FMO DATABASE

FMODB ID: 5J1NZ

Calculation Name: 4YPC-A-Xray372

Preferred Name: Vimentin

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4YPC

Chain ID: A

ChEMBL ID: CHEMBL3712854

UniProt ID: P08670

Base Structure: X-ray

Registration Date: 2023-09-23

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	83
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-399996.280446
FMO2-HF: Nuclear repulsion	365120.918844
FMO2-HF: Total energy	-34875.361602
FMO2-MP2: Total energy	-34976.920578

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:161:VAL)

Summations of interaction energy for fragment #1(A:161:VAL)

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.
-0.935	0.851	-0.004	-0.815	-0.968	0.004

Interaction energy analysis for fragmet #1(A:161:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / 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

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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	163	GLN	0	-0.054	-0.042	3.651	-1.230	0.556	-0.004	-0.815	-0.968	0.004
4	A	164	LEU	0	0.043	0.029	6.262	0.592	0.592	0.000	0.000	0.000	0.000
5	A	165	THR	0	-0.008	-0.019	9.597	0.201	0.201	0.000	0.000	0.000	0.000
6	A	166	ASN	0	0.000	0.007	10.594	0.019	0.019	0.000	0.000	0.000	0.000
7	A	167	ASP	-1	-0.861	-0.943	11.208	-0.909	-0.909	0.000	0.000	0.000	0.000
8	A	168	LYS	1	0.849	0.907	14.087	0.685	0.685	0.000	0.000	0.000	0.000
9	A	169	ALA	0	0.011	0.017	15.921	0.066	0.066	0.000	0.000	0.000	0.000
10	A	170	ARG	1	0.915	0.962	17.309	0.392	0.392	0.000	0.000	0.000	0.000
11	A	171	VAL	0	0.000	-0.009	17.745	0.047	0.047	0.000	0.000	0.000	0.000
12	A	172	GLU	-1	-0.852	-0.917	19.517	-0.433	-0.433	0.000	0.000	0.000	0.000
13	A	173	VAL	0	0.042	0.026	21.924	0.031	0.031	0.000	0.000	0.000	0.000
14	A	174	GLU	-1	-0.862	-0.927	22.564	-0.239	-0.239	0.000	0.000	0.000	0.000
15	A	175	ARG	1	0.786	0.886	23.684	0.290	0.290	0.000	0.000	0.000	0.000
16	A	176	ASP	-1	-0.829	-0.911	25.905	-0.220	-0.220	0.000	0.000	0.000	0.000
17	A	177	ASN	0	-0.024	-0.018	27.486	0.026	0.026	0.000	0.000	0.000	0.000
18	A	178	LEU	0	0.013	0.012	27.215	0.013	0.013	0.000	0.000	0.000	0.000
19	A	179	ALA	0	-0.044	-0.023	29.865	0.013	0.013	0.000	0.000	0.000	0.000
20	A	180	GLU	-1	-0.923	-0.959	31.632	-0.146	-0.146	0.000	0.000	0.000	0.000
21	A	181	ASP	-1	-0.907	-0.946	34.035	-0.121	-0.121	0.000	0.000	0.000	0.000
22	A	182	ILE	0	-0.075	-0.053	31.966	0.009	0.009	0.000	0.000	0.000	0.000
23	A	183	MET	0	-0.041	-0.018	35.339	0.009	0.009	0.000	0.000	0.000	0.000
24	A	184	ARG	1	0.908	0.942	37.402	0.105	0.105	0.000	0.000	0.000	0.000
25	A	185	LEU	0	0.007	0.006	38.104	0.007	0.007	0.000	0.000	0.000	0.000
26	A	186	ARG	1	0.938	0.980	35.145	0.128	0.128	0.000	0.000	0.000	0.000
27	A	187	GLU	-1	-0.871	-0.926	41.207	-0.097	-0.097	0.000	0.000	0.000	0.000
28	A	188	LYS	1	0.812	0.897	43.638	0.079	0.079	0.000	0.000	0.000	0.000
29	A	189	LEU	0	0.010	0.012	42.953	0.004	0.004	0.000	0.000	0.000	0.000
30	A	190	GLN	0	-0.011	-0.029	42.943	0.000	0.000	0.000	0.000	0.000	0.000
31	A	191	GLU	-1	-0.852	-0.910	46.924	-0.072	-0.072	0.000	0.000	0.000	0.000
32	A	192	GLU	-1	-0.867	-0.925	48.500	-0.064	-0.064	0.000	0.000	0.000	0.000
33	A	193	MET	0	-0.077	-0.036	47.482	0.002	0.002	0.000	0.000	0.000	0.000
34	A	194	LEU	0	0.051	0.024	50.743	0.003	0.003	0.000	0.000	0.000	0.000
35	A	195	GLN	0	-0.039	-0.026	52.346	0.005	0.005	0.000	0.000	0.000	0.000
36	A	196	ARG	1	0.772	0.871	52.688	0.058	0.058	0.000	0.000	0.000	0.000
37	A	197	GLU	-1	-0.888	-0.940	52.654	-0.059	-0.059	0.000	0.000	0.000	0.000
38	A	198	GLU	-1	-0.946	-0.962	56.568	-0.047	-0.047	0.000	0.000	0.000	0.000
39	A	199	ALA	0	-0.008	-0.003	58.764	0.002	0.002	0.000	0.000	0.000	0.000
40	A	200	GLU	-1	-0.820	-0.901	57.686	-0.046	-0.046	0.000	0.000	0.000	0.000
41	A	201	ASN	0	-0.080	-0.049	60.082	0.003	0.003	0.000	0.000	0.000	0.000
42	A	202	THR	0	-0.011	-0.005	63.093	0.002	0.002	0.000	0.000	0.000	0.000
43	A	203	LEU	0	0.008	0.001	62.336	0.002	0.002	0.000	0.000	0.000	0.000
44	A	204	GLN	0	-0.057	-0.020	65.170	0.002	0.002	0.000	0.000	0.000	0.000
45	A	205	SER	0	0.011	-0.005	66.923	0.001	0.001	0.000	0.000	0.000	0.000
46	A	206	PHE	0	0.019	0.013	67.396	0.001	0.001	0.000	0.000	0.000	0.000
47	A	207	ARG	1	0.807	0.885	69.183	0.032	0.032	0.000	0.000	0.000	0.000
48	A	208	GLN	0	-0.004	-0.005	71.053	0.002	0.002	0.000	0.000	0.000	0.000
49	A	209	ASP	-1	-0.859	-0.920	73.093	-0.030	-0.030	0.000	0.000	0.000	0.000
50	A	210	VAL	0	-0.035	-0.023	73.545	0.001	0.001	0.000	0.000	0.000	0.000
51	A	211	ASP	-1	-0.823	-0.878	74.529	-0.028	-0.028	0.000	0.000	0.000	0.000
52	A	212	ASN	0	-0.015	-0.020	76.691	0.002	0.002	0.000	0.000	0.000	0.000
53	A	213	ALA	0	-0.015	-0.001	78.887	0.001	0.001	0.000	0.000	0.000	0.000
54	A	214	SER	0	-0.059	-0.062	79.036	0.001	0.001	0.000	0.000	0.000	0.000
55	A	215	LEU	0	-0.022	0.010	80.789	0.001	0.001	0.000	0.000	0.000	0.000
56	A	216	ALA	0	0.015	0.007	83.590	0.001	0.001	0.000	0.000	0.000	0.000
57	A	217	ARG	1	0.906	0.956	80.910	0.025	0.025	0.000	0.000	0.000	0.000
58	A	218	LEU	0	0.009	0.020	85.673	0.001	0.001	0.000	0.000	0.000	0.000
59	A	219	ASP	-1	-0.808	-0.903	87.607	-0.020	-0.020	0.000	0.000	0.000	0.000
60	A	220	LEU	0	-0.037	-0.016	88.107	0.001	0.001	0.000	0.000	0.000	0.000
61	A	221	GLU	-1	-0.895	-0.948	87.514	-0.021	-0.021	0.000	0.000	0.000	0.000
62	A	222	ARG	1	0.819	0.896	89.251	0.020	0.020	0.000	0.000	0.000	0.000
63	A	223	LYS	1	0.844	0.906	92.542	0.020	0.020	0.000	0.000	0.000	0.000
64	A	224	VAL	0	-0.026	-0.010	94.117	0.000	0.000	0.000	0.000	0.000	0.000
65	A	225	GLU	-1	-0.823	-0.904	94.440	-0.018	-0.018	0.000	0.000	0.000	0.000
66	A	226	SER	0	-0.016	-0.007	97.969	0.000	0.000	0.000	0.000	0.000	0.000
67	A	227	LEU	0	-0.011	-0.007	98.356	0.000	0.000	0.000	0.000	0.000	0.000
68	A	228	GLN	0	-0.047	-0.030	98.114	0.000	0.000	0.000	0.000	0.000	0.000
69	A	229	GLU	-1	-0.945	-0.963	101.488	-0.015	-0.015	0.000	0.000	0.000	0.000
70	A	230	GLU	-1	-0.911	-0.955	102.955	-0.015	-0.015	0.000	0.000	0.000	0.000
71	A	231	ILE	0	-0.033	-0.019	103.483	0.000	0.000	0.000	0.000	0.000	0.000
72	A	232	ALA	0	0.001	0.000	106.262	0.000	0.000	0.000	0.000	0.000	0.000
73	A	233	PHE	0	-0.038	-0.023	108.020	0.000	0.000	0.000	0.000	0.000	0.000
74	A	234	LEU	0	-0.007	-0.015	108.735	0.000	0.000	0.000	0.000	0.000	0.000
75	A	235	LYS	1	0.811	0.887	110.105	0.013	0.013	0.000	0.000	0.000	0.000
76	A	236	LYS	1	0.916	0.986	111.737	0.013	0.013	0.000	0.000	0.000	0.000
77	A	237	LEU	0	-0.048	-0.019	114.150	0.000	0.000	0.000	0.000	0.000	0.000
78	A	238	HIS	0	-0.020	-0.024	114.450	0.000	0.000	0.000	0.000	0.000	0.000
79	A	239	GLU	-1	-0.839	-0.888	114.492	-0.013	-0.013	0.000	0.000	0.000	0.000
80	A	240	GLU	-1	-0.992	-1.002	116.435	-0.012	-0.012	0.000	0.000	0.000	0.000
81	A	241	GLU	-1	-0.942	-0.955	119.869	-0.011	-0.011	0.000	0.000	0.000	0.000
82	A	242	ILE	0	-0.043	-0.025	122.026	0.000	0.000	0.000	0.000	0.000	0.000
83	A	243	GLN	0	-0.040	-0.011	122.239	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:161:VAL)