FMO DATABASE

FMODB ID: R8858

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

Total energy (hartree)

FMO2-HF: Electronic energy	-712133.060818
FMO2-HF: Nuclear repulsion	674633.189006
FMO2-HF: Total energy	-37499.871812
FMO2-MP2: Total energy	-37610.853644

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.
-13.473	-4.459	3.726	-5.406	-7.334	-0.043

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 : 0.975 / q_NPA : 0.998

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	-0.004	0.005	2.910	-0.796	3.316	0.092	-2.039	-2.166	0.003
4	A	12	LEU	0	-0.015	-0.017	2.329	-34.238	-30.091	3.596	-3.227	-4.516	-0.045
5	A	13	THR	0	0.038	0.020	3.774	9.467	9.739	0.005	-0.043	-0.234	0.000
6	A	14	LEU	0	-0.025	0.005	5.706	-4.146	-4.146	0.000	0.000	0.000	0.000
7	A	15	TRP	0	-0.021	-0.013	8.295	0.845	0.845	0.000	0.000	0.000	0.000
8	A	16	LEU	0	0.023	0.012	11.937	-0.240	-0.240	0.000	0.000	0.000	0.000
9	A	17	ASP	-1	-0.772	-0.891	14.688	-15.314	-15.314	0.000	0.000	0.000	0.000
10	A	18	ASP	-1	-0.889	-0.945	16.457	-16.277	-16.277	0.000	0.000	0.000	0.000
11	A	19	LYS	1	0.851	0.928	16.106	16.237	16.237	0.000	0.000	0.000	0.000
12	A	20	MET	0	-0.013	0.003	9.673	-0.405	-0.405	0.000	0.000	0.000	0.000
13	A	21	PHE	0	0.016	0.013	10.688	1.346	1.346	0.000	0.000	0.000	0.000
14	A	22	THR	0	-0.009	-0.023	6.557	-2.492	-2.492	0.000	0.000	0.000	0.000
15	A	23	GLY	0	0.027	0.013	7.446	4.381	4.381	0.000	0.000	0.000	0.000
16	A	24	LEU	0	-0.023	-0.016	6.744	-6.590	-6.590	0.000	0.000	0.000	0.000
17	A	25	ILE	0	-0.003	0.001	3.184	1.879	2.362	0.033	-0.097	-0.418	-0.001
18	A	26	ASN	0	-0.002	-0.003	7.356	1.959	1.959	0.000	0.000	0.000	0.000
19	A	27	THR	0	0.058	0.023	9.663	1.697	1.697	0.000	0.000	0.000	0.000
20	A	28	GLY	0	0.026	0.022	12.192	1.492	1.492	0.000	0.000	0.000	0.000
21	A	29	ALA	0	-0.011	0.004	14.791	1.509	1.509	0.000	0.000	0.000	0.000
22	A	30	ASP	-1	-0.914	-0.971	15.755	-16.282	-16.282	0.000	0.000	0.000	0.000
23	A	31	VAL	0	-0.023	0.001	17.469	-0.237	-0.237	0.000	0.000	0.000	0.000
24	A	32	THR	0	-0.013	-0.030	13.212	-1.460	-1.460	0.000	0.000	0.000	0.000
25	A	33	ILE	0	-0.062	-0.025	14.721	1.439	1.439	0.000	0.000	0.000	0.000
26	A	34	ILE	0	0.001	0.004	13.887	-1.550	-1.550	0.000	0.000	0.000	0.000
27	A	35	LYS	1	0.816	0.895	15.756	19.698	19.698	0.000	0.000	0.000	0.000
28	A	36	LEU	0	0.024	-0.019	18.484	-0.092	-0.092	0.000	0.000	0.000	0.000
29	A	37	GLU	-1	-0.909	-0.938	19.964	-15.880	-15.880	0.000	0.000	0.000	0.000
30	A	38	ASP	-1	-0.775	-0.857	15.284	-19.972	-19.972	0.000	0.000	0.000	0.000
31	A	39	TRP	0	-0.058	-0.048	18.399	-0.876	-0.876	0.000	0.000	0.000	0.000
32	A	40	PRO	0	-0.008	0.001	19.106	0.745	0.745	0.000	0.000	0.000	0.000
33	A	41	PRO	0	0.040	0.013	22.186	0.242	0.242	0.000	0.000	0.000	0.000
34	A	42	ASN	0	-0.037	-0.022	25.690	0.490	0.490	0.000	0.000	0.000	0.000
35	A	43	TRP	0	-0.021	-0.001	17.742	0.043	0.043	0.000	0.000	0.000	0.000
36	A	44	PRO	0	0.013	0.012	25.060	0.063	0.063	0.000	0.000	0.000	0.000
37	A	45	ILE	0	0.033	0.018	23.928	-0.543	-0.543	0.000	0.000	0.000	0.000
38	A	46	THR	0	-0.020	-0.009	26.691	0.476	0.476	0.000	0.000	0.000	0.000
39	A	47	ASP	-1	-0.790	-0.877	27.925	-10.889	-10.889	0.000	0.000	0.000	0.000
40	A	48	THR	0	-0.015	0.001	25.688	0.089	0.089	0.000	0.000	0.000	0.000
41	A	49	LEU	0	0.042	0.012	28.964	0.079	0.079	0.000	0.000	0.000	0.000
42	A	50	THR	0	-0.038	-0.024	25.163	0.151	0.151	0.000	0.000	0.000	0.000
43	A	51	ASN	0	-0.010	-0.008	27.727	-0.054	-0.054	0.000	0.000	0.000	0.000
44	A	52	LEU	0	0.022	0.027	21.516	-0.243	-0.243	0.000	0.000	0.000	0.000
45	A	53	ARG	1	1.003	0.988	21.258	13.392	13.392	0.000	0.000	0.000	0.000
46	A	54	GLY	0	-0.051	-0.033	22.072	-0.482	-0.482	0.000	0.000	0.000	0.000
47	A	55	ILE	0	0.009	0.014	20.813	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	56	GLY	0	0.027	0.025	25.100	0.270	0.270	0.000	0.000	0.000	0.000
49	A	57	GLN	0	0.054	0.000	28.689	-0.131	-0.131	0.000	0.000	0.000	0.000
50	A	58	SER	0	0.004	0.005	31.097	-0.087	-0.087	0.000	0.000	0.000	0.000
51	A	59	ASN	0	-0.027	-0.007	24.306	0.281	0.281	0.000	0.000	0.000	0.000
52	A	60	ASN	0	-0.024	-0.002	27.745	-0.316	-0.316	0.000	0.000	0.000	0.000
53	A	61	PRO	0	0.041	0.034	25.033	-0.270	-0.270	0.000	0.000	0.000	0.000
54	A	62	LYS	1	0.812	0.891	24.717	11.528	11.528	0.000	0.000	0.000	0.000
55	A	63	GLN	0	0.008	0.004	22.022	0.040	0.040	0.000	0.000	0.000	0.000
56	A	64	SER	0	0.052	0.028	21.264	0.619	0.619	0.000	0.000	0.000	0.000
57	A	65	SER	0	-0.025	-0.033	23.333	0.148	0.148	0.000	0.000	0.000	0.000
58	A	66	LYS	1	0.901	0.950	24.215	11.686	11.686	0.000	0.000	0.000	0.000
59	A	67	TYR	0	-0.007	0.001	20.248	-0.137	-0.137	0.000	0.000	0.000	0.000
60	A	68	LEU	0	-0.007	0.008	17.483	0.357	0.357	0.000	0.000	0.000	0.000
61	A	69	THR	0	0.003	-0.008	16.471	-0.255	-0.255	0.000	0.000	0.000	0.000
62	A	70	TRP	0	-0.049	-0.017	9.907	-1.438	-1.438	0.000	0.000	0.000	0.000
63	A	71	ARG	1	0.923	0.962	11.833	20.738	20.738	0.000	0.000	0.000	0.000
64	A	72	ASP	-1	-0.728	-0.856	6.622	-34.885	-34.885	0.000	0.000	0.000	0.000
65	A	73	LYS	1	0.853	0.898	5.260	40.309	40.309	0.000	0.000	0.000	0.000
66	A	74	GLU	-1	-0.920	-0.940	8.250	-29.460	-29.460	0.000	0.000	0.000	0.000
67	A	75	ASN	0	-0.057	-0.018	10.622	2.127	2.127	0.000	0.000	0.000	0.000
68	A	76	ASN	0	-0.009	-0.002	9.572	4.307	4.307	0.000	0.000	0.000	0.000
69	A	77	SER	0	-0.032	-0.055	12.166	-0.556	-0.556	0.000	0.000	0.000	0.000
70	A	78	GLY	0	0.055	0.031	14.242	0.535	0.535	0.000	0.000	0.000	0.000
71	A	79	LEU	0	-0.025	0.000	16.039	0.236	0.236	0.000	0.000	0.000	0.000
72	A	80	ILE	0	-0.009	0.004	13.665	-0.160	-0.160	0.000	0.000	0.000	0.000
73	A	81	LYS	1	0.834	0.913	17.590	13.227	13.227	0.000	0.000	0.000	0.000
74	A	82	PRO	0	0.011	0.027	16.467	0.363	0.363	0.000	0.000	0.000	0.000
75	A	83	PHE	0	0.026	-0.010	18.534	1.031	1.031	0.000	0.000	0.000	0.000
76	A	84	VAL	0	0.000	0.009	19.002	-0.961	-0.961	0.000	0.000	0.000	0.000
77	A	85	ILE	0	-0.035	-0.018	20.405	0.835	0.835	0.000	0.000	0.000	0.000
78	A	86	PRO	0	0.061	0.039	21.541	-0.670	-0.670	0.000	0.000	0.000	0.000
79	A	87	ASN	0	-0.017	-0.025	23.185	0.058	0.058	0.000	0.000	0.000	0.000
80	A	88	LEU	0	-0.011	0.015	16.430	0.072	0.072	0.000	0.000	0.000	0.000
81	A	89	PRO	0	0.009	0.001	16.712	-0.279	-0.279	0.000	0.000	0.000	0.000
82	A	90	VAL	0	0.000	-0.007	12.082	-0.795	-0.795	0.000	0.000	0.000	0.000
83	A	91	ASN	0	-0.006	-0.017	11.603	2.341	2.341	0.000	0.000	0.000	0.000
84	A	92	LEU	0	-0.043	-0.018	11.279	-2.029	-2.029	0.000	0.000	0.000	0.000
85	A	93	TRP	0	-0.015	-0.013	6.842	3.406	3.406	0.000	0.000	0.000	0.000
86	A	94	GLY	0	0.071	0.034	10.650	-0.758	-0.758	0.000	0.000	0.000	0.000
87	A	95	ARG	1	0.855	0.899	12.403	16.599	16.599	0.000	0.000	0.000	0.000
88	A	96	ASP	-1	-0.778	-0.838	14.261	-20.220	-20.220	0.000	0.000	0.000	0.000
89	A	97	LEU	0	0.022	0.012	9.488	0.277	0.277	0.000	0.000	0.000	0.000
90	A	98	LEU	0	-0.026	-0.025	7.532	-0.954	-0.954	0.000	0.000	0.000	0.000
91	A	99	SER	0	-0.080	-0.046	10.877	-0.305	-0.305	0.000	0.000	0.000	0.000
92	A	100	GLN	0	-0.008	-0.021	13.365	1.080	1.080	0.000	0.000	0.000	0.000
93	A	101	MET	0	-0.064	-0.011	6.657	-1.202	-1.202	0.000	0.000	0.000	0.000
94	A	102	LYS	1	0.879	0.926	9.665	24.013	24.013	0.000	0.000	0.000	0.000
95	A	103	ILE	0	-0.002	0.011	5.789	-2.748	-2.748	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:9:LYS)