FMO DATABASE

FMODB ID: 662MZ

Calculation Name: 2YAD-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YAD

Chain ID: E

ChEMBL ID:

UniProt ID: P11686

Base Structure: X-ray

Registration Date: 2023-06-20

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	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	76
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-487063.541189
FMO2-HF: Nuclear repulsion	455834.84778
FMO2-HF: Total energy	-31228.693409
FMO2-MP2: Total energy	-31315.293806

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(E:89:VAL)

Summations of interaction energy for fragment #1(E:89: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.
-6.216	-0.739	3.858	-3.042	-6.293	-0.013

Interaction energy analysis for fragmet #1(E:89:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / q_NPA : -0.016

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	E	91	THR	0	-0.029	-0.003	3.059	-1.960	0.155	0.239	-0.961	-1.392	-0.002
4	E	92	ALA	0	0.035	0.028	4.550	0.407	0.489	-0.001	-0.006	-0.075	0.000
5	E	93	THR	0	-0.020	-0.012	6.925	-0.018	-0.018	0.000	0.000	0.000	0.000
6	E	94	PHE	0	-0.016	-0.012	9.336	0.064	0.064	0.000	0.000	0.000	0.000
7	E	95	SER	0	0.030	0.018	13.526	-0.006	-0.006	0.000	0.000	0.000	0.000
8	E	96	ILE	0	-0.031	-0.018	16.757	0.000	0.000	0.000	0.000	0.000	0.000
9	E	97	GLY	0	0.014	0.015	19.544	0.004	0.004	0.000	0.000	0.000	0.000
10	E	98	SER	0	-0.028	-0.024	22.807	-0.001	-0.001	0.000	0.000	0.000	0.000
11	E	99	THR	0	-0.022	-0.029	23.486	0.008	0.008	0.000	0.000	0.000	0.000
12	E	100	GLY	0	0.031	0.042	20.704	-0.006	-0.006	0.000	0.000	0.000	0.000
13	E	101	LEU	0	-0.039	-0.026	16.036	0.003	0.003	0.000	0.000	0.000	0.000
14	E	102	VAL	0	-0.008	-0.005	12.327	-0.009	-0.009	0.000	0.000	0.000	0.000
15	E	103	VAL	0	0.008	0.011	8.904	-0.006	-0.006	0.000	0.000	0.000	0.000
16	E	104	TYR	0	-0.025	-0.025	7.163	0.036	0.036	0.000	0.000	0.000	0.000
17	E	105	ASP	-1	-0.842	-0.944	5.635	-2.244	-2.244	0.000	0.000	0.000	0.000
18	E	106	TYR	0	0.031	-0.003	2.492	-0.808	0.047	0.848	-0.361	-1.343	0.002
19	E	107	GLN	0	-0.009	-0.004	2.184	-3.450	-1.166	2.773	-1.694	-3.363	-0.013
20	E	108	GLN	0	0.001	0.003	4.593	0.492	0.633	-0.001	-0.020	-0.120	0.000
21	E	109	LEU	0	-0.013	0.004	7.387	0.318	0.318	0.000	0.000	0.000	0.000
22	E	110	LEU	0	-0.031	-0.016	9.035	0.239	0.239	0.000	0.000	0.000	0.000
23	E	111	ILE	0	0.017	0.009	9.614	-0.117	-0.117	0.000	0.000	0.000	0.000
24	E	112	ALA	0	-0.001	0.008	12.008	0.065	0.065	0.000	0.000	0.000	0.000
25	E	113	TYR	0	0.016	-0.001	14.199	-0.007	-0.007	0.000	0.000	0.000	0.000
26	E	114	LYS	1	0.923	0.954	16.872	0.209	0.209	0.000	0.000	0.000	0.000
27	E	115	PRO	0	0.035	0.027	19.397	0.005	0.005	0.000	0.000	0.000	0.000
28	E	116	ALA	0	0.055	0.034	22.383	0.013	0.013	0.000	0.000	0.000	0.000
29	E	117	PRO	0	-0.013	-0.011	23.629	-0.010	-0.010	0.000	0.000	0.000	0.000
30	E	118	GLY	0	0.017	0.009	24.555	0.007	0.007	0.000	0.000	0.000	0.000
31	E	119	THR	0	-0.006	-0.001	24.419	0.000	0.000	0.000	0.000	0.000	0.000
32	E	148	CYS	0	-0.103	-0.040	23.533	0.009	0.009	0.000	0.000	0.000	0.000
33	E	121	CYS	0	-0.054	-0.039	16.551	0.014	0.014	0.000	0.000	0.000	0.000
34	E	122	TYR	0	0.042	0.037	19.204	0.009	0.009	0.000	0.000	0.000	0.000
35	E	123	ILE	0	-0.011	-0.005	15.162	-0.041	-0.041	0.000	0.000	0.000	0.000
36	E	124	MET	0	-0.026	-0.004	15.333	0.049	0.049	0.000	0.000	0.000	0.000
37	E	125	LYS	1	0.899	0.951	11.918	0.664	0.664	0.000	0.000	0.000	0.000
38	E	126	ILE	0	-0.025	-0.013	8.616	0.055	0.055	0.000	0.000	0.000	0.000
39	E	127	ALA	0	0.012	0.007	12.080	-0.048	-0.048	0.000	0.000	0.000	0.000
40	E	128	PRO	0	0.017	-0.013	10.228	-0.013	-0.013	0.000	0.000	0.000	0.000
41	E	129	GLU	-1	-0.904	-0.955	8.962	-0.635	-0.635	0.000	0.000	0.000	0.000
42	E	130	SER	0	-0.050	-0.011	11.730	0.085	0.085	0.000	0.000	0.000	0.000
43	E	131	ILE	0	-0.038	-0.015	7.137	0.008	0.008	0.000	0.000	0.000	0.000
44	E	132	PRO	0	-0.005	0.019	11.360	0.053	0.053	0.000	0.000	0.000	0.000
45	E	133	SER	0	0.060	0.017	12.492	-0.037	-0.037	0.000	0.000	0.000	0.000
46	E	134	LEU	0	0.110	0.048	13.809	-0.007	-0.007	0.000	0.000	0.000	0.000
47	E	135	GLU	-1	-0.910	-0.959	15.178	-0.135	-0.135	0.000	0.000	0.000	0.000
48	E	136	ALA	0	-0.076	-0.040	17.144	0.016	0.016	0.000	0.000	0.000	0.000
49	E	137	LEU	0	-0.016	-0.002	14.159	0.010	0.010	0.000	0.000	0.000	0.000
50	E	138	THR	0	0.021	-0.006	17.753	0.011	0.011	0.000	0.000	0.000	0.000
51	E	139	ARG	1	0.964	0.989	20.301	0.180	0.180	0.000	0.000	0.000	0.000
52	E	140	LYS	1	0.934	0.988	19.219	0.289	0.289	0.000	0.000	0.000	0.000
53	E	141	VAL	0	0.032	0.011	19.615	0.006	0.006	0.000	0.000	0.000	0.000
54	E	142	HIS	0	0.069	0.052	22.326	0.007	0.007	0.000	0.000	0.000	0.000
55	E	143	ASN	0	-0.053	-0.040	25.441	0.016	0.016	0.000	0.000	0.000	0.000
56	E	144	PHE	0	-0.060	-0.043	23.937	0.002	0.002	0.000	0.000	0.000	0.000
57	E	145	GLN	0	-0.057	-0.020	26.311	0.008	0.008	0.000	0.000	0.000	0.000
58	E	146	MET	0	-0.074	-0.025	19.695	-0.004	-0.004	0.000	0.000	0.000	0.000
59	E	147	GLU	-1	-0.863	-0.947	24.168	-0.164	-0.164	0.000	0.000	0.000	0.000
60	E	180	PHE	0	-0.009	-0.016	15.220	-0.005	-0.005	0.000	0.000	0.000	0.000
61	E	181	LEU	0	0.022	0.007	13.548	-0.023	-0.023	0.000	0.000	0.000	0.000
62	E	182	GLY	0	0.091	0.057	10.358	-0.146	-0.146	0.000	0.000	0.000	0.000
63	E	183	MET	0	-0.008	-0.006	10.236	0.080	0.080	0.000	0.000	0.000	0.000
64	E	184	ALA	0	0.014	0.014	9.308	0.077	0.077	0.000	0.000	0.000	0.000
65	E	185	VAL	0	0.066	0.022	10.636	0.077	0.077	0.000	0.000	0.000	0.000
66	E	186	SER	0	-0.025	-0.029	12.995	0.079	0.079	0.000	0.000	0.000	0.000
67	E	187	THR	0	-0.040	-0.010	14.611	0.065	0.065	0.000	0.000	0.000	0.000
68	E	188	LEU	0	-0.006	0.002	14.262	0.035	0.035	0.000	0.000	0.000	0.000
69	E	190	GLY	0	0.048	0.046	18.596	0.011	0.011	0.000	0.000	0.000	0.000
70	E	191	GLU	-1	-0.971	-0.992	20.737	-0.096	-0.096	0.000	0.000	0.000	0.000
71	E	192	VAL	0	-0.044	-0.007	21.542	0.012	0.012	0.000	0.000	0.000	0.000
72	E	193	PRO	0	-0.012	0.002	23.128	-0.014	-0.014	0.000	0.000	0.000	0.000
73	E	194	LEU	0	-0.008	-0.010	19.045	-0.017	-0.017	0.000	0.000	0.000	0.000
74	E	195	TYR	0	0.015	0.001	21.706	0.015	0.015	0.000	0.000	0.000	0.000
75	E	196	TYR	0	0.005	-0.002	17.964	-0.014	-0.014	0.000	0.000	0.000	0.000
76	E	197	ILE	0	-0.018	-0.017	19.952	0.013	0.013	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(E:89:VAL)