FMO DATABASE

FMODB ID: ZVVYN

Calculation Name: 3SQF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3SQF

Chain ID: A

ChEMBL ID:

UniProt ID: P07570

Base Structure: X-ray

Registration Date: 2023-09-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	95
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-712726.356087
FMO2-HF: Nuclear repulsion	675227.26636
FMO2-HF: Total energy	-37499.089727
FMO2-MP2: Total energy	-37610.137927

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:9:LYS)

Summations of interaction energy for fragment #1(A:9:LYS)

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.
-1.887	5.488	4.23	-4.905	-6.7	-0.054

Interaction energy analysis for fragmet #1(A:9:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.936 / q_NPA : 0.959

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	11	SER	0	-0.016	0.010	2.622	-0.081	3.159	0.213	-1.496	-1.958	-0.004
4	A	12	LEU	0	0.010	-0.005	2.253	-31.196	-27.615	4.010	-3.352	-4.239	-0.049
5	A	13	THR	0	0.035	0.011	3.610	8.339	8.556	0.006	-0.022	-0.202	-0.001
6	A	14	LEU	0	-0.025	0.003	6.134	-4.144	-4.144	0.000	0.000	0.000	0.000
7	A	15	TRP	0	-0.027	-0.013	8.737	0.568	0.568	0.000	0.000	0.000	0.000
8	A	16	LEU	0	0.008	-0.001	12.344	-0.269	-0.269	0.000	0.000	0.000	0.000
9	A	17	ASP	-1	-0.805	-0.911	15.147	-15.048	-15.048	0.000	0.000	0.000	0.000
10	A	18	ASP	-1	-0.963	-0.991	16.832	-16.094	-16.094	0.000	0.000	0.000	0.000
11	A	19	LYS	1	0.951	0.979	16.712	15.829	15.829	0.000	0.000	0.000	0.000
12	A	20	MET	0	-0.025	-0.006	10.082	-0.637	-0.637	0.000	0.000	0.000	0.000
13	A	21	PHE	0	0.016	0.017	11.257	1.262	1.262	0.000	0.000	0.000	0.000
14	A	22	THR	0	-0.003	-0.020	6.759	-2.298	-2.298	0.000	0.000	0.000	0.000
15	A	23	GLY	0	0.016	0.010	7.252	4.058	4.058	0.000	0.000	0.000	0.000
16	A	24	LEU	0	-0.017	-0.010	6.721	-6.123	-6.123	0.000	0.000	0.000	0.000
17	A	25	ILE	0	0.004	0.003	3.993	2.033	2.297	0.002	-0.034	-0.231	0.000
18	A	26	ASN	0	-0.006	-0.006	7.355	1.777	1.777	0.000	0.000	0.000	0.000
19	A	27	THR	0	0.034	0.008	9.416	1.885	1.885	0.000	0.000	0.000	0.000
20	A	28	GLY	0	0.043	0.023	12.313	1.336	1.336	0.000	0.000	0.000	0.000
21	A	29	ALA	0	-0.027	-0.008	14.856	1.416	1.416	0.000	0.000	0.000	0.000
22	A	30	ASP	-1	-0.921	-0.979	16.003	-15.917	-15.917	0.000	0.000	0.000	0.000
23	A	31	VAL	0	-0.003	0.016	17.833	-0.299	-0.299	0.000	0.000	0.000	0.000
24	A	32	THR	0	-0.006	-0.026	13.500	-1.377	-1.377	0.000	0.000	0.000	0.000
25	A	33	ILE	0	-0.031	-0.008	14.894	1.344	1.344	0.000	0.000	0.000	0.000
26	A	34	ILE	0	-0.021	-0.005	13.964	-1.465	-1.465	0.000	0.000	0.000	0.000
27	A	35	LYS	1	0.943	0.978	14.991	19.833	19.833	0.000	0.000	0.000	0.000
28	A	36	LEU	0	0.014	-0.023	18.403	-0.098	-0.098	0.000	0.000	0.000	0.000
29	A	37	GLU	-1	-0.983	-0.990	19.982	-15.231	-15.231	0.000	0.000	0.000	0.000
30	A	38	ASP	-1	-0.817	-0.890	15.194	-19.701	-19.701	0.000	0.000	0.000	0.000
31	A	39	TRP	0	-0.081	-0.062	18.484	-0.854	-0.854	0.000	0.000	0.000	0.000
32	A	40	PRO	0	-0.023	-0.004	19.298	0.718	0.718	0.000	0.000	0.000	0.000
33	A	41	PRO	0	0.040	0.008	22.469	0.249	0.249	0.000	0.000	0.000	0.000
34	A	42	ASN	0	-0.027	-0.015	26.008	0.573	0.573	0.000	0.000	0.000	0.000
35	A	43	TRP	0	-0.007	0.008	18.170	0.040	0.040	0.000	0.000	0.000	0.000
36	A	44	PRO	0	0.013	0.010	25.223	0.058	0.058	0.000	0.000	0.000	0.000
37	A	45	ILE	0	0.021	0.010	23.971	-0.539	-0.539	0.000	0.000	0.000	0.000
38	A	46	THR	0	-0.010	-0.003	26.638	0.427	0.427	0.000	0.000	0.000	0.000
39	A	47	ASP	-1	-0.839	-0.911	27.983	-10.555	-10.555	0.000	0.000	0.000	0.000
40	A	48	THR	0	-0.022	-0.017	25.880	0.210	0.210	0.000	0.000	0.000	0.000
41	A	49	LEU	0	0.032	0.004	29.114	0.088	0.088	0.000	0.000	0.000	0.000
42	A	50	THR	0	-0.030	-0.014	25.334	0.077	0.077	0.000	0.000	0.000	0.000
43	A	51	ASN	0	-0.024	-0.009	27.988	-0.015	-0.015	0.000	0.000	0.000	0.000
44	A	52	LEU	0	0.021	0.024	22.339	-0.256	-0.256	0.000	0.000	0.000	0.000
45	A	53	ARG	1	1.003	0.985	21.254	13.052	13.052	0.000	0.000	0.000	0.000
46	A	54	GLY	0	-0.052	-0.031	22.027	-0.459	-0.459	0.000	0.000	0.000	0.000
47	A	55	ILE	0	0.006	0.015	20.812	0.007	0.007	0.000	0.000	0.000	0.000
48	A	56	GLY	0	0.026	0.022	25.013	0.261	0.261	0.000	0.000	0.000	0.000
49	A	57	GLN	0	0.063	0.000	28.608	-0.077	-0.077	0.000	0.000	0.000	0.000
50	A	58	SER	0	-0.002	0.004	31.098	-0.104	-0.104	0.000	0.000	0.000	0.000
51	A	59	ASN	0	0.001	0.005	24.006	0.216	0.216	0.000	0.000	0.000	0.000
52	A	60	ASN	0	-0.055	-0.023	27.812	-0.304	-0.304	0.000	0.000	0.000	0.000
53	A	61	PRO	0	0.021	0.026	25.224	-0.292	-0.292	0.000	0.000	0.000	0.000
54	A	62	LYS	1	0.924	0.965	24.781	11.677	11.677	0.000	0.000	0.000	0.000
55	A	63	GLN	0	-0.044	-0.032	22.155	-0.030	-0.030	0.000	0.000	0.000	0.000
56	A	64	SER	0	0.022	0.013	21.227	0.550	0.550	0.000	0.000	0.000	0.000
57	A	65	SER	0	-0.020	-0.041	23.331	0.172	0.172	0.000	0.000	0.000	0.000
58	A	66	LYS	1	0.899	0.946	24.514	11.553	11.553	0.000	0.000	0.000	0.000
59	A	67	TYR	0	-0.017	-0.005	20.824	-0.063	-0.063	0.000	0.000	0.000	0.000
60	A	68	LEU	0	0.001	0.011	17.678	0.349	0.349	0.000	0.000	0.000	0.000
61	A	69	THR	0	0.028	0.017	16.436	-0.259	-0.259	0.000	0.000	0.000	0.000
62	A	70	TRP	0	-0.057	-0.012	10.086	-1.291	-1.291	0.000	0.000	0.000	0.000
63	A	71	ARG	1	0.933	0.962	12.096	20.364	20.364	0.000	0.000	0.000	0.000
64	A	72	ASP	-1	-0.747	-0.876	6.736	-35.081	-35.081	0.000	0.000	0.000	0.000
65	A	73	LYS	1	0.929	0.942	4.517	48.267	48.340	-0.001	-0.001	-0.070	0.000
66	A	74	GLU	-1	-0.990	-0.983	8.313	-28.047	-28.047	0.000	0.000	0.000	0.000
67	A	75	ASN	0	-0.046	-0.009	10.499	2.020	2.020	0.000	0.000	0.000	0.000
68	A	76	ASN	0	-0.035	-0.021	9.647	4.195	4.195	0.000	0.000	0.000	0.000
69	A	77	SER	0	-0.026	-0.041	12.308	-0.504	-0.504	0.000	0.000	0.000	0.000
70	A	78	GLY	0	0.054	0.019	14.423	0.492	0.492	0.000	0.000	0.000	0.000
71	A	79	LEU	0	-0.027	-0.001	16.298	0.264	0.264	0.000	0.000	0.000	0.000
72	A	80	ILE	0	0.010	0.010	13.865	-0.141	-0.141	0.000	0.000	0.000	0.000
73	A	81	LYS	1	0.901	0.966	17.939	12.975	12.975	0.000	0.000	0.000	0.000
74	A	82	PRO	0	0.008	0.030	16.563	0.378	0.378	0.000	0.000	0.000	0.000
75	A	83	PHE	0	0.015	-0.007	18.632	0.985	0.985	0.000	0.000	0.000	0.000
76	A	84	VAL	0	0.010	0.015	19.061	-0.934	-0.934	0.000	0.000	0.000	0.000
77	A	85	ILE	0	-0.055	-0.028	20.178	0.805	0.805	0.000	0.000	0.000	0.000
78	A	86	PRO	0	0.068	0.039	21.516	-0.655	-0.655	0.000	0.000	0.000	0.000
79	A	87	ASN	0	-0.025	-0.024	22.992	0.133	0.133	0.000	0.000	0.000	0.000
80	A	88	LEU	0	0.009	0.021	16.319	0.067	0.067	0.000	0.000	0.000	0.000
81	A	89	PRO	0	0.010	-0.001	16.708	-0.296	-0.296	0.000	0.000	0.000	0.000
82	A	90	VAL	0	-0.018	-0.010	11.837	-0.750	-0.750	0.000	0.000	0.000	0.000
83	A	91	ASN	0	-0.003	-0.011	11.480	2.257	2.257	0.000	0.000	0.000	0.000
84	A	92	LEU	0	-0.035	-0.015	11.260	-1.947	-1.947	0.000	0.000	0.000	0.000
85	A	93	TRP	0	0.004	-0.004	7.000	3.121	3.121	0.000	0.000	0.000	0.000
86	A	94	GLY	0	0.056	0.028	10.907	-0.698	-0.698	0.000	0.000	0.000	0.000
87	A	95	ARG	1	0.873	0.924	12.797	16.162	16.162	0.000	0.000	0.000	0.000
88	A	96	ASP	-1	-0.795	-0.853	14.666	-19.808	-19.808	0.000	0.000	0.000	0.000
89	A	97	LEU	0	0.021	0.011	9.668	0.159	0.159	0.000	0.000	0.000	0.000
90	A	98	LEU	0	-0.027	-0.023	8.036	-0.902	-0.902	0.000	0.000	0.000	0.000
91	A	99	SER	0	-0.082	-0.046	11.114	-0.471	-0.471	0.000	0.000	0.000	0.000
92	A	100	GLN	0	0.008	-0.012	13.574	0.995	0.995	0.000	0.000	0.000	0.000
93	A	101	MET	0	-0.062	-0.011	7.652	-1.593	-1.593	0.000	0.000	0.000	0.000
94	A	102	LYS	1	0.906	0.955	9.619	24.394	24.394	0.000	0.000	0.000	0.000
95	A	103	ILE	0	-0.014	0.007	6.012	-2.974	-2.974	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:9:LYS)