https://github.com/google-deepmind/alphafold3/blob/main/WEIGHTS_TERMS_OF_USE.md.
;
1 license    https://github.com/google-deepmind/alphafold3/blob/main/OUTPUT_TERMS_OF_USE.md 
;AlphaFold 3 and its output are not intended for, have not been validated for,
and are not approved for clinical use. They are provided "as-is" without any
warranty of any kind, whether expressed or implied. No warranty is given that
use shall not infringe the rights of any third party.
;
2 disclaimer ?                                                                              
#
loop_
_pdbx_nonpoly_scheme.asym_id
_pdbx_nonpoly_scheme.auth_seq_num
_pdbx_nonpoly_scheme.entity_id
_pdbx_nonpoly_scheme.mon_id
_pdbx_nonpoly_scheme.pdb_ins_code
_pdbx_nonpoly_scheme.pdb_seq_num
_pdbx_nonpoly_scheme.pdb_strand_id
A 1 1 AMP . 1 A 
B 1 2 AMP . 1 B 
#
_software.classification other
_software.date           ?
_software.description    "Structure prediction"
_software.name           AlphaFold
_software.pdbx_ordinal   1
_software.type           package
_software.version        "AlphaFold-beta-20231127 (25b635fa27adb4b12654a9dc6367a96b1463ec03aa886066ffc6cf0691bbe007)"
#
loop_
_struct_asym.entity_id
_struct_asym.id
1 A 
2 B 
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_alt_id
_atom_site.label_comp_id
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.label_seq_id
_atom_site.pdbx_PDB_ins_code
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.auth_seq_id
_atom_site.auth_asym_id
_atom_site.pdbx_PDB_model_num
HETATM 1  P P     . AMP A 1 . ? -5.348 -1.318 -6.331 1.00 60.61 1 A 1 
HETATM 2  O O1P   . AMP A 1 . ? -6.276 -2.332 -6.950 1.00 56.94 1 A 1 
HETATM 3  O O2P   . AMP A 1 . ? -6.070 -0.127 -5.751 1.00 59.95 1 A 1 
HETATM 4  O O3P   . AMP A 1 . ? -4.203 -0.929 -7.230 1.00 56.41 1 A 1 
HETATM 5  O "O5'" . AMP A 1 . ? -4.677 -2.042 -5.060 1.00 52.08 1 A 1 
HETATM 6  C "C5'" . AMP A 1 . ? -4.321 -3.409 -5.114 1.00 65.71 1 A 1 
HETATM 7  C "C4'" . AMP A 1 . ? -3.785 -3.865 -3.770 1.00 54.80 1 A 1 
HETATM 8  O "O4'" . AMP A 1 . ? -2.465 -3.325 -3.591 1.00 55.09 1 A 1 
HETATM 9  C "C3'" . AMP A 1 . ? -4.597 -3.380 -2.569 1.00 55.18 1 A 1 
HETATM 10 O "O3'" . AMP A 1 . ? -5.696 -4.221 -2.281 1.00 52.39 1 A 1 
HETATM 11 C "C2'" . AMP A 1 . ? -3.576 -3.445 -1.454 1.00 51.60 1 A 1 
HETATM 12 O "O2'" . AMP A 1 . ? -3.456 -4.773 -0.922 1.00 41.43 1 A 1 
HETATM 13 C "C1'" . AMP A 1 . ? -2.282 -3.089 -2.201 1.00 54.50 1 A 1 
HETATM 14 N N9    . AMP A 1 . ? -1.919 -1.666 -1.988 1.00 74.43 1 A 1 
HETATM 15 C C8    . AMP A 1 . ? -2.469 -0.586 -2.594 1.00 65.95 1 A 1 
HETATM 16 N N7    . AMP A 1 . ? -1.918 0.516  -2.150 1.00 64.69 1 A 1 
HETATM 17 C C5    . AMP A 1 . ? -0.978 0.143  -1.247 1.00 69.69 1 A 1 
HETATM 18 C C6    . AMP A 1 . ? -0.061 0.823  -0.449 1.00 66.37 1 A 1 
HETATM 19 N N6    . AMP A 1 . ? 0.035  2.161  -0.476 1.00 61.29 1 A 1 
HETATM 20 N N1    . AMP A 1 . ? 0.742  0.109  0.344  1.00 62.07 1 A 1 
HETATM 21 C C2    . AMP A 1 . ? 0.705  -1.212 0.399  1.00 56.89 1 A 1 
HETATM 22 N N3    . AMP A 1 . ? -0.129 -1.934 -0.332 1.00 57.15 1 A 1 
HETATM 23 C C4    . AMP A 1 . ? -0.964 -1.256 -1.136 1.00 70.31 1 A 1 
HETATM 24 P P     . AMP B 2 . ? 1.040  5.880  4.895  1.00 60.78 1 B 1 
HETATM 25 O O1P   . AMP B 2 . ? 2.515  6.174  4.972  1.00 52.12 1 B 1 
HETATM 26 O O2P   . AMP B 2 . ? 0.288  6.313  6.135  1.00 56.03 1 B 1 
HETATM 27 O O3P   . AMP B 2 . ? 0.393  6.328  3.611  1.00 57.55 1 B 1 
HETATM 28 O "O5'" . AMP B 2 . ? 0.927  4.269  4.865  1.00 56.42 1 B 1 
HETATM 29 C "C5'" . AMP B 2 . ? 1.386  3.479  5.936  1.00 67.11 1 B 1 
HETATM 30 C "C4'" . AMP B 2 . ? 1.416  2.011  5.538  1.00 53.24 1 B 1 
HETATM 31 O "O4'" . AMP B 2 . ? 0.074  1.535  5.413  1.00 55.65 1 B 1 
HETATM 32 C "C3'" . AMP B 2 . ? 2.083  1.757  4.193  1.00 57.54 1 B 1 
HETATM 33 O "O3'" . AMP B 2 . ? 3.491  1.638  4.307  1.00 54.98 1 B 1 
HETATM 34 C "C2'" . AMP B 2 . ? 1.455  0.440  3.786  1.00 57.80 1 B 1 
HETATM 35 O "O2'" . AMP B 2 . ? 2.125  -0.670 4.390  1.00 48.59 1 B 1 
HETATM 36 C "C1'" . AMP B 2 . ? 0.054  0.556  4.384  1.00 55.29 1 B 1 
HETATM 37 N N9    . AMP B 2 . ? -0.945 0.952  3.370  1.00 77.71 1 B 1 
HETATM 38 C C8    . AMP B 2 . ? -1.209 2.211  2.938  1.00 70.81 1 B 1 
HETATM 39 N N7    . AMP B 2 . ? -2.143 2.199  2.017  1.00 70.12 1 B 1 
HETATM 40 C C5    . AMP B 2 . ? -2.506 0.904  1.851  1.00 74.08 1 B 1 
HETATM 41 C C6    . AMP B 2 . ? -3.430 0.241  1.047  1.00 70.44 1 B 1 
HETATM 42 N N6    . AMP B 2 . ? -4.222 0.897  0.193  1.00 63.59 1 B 1 
HETATM 43 N N1    . AMP B 2 . ? -3.521 -1.078 1.160  1.00 65.36 1 B 1 
HETATM 44 C C2    . AMP B 2 . ? -2.781 -1.788 1.999  1.00 61.64 1 B 1 
HETATM 45 N N3    . AMP B 2 . ? -1.882 -1.242 2.808  1.00 61.71 1 B 1 
HETATM 46 C C4    . AMP B 2 . ? -1.749 0.094  2.721  1.00 73.92 1 B 1 
#
