FMO DATABASE

FMODB ID: 1725Z

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	OptHSide
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	-194674.94123
FMO2-HF: Nuclear repulsion	174622.651808
FMO2-HF: Total energy	-20052.289421
FMO2-MP2: Total energy	-20109.840917

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.
-7.74	-3.794	0.549	-1.631	-2.863	0.005

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 : -0.014 / q_NPA : -0.019

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	-0.016	-0.002	2.864	-3.156	-0.651	0.080	-0.971	-1.614	0.003
4	A	147	GLY	0	0.004	0.004	2.354	-2.006	-0.890	0.466	-0.607	-0.974	0.002
5	A	148	ASP	-1	-0.867	-0.936	3.731	-3.208	-2.883	0.003	-0.053	-0.275	0.000
6	A	149	LEU	0	-0.029	-0.024	5.938	0.597	0.597	0.000	0.000	0.000	0.000
7	A	150	TYR	0	0.020	0.017	7.081	0.207	0.207	0.000	0.000	0.000	0.000
8	A	151	GLU	-1	-0.951	-0.964	8.668	-0.831	-0.831	0.000	0.000	0.000	0.000
9	A	152	GLU	-1	-0.849	-0.926	10.127	-0.144	-0.144	0.000	0.000	0.000	0.000
10	A	153	GLU	-1	-0.942	-0.956	11.951	0.389	0.389	0.000	0.000	0.000	0.000
11	A	154	MET	0	-0.006	-0.011	13.368	0.022	0.022	0.000	0.000	0.000	0.000
12	A	155	ARG	1	0.846	0.925	14.307	0.247	0.247	0.000	0.000	0.000	0.000
13	A	156	GLU	-1	-0.720	-0.820	16.077	0.065	0.065	0.000	0.000	0.000	0.000
14	A	157	LEU	0	-0.027	-0.020	17.193	0.015	0.015	0.000	0.000	0.000	0.000
15	A	158	ARG	1	0.896	0.943	18.943	0.139	0.139	0.000	0.000	0.000	0.000
16	A	159	ARG	1	0.822	0.884	20.367	-0.018	-0.018	0.000	0.000	0.000	0.000
17	A	160	GLN	0	-0.070	-0.053	21.550	0.007	0.007	0.000	0.000	0.000	0.000
18	A	161	VAL	0	0.008	0.011	23.516	0.004	0.004	0.000	0.000	0.000	0.000
19	A	162	ASP	-1	-0.850	-0.912	24.698	-0.077	-0.077	0.000	0.000	0.000	0.000
20	A	163	GLN	0	-0.089	-0.040	26.378	0.001	0.001	0.000	0.000	0.000	0.000
21	A	164	LEU	0	0.016	0.003	27.326	0.002	0.002	0.000	0.000	0.000	0.000
22	A	165	THR	0	-0.064	-0.040	28.616	0.000	0.000	0.000	0.000	0.000	0.000
23	A	166	ASN	0	-0.016	-0.015	30.801	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	167	ASP	-1	-0.819	-0.904	32.059	0.014	0.014	0.000	0.000	0.000	0.000
25	A	168	LYS	1	0.833	0.909	33.749	0.006	0.006	0.000	0.000	0.000	0.000
26	A	169	ALA	0	0.009	0.005	35.338	0.001	0.001	0.000	0.000	0.000	0.000
27	A	170	ARG	1	0.804	0.869	35.686	-0.011	-0.011	0.000	0.000	0.000	0.000
28	A	171	VAL	0	0.005	0.012	38.141	0.002	0.002	0.000	0.000	0.000	0.000
29	A	172	GLU	-1	-0.832	-0.895	39.130	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	173	VAL	0	0.015	0.017	41.500	0.000	0.000	0.000	0.000	0.000	0.000
31	A	174	GLU	-1	-0.875	-0.927	41.365	0.012	0.012	0.000	0.000	0.000	0.000
32	A	175	ARG	1	0.763	0.835	42.195	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	176	ASP	-1	-0.813	-0.887	45.371	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	177	ASN	0	-0.005	-0.001	47.468	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	178	LEU	0	0.015	0.011	47.993	0.001	0.001	0.000	0.000	0.000	0.000
36	A	179	ALA	0	-0.037	-0.010	50.438	0.001	0.001	0.000	0.000	0.000	0.000
37	A	180	GLU	-1	-0.853	-0.924	51.790	-0.005	-0.005	0.000	0.000	0.000	0.000
38	A	181	ASP	-1	-0.877	-0.919	53.229	0.002	0.002	0.000	0.000	0.000	0.000
39	A	182	ILE	0	-0.065	-0.038	53.761	0.001	0.001	0.000	0.000	0.000	0.000
40	A	183	MET	0	-0.030	-0.019	55.587	0.000	0.000	0.000	0.000	0.000	0.000
41	A	184	ARG	1	0.897	0.918	54.123	0.002	0.002	0.000	0.000	0.000	0.000
42	A	185	LEU	0	-0.089	-0.051	58.144	0.000	0.000	0.000	0.000	0.000	0.000
43	A	186	ARG	1	0.913	0.955	58.243	-0.007	-0.007	0.000	0.000	0.000	0.000
44	A	187	GLU	-1	-0.948	-0.959	61.531	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	188	LYS	1	0.867	0.941	62.041	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	189	LEU	0	-0.023	0.009	66.278	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)