Your cif-file contains coordinates, but as far as I could see it does not
contain bond lengths, and angles and their deviations. That is what coot
complains about.
Unless your cif-file describes a modified spermine you could use the
spermine already described in the refmac5 library:
In coot, go to the "File->Get Monomer" menu and enter the three letter
code SPM.
It should load a spermine together with geometric restrains (have a look
at $CLIB/data/monomers/s/SPM.cif to compare with your cif-file and see
that it contains bond length information etc.).
Tim
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
On Tue, 22 Jan 2008, Vineet Gaur wrote:
Hi all
I am using COOT for model building and refinement.
i have to introducea ligand in my model
i have downloaded .cif file from RCSB.
However while importing the cif file i m getting the warning message of
having No restraints in the CIF file
is there any problem in the format of the following cif file
data_SPM
#
_chem_comp.id SPM
_chem_comp.name SPERMINE
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAI
_chem_comp.formula "C10 H26 N4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2007-08-16
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 202.340
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code SPM
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1DPL
_chem_comp.pdbx_processing_site ?
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_ordinal
SPM N1 N1 N 0 1 N N N -1.386 5.560 25.140 -0.292 0.012 7.961 1
SPM C2 C2 C 0 1 N N N -2.248 4.344 25.282 0.514 -0.023 6.734 2
SPM C3 C3 C 0 1 N N N -1.844 3.214 24.376 -0.408 0.014 5.515 3
SPM C4 C4 C 0 1 N N N -2.834 2.063 24.495 0.432 -0.022 4.237 4
SPM N5 N5 N 0 1 N N N -2.313 0.871 23.720 -0.453 0.013 3.066 5
SPM C6 C6 C 0 1 N N N -3.235 -0.310 23.760 0.411 -0.024 1.880 6
SPM C7 C7 C 0 1 N N N -2.669 -1.391 22.871 -0.451 0.011 0.617 7
SPM C8 C8 C 0 1 N N N -3.306 -2.753 23.219 0.450 -0.028 -0.617 8
SPM C9 C9 C 0 1 N N N -2.886 -3.777 22.188 -0.412 0.006 -1.880 9
SPM N10 N10 N 0 1 N N N -3.212 -5.172 22.585 0.453 -0.031 -3.066 10
SPM C11 C11 C 0 1 N N N -2.084 -5.778 23.391 -0.433 0.005 -4.237 11
SPM C12 C12 C 0 1 N N N -2.443 -7.162 23.912 0.407 -0.032 -5.515 12
SPM C13 C13 C 0 1 N N N -1.448 -8.158 23.367 -0.515 0.005 -6.734 13
SPM N14 N14 N 0 1 N N N -0.553 -8.726 24.427 0.292 -0.029 -7.961 14
SPM HN11 1HN1 H 0 0 N N N -1.660 6.326 25.754 -0.739 0.916 7.988 15
SPM HN12 2HN1 H 0 0 N N N -1.355 5.869 24.168 0.354 -0.014 8.735 16
SPM H21 1H2 H 0 1 N N N -2.281 4.005 26.343 1.181 0.838 6.713 17
SPM H22 2H2 H 0 1 N N N -3.322 4.602 25.135 1.105 -0.939 6.715 18
SPM H31 1H3 H 0 1 N N N -1.722 3.550 23.320 -1.074 -0.847 5.536 19
SPM H32 2H3 H 0 1 N N N -0.796 2.883 24.565 -0.999 0.930 5.534 20
SPM H41 1H4 H 0 1 N N N -3.061 1.809 25.556 1.098 0.839 4.215 21
SPM H42 2H4 H 0 1 N N N -3.862 2.355 24.178 1.023 -0.938 4.217 22
SPM HN5 HN5 H 0 1 N N N -1.378 0.612 24.037 -0.976 -0.849 3.071 23
SPM H61 1H6 H 0 1 N N N -3.427 -0.667 24.798 1.078 0.838 1.889 24
SPM H62 2H6 H 0 1 N N N -4.284 -0.042 23.493 1.002 -0.940 1.891 25
SPM H71 1H7 H 0 1 N N N -2.780 -1.142 21.789 -1.117 -0.851 0.608 26
SPM H72 2H7 H 0 1 N N N -1.555 -1.427 22.916 -1.042 0.927 0.607 27
SPM H81 1H8 H 0 1 N N N -3.068 -3.077 24.258 1.117 0.833 -0.608 28
SPM H82 2H8 H 0 1 N N N -4.414 -2.687 23.323 1.041 -0.944 -0.607 29
SPM H91 1H9 H 0 1 N N N -3.319 -3.536 21.189 -1.079 -0.855 -1.889 30
SPM H92 2H9 H 0 1 N N N -1.802 -3.675 21.945 -1.003 0.922 -1.891 31
SPM HN0 HN0 H 0 1 N N N -3.451 -5.748 21.778 0.976 0.831 -3.071 32
SPM H111 1H11 H 0 0 N N N -1.133 -5.797 22.808 -1.099 -0.857 -4.215 33
SPM H112 2H11 H 0 0 N N N -1.767 -5.101 24.219 -1.023 0.921 -4.217 34
SPM H121 1H12 H 0 0 N N N -2.512 -7.194 25.024 1.074 0.830 -5.536 35
SPM H122 2H12 H 0 0 N N N -3.497 -7.443 23.683 0.998 -0.948 -5.534 36
SPM H131 1H13 H 0 0 N N N -1.964 -8.969 22.803 -1.181 -0.856 -6.713 37
SPM H132 2H13 H 0 0 N N N -0.851 -7.712 22.537 -1.105 0.921 -6.714 38
SPM HN41 1HN4 H 0 0 N N N 0.119 -9.398 24.058 -0.354 -0.003 -8.735 39
SPM HN42 2HN4 H 0 0 N N N -1.099 -9.133 25.186 0.814 0.833 -7.990 40
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
SPM N1 C2 SING N N 1
SPM N1 HN11 SING N N 2
SPM N1 HN12 SING N N 3
SPM C2 C3 SING N N 4
SPM C2 H21 SING N N 5
SPM C2 H22 SING N N 6
SPM C3 C4 SING N N 7
SPM C3 H31 SING N N 8
SPM C3 H32 SING N N 9
SPM C4 N5 SING N N 10
SPM C4 H41 SING N N 11
SPM C4 H42 SING N N 12
SPM N5 C6 SING N N 13
SPM N5 HN5 SING N N 14
SPM C6 C7 SING N N 15
SPM C6 H61 SING N N 16
SPM C6 H62 SING N N 17
SPM C7 C8 SING N N 18
SPM C7 H71 SING N N 19
SPM C7 H72 SING N N 20
SPM C8 C9 SING N N 21
SPM C8 H81 SING N N 22
SPM C8 H82 SING N N 23
SPM C9 N10 SING N N 24
SPM C9 H91 SING N N 25
SPM C9 H92 SING N N 26
SPM N10 C11 SING N N 27
SPM N10 HN0 SING N N 28
SPM C11 C12 SING N N 29
SPM C11 H111 SING N N 30
SPM C11 H112 SING N N 31
SPM C12 C13 SING N N 32
SPM C12 H121 SING N N 33
SPM C12 H122 SING N N 34
SPM C13 N14 SING N N 35
SPM C13 H131 SING N N 36
SPM C13 H132 SING N N 37
SPM N14 HN41 SING N N 38
SPM N14 HN42 SING N N 39
#
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
SPM SMILES ACDLabs 10.04 NCCCNCCCCNCCCN
SPM InChI InChI 1.01
InChI=1/C10H26N4/c11-5-3-9-13-7-1-2-8-14-10-4-6-12/h13-14H,1-12H2
SPM SMILES_CANONICAL CACTVS 3.341 NCCCNCCCCNCCCN
SPM SMILES CACTVS 3.341 NCCCNCCCCNCCCN
SPM SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C(CCNCCCN)CNCCCN
SPM SMILES "OpenEye OEToolkits" 1.5.0 C(CCNCCCN)CNCCCN
#
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
SPM "SYSTEMATIC NAME" ACDLabs 10.04
"N,N'-bis(3-aminopropyl)butane-1,4-diamine"
SPM "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0
"N,N'-bis(3-aminopropyl)butane-1,4-diamine"
#
thanks
Vineet
