The FDAT file is the numeric data file used by the program RPluto.
The file consists of formatted 80-byte records containing the information fields of the DATA category of CSD.
Each entry is composed of up to 7 possible record types.
Record type 1 is mandatory but all other record types are optional.
This is because the CSD files contain a number of entries for which some or all of the numerical data was not reported in the relevant publication.
Record types are:
Record types 1, 2 and 5 are single-line records. Other types may need more than one line to encompass the information.
Record type 4 is normally present only if the space group and record type 6 are both present.
Record type 5 is normally present only when type 6 is present.
Record type 7 is present only when record type 6 is present and the entry is error-free.
The format of the record is: (1H#,A8,2I1,I6,6X,11I3,22I1,I2)
The contents of the record are:
Cols. 1-9 #REFCOD Start-of-entry marker # and CSD reference code. 10 SYS Crystal system: 0 = unknown 1 = anorthic 2 = monoclinic 3 = orthorhombic 4 = tetragonal 5 = hexagonal or trigonal with P-lattice type> 6 = cubic 7 = trigonal with R-lattice symbol 11 CAT Structural category, always 3 at present. 12-17 ADAT Accession date, eg. 890401 = 1st April 1989; all entries prior to 31 Dec 1971 have accession date 711231. 18-23 IW Not used. 24-26 NCARDS No. of records in entry, including directory. 27-29 NRFAC No. of characters in R-factor field (record 3)> 30-32 NREM No. of characters in text REMARK field (record 3) 33-35 NDIS No. of characters in text DISORDER description (record 3) 36-38 NERR No. of characters in text ERROR description (record 3) 39-41 NOPR No. of symmetry positions (record 4) 42-44 NRAD No. of element types in RADIUS record (record 5) 45-47 NAT No. of ATOMs (record 6) 48-50 NSAT No. of SATOMs (symmetry-generated atoms) (record 6) 51-53 NBND Not used. 54-56 NCON No. of crystallographic connectivity integers (record 7) 57 CELL Absence (0) or presence (1) of unit cell record (record 2) 58 INTF Intensity data measurement flag 0 = unknown 1 = visual 2 = densitometer 3 = diffractometer 59 ATFOR Atom coordinate format type 0 = no atoms present 2 = atoms present with format coordinates x 105 60 CENT Centre of symmetry at origin 0 = unknown (record 4 absent) 1 = centre at origin 2 = no centre at origin 61 ERR Error status flag 0 = no errors 1 = error(s) in entry still unresolved (about 1.8% of CSD) 62 RPA Refer problem to author 0 = no referral 1 = problem referred back to author 63 TD Set to 1 if entry is disordered to extent where all coordinates have been removed. 64 PD Set to 1 if entry is disordered, and a few coordinates may have been removed or suppressed. 65 NU Not used. 66 CBL Set to 1 for presence in paper of bond lengths corrected for thermal motion. 67 AS Average esd. of C-C bonds, 0 = unknown 1 = 0.001-0.005Å 2 = 0.006-0.010Å 3 = 0.011-0.030Å 4 = 0.031Å+ 68 POL Set to 1 for polymeric structure. 69-78 The remaining 10(I1) fields are either unused (=0), or relate to CSD processing. They are of little interest to users. 79-80 YEAR Year of publication (final two digits of 19[nn]).
The format of the record is: (6I6,6I1,6I2,2I3,I3,A8,I3,I2,4X)
The following items are recorded:
Cols. 1-36 CELLD (6I6) Cell parameters a, b, c, alpha, beta, gamma, all multiplied by 10Pn, where the Pn are precision digits for a.... gamma, n = 1 ..... 6. 37-42 PREC (6I1) Precision digits P1 (for a) .... P6 (for gamma). 43-54 CESD (6I2) Cell parameter esd's multiplied by 10Pn, as above. 55-60 DENS (2I3) 100 x Dm, 100 x Dx. 61-63 NSPG (I3) Space group number or aspect number. 64-71 SPG (A8) Space group symbol or aspect symbol. 72-74 Z (I3) Z-value, i.e. no. of formula units per cell. 75-76 ITOL (I2) 100 x tolerance value (usually 0.4).
The textual information is divided into 4 fields and the division into fields of continuous text is accomplished using the directory elements NRFAC, NREM, NDIS, NERR, in record 1.
The format of the record is: (5(3I1,I2,3I1,I2,3I1,I2),5X)
This record carries the general equivalent positions of the space group, except those related by a centre of symmetry. Lattice centring operations are included.
The record is present only if atomic coordinates and space group are recorded.
The position x(p), y(p), z(p) is generated from x, y, z by the matrix transformation:
[X(p)] = [Rij] . [X] + [T]
Here Rij is a 3x3 rotation matrix, and T is a 3x1 translation vector. For each position the order of information (repeated for subsequent positions) is:
R11 R12 R13 T1 R21 R22 R23 T2 R31 R32 R33 T3
The format of the record is: (16(A2,I3))
The element symbol (A2) and 100 x R(el) are recorded.
These are the radii actually used to prepare the CSD entry. In general these will correspond to standard values, unless bonding situations have been encountered which require a change in the standard value.
The format of the records is: (A5,3I7,1X,A5,3I7,1X,A5,3I7)
Each atom has a left-adjusted atom label [A5]. This always begins with a valid element symbol, which is then followed by at least one digit. Succeeding characters may be numbers and/or prime characters (').
For symmetry-related atoms, a letter is added to the symbol for the basic atom [C11 would generate C11A etc.]. The symbol A refers to the second symmetry position, B the third, etc.
The coordinates x, y, z then follow. They are multiplied by 105.
Any symmetry-related atoms (SATOM) are encoded in records of type 6, and follow on continuously from the asymmetric unit atom coordinates (ATOM). The number of lines of atomic coordinates to be expected can be deduced from NAT + NSAT in the directory record (record 1).
The format may take one of the following forms:
In each case the record contains a sequence of integers. Their ordering and meaning are illustrated by the following example:
Consider the 12-atom structure:
The atom numbers are the sequence numbers in the total list of atoms and symmetry-related atoms (record 6).
The connectivity matrix for the above structure could be represented as follows:
FROM TO1 10 2 3 4 8 9 3 2 4 2 5 12 5 4 6 6 5 7 9 7 6 8 8 2 7 9 2 6 10 11 10 9 1 11 9 12 4
This is a redundant table since each connection occurs twice.
We can code the connections of the first column of the TO list by implying the FROM atom. Thus:
The bond 3-0 is a "dummy" bond; atom 3 has only one connection and it has already been specified, viz. 2-3.
Two bonds have not been accounted for viz. 6-9 and 7-8. We code these by simply adding these 2 pairs of integers to the above sequence. Thus the full sequence of integers is: 10 3 0 2 4 5 6 2 2 9 9 4 6 9 7 8
In general, for an N-atom structure (atoms and symmetry-related atoms) interpret the first N integers as having implied FROM atoms and treat any further integers as FROM-TO pairs.
#AABHTZ 13770506 18 9 0 0 0 1 5 35 0 0 37132100000000000000000076 11372 10272 7359 10875 7107 9616333222 9 5 9 6 4 8 0 0 2P-1 240 R=0.0410 211 0121 0112 0 C 68H 23O 68N 68CL 99 CL1 -33550 9980 10610 CL2 -64070 -30840 32700 C1 -47750 3880 23070 C2 -57270 13370 34240 C3 -68450 9160 44830 C4 -70210 -4450 44470 C5 -60690 -13870 32950 C6 -49040 -10070 21810 C7 -38440 -19380 8860 N8 -36680 -29770 13510 N9 -26290 -38000 990 C10 -18570 -36530 -17520 N11 -21960 -38590 -33470 N12 -11480 -36040 -48430 C13 -2540 -32560 -40600 N14 -6420 -32680 -21040 N15 230 -28370 -7410 C16 -3050 -16060 7440 C17 4050 -12440 22150 O18 -11020 -8830 7930 C19 -23940 -48600 7180 C20 -33070 -50930 25480 O21 -14540 -55420 -2960 H2 -55800 23200 34700 H3 -75200 15700 53100 H4 -78400 -7800 53000 H7 -32600 -17500 -3200 H13 5700 -29600 -46900 H15 4600 -34000 -5700 H171 8100 -3600 21700 H172 10500 -19800 18900 H173 -600 -10700 33300 H201 -31300 -59800 27500 H202 -32900 -45100 37400 H203 -41300 -52500 24300 3 7 4 5 6 7 8 3 8 910111213141216171818112121 4 5 6 915171919192222221516
Notes:
Record type 1 (Directory Information) corresponds to the following values of items:
SYS 1 CAT 3 ADAT 770506 NCARDS 18 NRFAC 9 NREM 0 NDIS 0 NERR 0 NOPR 1 NRAD 5 NAT 35 NSAT 0 NBND 0 NCON 37 CELL 1 INTF 3 ATFOR 2 CENT 1 ERR 0 RPA 0 TD 0 PD 0 CBL 0 AS 0 POL 0 YEAR 76
Record type 2 (Unit Cell)
CELLD 11372 10272 7359 10875 7107 9616 PREC 333222 CESD 9 5 9 6 4 8 DENS 0 0 NSPG 2 SPG P-1 Z 2 ITOL 40
Thus cell parameters are:
11.372(9) 10.272(5) 7.359(9) 108.75(6) 71.07(4) 96.16(8)
Record type 3 (Text Information)
R=0.0410 Note that in record 1 NRFAC=9 i.e. number of characters plus a blank
Record type 4 (Symmetry Positions)
One symmetry position 211 0121 0112 0
Record type 5 (Radius Values)
C 68H 23O 68N 68CL 99
This indicates radii (in Å) for 5 elements: C 0.68 H 0.23 O 0.68 N 0.68 CL 0.99
Record type 6 (Atomic Coordinates)
Coordinates for 35 atoms are recorded. Each fractional coordinate has been multiplied by 105.
Record type 7 (Crystallographic Connection Table)
37 crystallographic connectivity integers are recorded. Since NAT + NSAT < 100 these are in format (40I2).
#AACFAZ1033831006 27 9 0 0 0 4 5 29 29 0 64132100000000000000000083 20132 6162 19954 90 90 90333000 4 1 3 0 0 0141142 60Pbcn 440 R=0.0720 211 0121 0112 0011 6121 6112 0211 0101 0112 6011 6101 6112 6 C 68H 23O 68N 68CL 99 CL1 47060 102730 33580 C1 41150 82580 34520 C2 37970 79280 40600 C3 33310 63010 41020 C4 31860 49900 35580 C5 35250 53030 29640 C6 39960 69530 29050 C7 39690 93120 46620 C8 39710 81720 53280 C9 44000 63090 54410 N10 48000 58940 49490 C11 43510 50330 60740 C12 35500 92050 57370 C13 32330 110060 53700 C14 29810 99400 67690 O1 34430 87220 63850 O2 28360 123460 55520 O3 34650 110000 47370 H3 30700 60000 45500 H4 28200 38400 35800 H5 34300 43000 25700 H6 42800 72500 24500 H7 44100 100900 45800 H111 45500 35900 60400 H112 44100 57700 65100 H113 39400 50000 62500 H141 29700 94100 72500 H142 30900 115100 68400 H143 25300 100900 65300 N10D 52000 41060 50510 C9D 56000 36910 45590 C8D 60290 18280 46720 C11D 56490 49670 39260 C7D 60310 6880 53380 C12D 64500 7950 42630 H111D 54500 64100 39600 H112D 55900 42300 34900 H113D 60600 50000 37500 C2D 62030 20720 59400 O3D 65350 -10000 52630 H7D 55900 -900 54200 C13D 67670 -10060 46300 O1D 65570 12780 36150 C1D 58850 17420 65480 C3D 66690 36990 58980 O2D 71640 -23460 44480 C14D 70190 600 32310 CL1D 52940 -2730 66420 C6D 60040 30470 70950 C4D 68140 50100 64420 H3D 69300 40000 54500 H141D 70300 5900 27500 H142D 69100 -15100 31600 H143D 74700 -900 34700 C5D 64750 46970 70360 H6D 57200 27500 75500 H4D 71800 61600 64200 H5D 65700 57000 74300 2 3 4 5 6 7 2 3 8 91010 913161314 8 4 5 6 7 81212121515151130313132323333333434 343535393942434444454547474749495055141840425055
Notes:
Record type 4 (Symmetry Information)
Orthorhombic cell with space group Pbcn. A centre of symmetry at the origin is present (CENT = 1) so only 4 general positions are given (NOPR = 4):
211 0121 0112 0 x, y, z 011 6121 6112 0 1/2-x, 1/2+y, z 211 0101 0112 6 x, -y, 1/2+z 011 6101 6112 6 1/2-x, 1/2-y, 1/2+z
The remaining 4 operators are generated by applying the centre of symmetry operator to this set of 4, giving a total of 8 operators.
Record type 6 (Atomic Coordinates)
The total number of atoms is 58, consisting of NAT (=29) reference atoms plus NSAT (=29) symmetry-related atoms. The latter begin with label N10D and were generated with symmetry operator 5 in the expanded list, i.e. symmetry operator -x, -y, -z.