FMO DATABASE

FMODB ID: 3J77L

Calculation Name: 1Y7Y-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Y7Y

Chain ID: A

ChEMBL ID:

UniProt ID: Q7X0F0

Base Structure: X-ray

Registration Date: 2023-09-22

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	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	69
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-417034.559558
FMO2-HF: Nuclear repulsion	390413.858565
FMO2-HF: Total energy	-26620.700993
FMO2-MP2: Total energy	-26700.921206

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:5:HIS)

Summations of interaction energy for fragment #1(A:5: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.
-29.666	-24.778	12.11	-5.96	-11.037	-0.049

Interaction energy analysis for fragmet #1(A:5:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / q_NPA : 0.000

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	7	HIS	0	-0.005	-0.016	2.623	-12.343	-5.824	3.936	-2.946	-7.509	-0.001
4	A	8	TYR	0	-0.044	-0.022	3.623	-0.207	-0.132	0.042	0.289	-0.407	0.001
5	A	9	ALA	0	0.027	0.017	3.788	0.132	0.351	0.002	-0.039	-0.181	0.000
6	A	10	ASP	-1	-0.815	-0.895	1.816	-29.179	-31.180	8.131	-3.260	-2.869	-0.049
7	A	11	LEU	0	-0.010	-0.007	4.980	1.701	1.777	-0.001	-0.004	-0.071	0.000
8	A	12	VAL	0	-0.025	-0.014	8.151	0.755	0.755	0.000	0.000	0.000	0.000
9	A	13	LYS	1	0.905	0.958	5.327	6.434	6.434	0.000	0.000	0.000	0.000
10	A	14	PHE	0	0.006	0.000	9.020	0.582	0.582	0.000	0.000	0.000	0.000
11	A	15	GLY	0	0.018	0.002	10.886	0.403	0.403	0.000	0.000	0.000	0.000
12	A	16	GLN	0	0.005	-0.014	12.208	0.072	0.072	0.000	0.000	0.000	0.000
13	A	17	ARG	1	0.851	0.928	13.369	1.348	1.348	0.000	0.000	0.000	0.000
14	A	18	LEU	0	0.051	0.028	14.996	0.190	0.190	0.000	0.000	0.000	0.000
15	A	19	ARG	1	0.903	0.953	17.091	0.942	0.942	0.000	0.000	0.000	0.000
16	A	20	GLU	-1	-0.918	-0.947	17.105	-0.975	-0.975	0.000	0.000	0.000	0.000
17	A	21	LEU	0	-0.002	-0.001	17.771	0.095	0.095	0.000	0.000	0.000	0.000
18	A	22	ARG	1	0.768	0.841	21.006	0.802	0.802	0.000	0.000	0.000	0.000
19	A	23	THR	0	-0.129	-0.092	22.380	0.077	0.077	0.000	0.000	0.000	0.000
20	A	24	ALA	0	0.019	0.023	23.761	0.053	0.053	0.000	0.000	0.000	0.000
21	A	25	LYS	1	0.860	0.924	25.339	0.595	0.595	0.000	0.000	0.000	0.000
22	A	26	GLY	0	0.008	0.027	27.456	0.029	0.029	0.000	0.000	0.000	0.000
23	A	27	LEU	0	-0.020	0.016	26.433	0.019	0.019	0.000	0.000	0.000	0.000
24	A	28	SER	0	0.106	0.052	26.825	-0.038	-0.038	0.000	0.000	0.000	0.000
25	A	29	GLN	0	-0.047	-0.059	21.718	0.044	0.044	0.000	0.000	0.000	0.000
26	A	30	GLU	-1	-0.949	-0.964	25.529	-0.425	-0.425	0.000	0.000	0.000	0.000
27	A	31	THR	0	0.021	-0.009	28.616	0.012	0.012	0.000	0.000	0.000	0.000
28	A	32	LEU	0	0.069	0.056	21.886	0.000	0.000	0.000	0.000	0.000	0.000
29	A	33	ALA	0	-0.065	-0.025	25.462	-0.019	-0.019	0.000	0.000	0.000	0.000
30	A	34	PHE	0	0.022	0.010	26.342	0.005	0.005	0.000	0.000	0.000	0.000
31	A	35	LEU	0	0.046	0.025	28.176	0.008	0.008	0.000	0.000	0.000	0.000
32	A	36	SER	0	-0.041	-0.019	24.258	-0.012	-0.012	0.000	0.000	0.000	0.000
33	A	37	GLY	0	-0.023	-0.020	26.301	-0.013	-0.013	0.000	0.000	0.000	0.000
34	A	38	LEU	0	-0.097	-0.033	21.841	-0.016	-0.016	0.000	0.000	0.000	0.000
35	A	39	ASP	-1	-0.782	-0.907	25.081	-0.589	-0.589	0.000	0.000	0.000	0.000
36	A	40	ARG	1	0.984	0.972	24.550	0.461	0.461	0.000	0.000	0.000	0.000
37	A	41	SER	0	-0.003	0.001	23.885	-0.046	-0.046	0.000	0.000	0.000	0.000
38	A	42	TYR	0	-0.013	-0.004	18.399	-0.093	-0.093	0.000	0.000	0.000	0.000
39	A	43	VAL	0	0.062	0.027	19.649	-0.104	-0.104	0.000	0.000	0.000	0.000
40	A	44	GLY	0	-0.018	-0.002	19.319	-0.085	-0.085	0.000	0.000	0.000	0.000
41	A	45	GLY	0	-0.065	-0.059	18.402	-0.051	-0.051	0.000	0.000	0.000	0.000
42	A	46	VAL	0	0.002	0.003	14.584	-0.124	-0.124	0.000	0.000	0.000	0.000
43	A	47	GLU	-1	-0.769	-0.851	14.514	-1.044	-1.044	0.000	0.000	0.000	0.000
44	A	48	ARG	1	0.940	0.982	15.201	0.771	0.771	0.000	0.000	0.000	0.000
45	A	49	GLY	0	0.048	0.034	11.753	-0.018	-0.018	0.000	0.000	0.000	0.000
46	A	50	GLN	0	-0.074	-0.033	11.917	0.010	0.010	0.000	0.000	0.000	0.000
47	A	51	ARG	1	0.863	0.942	14.266	1.061	1.061	0.000	0.000	0.000	0.000
48	A	52	ASN	0	0.054	0.023	11.422	-0.403	-0.403	0.000	0.000	0.000	0.000
49	A	53	VAL	0	-0.021	0.006	13.070	0.209	0.209	0.000	0.000	0.000	0.000
50	A	54	SER	0	0.008	-0.005	14.206	-0.131	-0.131	0.000	0.000	0.000	0.000
51	A	55	LEU	0	0.114	0.057	16.260	0.007	0.007	0.000	0.000	0.000	0.000
52	A	56	VAL	0	0.050	0.019	17.306	0.039	0.039	0.000	0.000	0.000	0.000
53	A	57	ASN	0	0.048	0.000	19.069	0.115	0.115	0.000	0.000	0.000	0.000
54	A	58	ILE	0	0.023	0.020	13.703	0.039	0.039	0.000	0.000	0.000	0.000
55	A	59	LEU	0	-0.006	-0.011	18.083	0.044	0.044	0.000	0.000	0.000	0.000
56	A	60	LYS	1	0.905	0.986	21.285	0.700	0.700	0.000	0.000	0.000	0.000
57	A	61	LEU	0	-0.034	-0.023	18.544	0.048	0.048	0.000	0.000	0.000	0.000
58	A	62	ALA	0	0.016	0.007	20.145	0.030	0.030	0.000	0.000	0.000	0.000
59	A	63	THR	0	0.022	0.001	21.912	0.059	0.059	0.000	0.000	0.000	0.000
60	A	64	ALA	0	-0.044	-0.016	24.968	0.042	0.042	0.000	0.000	0.000	0.000
61	A	65	LEU	0	-0.053	-0.024	21.109	0.026	0.026	0.000	0.000	0.000	0.000
62	A	66	ASP	-1	-0.955	-0.964	25.175	-0.445	-0.445	0.000	0.000	0.000	0.000
63	A	67	ILE	0	-0.057	-0.018	20.136	0.000	0.000	0.000	0.000	0.000	0.000
64	A	68	GLU	-1	-0.805	-0.896	21.947	-0.580	-0.580	0.000	0.000	0.000	0.000
65	A	69	PRO	0	0.034	0.008	18.380	-0.073	-0.073	0.000	0.000	0.000	0.000
66	A	70	ARG	1	0.855	0.906	16.650	0.496	0.496	0.000	0.000	0.000	0.000
67	A	71	GLU	-1	-0.875	-0.939	16.389	-0.790	-0.790	0.000	0.000	0.000	0.000
68	A	72	LEU	0	-0.037	-0.021	14.768	-0.046	-0.046	0.000	0.000	0.000	0.000
69	A	73	PHE	0	-0.046	-0.006	10.322	-0.272	-0.272	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:HIS)