FMO DATABASE

FMODB ID: V58V1

Calculation Name: 3SSU-A-Xray372

Preferred Name: Vimentin

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3SSU

Chain ID: A

ChEMBL ID: CHEMBL3712854

UniProt ID: P08670

Base Structure: X-ray

Registration Date: 2023-06-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	46
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-194456.727069
FMO2-HF: Nuclear repulsion	174404.934935
FMO2-HF: Total energy	-20051.792134
FMO2-MP2: Total energy	-20109.357005

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:144:SER)

Summations of interaction energy for fragment #1(A:144:SER)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-6.53	-2.655	0.58	-1.55	-2.905	0.003

Interaction energy analysis for fragmet #1(A:144:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.008 / q_NPA : -0.014

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

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X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	146	LEU	0	-0.008	-0.002	2.664	-3.020	-0.583	0.120	-0.910	-1.647	0.002
4	A	147	GLY	0	-0.004	0.000	2.361	-1.797	-0.702	0.457	-0.592	-0.959	0.001
5	A	148	ASP	-1	-0.846	-0.926	3.734	-2.272	-1.929	0.003	-0.048	-0.299	0.000
6	A	149	LEU	0	-0.036	-0.022	5.944	0.562	0.562	0.000	0.000	0.000	0.000
7	A	150	TYR	0	0.030	0.016	7.130	0.098	0.098	0.000	0.000	0.000	0.000
8	A	151	GLU	-1	-0.948	-0.961	8.677	-0.750	-0.750	0.000	0.000	0.000	0.000
9	A	152	GLU	-1	-0.957	-0.992	10.074	-0.063	-0.063	0.000	0.000	0.000	0.000
10	A	153	GLU	-1	-0.951	-0.961	11.954	0.356	0.356	0.000	0.000	0.000	0.000
11	A	154	MET	0	-0.012	-0.012	13.269	0.018	0.018	0.000	0.000	0.000	0.000
12	A	155	ARG	1	0.939	0.984	14.513	0.175	0.175	0.000	0.000	0.000	0.000
13	A	156	GLU	-1	-0.782	-0.902	16.084	0.094	0.094	0.000	0.000	0.000	0.000
14	A	157	LEU	0	-0.011	-0.012	17.575	0.012	0.012	0.000	0.000	0.000	0.000
15	A	158	ARG	1	0.920	0.954	18.947	0.133	0.133	0.000	0.000	0.000	0.000
16	A	159	ARG	1	0.882	0.949	20.370	-0.034	-0.034	0.000	0.000	0.000	0.000
17	A	160	GLN	0	-0.062	-0.036	21.934	0.001	0.001	0.000	0.000	0.000	0.000
18	A	161	VAL	0	0.012	0.012	23.521	0.003	0.003	0.000	0.000	0.000	0.000
19	A	162	ASP	-1	-0.880	-0.931	24.782	-0.059	-0.059	0.000	0.000	0.000	0.000
20	A	163	GLN	0	-0.074	-0.024	26.384	0.006	0.006	0.000	0.000	0.000	0.000
21	A	164	LEU	0	0.007	-0.002	27.051	0.001	0.001	0.000	0.000	0.000	0.000
22	A	165	THR	0	-0.069	-0.032	28.642	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	166	ASN	0	-0.012	-0.016	30.807	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	167	ASP	-1	-0.905	-0.968	32.251	0.024	0.024	0.000	0.000	0.000	0.000
25	A	168	LYS	1	0.911	0.960	33.754	0.000	0.000	0.000	0.000	0.000	0.000
26	A	169	ALA	0	0.012	0.015	35.345	0.000	0.000	0.000	0.000	0.000	0.000
27	A	170	ARG	1	0.936	0.961	35.173	-0.018	-0.018	0.000	0.000	0.000	0.000
28	A	171	VAL	0	-0.012	0.002	37.600	0.001	0.001	0.000	0.000	0.000	0.000
29	A	172	GLU	-1	-0.955	-0.982	39.152	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	173	VAL	0	0.040	0.026	41.502	0.000	0.000	0.000	0.000	0.000	0.000
31	A	174	GLU	-1	-0.945	-0.972	41.903	0.019	0.019	0.000	0.000	0.000	0.000
32	A	175	ARG	1	0.810	0.880	42.558	-0.005	-0.005	0.000	0.000	0.000	0.000
33	A	176	ASP	-1	-0.814	-0.900	45.382	0.001	0.001	0.000	0.000	0.000	0.000
34	A	177	ASN	0	0.006	0.002	47.469	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	178	LEU	0	0.020	0.018	48.244	0.000	0.000	0.000	0.000	0.000	0.000
36	A	179	ALA	0	-0.030	-0.008	50.448	0.001	0.001	0.000	0.000	0.000	0.000
37	A	180	GLU	-1	-0.903	-0.964	51.312	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	181	ASP	-1	-0.940	-0.964	53.019	0.006	0.006	0.000	0.000	0.000	0.000
39	A	182	ILE	0	-0.067	-0.043	54.300	0.000	0.000	0.000	0.000	0.000	0.000
40	A	183	MET	0	-0.009	-0.008	55.612	0.000	0.000	0.000	0.000	0.000	0.000
41	A	184	ARG	1	0.969	0.978	55.066	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	185	LEU	0	-0.090	-0.052	58.265	0.000	0.000	0.000	0.000	0.000	0.000
43	A	186	ARG	1	0.919	0.961	58.173	-0.009	-0.009	0.000	0.000	0.000	0.000
44	A	187	GLU	-1	-0.952	-0.959	61.906	0.000	0.000	0.000	0.000	0.000	0.000
45	A	188	LYS	1	0.855	0.938	61.960	-0.005	-0.005	0.000	0.000	0.000	0.000
46	A	189	LEU	0	-0.018	0.010	66.284	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:144:SER)