Volume 2 Chapter 10 Search Menu SAVE BCCAB

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SAVE CIF

Function

SAVE CIF is used to specify that a CIF/MIF file should be written, containing all hits kept in a search.

Basic QUEST Procedure

Type SAVE CIF. See SAVE for more information about use of this control command in Basic QUEST.

Remarks

This is the first attempt at writing a combined CIF/MIF output file from the CSD. It is envisaged to unite the 3D information, expressed by CIF datanames, with the CSD chemical information, expressed by MIF datanames. As such, it should be regarded as a prototype. Potential users are urged to consult the published CIF and MIF file specifications

CIF -  Hall, Allen, Brown.        Acta Cryst.          (1991) A47,       
                                                       655-685.          

MIF -  Allen, Barnard, Cook &     J.Chem.Inf.Comp.Sci. (1995) 35,        
       Hall.                                           412-427.          

The CIF/MIF file uses THREE loops to represent the 3D and 2D structure.

The _atom_site loop represents the crystal structure. This loop includes all H-atoms located in the experiment and also any symmetry-generated atoms bonded to atoms of the asymmetric unit. This loop omits any atoms suppressed during building of the CSD entry. The _ccdc_atom_site_atom_id_number then links this loop to the following two loops, which would normally contain the 2D chemical information.

The _atom loop contains the chemical atom properties of the non-H atoms and, by CSD convention, H-atoms that have >1 connection. Atoms in this loop are tied to _atom_site_ data via the linking number. Atoms only occur in this loop if CSD 2D/3D graph matching has been successful for the bonded unit containing this atom.

The _bond_ loop carries the full crystal connectivity, including bonds to located H-atoms. H-atoms not located in the structure are NOT added to this loop. Where the bond occurs in a unit for which 2D/3D graph matching has been successful, then CCDC bond-type and bond-environment information is added.

Data Items

The set of data items and loops are given below followed by an example of the output for a CSD entry.

data_CSD_CIF/MIF_[refcode]
_audit_creation_date            yyyy-mm-dd
_audit creation_method          CSD-QUEST3D-V5
_database_coden_CSD             [refcode]

These are general header items for the entry including the CSD accession date (*ADATe).

_symmetry_cell_setting          triclinic, monoclinic, etc.
_symmetry_space_group_name_H-M  'P 21/c'
_symmetry_Int_Tables_number     14

The dataname _symmetry_space_group_name_H-M may be substituted by _ccdc_symmetry_space_group_name for certain CSD entries.

loop_
_symmetry_equiv_pos_id
_symmetry_equiv_pos_as_xyz

Each symmetry equivalent position is numbered and those related by a centre of symmetry follow the CSD-stored ones.

_cell_length_a                  6.801(3)
_cell_length_b                 15.272(4)
_cell_length_c                  8.049(2)
_cell_angle_alpha              90
_cell_angle_beta              102.46(8)
_cell_angle_gamma              90
_cell_formula_units_Z          4 
_ccdc_flag_disorder            'yes' or 'no'  (screen 35)
_ccdc_flag_error               'yes' or 'no'  (screen 34)
_ccdc_flag_match               'full' or      (screen 85)
                               'partial' or   (screen 84)
                               'none'         (screen 82,83,86)
_ccdc_flag_sigma(C-C) 'none','1','2','3','4'  (screens 73,74-77)
_ccdc_R_factor                  0.074

These are various CSD entry flags which do not have standard CIF/MIF datanames. The CCDC stores the lowest of the standard R-factors cited, so this does not correspond to the standard CIF datanames.

loop_
_atom_type_symbol
_atom_type_radius_bond

The _atom_type_symbol corresponds to one of the _atom_site_type_symbol 's in the _atom_site_ loop below. The _atom_type_radius_bond is the covalent radius for this atom type that was used in assembling the connectivity in the _bond_ loop below.

loop_
_ccdc_atom_site_atom_id_number
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_ccdc_atom_site_symmetry
_ccdc_atom_site_base

e.g.

15 C3G C 0.3328 0.23847 0.0632 8_555 7

The _ccdc_atom_site_atom_id_number is a simple ascending number assigned to each atom in the loop. It links to the atom_ and bond_ loops given below. They will normally be sequential numbers unless suppressed atoms are present in the CSD atom list. Until we have a fully operational disorder treatment, we will NOT output secondary sites. This means that the atom sequence may be interrupted in its ascent, so that the _ccdc_atom_site_atom_id_number' s still tie correctly to the crystal connectivity expression in the bond_ loop below.

The _ccdc_atom_site_symmetry is a string of the form n_mmm where n is the _symmetry_equiv_pos_id (see above) and mmm are translational operations. In the example line above atom 15 (C3G) is symmetry- -related to atom 7 (_ccdc_atom_site_base) by symmetry operation number 8 in the list accompanied by cell translations of x+0.0, y+0.0, z+0.0. Thus _ccdc_atom_site_symmetry will always be 1_555 for atoms in the asymmetric unit (CSD ATOMS) and something different for symmetry-generated atoms (CSD SATOMS).


loop_
_atom_id
_atom_type
_atom_attach_nh
_atom_attach_h
_atom_charge

e.g.

2 O 1 0 -1

This loop describes the CSD chemical attributes for each of the _ccdc_atom_site_atom_id_number's in the _atom_site loop above. In the example line above oxygen atom number 2 has 1 connected non-hydrogen atom, no attached hydrogens, and a CSD charge of -1.

The CSD chemical connectivity only stores one copy of each unique chemical moiety (residue). However, if there are two molecules in the asymmetric unit, then atom properties for the second residue will be repeated in this loop.

If any crystal atom is not matched to an atom in the CSD chemical connectivity, then it will not have an entry in this loop. If the CSD entry is completely unmatched, then this loop will NOT exist.

loop_
_bond_id_1             _ccdc_atom_site_atom_id_number for atom 1
_bond_id_2             _ccdc_atom_site_atom_id_number for atom 2
_bond_type_ccdc        CCDC bond type from MIF specification
_bond_environment      ring or chain from MIF specification

e.g.

1  2  S chain

Chemical bond types and environments will be added for all pairs of 3D atoms that are matched to 2D atoms in the CSD. Otherwise these two items will be denoted by '?'. For totally unmatched entries, ALL _bond_type's and _bond_environment's will be denoted with '?' and the bond loop will indicate the crystal connectivity.

Example

data_CSD_CIF/MIF_AMPICR01
_audit_creation_date 96-06-26
_audit_creation_method CSD-QUEST3D-V5
_database_coden_CSD AMPICR01
_symmetry_cell_setting orthorhombic
_symmetry_space_group_name_H-M  'I b c a'
_symmetry_Int_Tables_number 73

loop_
_symmetry_equiv_pos_id
_symmetry_equiv_pos_as_xyz
  1  x,y,z
  2  -x,1/2-y,z
  3  x,-y,1/2-z
  4  -x,1/2+y,1/2-z
  5  1/2+x,1/2+y,1/2+z
  6  1/2-x,-y,1/2+z
  7  1/2+x,1/2-y,-z
  8  1/2-x,y,-z
  9  -x,-y,-z
 10  x,-1/2+y,-z
 11  -x,y,-1/2+z
 12  x,-1/2-y,-1/2+z
 13  -1/2-x,-1/2-y,-1/2-z
 14  -1/2+x,y,-1/2-z
 15  -1/2-x,-1/2+y,z
 16  -1/2+x,-y,z
_cell_length_a 13.474(4)
_cell_length_b 19.790(7)
_cell_length_c 7.131(4)
_cell_angle_alpha 90
_cell_angle_beta 90
_cell_angle_gamma 90
_cell_formula_units_Z 8
_ccdc_flag_disorder no
_ccdc_flag_error no
_ccdc_flag_match full
_ccdc_flag_sigma(C-C) 1
_ccdc_R_factor 4.00

loop_
_atom_type_symbol
_atom_type_radius_bond
C 0.68
H 0.23
N 0.68
O 0.68

loop_
_ccdc_atom_site_atom_id_number
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_ccdc_atom_site_symmetry
_ccdc_atom_site_base
1 C1 C 0.2500 0.1280(1) 0.0 1_555 1
2 O1 O 0.2500 0.06477(7) 0.0 1_555 2
3 C2 C 0.1668(1) 0.16901(8) -0.0608(2) 1_555 3
4 N1 N 0.0776(1) 0.13664(7) -0.1342(2) 1_555 4
5 O2 O 0.05679(9) 0.07942(7) -0.0825(2) 1_555 5
6 O3 O 0.02663(9) 0.16864(7) -0.2449(2) 1_555 6
7 C3 C 0.1672(1) 0.23847(8) -0.0632(2) 1_555 7
8 C4 C 0.2500 0.2725(1) 0.0 1_555 8
9 N2 N 0.2500 0.3458(1) 0.0 1_555 9
10 O4 O 0.1773(1) 0.37478(7) -0.0604(2) 1_555 10
11 N3 N 0.1165(2) 0.0 0.2500 1_555 11
12 H1 H 0.111(1) 0.261(1) -0.112(3) 1_555 12
13 H2 H 0.153(2) 0.017(1) 0.148(3) 1_555 13
14 H3 H 0.076(2) 0.030(1) 0.301(3) 1_555 14
15 C3G C 0.3328 0.23847 0.0632 8_555 7
16 C2G C 0.3332 0.16901 0.0608 8_555 3
17 N1G N 0.4224 0.13664 0.1342 8_555 4
18 O2G O 0.44321 0.07942 0.0825 8_555 5
19 O3G O 0.47337 0.16864 0.2449 8_555 6
20 H1G H 0.389 0.261 0.112 8_555 12
21 O4G O 0.3227 0.37478 0.0604 8_555 10
22 H2B H 0.153 -0.017 0.352 3_555 13
23 H3B H 0.076 -0.030 0.199 3_555 14

loop_
_atom_id
_atom_type
_atom_attach_nh
_atom_attach_h
_atom_charge
1 C 3 0 0
2 O 1 0 -1
3 C 3 0 0
4 N 3 0 0
5 O 1 0 0
6 O 1 0 0
7 C 2 1 0
8 C 3 0 0
9 N 3 0 0
10 O 1 0 0
11 N 0 4 1
15 C 2 1 0
16 C 3 0 0
17 N 3 0 0
18 O 1 0 0
19 O 1 0 0
21 O 1 0 0

loop_
_bond_id_1
_bond_id_2
_bond_type_ccdc
_bond_environment
1 2 S chain
3 1 A ring
4 3 S chain
5 4 D chain
6 4 D chain
7 3 A ring
8 7 A ring
9 8 S chain
10 9 D chain
11 13 S chain
12 7 S chain
14 11 S chain
15 8 A ring
16 1 A ring
17 16 S chain
18 17 D chain
19 17 D chain
20 15 S chain
21 9 D chain
22 11 S chain
23 11 S chain
15 16 A ring

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Volume 2 Chapter 10 Search Menu SAVE COORD.