FMO DATABASE

FMODB ID: G6L81

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	OptAll
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	-194634.461562
FMO2-HF: Nuclear repulsion	174581.939129
FMO2-HF: Total energy	-20052.522433
FMO2-MP2: Total energy	-20110.015661

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.
-6.253	-3.133	0.027	-1.306	-1.842	-0.002

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 : 0.004 / q_NPA : -0.009

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	-0.017	0.006	3.409	-2.023	-0.111	0.009	-0.856	-1.066	0.000
4	A	147	GLY	0	0.016	0.008	3.230	-0.001	0.501	0.005	-0.153	-0.354	0.000
5	A	148	ASP	-1	-0.867	-0.944	3.793	-4.844	-4.138	0.013	-0.297	-0.422	-0.002
6	A	149	LEU	0	-0.023	-0.021	6.048	0.737	0.737	0.000	0.000	0.000	0.000
7	A	150	TYR	0	0.019	0.017	7.421	0.262	0.262	0.000	0.000	0.000	0.000
8	A	151	GLU	-1	-0.951	-0.961	8.824	-0.998	-0.998	0.000	0.000	0.000	0.000
9	A	152	GLU	-1	-0.839	-0.917	10.441	-0.221	-0.221	0.000	0.000	0.000	0.000
10	A	153	GLU	-1	-0.951	-0.973	12.149	0.121	0.121	0.000	0.000	0.000	0.000
11	A	154	MET	0	-0.016	-0.014	13.423	0.073	0.073	0.000	0.000	0.000	0.000
12	A	155	ARG	1	0.823	0.911	14.192	0.432	0.432	0.000	0.000	0.000	0.000
13	A	156	GLU	-1	-0.744	-0.825	16.462	-0.032	-0.032	0.000	0.000	0.000	0.000
14	A	157	LEU	0	0.002	-0.003	16.976	0.027	0.027	0.000	0.000	0.000	0.000
15	A	158	ARG	1	0.821	0.879	19.075	0.225	0.225	0.000	0.000	0.000	0.000
16	A	159	ARG	1	0.792	0.866	20.576	0.095	0.095	0.000	0.000	0.000	0.000
17	A	160	GLN	0	-0.057	-0.048	21.831	0.020	0.020	0.000	0.000	0.000	0.000
18	A	161	VAL	0	0.030	0.019	23.730	0.013	0.013	0.000	0.000	0.000	0.000
19	A	162	ASP	-1	-0.794	-0.859	24.355	-0.160	-0.160	0.000	0.000	0.000	0.000
20	A	163	GLN	0	-0.060	-0.033	26.503	0.007	0.007	0.000	0.000	0.000	0.000
21	A	164	LEU	0	0.005	-0.005	27.426	0.009	0.009	0.000	0.000	0.000	0.000
22	A	165	THR	0	-0.051	-0.030	28.980	0.006	0.006	0.000	0.000	0.000	0.000
23	A	166	ASN	0	-0.033	-0.012	31.049	0.002	0.002	0.000	0.000	0.000	0.000
24	A	167	ASP	-1	-0.802	-0.898	32.369	-0.034	-0.034	0.000	0.000	0.000	0.000
25	A	168	LYS	1	0.827	0.914	33.885	0.049	0.049	0.000	0.000	0.000	0.000
26	A	169	ALA	0	0.015	-0.001	35.546	0.004	0.004	0.000	0.000	0.000	0.000
27	A	170	ARG	1	0.774	0.863	35.934	0.030	0.030	0.000	0.000	0.000	0.000
28	A	171	VAL	0	0.017	0.004	38.278	0.003	0.003	0.000	0.000	0.000	0.000
29	A	172	GLU	-1	-0.827	-0.888	39.626	-0.037	-0.037	0.000	0.000	0.000	0.000
30	A	173	VAL	0	0.017	0.016	41.682	0.002	0.002	0.000	0.000	0.000	0.000
31	A	174	GLU	-1	-0.873	-0.926	41.406	-0.020	-0.020	0.000	0.000	0.000	0.000
32	A	175	ARG	1	0.738	0.821	42.439	0.031	0.031	0.000	0.000	0.000	0.000
33	A	176	ASP	-1	-0.805	-0.875	45.695	-0.027	-0.027	0.000	0.000	0.000	0.000
34	A	177	ASN	0	0.011	0.004	47.130	0.000	0.000	0.000	0.000	0.000	0.000
35	A	178	LEU	0	0.009	0.012	47.971	0.002	0.002	0.000	0.000	0.000	0.000
36	A	179	ALA	0	-0.031	-0.014	50.502	0.002	0.002	0.000	0.000	0.000	0.000
37	A	180	GLU	-1	-0.829	-0.911	51.742	-0.024	-0.024	0.000	0.000	0.000	0.000
38	A	181	ASP	-1	-0.860	-0.919	53.639	-0.018	-0.018	0.000	0.000	0.000	0.000
39	A	182	ILE	0	-0.061	-0.034	53.666	0.002	0.002	0.000	0.000	0.000	0.000
40	A	183	MET	0	-0.062	-0.023	55.704	0.001	0.001	0.000	0.000	0.000	0.000
41	A	184	ARG	1	0.876	0.907	53.823	0.022	0.022	0.000	0.000	0.000	0.000
42	A	185	LEU	0	-0.079	-0.037	58.282	0.001	0.001	0.000	0.000	0.000	0.000
43	A	186	ARG	1	0.921	0.958	57.980	0.010	0.010	0.000	0.000	0.000	0.000
44	A	187	GLU	-1	-0.932	-0.970	61.394	-0.017	-0.017	0.000	0.000	0.000	0.000
45	A	188	LYS	1	0.871	0.951	61.994	0.014	0.014	0.000	0.000	0.000	0.000
46	A	189	LEU	0	-0.039	-0.001	66.561	0.001	0.001	0.000	0.000	0.000	0.000

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