FMO DATABASE

FMODB ID: YV5V2

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:

Apendix: None

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	83
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-400715.608905
FMO2-HF: Nuclear repulsion	365839.883084
FMO2-HF: Total energy	-34875.725822
FMO2-MP2: Total energy	-34977.287247

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.
-1.07	0.568	0.001	-0.79	-0.848	0.002

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 : -0.009 / q_NPA : -0.005

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	-0.027	-0.029	3.691	-1.152	0.486	0.001	-0.790	-0.848	0.002
4	A	164	LEU	0	0.021	0.013	6.127	0.492	0.492	0.000	0.000	0.000	0.000
5	A	165	THR	0	-0.005	-0.003	9.438	0.223	0.223	0.000	0.000	0.000	0.000
6	A	166	ASN	0	0.019	0.002	10.478	0.044	0.044	0.000	0.000	0.000	0.000
7	A	167	ASP	-1	-0.857	-0.925	10.776	-1.042	-1.042	0.000	0.000	0.000	0.000
8	A	168	LYS	1	0.828	0.880	13.700	0.714	0.714	0.000	0.000	0.000	0.000
9	A	169	ALA	0	0.009	0.021	15.388	0.081	0.081	0.000	0.000	0.000	0.000
10	A	170	ARG	1	0.881	0.934	16.884	0.407	0.407	0.000	0.000	0.000	0.000
11	A	171	VAL	0	0.003	-0.001	18.018	0.050	0.050	0.000	0.000	0.000	0.000
12	A	172	GLU	-1	-0.855	-0.915	18.728	-0.468	-0.468	0.000	0.000	0.000	0.000
13	A	173	VAL	0	0.050	0.028	21.439	0.034	0.034	0.000	0.000	0.000	0.000
14	A	174	GLU	-1	-0.849	-0.915	22.142	-0.265	-0.265	0.000	0.000	0.000	0.000
15	A	175	ARG	1	0.767	0.859	23.399	0.319	0.319	0.000	0.000	0.000	0.000
16	A	176	ASP	-1	-0.815	-0.881	25.831	-0.241	-0.241	0.000	0.000	0.000	0.000
17	A	177	ASN	0	-0.010	-0.010	27.019	0.028	0.028	0.000	0.000	0.000	0.000
18	A	178	LEU	0	0.030	0.013	27.421	0.013	0.013	0.000	0.000	0.000	0.000
19	A	179	ALA	0	-0.037	-0.015	30.046	0.012	0.012	0.000	0.000	0.000	0.000
20	A	180	GLU	-1	-0.948	-0.972	31.726	-0.152	-0.152	0.000	0.000	0.000	0.000
21	A	181	ASP	-1	-0.908	-0.950	33.729	-0.135	-0.135	0.000	0.000	0.000	0.000
22	A	182	ILE	0	-0.058	-0.044	32.461	0.010	0.010	0.000	0.000	0.000	0.000
23	A	183	MET	0	-0.020	0.011	35.099	0.008	0.008	0.000	0.000	0.000	0.000
24	A	184	ARG	1	0.905	0.938	37.668	0.111	0.111	0.000	0.000	0.000	0.000
25	A	185	LEU	0	-0.006	-0.001	37.978	0.008	0.008	0.000	0.000	0.000	0.000
26	A	186	ARG	1	0.893	0.945	35.852	0.140	0.140	0.000	0.000	0.000	0.000
27	A	187	GLU	-1	-0.857	-0.919	41.077	-0.106	-0.106	0.000	0.000	0.000	0.000
28	A	188	LYS	1	0.810	0.890	43.790	0.085	0.085	0.000	0.000	0.000	0.000
29	A	189	LEU	0	0.020	0.015	43.514	0.004	0.004	0.000	0.000	0.000	0.000
30	A	190	GLN	0	-0.014	-0.023	43.300	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	191	GLU	-1	-0.847	-0.903	47.451	-0.078	-0.078	0.000	0.000	0.000	0.000
32	A	192	GLU	-1	-0.852	-0.923	48.813	-0.072	-0.072	0.000	0.000	0.000	0.000
33	A	193	MET	0	-0.086	-0.040	48.053	0.002	0.002	0.000	0.000	0.000	0.000
34	A	194	LEU	0	0.041	0.021	50.964	0.003	0.003	0.000	0.000	0.000	0.000
35	A	195	GLN	0	-0.038	-0.026	52.564	0.005	0.005	0.000	0.000	0.000	0.000
36	A	196	ARG	1	0.741	0.845	52.885	0.066	0.066	0.000	0.000	0.000	0.000
37	A	197	GLU	-1	-0.854	-0.905	53.146	-0.066	-0.066	0.000	0.000	0.000	0.000
38	A	198	GLU	-1	-0.929	-0.952	57.238	-0.051	-0.051	0.000	0.000	0.000	0.000
39	A	199	ALA	0	-0.006	0.003	59.425	0.003	0.003	0.000	0.000	0.000	0.000
40	A	200	GLU	-1	-0.812	-0.906	57.715	-0.054	-0.054	0.000	0.000	0.000	0.000
41	A	201	ASN	0	-0.070	-0.043	60.657	0.003	0.003	0.000	0.000	0.000	0.000
42	A	202	THR	0	-0.014	0.004	63.665	0.002	0.002	0.000	0.000	0.000	0.000
43	A	203	LEU	0	-0.009	-0.013	62.792	0.002	0.002	0.000	0.000	0.000	0.000
44	A	204	GLN	0	-0.053	-0.021	65.529	0.002	0.002	0.000	0.000	0.000	0.000
45	A	205	SER	0	-0.008	-0.011	67.322	0.002	0.002	0.000	0.000	0.000	0.000
46	A	206	PHE	0	0.028	0.004	68.045	0.001	0.001	0.000	0.000	0.000	0.000
47	A	207	ARG	1	0.768	0.859	69.757	0.036	0.036	0.000	0.000	0.000	0.000
48	A	208	GLN	0	0.028	0.017	71.627	0.002	0.002	0.000	0.000	0.000	0.000
49	A	209	ASP	-1	-0.861	-0.922	73.406	-0.034	-0.034	0.000	0.000	0.000	0.000
50	A	210	VAL	0	-0.025	-0.020	74.042	0.001	0.001	0.000	0.000	0.000	0.000
51	A	211	ASP	-1	-0.799	-0.852	74.740	-0.032	-0.032	0.000	0.000	0.000	0.000
52	A	212	ASN	0	-0.046	-0.045	77.136	0.002	0.002	0.000	0.000	0.000	0.000
53	A	213	ALA	0	0.005	0.006	79.371	0.001	0.001	0.000	0.000	0.000	0.000
54	A	214	SER	0	-0.038	-0.034	79.677	0.001	0.001	0.000	0.000	0.000	0.000
55	A	215	LEU	0	-0.027	-0.004	80.957	0.001	0.001	0.000	0.000	0.000	0.000
56	A	216	ALA	0	0.013	0.007	83.836	0.001	0.001	0.000	0.000	0.000	0.000
57	A	217	ARG	1	0.865	0.932	81.910	0.027	0.027	0.000	0.000	0.000	0.000
58	A	218	LEU	0	0.011	0.014	85.972	0.001	0.001	0.000	0.000	0.000	0.000
59	A	219	ASP	-1	-0.831	-0.917	87.850	-0.022	-0.022	0.000	0.000	0.000	0.000
60	A	220	LEU	0	-0.027	-0.004	88.583	0.001	0.001	0.000	0.000	0.000	0.000
61	A	221	GLU	-1	-0.868	-0.931	87.494	-0.024	-0.024	0.000	0.000	0.000	0.000
62	A	222	ARG	1	0.834	0.891	89.415	0.023	0.023	0.000	0.000	0.000	0.000
63	A	223	LYS	1	0.808	0.889	92.761	0.023	0.023	0.000	0.000	0.000	0.000
64	A	224	VAL	0	-0.028	-0.008	94.351	0.000	0.000	0.000	0.000	0.000	0.000
65	A	225	GLU	-1	-0.836	-0.906	94.576	-0.021	-0.021	0.000	0.000	0.000	0.000
66	A	226	SER	0	-0.025	-0.023	98.265	0.000	0.000	0.000	0.000	0.000	0.000
67	A	227	LEU	0	0.017	0.007	98.952	0.000	0.000	0.000	0.000	0.000	0.000
68	A	228	GLN	0	-0.044	-0.023	98.472	0.000	0.000	0.000	0.000	0.000	0.000
69	A	229	GLU	-1	-0.939	-0.959	102.096	-0.018	-0.018	0.000	0.000	0.000	0.000
70	A	230	GLU	-1	-0.901	-0.939	103.000	-0.018	-0.018	0.000	0.000	0.000	0.000
71	A	231	ILE	0	-0.031	-0.022	103.946	0.000	0.000	0.000	0.000	0.000	0.000
72	A	232	ALA	0	-0.010	-0.003	106.736	0.000	0.000	0.000	0.000	0.000	0.000
73	A	233	PHE	0	-0.023	-0.011	108.472	0.000	0.000	0.000	0.000	0.000	0.000
74	A	234	LEU	0	-0.007	-0.019	109.118	0.000	0.000	0.000	0.000	0.000	0.000
75	A	235	LYS	1	0.791	0.874	110.883	0.015	0.015	0.000	0.000	0.000	0.000
76	A	236	LYS	1	0.876	0.924	112.814	0.014	0.014	0.000	0.000	0.000	0.000
77	A	237	LEU	0	-0.088	-0.028	114.720	0.000	0.000	0.000	0.000	0.000	0.000
78	A	238	HIS	0	-0.018	-0.028	114.819	0.000	0.000	0.000	0.000	0.000	0.000
79	A	239	GLU	-1	-0.824	-0.881	114.813	-0.014	-0.014	0.000	0.000	0.000	0.000
80	A	240	GLU	-1	-0.945	-0.972	116.302	-0.014	-0.014	0.000	0.000	0.000	0.000
81	A	241	GLU	-1	-0.901	-0.905	119.268	-0.013	-0.013	0.000	0.000	0.000	0.000
82	A	242	ILE	0	-0.044	-0.032	121.979	0.000	0.000	0.000	0.000	0.000	0.000
83	A	243	GLN	0	-0.047	-0.016	122.091	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)