FMO DATABASE

FMODB ID: VQN91

Calculation Name: 1RIY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1RIY

Chain ID: A

ChEMBL ID:

UniProt ID: P36206

Base Structure: X-ray

Registration Date: 2023-09-23

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	71
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-385803.080723
FMO2-HF: Nuclear repulsion	358541.804706
FMO2-HF: Total energy	-27261.276016
FMO2-MP2: Total energy	-27342.735175

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:1:MET)

Summations of interaction energy for fragment #1(A:1:MET)

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.
-19.021	-11.908	12.526	-6.753	-12.888	-0.029

Interaction energy analysis for fragmet #1(A:1:MET)

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 : 0.017

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	3	LYS	1	0.925	0.936	2.750	-2.476	1.216	0.393	-2.138	-1.948	-0.004
4	A	4	LYS	1	0.894	0.931	5.392	0.881	1.044	-0.001	-0.007	-0.154	0.000
5	A	5	GLU	-1	-0.811	-0.900	2.231	-6.530	-4.525	4.925	-2.968	-3.963	-0.027
6	A	6	LEU	0	0.005	-0.001	2.927	1.351	3.719	2.424	-1.613	-3.180	0.000
7	A	7	ILE	0	-0.001	-0.005	3.754	0.664	-0.171	0.033	1.184	-0.382	-0.001
8	A	8	ASP	-1	-0.749	-0.858	6.734	0.767	0.767	0.000	0.000	0.000	0.000
9	A	9	ARG	1	0.853	0.911	2.806	-5.993	-6.273	4.752	-1.211	-3.261	0.003
10	A	10	VAL	0	-0.003	-0.003	5.977	-0.745	-0.745	0.000	0.000	0.000	0.000
11	A	11	ALA	0	-0.011	0.003	8.066	-0.485	-0.485	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.964	0.980	9.904	-1.430	-1.430	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.902	0.947	5.216	-2.879	-2.879	0.000	0.000	0.000	0.000
14	A	14	ALA	0	0.005	-0.001	11.105	-0.170	-0.170	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.024	0.040	13.538	-0.134	-0.134	0.000	0.000	0.000	0.000
16	A	16	ALA	0	-0.006	0.007	14.002	-0.114	-0.114	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.956	0.958	14.562	-0.295	-0.295	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.907	0.925	10.984	-0.770	-0.770	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.933	0.985	13.297	-0.234	-0.234	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.814	-0.910	15.860	0.346	0.346	0.000	0.000	0.000	0.000
21	A	21	VAL	0	0.029	0.024	9.655	-0.010	-0.010	0.000	0.000	0.000	0.000
22	A	22	LYS	1	0.927	0.958	11.654	0.088	0.088	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.001	0.011	12.614	-0.075	-0.075	0.000	0.000	0.000	0.000
24	A	24	ILE	0	0.062	0.041	14.453	-0.053	-0.053	0.000	0.000	0.000	0.000
25	A	25	LEU	0	-0.002	-0.002	8.060	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	26	ASP	-1	-0.810	-0.918	12.242	-0.145	-0.145	0.000	0.000	0.000	0.000
27	A	27	THR	0	0.037	0.015	14.192	-0.079	-0.079	0.000	0.000	0.000	0.000
28	A	28	ILE	0	-0.046	-0.006	13.632	-0.026	-0.026	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.052	-0.035	10.400	-0.065	-0.065	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.864	-0.917	14.922	-0.203	-0.203	0.000	0.000	0.000	0.000
31	A	31	THR	0	0.016	-0.001	18.290	-0.016	-0.016	0.000	0.000	0.000	0.000
32	A	32	ILE	0	-0.055	-0.032	15.127	-0.008	-0.008	0.000	0.000	0.000	0.000
33	A	33	THR	0	-0.030	-0.030	17.247	-0.050	-0.050	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.901	-0.947	19.551	-0.035	-0.035	0.000	0.000	0.000	0.000
35	A	35	ALA	0	-0.004	-0.009	22.078	-0.004	-0.004	0.000	0.000	0.000	0.000
36	A	36	LEU	0	-0.065	-0.030	18.334	-0.012	-0.012	0.000	0.000	0.000	0.000
37	A	37	ALA	0	-0.032	-0.010	22.797	-0.009	-0.009	0.000	0.000	0.000	0.000
38	A	38	LYS	1	0.822	0.908	25.020	0.001	0.001	0.000	0.000	0.000	0.000
39	A	39	GLY	0	-0.103	-0.051	26.281	0.008	0.008	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.811	-0.882	25.318	0.016	0.016	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.855	0.918	23.379	-0.051	-0.051	0.000	0.000	0.000	0.000
42	A	42	ILE	0	0.038	0.027	19.168	0.020	0.020	0.000	0.000	0.000	0.000
43	A	43	GLN	0	-0.021	-0.019	19.981	-0.026	-0.026	0.000	0.000	0.000	0.000
44	A	44	ILE	0	0.053	0.032	15.556	0.013	0.013	0.000	0.000	0.000	0.000
45	A	45	VAL	0	0.055	0.018	17.804	0.002	0.002	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.022	0.010	16.870	0.042	0.042	0.000	0.000	0.000	0.000
47	A	47	PHE	0	-0.042	-0.015	9.968	0.065	0.065	0.000	0.000	0.000	0.000
48	A	48	GLY	0	0.053	0.010	14.862	-0.057	-0.057	0.000	0.000	0.000	0.000
49	A	49	SER	0	-0.067	-0.023	17.126	0.018	0.018	0.000	0.000	0.000	0.000
50	A	50	PHE	0	0.051	0.028	12.996	-0.040	-0.040	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.801	-0.885	18.999	-0.018	-0.018	0.000	0.000	0.000	0.000
52	A	52	VAL	0	0.065	0.041	21.580	-0.032	-0.032	0.000	0.000	0.000	0.000
53	A	53	ARG	1	0.808	0.889	23.889	0.095	0.095	0.000	0.000	0.000	0.000
54	A	54	LYS	1	1.047	1.035	26.009	0.086	0.086	0.000	0.000	0.000	0.000
55	A	74	ARG	1	0.989	0.985	27.534	0.165	0.165	0.000	0.000	0.000	0.000
56	A	75	LYS	1	0.934	0.961	26.353	0.125	0.125	0.000	0.000	0.000	0.000
57	A	76	VAL	0	0.043	0.028	21.501	-0.019	-0.019	0.000	0.000	0.000	0.000
58	A	77	PRO	0	0.050	0.026	18.228	0.040	0.040	0.000	0.000	0.000	0.000
59	A	78	LYS	1	0.955	0.981	18.751	0.122	0.122	0.000	0.000	0.000	0.000
60	A	79	PHE	0	0.045	0.017	13.607	0.033	0.033	0.000	0.000	0.000	0.000
61	A	80	LYS	1	0.804	0.896	17.197	0.020	0.020	0.000	0.000	0.000	0.000
62	A	81	PRO	0	0.057	0.043	14.899	0.047	0.047	0.000	0.000	0.000	0.000
63	A	82	GLY	0	0.047	0.002	16.721	-0.016	-0.016	0.000	0.000	0.000	0.000
64	A	83	LYS	1	0.865	0.919	17.841	-0.094	-0.094	0.000	0.000	0.000	0.000
65	A	84	ALA	0	0.082	0.031	16.769	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	85	LEU	0	-0.010	-0.003	10.809	0.026	0.026	0.000	0.000	0.000	0.000
67	A	86	LYS	1	0.915	0.945	14.354	-0.030	-0.030	0.000	0.000	0.000	0.000
68	A	87	GLU	-1	-0.773	-0.867	16.800	0.069	0.069	0.000	0.000	0.000	0.000
69	A	88	LYS	1	0.921	0.976	9.773	-0.609	-0.609	0.000	0.000	0.000	0.000
70	A	89	VAL	0	-0.031	-0.017	11.015	0.024	0.024	0.000	0.000	0.000	0.000
71	A	90	LYS	1	0.867	0.948	13.658	-0.113	-0.113	0.000	0.000	0.000	0.000

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