FMO DATABASE

FMODB ID: 9GRK2

Calculation Name: 3LAY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LAY

Chain ID: A

ChEMBL ID:

UniProt ID: Q9L9I0

Base Structure: X-ray

Registration Date: 2023-03-14

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	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	79
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-451121.8591
FMO2-HF: Nuclear repulsion	419956.11705
FMO2-HF: Total energy	-31165.742049
FMO2-MP2: Total energy	-31256.569505

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:44:LEU)

Summations of interaction energy for fragment #1(A:44: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.
-5.192	-0.798	0.455	-2.061	-2.787	-0.006

Interaction energy analysis for fragmet #1(A:44:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.040 / q_NPA : 0.010

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	46	THR	0	0.033	0.012	3.896	-1.429	0.057	-0.012	-0.801	-0.673	0.004
4	A	47	GLU	-1	-0.847	-0.933	6.813	-1.671	-1.671	0.000	0.000	0.000	0.000
5	A	48	GLN	0	-0.010	0.012	2.914	-3.252	-1.799	0.280	-0.771	-0.962	-0.007
6	A	49	GLN	0	0.024	0.010	2.800	0.228	1.472	0.185	-0.454	-0.974	-0.003
7	A	50	ALA	0	-0.004	0.000	5.456	0.609	0.609	0.000	0.000	0.000	0.000
8	A	51	THR	0	-0.058	-0.042	7.853	0.364	0.364	0.000	0.000	0.000	0.000
9	A	52	ALA	0	0.034	0.013	6.096	0.220	0.220	0.000	0.000	0.000	0.000
10	A	53	GLN	0	-0.031	-0.015	8.117	0.192	0.192	0.000	0.000	0.000	0.000
11	A	54	LYS	1	0.924	0.972	10.725	0.557	0.557	0.000	0.000	0.000	0.000
12	A	55	ILE	0	-0.001	0.002	9.962	0.048	0.048	0.000	0.000	0.000	0.000
13	A	56	TYR	0	-0.001	-0.007	12.280	0.065	0.065	0.000	0.000	0.000	0.000
14	A	57	ASP	-1	-0.854	-0.926	13.954	-0.062	-0.062	0.000	0.000	0.000	0.000
15	A	58	ASP	-1	-0.829	-0.879	16.174	-0.031	-0.031	0.000	0.000	0.000	0.000
16	A	59	TYR	0	0.017	0.004	16.559	0.024	0.024	0.000	0.000	0.000	0.000
17	A	60	TYR	0	-0.022	-0.020	17.878	0.013	0.013	0.000	0.000	0.000	0.000
18	A	61	THR	0	0.005	-0.012	19.710	0.002	0.002	0.000	0.000	0.000	0.000
19	A	62	GLN	0	-0.065	-0.045	20.788	0.007	0.007	0.000	0.000	0.000	0.000
20	A	63	THR	0	-0.050	-0.009	21.171	0.002	0.002	0.000	0.000	0.000	0.000
21	A	64	SER	0	-0.031	-0.012	23.660	0.005	0.005	0.000	0.000	0.000	0.000
22	A	65	ALA	0	0.027	0.007	25.365	0.006	0.006	0.000	0.000	0.000	0.000
23	A	66	LEU	0	0.041	0.022	26.039	0.003	0.003	0.000	0.000	0.000	0.000
24	A	67	ARG	1	0.964	0.979	23.560	-0.126	-0.126	0.000	0.000	0.000	0.000
25	A	68	GLN	0	0.021	0.005	27.408	0.001	0.001	0.000	0.000	0.000	0.000
26	A	69	GLN	0	0.001	0.000	30.243	0.002	0.002	0.000	0.000	0.000	0.000
27	A	70	LEU	0	0.013	0.014	28.498	0.002	0.002	0.000	0.000	0.000	0.000
28	A	71	ILE	0	-0.066	-0.038	27.770	0.005	0.005	0.000	0.000	0.000	0.000
29	A	72	SER	0	0.007	0.005	32.085	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	73	LYS	1	0.779	0.861	35.271	-0.037	-0.037	0.000	0.000	0.000	0.000
31	A	74	ARG	1	0.977	0.990	30.056	-0.091	-0.091	0.000	0.000	0.000	0.000
32	A	75	TYR	0	0.005	0.002	32.714	0.003	0.003	0.000	0.000	0.000	0.000
33	A	76	GLU	-1	-0.836	-0.901	37.889	0.037	0.037	0.000	0.000	0.000	0.000
34	A	77	TYR	0	0.002	-0.005	38.592	0.000	0.000	0.000	0.000	0.000	0.000
35	A	78	ASN	0	-0.030	-0.032	37.133	0.000	0.000	0.000	0.000	0.000	0.000
36	A	79	ALA	0	0.014	0.029	40.892	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	80	LEU	0	-0.029	-0.020	43.540	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	81	LEU	0	-0.032	-0.024	41.402	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	82	THR	0	-0.066	-0.043	43.759	0.000	0.000	0.000	0.000	0.000	0.000
40	A	83	ALA	0	0.002	0.018	46.464	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	84	SER	0	-0.004	-0.012	49.438	0.001	0.001	0.000	0.000	0.000	0.000
42	A	85	SER	0	-0.043	-0.024	52.453	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	86	PRO	0	0.015	0.017	48.655	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	87	ASP	-1	-0.757	-0.862	49.241	0.030	0.030	0.000	0.000	0.000	0.000
45	A	88	THR	0	0.036	0.001	48.019	0.000	0.000	0.000	0.000	0.000	0.000
46	A	89	ALA	0	-0.007	0.011	47.343	0.001	0.001	0.000	0.000	0.000	0.000
47	A	90	LYS	1	0.866	0.912	46.548	-0.028	-0.028	0.000	0.000	0.000	0.000
48	A	91	ILE	0	0.009	0.015	43.270	0.001	0.001	0.000	0.000	0.000	0.000
49	A	92	ASN	0	0.006	-0.013	42.540	0.005	0.005	0.000	0.000	0.000	0.000
50	A	93	ALA	0	-0.045	-0.012	42.517	0.001	0.001	0.000	0.000	0.000	0.000
51	A	94	VAL	0	0.047	0.020	39.264	0.001	0.001	0.000	0.000	0.000	0.000
52	A	95	ALA	0	-0.006	-0.003	38.449	0.003	0.003	0.000	0.000	0.000	0.000
53	A	96	LYS	1	0.991	1.000	37.410	-0.035	-0.035	0.000	0.000	0.000	0.000
54	A	97	GLU	-1	-0.845	-0.905	37.179	0.036	0.036	0.000	0.000	0.000	0.000
55	A	98	MET	0	-0.045	-0.019	33.629	0.002	0.002	0.000	0.000	0.000	0.000
56	A	99	GLU	-1	-0.913	-0.954	32.836	0.060	0.060	0.000	0.000	0.000	0.000
57	A	100	SER	0	0.005	0.006	32.471	0.001	0.001	0.000	0.000	0.000	0.000
58	A	101	LEU	0	-0.045	-0.016	31.229	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	102	GLY	0	0.020	0.006	28.741	0.003	0.003	0.000	0.000	0.000	0.000
60	A	103	GLN	0	-0.004	-0.013	27.679	0.003	0.003	0.000	0.000	0.000	0.000
61	A	104	LYS	1	0.936	0.969	27.414	-0.033	-0.033	0.000	0.000	0.000	0.000
62	A	105	LEU	0	-0.039	-0.017	24.104	0.000	0.000	0.000	0.000	0.000	0.000
63	A	106	ASP	-1	-0.814	-0.880	23.240	0.148	0.148	0.000	0.000	0.000	0.000
64	A	107	GLU	-1	-0.924	-0.952	22.796	0.039	0.039	0.000	0.000	0.000	0.000
65	A	108	GLN	0	0.033	0.010	21.411	-0.006	-0.006	0.000	0.000	0.000	0.000
66	A	109	ARG	1	0.745	0.844	18.862	-0.173	-0.173	0.000	0.000	0.000	0.000
67	A	110	VAL	0	0.033	0.009	18.011	0.022	0.022	0.000	0.000	0.000	0.000
68	A	111	LYS	1	0.816	0.912	18.175	0.013	0.013	0.000	0.000	0.000	0.000
69	A	112	ARG	1	0.821	0.897	14.066	-0.302	-0.302	0.000	0.000	0.000	0.000
70	A	113	ASP	-1	-0.791	-0.886	13.735	0.307	0.307	0.000	0.000	0.000	0.000
71	A	114	VAL	0	-0.003	0.002	13.666	0.024	0.024	0.000	0.000	0.000	0.000
72	A	115	ALA	0	0.011	0.007	13.698	-0.023	-0.023	0.000	0.000	0.000	0.000
73	A	116	MET	0	-0.020	-0.007	7.132	-0.176	-0.176	0.000	0.000	0.000	0.000
74	A	117	ALA	0	0.018	0.008	9.224	0.010	0.010	0.000	0.000	0.000	0.000
75	A	118	GLN	0	-0.042	-0.026	11.201	-0.025	-0.025	0.000	0.000	0.000	0.000
76	A	119	ALA	0	-0.033	-0.002	7.856	-0.084	-0.084	0.000	0.000	0.000	0.000
77	A	120	GLY	0	0.000	0.000	7.239	-0.331	-0.331	0.000	0.000	0.000	0.000
78	A	121	ILE	0	-0.056	-0.031	3.686	-0.122	0.089	0.002	-0.035	-0.178	0.000
79	A	122	PRO	0	-0.004	0.003	4.831	-0.249	-0.249	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:44:LEU)