FMO DATABASE

FMODB ID: 22QYR

Calculation Name: 2YAD-F-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YAD

Chain ID: F

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	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	75
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-476792.106066
FMO2-HF: Nuclear repulsion	446038.523144
FMO2-HF: Total energy	-30753.582922
FMO2-MP2: Total energy	-30838.758432

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(F:89:VAL)

Summations of interaction energy for fragment #1(F: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.
-2.632	0.289	1.959	-1.623	-3.255	-0.004

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / 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

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	F	91	THR	0	-0.020	-0.018	3.562	-1.801	0.053	0.010	-0.898	-0.966	-0.001
4	F	92	ALA	0	-0.006	0.000	5.255	0.258	0.338	-0.001	-0.002	-0.076	0.000
5	F	93	THR	0	-0.008	0.014	7.487	-0.082	-0.082	0.000	0.000	0.000	0.000
6	F	94	PHE	0	-0.024	-0.018	8.805	0.031	0.031	0.000	0.000	0.000	0.000
7	F	95	SER	0	0.031	0.009	13.783	0.001	0.001	0.000	0.000	0.000	0.000
8	F	96	ILE	0	-0.031	-0.015	16.524	-0.010	-0.010	0.000	0.000	0.000	0.000
9	F	97	GLY	0	0.022	0.011	19.820	0.002	0.002	0.000	0.000	0.000	0.000
10	F	98	SER	0	0.004	-0.005	23.201	0.005	0.005	0.000	0.000	0.000	0.000
11	F	99	THR	0	-0.052	-0.038	24.169	0.008	0.008	0.000	0.000	0.000	0.000
12	F	100	GLY	0	0.025	0.040	21.041	0.001	0.001	0.000	0.000	0.000	0.000
13	F	101	LEU	0	-0.032	-0.019	17.047	0.011	0.011	0.000	0.000	0.000	0.000
14	F	102	VAL	0	0.010	-0.004	11.922	-0.020	-0.020	0.000	0.000	0.000	0.000
15	F	103	VAL	0	-0.006	-0.003	9.436	0.042	0.042	0.000	0.000	0.000	0.000
16	F	104	TYR	0	-0.045	-0.032	6.744	-0.017	-0.017	0.000	0.000	0.000	0.000
17	F	105	ASP	-1	-0.813	-0.937	5.956	-0.783	-0.783	0.000	0.000	0.000	0.000
18	F	106	TYR	0	0.015	-0.006	2.256	-0.900	-0.200	1.951	-0.694	-1.956	-0.003
19	F	107	GLN	0	-0.026	0.005	4.387	-0.253	0.034	-0.001	-0.029	-0.257	0.000
20	F	108	GLN	0	-0.035	-0.019	5.528	0.324	0.324	0.000	0.000	0.000	0.000
21	F	109	LEU	0	-0.022	-0.008	7.104	0.192	0.192	0.000	0.000	0.000	0.000
22	F	110	LEU	0	-0.046	-0.035	8.655	0.147	0.147	0.000	0.000	0.000	0.000
23	F	111	ILE	0	0.001	0.004	9.185	-0.048	-0.048	0.000	0.000	0.000	0.000
24	F	112	ALA	0	-0.001	0.005	11.662	0.021	0.021	0.000	0.000	0.000	0.000
25	F	113	TYR	0	0.007	-0.012	14.201	0.011	0.011	0.000	0.000	0.000	0.000
26	F	114	LYS	1	0.911	0.972	17.017	0.021	0.021	0.000	0.000	0.000	0.000
27	F	115	PRO	0	0.024	0.013	20.055	0.010	0.010	0.000	0.000	0.000	0.000
28	F	116	ALA	0	0.052	0.035	22.825	0.008	0.008	0.000	0.000	0.000	0.000
29	F	117	PRO	0	0.009	-0.001	24.193	-0.005	-0.005	0.000	0.000	0.000	0.000
30	F	118	GLY	0	0.017	0.011	25.173	-0.002	-0.002	0.000	0.000	0.000	0.000
31	F	119	THR	0	-0.021	-0.014	24.791	-0.006	-0.006	0.000	0.000	0.000	0.000
32	F	148	CYS	0	-0.131	-0.057	24.032	0.005	0.005	0.000	0.000	0.000	0.000
33	F	121	CYS	0	-0.074	-0.057	17.098	-0.001	-0.001	0.000	0.000	0.000	0.000
34	F	122	TYR	0	0.050	0.043	19.507	-0.005	-0.005	0.000	0.000	0.000	0.000
35	F	123	ILE	0	-0.026	-0.017	15.168	-0.013	-0.013	0.000	0.000	0.000	0.000
36	F	124	MET	0	0.021	0.026	14.974	0.015	0.015	0.000	0.000	0.000	0.000
37	F	125	LYS	1	0.911	0.963	12.337	0.432	0.432	0.000	0.000	0.000	0.000
38	F	126	ILE	0	-0.024	-0.007	8.198	0.043	0.043	0.000	0.000	0.000	0.000
39	F	127	ALA	0	0.041	0.022	11.181	-0.065	-0.065	0.000	0.000	0.000	0.000
40	F	128	PRO	0	0.028	-0.005	8.705	0.001	0.001	0.000	0.000	0.000	0.000
41	F	129	GLU	-1	-0.905	-0.953	9.745	-0.566	-0.566	0.000	0.000	0.000	0.000
42	F	130	SER	0	-0.072	-0.037	11.828	0.080	0.080	0.000	0.000	0.000	0.000
43	F	131	ILE	0	-0.022	0.008	6.286	0.025	0.025	0.000	0.000	0.000	0.000
44	F	132	PRO	0	-0.005	0.020	10.319	0.035	0.035	0.000	0.000	0.000	0.000
45	F	133	SER	0	0.081	0.033	11.296	-0.013	-0.013	0.000	0.000	0.000	0.000
46	F	134	LEU	0	0.096	0.040	12.901	0.005	0.005	0.000	0.000	0.000	0.000
47	F	135	GLU	-1	-0.823	-0.883	14.376	-0.071	-0.071	0.000	0.000	0.000	0.000
48	F	136	ALA	0	-0.005	0.004	15.610	0.011	0.011	0.000	0.000	0.000	0.000
49	F	137	LEU	0	-0.006	0.000	13.165	0.007	0.007	0.000	0.000	0.000	0.000
50	F	138	THR	0	0.023	-0.008	16.473	0.015	0.015	0.000	0.000	0.000	0.000
51	F	139	ARG	1	0.823	0.893	19.433	0.104	0.104	0.000	0.000	0.000	0.000
52	F	140	LYS	1	0.834	0.932	17.740	0.195	0.195	0.000	0.000	0.000	0.000
53	F	141	VAL	0	0.012	-0.017	18.772	0.003	0.003	0.000	0.000	0.000	0.000
54	F	142	HIS	0	0.014	0.020	21.405	0.007	0.007	0.000	0.000	0.000	0.000
55	F	143	ASN	0	-0.005	-0.021	23.896	0.010	0.010	0.000	0.000	0.000	0.000
56	F	144	PHE	0	-0.038	-0.031	22.326	-0.007	-0.007	0.000	0.000	0.000	0.000
57	F	145	GLN	0	-0.035	-0.008	25.039	-0.001	-0.001	0.000	0.000	0.000	0.000
58	F	146	MET	0	-0.072	-0.013	19.276	-0.002	-0.002	0.000	0.000	0.000	0.000
59	F	147	GLU	-1	-0.826	-0.918	24.154	-0.052	-0.052	0.000	0.000	0.000	0.000
60	F	181	LEU	0	0.018	-0.004	14.439	-0.003	-0.003	0.000	0.000	0.000	0.000
61	F	182	GLY	0	0.099	0.056	11.242	-0.058	-0.058	0.000	0.000	0.000	0.000
62	F	183	MET	0	-0.003	0.001	11.980	0.033	0.033	0.000	0.000	0.000	0.000
63	F	184	ALA	0	0.050	0.035	10.102	0.011	0.011	0.000	0.000	0.000	0.000
64	F	185	VAL	0	0.048	0.020	10.800	0.009	0.009	0.000	0.000	0.000	0.000
65	F	186	SER	0	-0.029	-0.034	13.376	0.009	0.009	0.000	0.000	0.000	0.000
66	F	187	THR	0	-0.029	-0.020	15.578	0.017	0.017	0.000	0.000	0.000	0.000
67	F	188	LEU	0	-0.029	-0.003	14.771	0.004	0.004	0.000	0.000	0.000	0.000
68	F	190	GLY	0	0.049	0.040	19.012	-0.004	-0.004	0.000	0.000	0.000	0.000
69	F	191	GLU	-1	-0.968	-1.001	21.588	0.014	0.014	0.000	0.000	0.000	0.000
70	F	192	VAL	0	-0.045	0.002	22.467	0.002	0.002	0.000	0.000	0.000	0.000
71	F	193	PRO	0	0.014	0.014	24.152	-0.006	-0.006	0.000	0.000	0.000	0.000
72	F	194	LEU	0	-0.008	-0.010	19.929	-0.006	-0.006	0.000	0.000	0.000	0.000
73	F	195	TYR	0	-0.004	-0.012	21.732	0.001	0.001	0.000	0.000	0.000	0.000
74	F	196	TYR	0	0.029	0.009	17.943	-0.016	-0.016	0.000	0.000	0.000	0.000
75	F	197	ILE	0	-0.015	-0.010	19.113	-0.002	-0.002	0.000	0.000	0.000	0.000

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