FMO DATABASE

FMODB ID: 723KK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-542962.572114
FMO2-HF: Nuclear repulsion	498817.024868
FMO2-HF: Total energy	-44145.547246
FMO2-MP2: Total energy	-44273.750699

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.
-2.272	0.612	5.477	-2.651	-5.708	-0.002

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 : 0.038 / q_NPA : 0.002

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

Sort

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	-0.860	-0.931	2.011	-1.178	1.536	1.494	-1.065	-3.142	-0.001
4	A	149	LEU	0	-0.009	-0.014	1.973	-0.973	-1.064	3.984	-1.558	-2.335	-0.001
5	A	150	TYR	0	-0.004	0.012	4.695	-0.244	0.017	-0.001	-0.028	-0.231	0.000
6	A	151	GLU	-1	-0.910	-0.960	6.822	0.175	0.175	0.000	0.000	0.000	0.000
7	A	152	GLU	-1	-0.967	-0.998	7.571	0.355	0.355	0.000	0.000	0.000	0.000
8	A	153	GLU	-1	-0.876	-0.923	8.625	-0.108	-0.108	0.000	0.000	0.000	0.000
9	A	154	MET	0	-0.086	-0.045	10.442	-0.007	-0.007	0.000	0.000	0.000	0.000
10	A	155	ARG	1	0.871	0.941	9.614	-0.278	-0.278	0.000	0.000	0.000	0.000
11	A	156	GLU	-1	-0.806	-0.908	13.175	0.045	0.045	0.000	0.000	0.000	0.000
12	A	157	LEU	0	0.010	0.003	14.519	-0.009	-0.009	0.000	0.000	0.000	0.000
13	A	158	ARG	1	0.891	0.936	13.816	-0.010	-0.010	0.000	0.000	0.000	0.000
14	A	159	ARG	1	0.927	0.988	17.980	-0.059	-0.059	0.000	0.000	0.000	0.000
15	A	160	GLN	0	-0.069	-0.043	17.823	-0.009	-0.009	0.000	0.000	0.000	0.000
16	A	161	VAL	0	0.000	-0.005	20.920	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	162	ASP	-1	-0.871	-0.937	22.548	0.020	0.020	0.000	0.000	0.000	0.000
18	A	163	GLN	0	-0.088	-0.030	23.958	0.003	0.003	0.000	0.000	0.000	0.000
19	A	164	LEU	0	0.016	-0.013	24.796	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	165	THR	0	-0.025	0.001	26.851	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	166	ASN	0	0.003	-0.003	28.599	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	167	ASP	-1	-0.930	-0.953	29.577	0.015	0.015	0.000	0.000	0.000	0.000
23	A	168	LYS	1	0.925	0.952	31.081	0.005	0.005	0.000	0.000	0.000	0.000
24	A	169	ALA	0	0.011	0.021	32.772	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	170	ARG	1	0.921	0.960	33.441	-0.011	-0.011	0.000	0.000	0.000	0.000
26	A	171	VAL	0	-0.020	-0.023	35.443	0.000	0.000	0.000	0.000	0.000	0.000
27	A	172	GLU	-1	-0.957	-0.981	36.575	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	173	VAL	0	0.034	0.028	38.930	0.000	0.000	0.000	0.000	0.000	0.000
29	A	174	GLU	-1	-0.937	-0.971	39.405	0.007	0.007	0.000	0.000	0.000	0.000
30	A	175	ARG	1	0.847	0.910	40.201	0.001	0.001	0.000	0.000	0.000	0.000
31	A	176	ASP	-1	-0.880	-0.926	42.343	0.000	0.000	0.000	0.000	0.000	0.000
32	A	177	ASN	0	0.019	0.007	44.896	0.000	0.000	0.000	0.000	0.000	0.000
33	A	178	LEU	0	-0.010	-0.004	45.149	0.000	0.000	0.000	0.000	0.000	0.000
34	A	179	ALA	0	-0.013	-0.023	47.388	0.000	0.000	0.000	0.000	0.000	0.000
35	A	180	GLU	-1	-0.924	-0.960	49.090	0.003	0.003	0.000	0.000	0.000	0.000
36	A	181	ASP	-1	-0.902	-0.953	51.297	0.003	0.003	0.000	0.000	0.000	0.000
37	A	182	ILE	0	-0.046	-0.021	51.280	0.000	0.000	0.000	0.000	0.000	0.000
38	A	183	MET	0	-0.062	-0.026	51.608	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	184	ARG	1	0.953	0.968	53.133	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	185	LEU	0	-0.050	-0.021	55.863	0.000	0.000	0.000	0.000	0.000	0.000
41	A	186	ARG	1	0.952	0.975	53.406	0.001	0.001	0.000	0.000	0.000	0.000
42	A	187	GLU	-1	-0.918	-0.944	59.164	0.000	0.000	0.000	0.000	0.000	0.000
43	A	188	LYS	1	0.956	0.979	61.542	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	189	LEU	0	-0.018	-0.001	61.040	0.000	0.000	0.000	0.000	0.000	0.000
45	A	190	GLN	0	-0.012	-0.028	62.238	0.000	0.000	0.000	0.000	0.000	0.000
46	A	191	GLU	-1	-0.938	-0.977	64.966	0.001	0.001	0.000	0.000	0.000	0.000
47	A	192	GLU	-1	-0.900	-0.952	66.590	0.001	0.001	0.000	0.000	0.000	0.000
48	A	193	MET	0	-0.107	-0.040	63.809	0.000	0.000	0.000	0.000	0.000	0.000
49	A	194	LEU	0	0.033	0.022	68.854	0.000	0.000	0.000	0.000	0.000	0.000
50	A	195	GLN	0	0.049	0.039	71.344	0.000	0.000	0.000	0.000	0.000	0.000
51	A	196	ARG	1	0.866	0.929	71.041	0.000	0.000	0.000	0.000	0.000	0.000
52	A	197	GLU	-1	-0.967	-0.997	72.530	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	198	GLU	-1	-0.915	-0.937	74.496	0.000	0.000	0.000	0.000	0.000	0.000
54	A	199	ALA	0	-0.026	-0.028	76.598	0.000	0.000	0.000	0.000	0.000	0.000
55	A	200	GLU	-1	-0.962	-0.994	75.199	0.000	0.000	0.000	0.000	0.000	0.000
56	A	201	ASN	0	0.003	0.002	77.431	0.000	0.000	0.000	0.000	0.000	0.000
57	A	202	THR	0	-0.019	-0.005	80.596	0.000	0.000	0.000	0.000	0.000	0.000
58	A	203	LEU	0	-0.055	-0.028	81.109	0.000	0.000	0.000	0.000	0.000	0.000
59	A	204	GLN	0	-0.020	0.000	81.831	0.000	0.000	0.000	0.000	0.000	0.000
60	A	205	SER	0	-0.069	-0.036	84.287	0.000	0.000	0.000	0.000	0.000	0.000
61	A	206	PHE	0	0.061	0.028	86.683	0.000	0.000	0.000	0.000	0.000	0.000
62	A	207	ARG	1	0.962	0.977	86.707	0.000	0.000	0.000	0.000	0.000	0.000
63	A	208	GLN	0	0.002	0.002	89.043	0.000	0.000	0.000	0.000	0.000	0.000
64	A	209	ASP	-1	-0.890	-0.934	91.679	0.000	0.000	0.000	0.000	0.000	0.000
65	A	210	VAL	0	-0.052	-0.025	90.768	0.000	0.000	0.000	0.000	0.000	0.000
66	A	211	ASP	-1	-0.904	-0.952	92.709	0.000	0.000	0.000	0.000	0.000	0.000
67	A	212	ASN	0	-0.006	-0.021	95.005	0.000	0.000	0.000	0.000	0.000	0.000
68	A	213	ALA	0	-0.052	-0.019	96.778	0.000	0.000	0.000	0.000	0.000	0.000
69	A	214	SER	0	-0.030	-0.018	96.923	0.000	0.000	0.000	0.000	0.000	0.000
70	A	215	LEU	0	0.025	0.011	98.585	0.000	0.000	0.000	0.000	0.000	0.000
71	A	216	ALA	0	0.032	0.042	101.221	0.000	0.000	0.000	0.000	0.000	0.000
72	A	217	ARG	1	0.872	0.925	100.732	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	218	LEU	0	0.017	0.012	101.155	0.000	0.000	0.000	0.000	0.000	0.000
74	A	219	ASP	-1	-0.910	-0.966	104.810	0.000	0.000	0.000	0.000	0.000	0.000
75	A	220	LEU	0	-0.118	-0.071	106.794	0.000	0.000	0.000	0.000	0.000	0.000
76	A	221	GLU	-1	-0.869	-0.936	105.190	0.000	0.000	0.000	0.000	0.000	0.000
77	A	222	ARG	1	0.910	0.979	108.928	0.000	0.000	0.000	0.000	0.000	0.000
78	A	223	LYS	1	0.924	0.953	110.775	0.000	0.000	0.000	0.000	0.000	0.000
79	A	224	VAL	0	-0.016	-0.015	112.187	0.000	0.000	0.000	0.000	0.000	0.000
80	A	225	GLU	-1	-0.903	-0.955	110.449	0.000	0.000	0.000	0.000	0.000	0.000
81	A	226	SER	0	-0.034	-0.008	114.568	0.000	0.000	0.000	0.000	0.000	0.000
82	A	227	LEU	0	0.009	-0.001	116.682	0.000	0.000	0.000	0.000	0.000	0.000
83	A	228	GLN	0	-0.048	-0.032	115.094	0.000	0.000	0.000	0.000	0.000	0.000
84	A	229	GLU	-1	-0.865	-0.928	116.616	0.000	0.000	0.000	0.000	0.000	0.000
85	A	230	GLU	-1	-0.944	-0.949	120.598	0.000	0.000	0.000	0.000	0.000	0.000
86	A	231	ILE	0	-0.022	-0.021	122.018	0.000	0.000	0.000	0.000	0.000	0.000
87	A	232	ALA	0	-0.064	-0.038	122.729	0.000	0.000	0.000	0.000	0.000	0.000
88	A	233	PHE	0	0.009	0.010	124.608	0.000	0.000	0.000	0.000	0.000	0.000
89	A	234	LEU	0	0.040	0.005	126.650	0.000	0.000	0.000	0.000	0.000	0.000
90	A	235	LYS	1	0.894	0.958	125.555	0.000	0.000	0.000	0.000	0.000	0.000
91	A	236	LYS	1	0.943	0.975	128.069	0.000	0.000	0.000	0.000	0.000	0.000
92	A	237	LEU	0	0.021	0.029	130.754	0.000	0.000	0.000	0.000	0.000	0.000
93	A	238	HIS	0	0.004	-0.011	131.836	0.000	0.000	0.000	0.000	0.000	0.000
94	A	239	GLU	-1	-0.977	-0.992	132.869	0.000	0.000	0.000	0.000	0.000	0.000
95	A	240	GLU	-1	-0.894	-0.939	135.090	0.000	0.000	0.000	0.000	0.000	0.000
96	A	241	GLU	-1	-1.012	-1.014	136.596	0.000	0.000	0.000	0.000	0.000	0.000
97	A	242	ILE	0	-0.041	-0.025	138.469	0.000	0.000	0.000	0.000	0.000	0.000
98	A	243	GLN	0	0.023	-0.001	139.808	0.000	0.000	0.000	0.000	0.000	0.000
99	A	244	GLU	-1	-0.989	-0.993	140.926	0.000	0.000	0.000	0.000	0.000	0.000
100	A	245	LEU	0	-0.050	-0.025	143.214	0.000	0.000	0.000	0.000	0.000	0.000
101	A	246	GLN	0	-0.044	-0.005	143.108	0.000	0.000	0.000	0.000	0.000	0.000
102	A	247	ALA	0	-0.063	-0.023	146.440	0.000	0.000	0.000	0.000	0.000	0.000
103	A	248	GLN	0	-0.010	-0.014	147.649	0.000	0.000	0.000	0.000	0.000	0.000
104	A	249	ILE	0	-0.037	0.000	149.886	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)