FMO DATABASE

FMODB ID: V5M21

Calculation Name: 3VFI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VFI

Chain ID: A

ChEMBL ID:

UniProt ID: C4NT42

Base Structure: X-ray

Registration Date: 2023-09-20

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	104
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-858100.282527
FMO2-HF: Nuclear repulsion	813898.404246
FMO2-HF: Total energy	-44201.878281
FMO2-MP2: Total energy	-44324.096057

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:2:LEU)

Summations of interaction energy for fragment #1(A:2: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.
-11.163	-2.322	10.213	-5.252	-13.804	-0.027

Interaction energy analysis for fragmet #1(A:2:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.007 / q_NPA : -0.008

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	4	SER	0	-0.015	-0.007	3.542	-2.164	-0.387	0.003	-0.866	-0.915	0.003
4	A	5	LEU	0	-0.046	-0.022	6.108	0.314	0.314	0.000	0.000	0.000	0.000
5	A	6	SER	0	0.049	0.004	9.006	-0.021	-0.021	0.000	0.000	0.000	0.000
6	A	7	ASP	-1	-0.737	-0.869	12.580	-0.208	-0.208	0.000	0.000	0.000	0.000
7	A	8	SER	0	-0.127	-0.061	15.588	0.030	0.030	0.000	0.000	0.000	0.000
8	A	9	ASP	-1	-0.802	-0.874	12.104	-0.137	-0.137	0.000	0.000	0.000	0.000
9	A	10	PHE	0	-0.011	-0.002	12.679	0.014	0.014	0.000	0.000	0.000	0.000
10	A	11	GLN	0	0.016	-0.012	14.362	0.014	0.014	0.000	0.000	0.000	0.000
11	A	12	LEU	0	0.022	0.017	15.468	0.006	0.006	0.000	0.000	0.000	0.000
12	A	13	GLU	-1	-0.794	-0.886	10.809	0.053	0.053	0.000	0.000	0.000	0.000
13	A	14	VAL	0	-0.041	-0.017	11.218	-0.024	-0.024	0.000	0.000	0.000	0.000
14	A	15	ARG	1	0.821	0.919	13.679	0.169	0.169	0.000	0.000	0.000	0.000
15	A	16	GLN	0	-0.017	-0.016	17.076	0.022	0.022	0.000	0.000	0.000	0.000
16	A	17	HIS	0	-0.050	0.001	12.278	-0.013	-0.013	0.000	0.000	0.000	0.000
17	A	18	PRO	0	-0.008	-0.003	15.410	-0.019	-0.019	0.000	0.000	0.000	0.000
18	A	19	ASP	-1	-0.854	-0.921	11.695	0.049	0.049	0.000	0.000	0.000	0.000
19	A	20	PRO	0	0.010	0.006	11.662	-0.035	-0.035	0.000	0.000	0.000	0.000
20	A	21	ILE	0	-0.031	-0.013	7.175	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	22	ILE	0	-0.011	0.007	5.974	0.052	0.052	0.000	0.000	0.000	0.000
22	A	23	ILE	0	0.002	-0.002	6.045	-0.216	-0.216	0.000	0.000	0.000	0.000
23	A	24	MET	0	-0.039	-0.003	5.496	0.124	0.124	0.000	0.000	0.000	0.000
24	A	25	PHE	0	0.030	0.000	7.301	-0.117	-0.117	0.000	0.000	0.000	0.000
25	A	26	THR	0	-0.036	-0.060	7.670	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	27	GLY	0	0.100	0.048	10.510	0.035	0.035	0.000	0.000	0.000	0.000
27	A	28	SER	0	0.038	0.027	12.992	-0.035	-0.035	0.000	0.000	0.000	0.000
28	A	29	TRP	0	-0.027	-0.011	14.516	0.006	0.006	0.000	0.000	0.000	0.000
29	A	30	CYS	0	0.033	0.041	13.697	0.013	0.013	0.000	0.000	0.000	0.000
30	A	31	GLN	0	0.061	0.022	13.786	-0.055	-0.055	0.000	0.000	0.000	0.000
31	A	32	PRO	0	-0.011	-0.022	13.975	-0.020	-0.020	0.000	0.000	0.000	0.000
32	A	33	CYS	0	0.032	0.024	10.130	-0.018	-0.018	0.000	0.000	0.000	0.000
33	A	34	LYS	1	0.842	0.927	9.244	0.247	0.247	0.000	0.000	0.000	0.000
34	A	35	LYS	1	0.936	0.963	10.189	0.237	0.237	0.000	0.000	0.000	0.000
35	A	36	MET	0	0.026	0.048	8.597	0.037	0.037	0.000	0.000	0.000	0.000
36	A	37	LYS	1	0.934	0.990	5.412	1.158	1.158	0.000	0.000	0.000	0.000
37	A	38	PRO	0	0.042	0.035	5.201	-0.076	-0.076	0.000	0.000	0.000	0.000
38	A	39	THR	0	-0.003	0.007	6.950	0.020	0.020	0.000	0.000	0.000	0.000
39	A	40	PHE	0	0.016	-0.002	2.421	-0.881	-0.257	1.674	-0.473	-1.824	-0.002
40	A	41	GLU	-1	-0.819	-0.891	2.239	-3.477	-2.957	3.276	-0.923	-2.873	-0.003
41	A	42	GLU	-1	-0.926	-0.964	3.402	-0.041	-0.144	0.010	0.249	-0.157	0.000
42	A	43	MET	0	-0.115	-0.049	6.260	0.142	0.142	0.000	0.000	0.000	0.000
43	A	44	ALA	0	0.037	0.014	2.405	-0.606	-0.208	1.235	-0.483	-1.149	-0.002
44	A	45	SER	0	-0.053	-0.032	4.377	0.197	0.293	-0.001	-0.018	-0.078	0.000
45	A	46	GLN	0	-0.013	-0.010	6.284	0.076	0.076	0.000	0.000	0.000	0.000
46	A	47	MET	0	-0.008	0.011	7.708	0.017	0.017	0.000	0.000	0.000	0.000
47	A	48	GLU	-1	-0.895	-0.937	6.783	0.694	0.694	0.000	0.000	0.000	0.000
48	A	49	GLY	0	-0.034	-0.014	7.966	0.019	0.019	0.000	0.000	0.000	0.000
49	A	50	ASP	-1	-0.967	-0.962	10.100	-0.038	-0.038	0.000	0.000	0.000	0.000
50	A	51	ILE	0	-0.062	-0.051	8.134	-0.020	-0.020	0.000	0.000	0.000	0.000
51	A	52	ARG	1	0.816	0.912	5.912	0.104	0.104	0.000	0.000	0.000	0.000
52	A	53	PHE	0	0.026	0.003	2.525	-1.115	-0.161	0.844	-0.355	-1.443	0.001
53	A	54	ALA	0	-0.018	-0.007	2.663	-3.501	-1.040	0.859	-1.395	-1.926	-0.017
54	A	55	TYR	0	-0.060	-0.085	2.429	-1.579	0.519	2.314	-0.988	-3.424	-0.007
55	A	56	MET	0	-0.023	0.001	5.328	0.064	0.080	-0.001	0.000	-0.015	0.000
56	A	57	ASP	-1	-0.833	-0.931	8.889	-0.490	-0.490	0.000	0.000	0.000	0.000
57	A	58	ALA	0	0.027	-0.013	11.069	0.055	0.055	0.000	0.000	0.000	0.000
58	A	59	GLU	-1	-1.016	-1.005	14.550	-0.212	-0.212	0.000	0.000	0.000	0.000
59	A	60	ASP	-1	-0.905	-0.936	12.479	-0.285	-0.285	0.000	0.000	0.000	0.000
60	A	61	ALA	0	-0.023	-0.017	12.580	0.014	0.014	0.000	0.000	0.000	0.000
61	A	62	GLU	-1	-0.869	-0.931	14.725	-0.148	-0.148	0.000	0.000	0.000	0.000
62	A	63	LYS	1	0.827	0.893	18.344	0.149	0.149	0.000	0.000	0.000	0.000
63	A	64	THR	0	0.020	-0.014	13.881	0.011	0.011	0.000	0.000	0.000	0.000
64	A	65	MET	0	0.006	0.008	14.980	-0.006	-0.006	0.000	0.000	0.000	0.000
65	A	66	ALA	0	-0.059	-0.006	17.299	0.014	0.014	0.000	0.000	0.000	0.000
66	A	67	GLU	-1	-0.856	-0.931	19.417	-0.147	-0.147	0.000	0.000	0.000	0.000
67	A	68	LEU	0	-0.032	-0.010	15.298	0.007	0.007	0.000	0.000	0.000	0.000
68	A	69	ASN	0	-0.068	-0.049	19.182	-0.005	-0.005	0.000	0.000	0.000	0.000
69	A	70	ILE	0	0.024	0.033	14.119	0.001	0.001	0.000	0.000	0.000	0.000
70	A	71	ARG	1	0.796	0.898	17.938	0.186	0.186	0.000	0.000	0.000	0.000
71	A	72	THR	0	0.017	0.014	16.757	-0.005	-0.005	0.000	0.000	0.000	0.000
72	A	73	LEU	0	0.011	0.073	12.996	-0.028	-0.028	0.000	0.000	0.000	0.000
73	A	74	PRO	0	-0.010	-0.055	10.332	0.029	0.029	0.000	0.000	0.000	0.000
74	A	75	SER	0	0.009	-0.033	11.743	0.056	0.056	0.000	0.000	0.000	0.000
75	A	76	LEU	0	-0.048	-0.012	8.010	-0.078	-0.078	0.000	0.000	0.000	0.000
76	A	77	ALA	0	0.025	0.022	10.206	0.060	0.060	0.000	0.000	0.000	0.000
77	A	78	LEU	0	0.002	0.021	10.631	-0.061	-0.061	0.000	0.000	0.000	0.000
78	A	79	PHE	0	0.003	-0.016	11.636	0.040	0.040	0.000	0.000	0.000	0.000
79	A	80	VAL	0	0.021	-0.008	13.516	-0.006	-0.006	0.000	0.000	0.000	0.000
80	A	81	ASP	-1	-0.836	-0.916	16.152	-0.074	-0.074	0.000	0.000	0.000	0.000
81	A	82	GLY	0	0.053	0.044	16.286	0.007	0.007	0.000	0.000	0.000	0.000
82	A	83	MET	0	-0.107	-0.059	17.273	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	84	ILE	0	-0.044	-0.023	15.230	-0.012	-0.012	0.000	0.000	0.000	0.000
84	A	85	ARG	1	0.863	0.938	16.037	0.134	0.134	0.000	0.000	0.000	0.000
85	A	86	GLU	-1	-0.845	-0.920	15.966	-0.158	-0.158	0.000	0.000	0.000	0.000
86	A	87	VAL	0	-0.034	-0.035	14.854	-0.036	-0.036	0.000	0.000	0.000	0.000
87	A	88	PHE	0	-0.027	-0.003	13.713	0.024	0.024	0.000	0.000	0.000	0.000
88	A	89	SER	0	0.006	-0.004	14.376	-0.031	-0.031	0.000	0.000	0.000	0.000
89	A	90	GLY	0	-0.009	-0.010	15.017	0.024	0.024	0.000	0.000	0.000	0.000
90	A	91	THR	0	-0.053	-0.048	12.767	-0.021	-0.021	0.000	0.000	0.000	0.000
91	A	92	MET	0	0.012	0.008	12.354	0.035	0.035	0.000	0.000	0.000	0.000
92	A	93	ASN	0	-0.027	-0.006	12.307	-0.031	-0.031	0.000	0.000	0.000	0.000
93	A	94	LYS	1	0.965	0.959	9.736	0.264	0.264	0.000	0.000	0.000	0.000
94	A	95	SER	0	-0.022	-0.016	12.502	0.002	0.002	0.000	0.000	0.000	0.000
95	A	96	ASP	-1	-0.852	-0.922	15.530	-0.169	-0.169	0.000	0.000	0.000	0.000
96	A	97	LEU	0	0.008	0.010	7.648	0.001	0.001	0.000	0.000	0.000	0.000
97	A	98	ARG	1	0.897	0.936	12.377	0.162	0.162	0.000	0.000	0.000	0.000
98	A	99	TYR	0	-0.058	-0.027	13.334	0.012	0.012	0.000	0.000	0.000	0.000
99	A	100	TRP	0	0.037	0.006	11.371	0.003	0.003	0.000	0.000	0.000	0.000
100	A	101	ILE	0	0.036	0.016	9.071	0.007	0.007	0.000	0.000	0.000	0.000
101	A	102	ASN	0	-0.004	-0.010	13.591	0.008	0.008	0.000	0.000	0.000	0.000
102	A	103	ASN	0	-0.048	-0.006	16.314	0.024	0.024	0.000	0.000	0.000	0.000
103	A	104	ASN	0	-0.024	-0.003	16.035	0.025	0.025	0.000	0.000	0.000	0.000
104	A	105	ILE	0	-0.054	-0.028	14.251	0.000	0.000	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:2:LEU)