FMO DATABASE

FMODB ID: 4J1LN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-399535.028906
FMO2-HF: Nuclear repulsion	364660.868694
FMO2-HF: Total energy	-34874.160211
FMO2-MP2: Total energy	-34975.722513

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.
-0.565	1.083	0.006	-0.653	-1.001	0.005

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 : -0.006 / q_NPA : 0.004

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	-0.053	-0.046	3.469	-1.116	0.532	0.006	-0.653	-1.001	0.005
4	A	164	LEU	0	0.059	0.040	6.277	0.615	0.615	0.000	0.000	0.000	0.000
5	A	165	THR	0	-0.018	-0.022	9.617	0.220	0.220	0.000	0.000	0.000	0.000
6	A	166	ASN	0	0.019	0.006	11.268	0.040	0.040	0.000	0.000	0.000	0.000
7	A	167	ASP	-1	-0.886	-0.946	11.245	-0.927	-0.927	0.000	0.000	0.000	0.000
8	A	168	LYS	1	0.939	0.966	13.813	0.778	0.778	0.000	0.000	0.000	0.000
9	A	169	ALA	0	0.020	0.019	15.915	0.065	0.065	0.000	0.000	0.000	0.000
10	A	170	ARG	1	0.974	0.991	17.112	0.455	0.455	0.000	0.000	0.000	0.000
11	A	171	VAL	0	0.001	-0.006	17.295	0.047	0.047	0.000	0.000	0.000	0.000
12	A	172	GLU	-1	-0.962	-0.985	19.320	-0.423	-0.423	0.000	0.000	0.000	0.000
13	A	173	VAL	0	0.039	0.019	21.937	0.031	0.031	0.000	0.000	0.000	0.000
14	A	174	GLU	-1	-0.922	-0.958	23.017	-0.226	-0.226	0.000	0.000	0.000	0.000
15	A	175	ARG	1	0.883	0.945	23.530	0.302	0.302	0.000	0.000	0.000	0.000
16	A	176	ASP	-1	-0.973	-0.988	25.703	-0.194	-0.194	0.000	0.000	0.000	0.000
17	A	177	ASN	0	0.058	0.020	27.309	0.025	0.025	0.000	0.000	0.000	0.000
18	A	178	LEU	0	0.004	0.007	27.254	0.014	0.014	0.000	0.000	0.000	0.000
19	A	179	ALA	0	-0.052	-0.028	29.635	0.013	0.013	0.000	0.000	0.000	0.000
20	A	180	GLU	-1	-0.914	-0.950	31.410	-0.153	-0.153	0.000	0.000	0.000	0.000
21	A	181	ASP	-1	-0.910	-0.952	33.863	-0.128	-0.128	0.000	0.000	0.000	0.000
22	A	182	ILE	0	-0.077	-0.052	31.829	0.010	0.010	0.000	0.000	0.000	0.000
23	A	183	MET	0	-0.039	-0.015	35.439	0.009	0.009	0.000	0.000	0.000	0.000
24	A	184	ARG	1	0.974	0.980	37.163	0.110	0.110	0.000	0.000	0.000	0.000
25	A	185	LEU	0	-0.029	-0.012	38.344	0.007	0.007	0.000	0.000	0.000	0.000
26	A	186	ARG	1	0.957	0.990	35.053	0.131	0.131	0.000	0.000	0.000	0.000
27	A	187	GLU	-1	-0.955	-0.980	41.002	-0.098	-0.098	0.000	0.000	0.000	0.000
28	A	188	LYS	1	0.980	0.985	43.395	0.092	0.092	0.000	0.000	0.000	0.000
29	A	189	LEU	0	-0.003	0.018	42.650	0.004	0.004	0.000	0.000	0.000	0.000
30	A	190	GLN	0	-0.028	-0.039	42.874	0.000	0.000	0.000	0.000	0.000	0.000
31	A	191	GLU	-1	-0.956	-0.968	46.697	-0.074	-0.074	0.000	0.000	0.000	0.000
32	A	192	GLU	-1	-0.896	-0.957	48.346	-0.066	-0.066	0.000	0.000	0.000	0.000
33	A	193	MET	0	-0.123	-0.061	47.328	0.002	0.002	0.000	0.000	0.000	0.000
34	A	194	LEU	0	0.061	0.031	50.543	0.003	0.003	0.000	0.000	0.000	0.000
35	A	195	GLN	0	0.009	0.013	52.997	0.002	0.002	0.000	0.000	0.000	0.000
36	A	196	ARG	1	0.844	0.915	52.604	0.060	0.060	0.000	0.000	0.000	0.000
37	A	197	GLU	-1	-0.946	-0.981	52.766	-0.061	-0.061	0.000	0.000	0.000	0.000
38	A	198	GLU	-1	-0.954	-0.966	56.368	-0.049	-0.049	0.000	0.000	0.000	0.000
39	A	199	ALA	0	-0.019	-0.004	58.573	0.002	0.002	0.000	0.000	0.000	0.000
40	A	200	GLU	-1	-0.868	-0.928	58.270	-0.047	-0.047	0.000	0.000	0.000	0.000
41	A	201	ASN	0	-0.010	-0.011	60.623	0.003	0.003	0.000	0.000	0.000	0.000
42	A	202	THR	0	-0.037	-0.025	62.889	0.002	0.002	0.000	0.000	0.000	0.000
43	A	203	LEU	0	0.001	0.000	62.171	0.002	0.002	0.000	0.000	0.000	0.000
44	A	204	GLN	0	-0.039	-0.014	64.994	0.002	0.002	0.000	0.000	0.000	0.000
45	A	205	SER	0	0.009	-0.008	66.751	0.001	0.001	0.000	0.000	0.000	0.000
46	A	206	PHE	0	0.021	0.023	67.465	0.001	0.001	0.000	0.000	0.000	0.000
47	A	207	ARG	1	0.924	0.966	69.019	0.034	0.034	0.000	0.000	0.000	0.000
48	A	208	GLN	0	-0.032	-0.024	70.910	0.002	0.002	0.000	0.000	0.000	0.000
49	A	209	ASP	-1	-0.870	-0.926	72.922	-0.032	-0.032	0.000	0.000	0.000	0.000
50	A	210	VAL	0	-0.053	-0.032	73.147	0.001	0.001	0.000	0.000	0.000	0.000
51	A	211	ASP	-1	-0.888	-0.929	75.135	-0.029	-0.029	0.000	0.000	0.000	0.000
52	A	212	ASN	0	0.002	-0.006	76.784	0.001	0.001	0.000	0.000	0.000	0.000
53	A	213	ALA	0	-0.025	-0.010	78.730	0.001	0.001	0.000	0.000	0.000	0.000
54	A	214	SER	0	-0.066	-0.073	78.809	0.001	0.001	0.000	0.000	0.000	0.000
55	A	215	LEU	0	-0.031	0.008	80.383	0.001	0.001	0.000	0.000	0.000	0.000
56	A	216	ALA	0	0.022	0.008	83.448	0.001	0.001	0.000	0.000	0.000	0.000
57	A	217	ARG	1	0.915	0.961	80.380	0.026	0.026	0.000	0.000	0.000	0.000
58	A	218	LEU	0	0.005	0.019	85.394	0.001	0.001	0.000	0.000	0.000	0.000
59	A	219	ASP	-1	-0.886	-0.958	87.487	-0.021	-0.021	0.000	0.000	0.000	0.000
60	A	220	LEU	0	-0.039	-0.023	87.842	0.001	0.001	0.000	0.000	0.000	0.000
61	A	221	GLU	-1	-0.923	-0.964	87.544	-0.022	-0.022	0.000	0.000	0.000	0.000
62	A	222	ARG	1	0.941	0.971	89.349	0.021	0.021	0.000	0.000	0.000	0.000
63	A	223	LYS	1	0.917	0.961	92.849	0.021	0.021	0.000	0.000	0.000	0.000
64	A	224	VAL	0	-0.010	-0.003	93.843	0.000	0.000	0.000	0.000	0.000	0.000
65	A	225	GLU	-1	-0.905	-0.952	94.531	-0.018	-0.018	0.000	0.000	0.000	0.000
66	A	226	SER	0	0.008	0.010	97.867	0.000	0.000	0.000	0.000	0.000	0.000
67	A	227	LEU	0	-0.036	-0.017	98.120	0.000	0.000	0.000	0.000	0.000	0.000
68	A	228	GLN	0	-0.039	-0.027	98.006	0.000	0.000	0.000	0.000	0.000	0.000
69	A	229	GLU	-1	-0.941	-0.964	101.038	-0.016	-0.016	0.000	0.000	0.000	0.000
70	A	230	GLU	-1	-0.937	-0.973	103.548	-0.016	-0.016	0.000	0.000	0.000	0.000
71	A	231	ILE	0	-0.033	-0.019	103.596	0.000	0.000	0.000	0.000	0.000	0.000
72	A	232	ALA	0	-0.012	-0.009	106.206	0.000	0.000	0.000	0.000	0.000	0.000
73	A	233	PHE	0	-0.034	-0.030	107.927	0.000	0.000	0.000	0.000	0.000	0.000
74	A	234	LEU	0	0.002	-0.010	108.554	0.000	0.000	0.000	0.000	0.000	0.000
75	A	235	LYS	1	0.942	0.967	108.244	0.015	0.015	0.000	0.000	0.000	0.000
76	A	236	LYS	1	0.912	0.997	111.786	0.013	0.013	0.000	0.000	0.000	0.000
77	A	237	LEU	0	-0.054	-0.023	113.941	0.000	0.000	0.000	0.000	0.000	0.000
78	A	238	HIS	0	-0.023	-0.028	114.170	0.000	0.000	0.000	0.000	0.000	0.000
79	A	239	GLU	-1	-0.941	-0.952	114.564	-0.013	-0.013	0.000	0.000	0.000	0.000
80	A	240	GLU	-1	-0.995	-0.991	116.941	-0.012	-0.012	0.000	0.000	0.000	0.000
81	A	241	GLU	-1	-0.902	-0.938	119.788	-0.012	-0.012	0.000	0.000	0.000	0.000
82	A	242	ILE	0	-0.082	-0.038	121.937	0.000	0.000	0.000	0.000	0.000	0.000
83	A	243	GLN	0	-0.064	-0.040	121.932	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)