FMO DATABASE

FMODB ID: 5367Z

Calculation Name: 2YAD-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YAD

Chain ID: C

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	81
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-533014.140333
FMO2-HF: Nuclear repulsion	499816.746088
FMO2-HF: Total energy	-33197.394245
FMO2-MP2: Total energy	-33289.914016

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(C:87:HIS)

Summations of interaction energy for fragment #1(C:87:HIS)

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.
-1.585	0.827	0.056	-0.986	-1.482	0.002

Interaction energy analysis for fragmet #1(C:87:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.006 / q_NPA : -0.025

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	C	89	VAL	0	-0.004	0.008	3.455	-0.740	1.655	0.057	-0.985	-1.467	0.002
4	C	90	THR	0	0.024	0.001	5.762	-0.858	-0.841	-0.001	-0.001	-0.015	0.000
5	C	91	THR	0	-0.041	-0.016	9.605	-0.236	-0.236	0.000	0.000	0.000	0.000
6	C	92	ALA	0	0.012	0.009	9.830	0.127	0.127	0.000	0.000	0.000	0.000
7	C	93	THR	0	-0.018	-0.003	11.858	-0.049	-0.049	0.000	0.000	0.000	0.000
8	C	94	PHE	0	-0.019	-0.010	11.134	-0.027	-0.027	0.000	0.000	0.000	0.000
9	C	95	SER	0	0.031	0.015	17.127	0.019	0.019	0.000	0.000	0.000	0.000
10	C	96	ILE	0	-0.022	-0.014	19.857	-0.027	-0.027	0.000	0.000	0.000	0.000
11	C	97	GLY	0	0.017	0.019	22.760	0.011	0.011	0.000	0.000	0.000	0.000
12	C	98	SER	0	-0.023	-0.020	25.764	0.002	0.002	0.000	0.000	0.000	0.000
13	C	99	THR	0	-0.017	-0.019	27.878	0.006	0.006	0.000	0.000	0.000	0.000
14	C	100	GLY	0	0.028	0.038	25.038	0.013	0.013	0.000	0.000	0.000	0.000
15	C	101	LEU	0	-0.030	-0.022	20.721	0.002	0.002	0.000	0.000	0.000	0.000
16	C	102	VAL	0	0.007	-0.003	16.930	-0.004	-0.004	0.000	0.000	0.000	0.000
17	C	103	VAL	0	0.007	0.012	15.512	0.018	0.018	0.000	0.000	0.000	0.000
18	C	104	TYR	0	-0.050	-0.050	12.031	-0.031	-0.031	0.000	0.000	0.000	0.000
19	C	105	ASP	-1	-0.834	-0.942	12.652	0.697	0.697	0.000	0.000	0.000	0.000
20	C	106	TYR	0	-0.008	-0.025	8.762	-0.124	-0.124	0.000	0.000	0.000	0.000
21	C	107	GLN	0	-0.020	0.002	10.086	0.200	0.200	0.000	0.000	0.000	0.000
22	C	108	GLN	0	-0.019	-0.014	11.787	-0.120	-0.120	0.000	0.000	0.000	0.000
23	C	109	LEU	0	-0.011	0.002	12.750	-0.080	-0.080	0.000	0.000	0.000	0.000
24	C	110	LEU	0	-0.035	-0.014	15.139	-0.079	-0.079	0.000	0.000	0.000	0.000
25	C	111	ILE	0	0.014	0.016	15.667	0.039	0.039	0.000	0.000	0.000	0.000
26	C	112	ALA	0	-0.015	0.010	17.824	-0.019	-0.019	0.000	0.000	0.000	0.000
27	C	113	TYR	0	0.016	-0.009	20.180	0.001	0.001	0.000	0.000	0.000	0.000
28	C	114	LYS	1	0.932	0.962	22.599	-0.139	-0.139	0.000	0.000	0.000	0.000
29	C	115	PRO	0	0.030	0.026	25.375	0.000	0.000	0.000	0.000	0.000	0.000
30	C	116	ALA	0	0.065	0.031	27.651	-0.006	-0.006	0.000	0.000	0.000	0.000
31	C	117	PRO	0	-0.031	-0.022	28.968	0.008	0.008	0.000	0.000	0.000	0.000
32	C	118	GLY	0	0.027	0.016	30.179	-0.007	-0.007	0.000	0.000	0.000	0.000
33	C	119	THR	0	0.003	0.001	30.462	-0.005	-0.005	0.000	0.000	0.000	0.000
34	C	120	CYS	0	-0.063	-0.030	30.156	0.004	0.004	0.000	0.000	0.000	0.000
35	C	121	CYS	0	-0.068	-0.053	23.365	-0.021	-0.021	0.000	0.000	0.000	0.000
36	C	122	TYR	0	0.045	0.029	25.235	-0.005	-0.005	0.000	0.000	0.000	0.000
37	C	123	ILE	0	-0.022	-0.010	21.604	0.013	0.013	0.000	0.000	0.000	0.000
38	C	124	MET	0	-0.008	-0.005	20.566	-0.026	-0.026	0.000	0.000	0.000	0.000
39	C	125	LYS	1	0.874	0.934	18.885	-0.145	-0.145	0.000	0.000	0.000	0.000
40	C	126	ILE	0	-0.034	-0.024	13.809	-0.034	-0.034	0.000	0.000	0.000	0.000
41	C	127	ALA	0	0.024	0.017	17.266	0.038	0.038	0.000	0.000	0.000	0.000
42	C	128	PRO	0	0.001	-0.010	13.184	-0.015	-0.015	0.000	0.000	0.000	0.000
43	C	129	GLU	-1	-0.882	-0.946	13.401	-0.172	-0.172	0.000	0.000	0.000	0.000
44	C	130	SER	0	-0.061	-0.027	15.908	-0.059	-0.059	0.000	0.000	0.000	0.000
45	C	131	ILE	0	0.019	0.021	10.499	0.062	0.062	0.000	0.000	0.000	0.000
46	C	132	PRO	0	-0.047	-0.014	14.022	-0.082	-0.082	0.000	0.000	0.000	0.000
47	C	133	SER	0	0.083	0.041	13.895	0.038	0.038	0.000	0.000	0.000	0.000
48	C	134	LEU	0	0.115	0.049	14.821	0.044	0.044	0.000	0.000	0.000	0.000
49	C	135	GLU	-1	-0.912	-0.950	16.575	-0.188	-0.188	0.000	0.000	0.000	0.000
50	C	136	ALA	0	-0.080	-0.043	18.375	0.026	0.026	0.000	0.000	0.000	0.000
51	C	137	LEU	0	-0.017	-0.011	17.652	0.022	0.022	0.000	0.000	0.000	0.000
52	C	138	THR	0	0.034	0.010	20.077	0.030	0.030	0.000	0.000	0.000	0.000
53	C	139	ARG	1	0.969	0.985	21.529	0.204	0.204	0.000	0.000	0.000	0.000
54	C	140	LYS	1	0.914	0.963	20.476	0.124	0.124	0.000	0.000	0.000	0.000
55	C	141	VAL	0	0.020	0.016	23.267	0.009	0.009	0.000	0.000	0.000	0.000
56	C	142	HIS	0	-0.044	-0.021	25.737	-0.001	-0.001	0.000	0.000	0.000	0.000
57	C	143	ASN	0	-0.024	-0.005	28.068	0.003	0.003	0.000	0.000	0.000	0.000
58	C	144	PHE	0	-0.051	-0.025	25.126	0.002	0.002	0.000	0.000	0.000	0.000
59	C	145	GLN	0	0.018	0.011	29.990	0.005	0.005	0.000	0.000	0.000	0.000
60	C	146	MET	0	-0.073	-0.040	25.698	0.005	0.005	0.000	0.000	0.000	0.000
61	C	147	GLU	-1	-0.865	-0.942	29.753	0.016	0.016	0.000	0.000	0.000	0.000
62	C	149	SER	0	0.037	0.017	33.304	0.003	0.003	0.000	0.000	0.000	0.000
63	C	150	LEU	0	-0.041	-0.012	36.479	-0.001	-0.001	0.000	0.000	0.000	0.000
64	C	151	GLN	0	-0.013	-0.011	34.233	0.002	0.002	0.000	0.000	0.000	0.000
65	C	180	PHE	0	0.034	0.020	20.751	-0.014	-0.014	0.000	0.000	0.000	0.000
66	C	181	LEU	0	-0.022	-0.012	21.243	0.023	0.023	0.000	0.000	0.000	0.000
67	C	182	GLY	0	0.083	0.043	17.998	0.011	0.011	0.000	0.000	0.000	0.000
68	C	183	MET	0	0.033	0.022	18.454	-0.043	-0.043	0.000	0.000	0.000	0.000
69	C	184	ALA	0	0.038	0.021	16.580	-0.036	-0.036	0.000	0.000	0.000	0.000
70	C	185	VAL	0	0.041	0.011	17.793	-0.041	-0.041	0.000	0.000	0.000	0.000
71	C	186	SER	0	-0.019	-0.029	20.192	-0.044	-0.044	0.000	0.000	0.000	0.000
72	C	187	THR	0	-0.046	-0.021	21.498	-0.019	-0.019	0.000	0.000	0.000	0.000
73	C	188	LEU	0	-0.037	-0.008	20.673	-0.023	-0.023	0.000	0.000	0.000	0.000
74	C	190	GLY	0	0.038	0.047	25.672	-0.012	-0.012	0.000	0.000	0.000	0.000
75	C	191	GLU	-1	-0.958	-0.987	28.018	0.135	0.135	0.000	0.000	0.000	0.000
76	C	192	VAL	0	-0.055	-0.007	28.589	-0.012	-0.012	0.000	0.000	0.000	0.000
77	C	193	PRO	0	-0.034	-0.013	30.257	0.007	0.007	0.000	0.000	0.000	0.000
78	C	194	LEU	0	0.009	0.003	26.185	0.002	0.002	0.000	0.000	0.000	0.000
79	C	195	TYR	0	0.013	0.018	28.229	-0.007	-0.007	0.000	0.000	0.000	0.000
80	C	196	TYR	0	0.029	0.010	24.440	0.003	0.003	0.000	0.000	0.000	0.000
81	C	197	ILE	0	-0.010	-0.003	24.847	-0.008	-0.008	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:87:HIS)