FMO DATABASE

FMODB ID: YV142

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

Total energy (hartree)

FMO2-HF: Electronic energy	-385537.885151
FMO2-HF: Nuclear repulsion	358277.074026
FMO2-HF: Total energy	-27260.811125
FMO2-MP2: Total energy	-27342.257494

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.
-12.565	-8.061	15.175	-6.285	-13.392	-0.041

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 : -0.030 / q_NPA : -0.008

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	0.932	0.940	2.601	-2.608	-0.222	0.793	-1.495	-1.684	-0.009
4	A	4	LYS	1	0.865	0.918	5.120	0.859	1.030	-0.001	-0.006	-0.164	0.000
5	A	5	GLU	-1	-0.808	-0.909	2.266	-6.350	-4.217	5.390	-3.492	-4.030	-0.036
6	A	6	LEU	0	-0.003	-0.005	2.731	1.021	3.163	2.830	-1.664	-3.308	0.001
7	A	7	ILE	0	-0.010	-0.011	3.761	0.850	-0.401	0.043	1.610	-0.402	-0.001
8	A	8	ASP	-1	-0.798	-0.888	6.480	0.316	0.316	0.000	0.000	0.000	0.000
9	A	9	ARG	1	0.884	0.932	1.883	-2.373	-3.450	6.120	-1.238	-3.804	0.004
10	A	10	VAL	0	0.000	0.002	6.011	-0.499	-0.499	0.000	0.000	0.000	0.000
11	A	11	ALA	0	-0.001	0.003	8.036	-0.366	-0.366	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.957	0.980	9.375	-0.719	-0.719	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.895	0.938	4.940	-1.682	-1.682	0.000	0.000	0.000	0.000
14	A	14	ALA	0	0.007	0.002	10.686	-0.109	-0.109	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.020	0.039	13.148	-0.087	-0.087	0.000	0.000	0.000	0.000
16	A	16	ALA	0	0.005	0.011	14.137	-0.067	-0.067	0.000	0.000	0.000	0.000
17	A	17	LYS	1	1.003	0.993	14.754	-0.168	-0.168	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.983	0.971	11.116	-0.300	-0.300	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.949	0.988	13.345	-0.115	-0.115	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.831	-0.922	15.906	0.232	0.232	0.000	0.000	0.000	0.000
21	A	21	VAL	0	-0.006	0.004	9.718	0.009	0.009	0.000	0.000	0.000	0.000
22	A	22	LYS	1	0.913	0.953	11.499	0.068	0.068	0.000	0.000	0.000	0.000
23	A	23	LEU	0	0.014	0.023	12.490	-0.047	-0.047	0.000	0.000	0.000	0.000
24	A	24	ILE	0	0.070	0.034	14.318	-0.031	-0.031	0.000	0.000	0.000	0.000
25	A	25	LEU	0	-0.012	-0.005	7.830	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	26	ASP	-1	-0.828	-0.924	12.120	-0.126	-0.126	0.000	0.000	0.000	0.000
27	A	27	THR	0	0.017	0.002	13.825	-0.052	-0.052	0.000	0.000	0.000	0.000
28	A	28	ILE	0	-0.046	-0.006	13.097	-0.013	-0.013	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.063	-0.046	9.995	-0.049	-0.049	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.874	-0.922	14.405	-0.101	-0.101	0.000	0.000	0.000	0.000
31	A	31	THR	0	0.021	0.005	17.793	-0.011	-0.011	0.000	0.000	0.000	0.000
32	A	32	ILE	0	-0.055	-0.029	14.692	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	33	THR	0	-0.029	-0.017	16.566	-0.035	-0.035	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.904	-0.955	19.064	-0.003	-0.003	0.000	0.000	0.000	0.000
35	A	35	ALA	0	0.025	0.010	21.788	-0.004	-0.004	0.000	0.000	0.000	0.000
36	A	36	LEU	0	-0.067	-0.032	18.380	-0.010	-0.010	0.000	0.000	0.000	0.000
37	A	37	ALA	0	-0.032	-0.010	22.708	-0.006	-0.006	0.000	0.000	0.000	0.000
38	A	38	LYS	1	0.936	0.977	24.766	-0.012	-0.012	0.000	0.000	0.000	0.000
39	A	39	GLY	0	-0.115	-0.059	26.194	0.004	0.004	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.910	-0.943	25.164	0.023	0.023	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.830	0.909	23.297	-0.030	-0.030	0.000	0.000	0.000	0.000
42	A	42	ILE	0	0.045	0.028	18.554	0.013	0.013	0.000	0.000	0.000	0.000
43	A	43	GLN	0	-0.007	-0.012	19.820	-0.014	-0.014	0.000	0.000	0.000	0.000
44	A	44	ILE	0	0.049	0.028	15.156	0.009	0.009	0.000	0.000	0.000	0.000
45	A	45	VAL	0	0.056	0.020	18.051	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.015	0.005	17.207	0.032	0.032	0.000	0.000	0.000	0.000
47	A	47	PHE	0	-0.041	-0.012	10.190	0.036	0.036	0.000	0.000	0.000	0.000
48	A	48	GLY	0	0.051	0.007	15.266	-0.054	-0.054	0.000	0.000	0.000	0.000
49	A	49	SER	0	-0.073	-0.024	17.386	0.018	0.018	0.000	0.000	0.000	0.000
50	A	50	PHE	0	0.059	0.027	13.050	-0.034	-0.034	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.853	-0.929	18.999	-0.008	-0.008	0.000	0.000	0.000	0.000
52	A	52	VAL	0	0.061	0.043	21.561	-0.021	-0.021	0.000	0.000	0.000	0.000
53	A	53	ARG	1	0.806	0.891	23.872	0.059	0.059	0.000	0.000	0.000	0.000
54	A	54	LYS	1	1.044	1.030	25.972	0.046	0.046	0.000	0.000	0.000	0.000
55	A	74	ARG	1	0.993	0.987	27.490	0.086	0.086	0.000	0.000	0.000	0.000
56	A	75	LYS	1	0.938	0.964	26.292	0.060	0.060	0.000	0.000	0.000	0.000
57	A	76	VAL	0	0.032	0.022	21.566	-0.009	-0.009	0.000	0.000	0.000	0.000
58	A	77	PRO	0	0.061	0.038	18.181	0.022	0.022	0.000	0.000	0.000	0.000
59	A	78	LYS	1	0.973	0.982	18.713	0.081	0.081	0.000	0.000	0.000	0.000
60	A	79	PHE	0	0.039	0.015	13.779	0.020	0.020	0.000	0.000	0.000	0.000
61	A	80	LYS	1	0.830	0.926	17.161	0.017	0.017	0.000	0.000	0.000	0.000
62	A	81	PRO	0	0.043	0.036	15.362	0.036	0.036	0.000	0.000	0.000	0.000
63	A	82	GLY	0	0.032	-0.010	17.024	-0.008	-0.008	0.000	0.000	0.000	0.000
64	A	83	LYS	1	0.866	0.922	18.116	-0.012	-0.012	0.000	0.000	0.000	0.000
65	A	84	ALA	0	0.082	0.029	17.200	-0.011	-0.011	0.000	0.000	0.000	0.000
66	A	85	LEU	0	0.001	0.005	11.066	0.004	0.004	0.000	0.000	0.000	0.000
67	A	86	LYS	1	0.957	0.964	14.583	0.009	0.009	0.000	0.000	0.000	0.000
68	A	87	GLU	-1	-0.773	-0.860	17.063	-0.044	-0.044	0.000	0.000	0.000	0.000
69	A	88	LYS	1	0.920	0.974	9.916	-0.316	-0.316	0.000	0.000	0.000	0.000
70	A	89	VAL	0	-0.036	-0.022	11.399	-0.016	-0.016	0.000	0.000	0.000	0.000
71	A	90	LYS	1	0.863	0.947	13.845	0.036	0.036	0.000	0.000	0.000	0.000

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