FMO DATABASE

FMODB ID: 6NL4Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-543509.441983
FMO2-HF: Nuclear repulsion	499362.065179
FMO2-HF: Total energy	-44147.376804
FMO2-MP2: Total energy	-44275.494258

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.
-10.205	-3.804	4.545	-4.707	-6.238	-0.022

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 : 0.055 / q_NPA : 0.025

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	-0.859	-0.943	2.503	-13.399	-7.150	1.712	-3.648	-4.313	-0.025
4	A	149	LEU	0	-0.015	-0.004	1.926	1.677	1.581	2.834	-1.036	-1.701	0.003
5	A	150	TYR	0	0.012	0.009	4.900	1.066	1.314	-0.001	-0.023	-0.224	0.000
6	A	151	GLU	-1	-0.785	-0.867	7.336	-0.538	-0.538	0.000	0.000	0.000	0.000
7	A	152	GLU	-1	-0.816	-0.892	7.604	-0.960	-0.960	0.000	0.000	0.000	0.000
8	A	153	GLU	-1	-0.921	-0.946	9.007	-0.480	-0.480	0.000	0.000	0.000	0.000
9	A	154	MET	0	-0.059	-0.038	10.905	0.286	0.286	0.000	0.000	0.000	0.000
10	A	155	ARG	1	0.720	0.836	9.958	1.352	1.352	0.000	0.000	0.000	0.000
11	A	156	GLU	-1	-0.761	-0.845	13.600	-0.325	-0.325	0.000	0.000	0.000	0.000
12	A	157	LEU	0	0.002	0.002	14.463	0.094	0.094	0.000	0.000	0.000	0.000
13	A	158	ARG	1	0.811	0.885	13.202	0.867	0.867	0.000	0.000	0.000	0.000
14	A	159	ARG	1	0.904	0.928	18.274	0.434	0.434	0.000	0.000	0.000	0.000
15	A	160	GLN	0	-0.072	-0.049	17.786	0.073	0.073	0.000	0.000	0.000	0.000
16	A	161	VAL	0	0.021	0.013	21.181	0.040	0.040	0.000	0.000	0.000	0.000
17	A	162	ASP	-1	-0.893	-0.929	22.270	-0.300	-0.300	0.000	0.000	0.000	0.000
18	A	163	GLN	0	-0.082	-0.042	24.123	0.016	0.016	0.000	0.000	0.000	0.000
19	A	164	LEU	0	0.007	-0.006	24.384	0.024	0.024	0.000	0.000	0.000	0.000
20	A	165	THR	0	-0.041	-0.023	26.647	0.023	0.023	0.000	0.000	0.000	0.000
21	A	166	ASN	0	-0.065	-0.045	28.033	0.026	0.026	0.000	0.000	0.000	0.000
22	A	167	ASP	-1	-0.794	-0.884	30.077	-0.151	-0.151	0.000	0.000	0.000	0.000
23	A	168	LYS	1	0.785	0.882	31.280	0.148	0.148	0.000	0.000	0.000	0.000
24	A	169	ALA	0	0.014	0.006	33.093	0.011	0.011	0.000	0.000	0.000	0.000
25	A	170	ARG	1	0.773	0.866	33.649	0.137	0.137	0.000	0.000	0.000	0.000
26	A	171	VAL	0	0.021	0.006	35.517	0.008	0.008	0.000	0.000	0.000	0.000
27	A	172	GLU	-1	-0.869	-0.914	36.324	-0.116	-0.116	0.000	0.000	0.000	0.000
28	A	173	VAL	0	0.050	0.028	39.128	0.007	0.007	0.000	0.000	0.000	0.000
29	A	174	GLU	-1	-0.868	-0.915	39.091	-0.100	-0.100	0.000	0.000	0.000	0.000
30	A	175	ARG	1	0.796	0.861	40.522	0.098	0.098	0.000	0.000	0.000	0.000
31	A	176	ASP	-1	-0.798	-0.879	43.045	-0.083	-0.083	0.000	0.000	0.000	0.000
32	A	177	ASN	0	-0.068	-0.039	44.399	0.006	0.006	0.000	0.000	0.000	0.000
33	A	178	LEU	0	0.026	0.010	44.940	0.004	0.004	0.000	0.000	0.000	0.000
34	A	179	ALA	0	-0.027	-0.011	47.379	0.004	0.004	0.000	0.000	0.000	0.000
35	A	180	GLU	-1	-0.832	-0.901	49.173	-0.059	-0.059	0.000	0.000	0.000	0.000
36	A	181	ASP	-1	-0.828	-0.900	51.169	-0.059	-0.059	0.000	0.000	0.000	0.000
37	A	182	ILE	0	-0.058	-0.031	51.063	0.003	0.003	0.000	0.000	0.000	0.000
38	A	183	MET	0	-0.088	-0.039	51.963	0.003	0.003	0.000	0.000	0.000	0.000
39	A	184	ARG	1	0.841	0.889	53.158	0.060	0.060	0.000	0.000	0.000	0.000
40	A	185	LEU	0	-0.041	-0.014	56.099	0.002	0.002	0.000	0.000	0.000	0.000
41	A	186	ARG	1	0.922	0.971	54.006	0.052	0.052	0.000	0.000	0.000	0.000
42	A	187	GLU	-1	-0.908	-0.954	59.387	-0.045	-0.045	0.000	0.000	0.000	0.000
43	A	188	LYS	1	0.901	0.951	61.599	0.040	0.040	0.000	0.000	0.000	0.000
44	A	189	LEU	0	-0.029	-0.012	60.956	0.001	0.001	0.000	0.000	0.000	0.000
45	A	190	GLN	0	0.000	-0.029	62.128	0.000	0.000	0.000	0.000	0.000	0.000
46	A	191	GLU	-1	-0.867	-0.915	65.306	-0.032	-0.032	0.000	0.000	0.000	0.000
47	A	192	GLU	-1	-0.882	-0.942	66.045	-0.034	-0.034	0.000	0.000	0.000	0.000
48	A	193	MET	0	-0.071	-0.035	63.818	0.001	0.001	0.000	0.000	0.000	0.000
49	A	194	LEU	0	0.047	0.029	68.937	0.001	0.001	0.000	0.000	0.000	0.000
50	A	195	GLN	0	-0.034	-0.028	71.496	0.002	0.002	0.000	0.000	0.000	0.000
51	A	196	ARG	1	0.722	0.848	70.350	0.029	0.029	0.000	0.000	0.000	0.000
52	A	197	GLU	-1	-0.890	-0.929	72.432	-0.027	-0.027	0.000	0.000	0.000	0.000
53	A	198	GLU	-1	-0.910	-0.944	74.845	-0.025	-0.025	0.000	0.000	0.000	0.000
54	A	199	ALA	0	0.008	0.015	77.035	0.001	0.001	0.000	0.000	0.000	0.000
55	A	200	GLU	-1	-0.862	-0.933	74.553	-0.026	-0.026	0.000	0.000	0.000	0.000
56	A	201	ASN	0	-0.052	-0.043	77.565	0.001	0.001	0.000	0.000	0.000	0.000
57	A	202	THR	0	-0.032	-0.020	80.784	0.001	0.001	0.000	0.000	0.000	0.000
58	A	203	LEU	0	-0.052	-0.026	81.903	0.001	0.001	0.000	0.000	0.000	0.000
59	A	204	GLN	0	-0.034	-0.018	81.501	0.000	0.000	0.000	0.000	0.000	0.000
60	A	205	SER	0	-0.006	-0.003	84.285	0.000	0.000	0.000	0.000	0.000	0.000
61	A	206	PHE	0	-0.004	0.005	86.836	0.001	0.001	0.000	0.000	0.000	0.000
62	A	207	ARG	1	0.844	0.895	87.354	0.018	0.018	0.000	0.000	0.000	0.000
63	A	208	GLN	0	0.046	0.029	89.286	0.001	0.001	0.000	0.000	0.000	0.000
64	A	209	ASP	-1	-0.872	-0.928	91.598	-0.018	-0.018	0.000	0.000	0.000	0.000
65	A	210	VAL	0	-0.041	-0.017	90.845	0.000	0.000	0.000	0.000	0.000	0.000
66	A	211	ASP	-1	-0.822	-0.896	92.329	-0.017	-0.017	0.000	0.000	0.000	0.000
67	A	212	ASN	0	-0.056	-0.045	95.065	0.001	0.001	0.000	0.000	0.000	0.000
68	A	213	ALA	0	-0.015	0.000	96.775	0.000	0.000	0.000	0.000	0.000	0.000
69	A	214	SER	0	-0.047	-0.019	96.972	0.000	0.000	0.000	0.000	0.000	0.000
70	A	215	LEU	0	0.010	0.000	98.960	0.000	0.000	0.000	0.000	0.000	0.000
71	A	216	ALA	0	0.052	0.028	101.314	0.000	0.000	0.000	0.000	0.000	0.000
72	A	217	ARG	1	0.775	0.870	101.354	0.015	0.015	0.000	0.000	0.000	0.000
73	A	218	LEU	0	0.029	0.008	101.630	0.000	0.000	0.000	0.000	0.000	0.000
74	A	219	ASP	-1	-0.885	-0.937	105.049	-0.013	-0.013	0.000	0.000	0.000	0.000
75	A	220	LEU	0	-0.115	-0.049	106.586	0.000	0.000	0.000	0.000	0.000	0.000
76	A	221	GLU	-1	-0.788	-0.873	105.171	-0.013	-0.013	0.000	0.000	0.000	0.000
77	A	222	ARG	1	0.837	0.882	108.923	0.011	0.011	0.000	0.000	0.000	0.000
78	A	223	LYS	1	0.871	0.926	110.495	0.012	0.012	0.000	0.000	0.000	0.000
79	A	224	VAL	0	-0.017	-0.015	112.483	0.000	0.000	0.000	0.000	0.000	0.000
80	A	225	GLU	-1	-0.876	-0.925	110.705	-0.011	-0.011	0.000	0.000	0.000	0.000
81	A	226	SER	0	0.008	-0.005	114.775	0.000	0.000	0.000	0.000	0.000	0.000
82	A	227	LEU	0	0.002	0.006	117.067	0.000	0.000	0.000	0.000	0.000	0.000
83	A	228	GLN	0	-0.045	-0.019	115.086	0.000	0.000	0.000	0.000	0.000	0.000
84	A	229	GLU	-1	-0.818	-0.884	116.423	-0.010	-0.010	0.000	0.000	0.000	0.000
85	A	230	GLU	-1	-0.941	-0.959	120.605	-0.010	-0.010	0.000	0.000	0.000	0.000
86	A	231	ILE	0	-0.015	-0.018	121.590	0.000	0.000	0.000	0.000	0.000	0.000
87	A	232	ALA	0	-0.056	-0.028	122.958	0.000	0.000	0.000	0.000	0.000	0.000
88	A	233	PHE	0	0.000	-0.002	124.787	0.000	0.000	0.000	0.000	0.000	0.000
89	A	234	LEU	0	0.021	0.006	126.670	0.000	0.000	0.000	0.000	0.000	0.000
90	A	235	LYS	1	0.893	0.958	125.102	0.010	0.010	0.000	0.000	0.000	0.000
91	A	236	LYS	1	0.830	0.882	128.869	0.008	0.008	0.000	0.000	0.000	0.000
92	A	237	LEU	0	0.002	0.020	130.901	0.000	0.000	0.000	0.000	0.000	0.000
93	A	238	HIS	0	0.038	0.001	132.237	0.000	0.000	0.000	0.000	0.000	0.000
94	A	239	GLU	-1	-0.857	-0.901	132.579	-0.008	-0.008	0.000	0.000	0.000	0.000
95	A	240	GLU	-1	-0.902	-0.956	135.406	-0.007	-0.007	0.000	0.000	0.000	0.000
96	A	241	GLU	-1	-0.984	-0.988	136.879	-0.008	-0.008	0.000	0.000	0.000	0.000
97	A	242	ILE	0	-0.025	-0.015	137.623	0.000	0.000	0.000	0.000	0.000	0.000
98	A	243	GLN	0	0.007	0.009	139.032	0.000	0.000	0.000	0.000	0.000	0.000
99	A	244	GLU	-1	-0.956	-0.983	141.373	-0.007	-0.007	0.000	0.000	0.000	0.000
100	A	245	LEU	0	-0.052	-0.020	142.649	0.000	0.000	0.000	0.000	0.000	0.000
101	A	246	GLN	0	-0.084	-0.033	143.702	0.000	0.000	0.000	0.000	0.000	0.000
102	A	247	ALA	0	-0.031	-0.011	146.161	0.000	0.000	0.000	0.000	0.000	0.000
103	A	248	GLN	0	-0.079	-0.056	146.268	0.000	0.000	0.000	0.000	0.000	0.000
104	A	249	ILE	0	-0.023	0.012	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)