FMO DATABASE

FMODB ID: 2J7MR

Calculation Name: 3UF1-A-Xray372

Preferred Name: Vimentin

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3UF1

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	104
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-543442.879756
FMO2-HF: Nuclear repulsion	499296.127838
FMO2-HF: Total energy	-44146.751919
FMO2-MP2: Total energy	-44274.952071

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:146:LEU)

Summations of interaction energy for fragment #1(A:146:LEU)

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.
-7.896	-2.026	5.8	-4.368	-7.302	-0.016

Interaction energy analysis for fragmet #1(A:146:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.076 / q_NPA : 0.032

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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Graph Options

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	148	ASP	-1	-0.877	-0.948	2.230	-10.759	-5.510	3.306	-3.347	-5.208	-0.018
4	A	149	LEU	0	0.003	-0.002	2.062	1.206	1.532	2.495	-0.983	-1.838	0.002
5	A	150	TYR	0	0.010	0.019	4.582	1.077	1.372	-0.001	-0.038	-0.256	0.000
6	A	151	GLU	-1	-0.796	-0.880	7.083	-0.467	-0.467	0.000	0.000	0.000	0.000
7	A	152	GLU	-1	-0.820	-0.890	7.385	-0.843	-0.843	0.000	0.000	0.000	0.000
8	A	153	GLU	-1	-0.927	-0.952	8.517	-0.468	-0.468	0.000	0.000	0.000	0.000
9	A	154	MET	0	-0.074	-0.041	10.371	0.299	0.299	0.000	0.000	0.000	0.000
10	A	155	ARG	1	0.747	0.838	9.790	1.297	1.297	0.000	0.000	0.000	0.000
11	A	156	GLU	-1	-0.766	-0.851	13.051	-0.315	-0.315	0.000	0.000	0.000	0.000
12	A	157	LEU	0	0.017	0.006	14.338	0.098	0.098	0.000	0.000	0.000	0.000
13	A	158	ARG	1	0.797	0.877	12.749	0.795	0.795	0.000	0.000	0.000	0.000
14	A	159	ARG	1	0.898	0.934	17.861	0.423	0.423	0.000	0.000	0.000	0.000
15	A	160	GLN	0	-0.075	-0.045	17.697	0.078	0.078	0.000	0.000	0.000	0.000
16	A	161	VAL	0	0.009	-0.002	20.677	0.037	0.037	0.000	0.000	0.000	0.000
17	A	162	ASP	-1	-0.867	-0.913	22.430	-0.267	-0.267	0.000	0.000	0.000	0.000
18	A	163	GLN	0	-0.103	-0.048	23.838	0.014	0.014	0.000	0.000	0.000	0.000
19	A	164	LEU	0	0.023	-0.009	24.328	0.022	0.022	0.000	0.000	0.000	0.000
20	A	165	THR	0	-0.036	-0.009	26.262	0.022	0.022	0.000	0.000	0.000	0.000
21	A	166	ASN	0	-0.055	-0.047	27.655	0.025	0.025	0.000	0.000	0.000	0.000
22	A	167	ASP	-1	-0.815	-0.880	29.664	-0.146	-0.146	0.000	0.000	0.000	0.000
23	A	168	LYS	1	0.796	0.880	30.970	0.137	0.137	0.000	0.000	0.000	0.000
24	A	169	ALA	0	-0.001	0.009	32.664	0.009	0.009	0.000	0.000	0.000	0.000
25	A	170	ARG	1	0.824	0.890	33.229	0.131	0.131	0.000	0.000	0.000	0.000
26	A	171	VAL	0	0.004	-0.008	35.216	0.007	0.007	0.000	0.000	0.000	0.000
27	A	172	GLU	-1	-0.855	-0.909	35.912	-0.107	-0.107	0.000	0.000	0.000	0.000
28	A	173	VAL	0	0.026	0.021	38.821	0.006	0.006	0.000	0.000	0.000	0.000
29	A	174	GLU	-1	-0.893	-0.942	38.849	-0.092	-0.092	0.000	0.000	0.000	0.000
30	A	175	ARG	1	0.796	0.874	40.139	0.090	0.090	0.000	0.000	0.000	0.000
31	A	176	ASP	-1	-0.817	-0.887	42.346	-0.078	-0.078	0.000	0.000	0.000	0.000
32	A	177	ASN	0	-0.015	-0.005	44.404	0.005	0.005	0.000	0.000	0.000	0.000
33	A	178	LEU	0	0.003	0.001	44.994	0.004	0.004	0.000	0.000	0.000	0.000
34	A	179	ALA	0	-0.023	-0.020	47.245	0.004	0.004	0.000	0.000	0.000	0.000
35	A	180	GLU	-1	-0.835	-0.909	48.986	-0.056	-0.056	0.000	0.000	0.000	0.000
36	A	181	ASP	-1	-0.830	-0.901	50.891	-0.055	-0.055	0.000	0.000	0.000	0.000
37	A	182	ILE	0	-0.056	-0.028	51.127	0.003	0.003	0.000	0.000	0.000	0.000
38	A	183	MET	0	-0.075	-0.030	51.597	0.003	0.003	0.000	0.000	0.000	0.000
39	A	184	ARG	1	0.829	0.881	52.759	0.056	0.056	0.000	0.000	0.000	0.000
40	A	185	LEU	0	-0.049	-0.014	56.119	0.002	0.002	0.000	0.000	0.000	0.000
41	A	186	ARG	1	0.955	0.969	53.523	0.047	0.047	0.000	0.000	0.000	0.000
42	A	187	GLU	-1	-0.914	-0.946	59.065	-0.041	-0.041	0.000	0.000	0.000	0.000
43	A	188	LYS	1	0.959	0.979	61.445	0.039	0.039	0.000	0.000	0.000	0.000
44	A	189	LEU	0	-0.018	-0.001	60.838	0.001	0.001	0.000	0.000	0.000	0.000
45	A	190	GLN	0	0.002	-0.025	61.846	0.000	0.000	0.000	0.000	0.000	0.000
46	A	191	GLU	-1	-0.903	-0.939	64.869	-0.030	-0.030	0.000	0.000	0.000	0.000
47	A	192	GLU	-1	-0.913	-0.955	66.265	-0.031	-0.031	0.000	0.000	0.000	0.000
48	A	193	MET	0	-0.090	-0.033	63.564	0.001	0.001	0.000	0.000	0.000	0.000
49	A	194	LEU	0	0.035	0.019	68.760	0.001	0.001	0.000	0.000	0.000	0.000
50	A	195	GLN	0	-0.014	-0.013	71.191	0.002	0.002	0.000	0.000	0.000	0.000
51	A	196	ARG	1	0.748	0.865	70.230	0.027	0.027	0.000	0.000	0.000	0.000
52	A	197	GLU	-1	-0.933	-0.966	72.202	-0.025	-0.025	0.000	0.000	0.000	0.000
53	A	198	GLU	-1	-0.934	-0.964	74.403	-0.023	-0.023	0.000	0.000	0.000	0.000
54	A	199	ALA	0	-0.012	-0.019	76.471	0.001	0.001	0.000	0.000	0.000	0.000
55	A	200	GLU	-1	-0.875	-0.937	74.386	-0.024	-0.024	0.000	0.000	0.000	0.000
56	A	201	ASN	0	-0.008	-0.004	77.126	0.001	0.001	0.000	0.000	0.000	0.000
57	A	202	THR	0	-0.008	0.002	80.505	0.001	0.001	0.000	0.000	0.000	0.000
58	A	203	LEU	0	-0.060	-0.030	81.502	0.001	0.001	0.000	0.000	0.000	0.000
59	A	204	GLN	0	-0.008	0.003	81.509	0.000	0.000	0.000	0.000	0.000	0.000
60	A	205	SER	0	-0.033	-0.021	84.199	0.000	0.000	0.000	0.000	0.000	0.000
61	A	206	PHE	0	0.004	0.007	86.583	0.000	0.000	0.000	0.000	0.000	0.000
62	A	207	ARG	1	0.862	0.919	87.012	0.017	0.017	0.000	0.000	0.000	0.000
63	A	208	GLN	0	0.041	0.020	88.954	0.001	0.001	0.000	0.000	0.000	0.000
64	A	209	ASP	-1	-0.869	-0.917	91.507	-0.016	-0.016	0.000	0.000	0.000	0.000
65	A	210	VAL	0	-0.040	-0.015	90.452	0.000	0.000	0.000	0.000	0.000	0.000
66	A	211	ASP	-1	-0.831	-0.911	92.222	-0.015	-0.015	0.000	0.000	0.000	0.000
67	A	212	ASN	0	-0.058	-0.056	94.918	0.001	0.001	0.000	0.000	0.000	0.000
68	A	213	ALA	0	-0.030	-0.008	96.654	0.000	0.000	0.000	0.000	0.000	0.000
69	A	214	SER	0	-0.017	-0.011	96.741	0.000	0.000	0.000	0.000	0.000	0.000
70	A	215	LEU	0	0.027	0.016	98.621	0.000	0.000	0.000	0.000	0.000	0.000
71	A	216	ALA	0	0.031	0.034	101.134	0.000	0.000	0.000	0.000	0.000	0.000
72	A	217	ARG	1	0.805	0.879	100.952	0.014	0.014	0.000	0.000	0.000	0.000
73	A	218	LEU	0	0.020	0.004	101.076	0.000	0.000	0.000	0.000	0.000	0.000
74	A	219	ASP	-1	-0.899	-0.953	104.722	-0.012	-0.012	0.000	0.000	0.000	0.000
75	A	220	LEU	0	-0.126	-0.070	106.449	0.000	0.000	0.000	0.000	0.000	0.000
76	A	221	GLU	-1	-0.812	-0.890	105.141	-0.012	-0.012	0.000	0.000	0.000	0.000
77	A	222	ARG	1	0.818	0.893	108.838	0.010	0.010	0.000	0.000	0.000	0.000
78	A	223	LYS	1	0.911	0.942	110.096	0.012	0.012	0.000	0.000	0.000	0.000
79	A	224	VAL	0	-0.021	-0.018	112.194	0.000	0.000	0.000	0.000	0.000	0.000
80	A	225	GLU	-1	-0.862	-0.919	110.628	-0.011	-0.011	0.000	0.000	0.000	0.000
81	A	226	SER	0	-0.003	0.001	114.480	0.000	0.000	0.000	0.000	0.000	0.000
82	A	227	LEU	0	0.004	-0.003	116.595	0.000	0.000	0.000	0.000	0.000	0.000
83	A	228	GLN	0	-0.050	-0.029	115.218	0.000	0.000	0.000	0.000	0.000	0.000
84	A	229	GLU	-1	-0.821	-0.880	116.243	-0.010	-0.010	0.000	0.000	0.000	0.000
85	A	230	GLU	-1	-0.955	-0.958	120.513	-0.009	-0.009	0.000	0.000	0.000	0.000
86	A	231	ILE	0	-0.015	-0.018	121.514	0.000	0.000	0.000	0.000	0.000	0.000
87	A	232	ALA	0	-0.061	-0.031	122.596	0.000	0.000	0.000	0.000	0.000	0.000
88	A	233	PHE	0	0.011	0.009	124.521	0.000	0.000	0.000	0.000	0.000	0.000
89	A	234	LEU	0	0.032	0.004	126.565	0.000	0.000	0.000	0.000	0.000	0.000
90	A	235	LYS	1	0.898	0.968	125.275	0.009	0.009	0.000	0.000	0.000	0.000
91	A	236	LYS	1	0.846	0.909	128.264	0.008	0.008	0.000	0.000	0.000	0.000
92	A	237	LEU	0	0.019	0.026	130.669	0.000	0.000	0.000	0.000	0.000	0.000
93	A	238	HIS	0	0.009	-0.010	131.828	0.000	0.000	0.000	0.000	0.000	0.000
94	A	239	GLU	-1	-0.886	-0.932	132.380	-0.008	-0.008	0.000	0.000	0.000	0.000
95	A	240	GLU	-1	-0.887	-0.942	135.008	-0.007	-0.007	0.000	0.000	0.000	0.000
96	A	241	GLU	-1	-1.010	-1.008	136.509	-0.007	-0.007	0.000	0.000	0.000	0.000
97	A	242	ILE	0	-0.023	-0.020	137.708	0.000	0.000	0.000	0.000	0.000	0.000
98	A	243	GLN	0	0.029	0.012	139.144	0.000	0.000	0.000	0.000	0.000	0.000
99	A	244	GLU	-1	-0.978	-0.989	141.041	-0.006	-0.006	0.000	0.000	0.000	0.000
100	A	245	LEU	0	-0.033	-0.021	142.768	0.000	0.000	0.000	0.000	0.000	0.000
101	A	246	GLN	0	-0.096	-0.033	143.427	0.000	0.000	0.000	0.000	0.000	0.000
102	A	247	ALA	0	-0.050	-0.016	146.333	0.000	0.000	0.000	0.000	0.000	0.000
103	A	248	GLN	0	-0.034	-0.025	146.359	0.000	0.000	0.000	0.000	0.000	0.000
104	A	249	ILE	0	-0.030	0.003	149.942	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:146:LEU)