FMO DATABASE

FMODB ID: 89KRY

Calculation Name: 5CR8-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5CR8

Chain ID: D

ChEMBL ID:

UniProt ID: Q04IN8

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	113
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-922658.039598
FMO2-HF: Nuclear repulsion	877146.00749
FMO2-HF: Total energy	-45512.032108
FMO2-MP2: Total energy	-45647.838692

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(D:359:ARG)

Summations of interaction energy for fragment #1(D:359:ARG)

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.
-77.787	-75.398	16.953	-7.507	-11.833	-0.075

Interaction energy analysis for fragmet #1(D:359:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.870 / q_NPA : 0.916

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	D	361	GLY	0	0.037	0.026	3.201	-8.661	-6.026	0.045	-1.303	-1.376	-0.005
4	D	362	ASP	-1	-0.912	-0.946	5.150	-21.237	-21.215	-0.001	-0.003	-0.019	0.000
5	D	363	LEU	0	-0.044	-0.026	8.846	-1.263	-1.263	0.000	0.000	0.000	0.000
6	D	364	LEU	0	0.005	0.001	11.395	1.529	1.529	0.000	0.000	0.000	0.000
7	D	365	LEU	0	-0.036	-0.020	14.561	-0.260	-0.260	0.000	0.000	0.000	0.000
8	D	366	ASP	-1	-0.838	-0.901	17.804	-12.819	-12.819	0.000	0.000	0.000	0.000
9	D	367	HIS	0	-0.003	0.013	21.056	-0.317	-0.317	0.000	0.000	0.000	0.000
10	D	368	SER	0	0.052	-0.010	24.305	0.548	0.548	0.000	0.000	0.000	0.000
11	D	369	GLY	0	-0.060	-0.015	27.177	0.366	0.366	0.000	0.000	0.000	0.000
12	D	370	ALA	0	-0.039	-0.021	28.830	0.102	0.102	0.000	0.000	0.000	0.000
13	D	371	TYR	0	-0.068	-0.056	26.577	0.199	0.199	0.000	0.000	0.000	0.000
14	D	372	VAL	0	0.037	0.022	29.984	-0.270	-0.270	0.000	0.000	0.000	0.000
15	D	373	ALA	0	-0.006	-0.006	25.008	-0.052	-0.052	0.000	0.000	0.000	0.000
16	D	374	GLN	0	0.013	0.009	25.162	-0.325	-0.325	0.000	0.000	0.000	0.000
17	D	375	TYR	0	0.022	0.001	18.806	-0.230	-0.230	0.000	0.000	0.000	0.000
18	D	376	TYR	0	-0.042	-0.049	19.916	0.381	0.381	0.000	0.000	0.000	0.000
19	D	377	ILE	0	-0.006	-0.008	13.875	-0.670	-0.670	0.000	0.000	0.000	0.000
20	D	378	THR	0	0.034	0.018	15.332	0.928	0.928	0.000	0.000	0.000	0.000
21	D	379	TRP	0	-0.017	-0.010	10.642	-1.404	-1.404	0.000	0.000	0.000	0.000
22	D	380	ASN	0	0.016	0.013	11.508	1.598	1.598	0.000	0.000	0.000	0.000
23	D	381	GLU	-1	-0.797	-0.877	10.094	-23.451	-23.451	0.000	0.000	0.000	0.000
24	D	382	LEU	0	-0.031	-0.012	8.836	1.167	1.167	0.000	0.000	0.000	0.000
25	D	383	SER	0	-0.065	-0.027	10.683	0.119	0.119	0.000	0.000	0.000	0.000
26	D	384	TYR	0	-0.005	-0.022	11.250	-0.301	-0.301	0.000	0.000	0.000	0.000
27	D	385	ASP	-1	-0.785	-0.882	15.707	-13.402	-13.402	0.000	0.000	0.000	0.000
28	D	386	HIS	0	-0.041	-0.029	19.190	-0.038	-0.038	0.000	0.000	0.000	0.000
29	D	387	GLN	0	-0.037	-0.016	21.651	0.724	0.724	0.000	0.000	0.000	0.000
30	D	388	GLY	0	-0.028	0.001	18.142	0.025	0.025	0.000	0.000	0.000	0.000
31	D	389	LYS	1	0.914	0.940	18.222	12.798	12.798	0.000	0.000	0.000	0.000
32	D	390	GLU	-1	-0.860	-0.935	13.489	-22.044	-22.044	0.000	0.000	0.000	0.000
33	D	391	VAL	0	-0.002	0.012	15.528	0.854	0.854	0.000	0.000	0.000	0.000
34	D	392	LEU	0	0.009	0.003	12.538	-1.280	-1.280	0.000	0.000	0.000	0.000
35	D	393	THR	0	0.010	-0.002	14.425	1.460	1.460	0.000	0.000	0.000	0.000
36	D	394	PRO	0	-0.030	-0.022	14.798	-1.260	-1.260	0.000	0.000	0.000	0.000
37	D	395	LYS	1	0.852	0.931	13.979	18.740	18.740	0.000	0.000	0.000	0.000
38	D	396	ALA	0	0.017	-0.004	16.107	-0.483	-0.483	0.000	0.000	0.000	0.000
39	D	397	TRP	0	0.039	0.024	16.566	0.216	0.216	0.000	0.000	0.000	0.000
40	D	398	ASP	-1	-0.890	-0.947	17.946	-14.143	-14.143	0.000	0.000	0.000	0.000
41	D	399	ARG	1	0.869	0.943	20.951	12.963	12.963	0.000	0.000	0.000	0.000
42	D	400	ASN	0	-0.019	-0.017	18.515	-0.116	-0.116	0.000	0.000	0.000	0.000
43	D	401	GLY	0	-0.006	0.000	22.278	0.413	0.413	0.000	0.000	0.000	0.000
44	D	402	GLN	0	-0.028	0.000	24.998	0.293	0.293	0.000	0.000	0.000	0.000
45	D	403	ASP	-1	-0.850	-0.918	26.398	-10.495	-10.495	0.000	0.000	0.000	0.000
46	D	404	LEU	0	-0.059	-0.029	23.554	0.067	0.067	0.000	0.000	0.000	0.000
47	D	405	THR	0	0.014	-0.002	27.664	0.063	0.063	0.000	0.000	0.000	0.000
48	D	406	ALA	0	-0.039	0.029	28.098	-0.190	-0.190	0.000	0.000	0.000	0.000
49	D	407	HIS	0	-0.102	-0.065	24.342	0.768	0.768	0.000	0.000	0.000	0.000
50	D	408	PHE	0	0.032	-0.009	21.454	-0.030	-0.030	0.000	0.000	0.000	0.000
51	D	409	THR	0	0.013	0.007	20.529	-0.437	-0.437	0.000	0.000	0.000	0.000
52	D	410	THR	0	-0.031	-0.016	17.734	0.487	0.487	0.000	0.000	0.000	0.000
53	D	411	SER	0	0.005	0.000	13.105	-0.726	-0.726	0.000	0.000	0.000	0.000
54	D	412	ILE	0	-0.060	-0.014	12.596	0.769	0.769	0.000	0.000	0.000	0.000
55	D	413	PRO	0	0.053	0.039	10.222	-1.872	-1.872	0.000	0.000	0.000	0.000
56	D	414	LEU	0	-0.030	-0.018	7.174	0.501	0.501	0.000	0.000	0.000	0.000
57	D	415	LYS	1	0.889	0.921	5.860	18.666	18.666	0.000	0.000	0.000	0.000
58	D	416	GLY	0	0.095	0.041	2.658	-2.984	-2.700	2.590	-1.657	-1.216	0.007
59	D	417	ASN	0	-0.089	-0.049	3.388	-4.519	-6.237	-0.021	2.277	-0.537	0.000
60	D	418	VAL	0	0.019	0.035	5.596	2.543	2.543	0.000	0.000	0.000	0.000
61	D	419	ARG	1	0.868	0.908	4.524	33.373	33.506	-0.001	-0.004	-0.128	0.000
62	D	420	ASN	0	0.048	0.018	8.852	0.978	0.978	0.000	0.000	0.000	0.000
63	D	421	LEU	0	-0.002	0.013	8.051	2.305	2.305	0.000	0.000	0.000	0.000
64	D	422	SER	0	-0.030	-0.004	10.415	0.139	0.139	0.000	0.000	0.000	0.000
65	D	423	VAL	0	0.006	0.008	12.737	0.599	0.599	0.000	0.000	0.000	0.000
66	D	424	LYS	1	0.799	0.886	15.275	14.835	14.835	0.000	0.000	0.000	0.000
67	D	425	ILE	0	0.029	0.010	17.928	0.136	0.136	0.000	0.000	0.000	0.000
68	D	426	ARG	1	0.899	0.982	21.324	12.163	12.163	0.000	0.000	0.000	0.000
69	D	427	GLU	-1	-0.731	-0.844	25.049	-10.524	-10.524	0.000	0.000	0.000	0.000
70	D	428	CYS	0	-0.067	-0.050	28.204	-0.027	-0.027	0.000	0.000	0.000	0.000
71	D	429	THR	0	-0.011	-0.016	31.272	0.256	0.256	0.000	0.000	0.000	0.000
72	D	430	GLY	0	0.025	0.042	35.063	-0.039	-0.039	0.000	0.000	0.000	0.000
73	D	431	LEU	0	-0.016	-0.024	37.619	-0.046	-0.046	0.000	0.000	0.000	0.000
74	D	432	ALA	0	-0.014	0.005	38.202	-0.144	-0.144	0.000	0.000	0.000	0.000
75	D	433	TRP	0	-0.010	-0.008	35.805	-0.049	-0.049	0.000	0.000	0.000	0.000
76	D	434	GLU	-1	-0.792	-0.883	30.807	-10.144	-10.144	0.000	0.000	0.000	0.000
77	D	435	TRP	0	-0.037	-0.023	34.270	-0.096	-0.096	0.000	0.000	0.000	0.000
78	D	436	TRP	0	0.046	0.014	26.836	-0.411	-0.411	0.000	0.000	0.000	0.000
79	D	437	ARG	1	0.733	0.841	28.813	10.249	10.249	0.000	0.000	0.000	0.000
80	D	438	THR	0	-0.034	-0.027	22.435	0.026	0.026	0.000	0.000	0.000	0.000
81	D	439	VAL	0	-0.004	0.009	23.054	0.153	0.153	0.000	0.000	0.000	0.000
82	D	440	TYR	0	-0.031	-0.066	13.705	-0.354	-0.354	0.000	0.000	0.000	0.000
83	D	441	GLU	-1	-0.819	-0.899	18.112	-14.485	-14.485	0.000	0.000	0.000	0.000
84	D	442	LYS	1	0.894	0.966	13.282	17.942	17.942	0.000	0.000	0.000	0.000
85	D	443	THR	0	0.042	0.009	13.634	0.229	0.229	0.000	0.000	0.000	0.000
86	D	444	ASP	-1	-0.934	-0.964	8.947	-30.761	-30.761	0.000	0.000	0.000	0.000
87	D	445	LEU	0	-0.023	-0.015	8.643	-1.760	-1.760	0.000	0.000	0.000	0.000
88	D	446	PRO	0	0.000	-0.008	4.270	-3.272	-3.186	-0.001	-0.006	-0.079	0.000
89	D	447	LEU	0	0.010	0.016	2.327	-1.026	1.200	1.176	-0.888	-2.514	-0.003
90	D	448	VAL	0	-0.035	-0.011	1.762	-39.727	-41.790	13.163	-5.708	-5.392	-0.073
91	D	449	ARG	1	0.884	0.931	3.922	32.110	32.336	-0.001	-0.029	-0.195	0.000
92	D	450	LYS	1	0.864	0.925	5.045	24.753	24.739	-0.001	-0.003	0.018	0.000
93	D	451	ARG	1	0.878	0.935	7.228	30.797	30.797	0.000	0.000	0.000	0.000
94	D	452	THR	0	-0.033	-0.019	10.437	1.167	1.167	0.000	0.000	0.000	0.000
95	D	453	ILE	0	0.007	0.008	13.115	0.162	0.162	0.000	0.000	0.000	0.000
96	D	454	SER	0	0.030	0.015	16.427	0.247	0.247	0.000	0.000	0.000	0.000
97	D	455	ILE	0	-0.017	-0.008	20.117	-0.045	-0.045	0.000	0.000	0.000	0.000
98	D	456	TRP	0	0.044	0.007	22.049	0.267	0.267	0.000	0.000	0.000	0.000
99	D	457	GLY	0	0.050	0.045	26.731	-0.033	-0.033	0.000	0.000	0.000	0.000
100	D	458	THR	0	-0.012	-0.022	29.937	0.190	0.190	0.000	0.000	0.000	0.000
101	D	459	THR	0	0.082	0.024	31.200	-0.109	-0.109	0.000	0.000	0.000	0.000
102	D	460	LEU	0	-0.005	0.019	32.080	-0.131	-0.131	0.000	0.000	0.000	0.000
103	D	461	TYR	0	-0.031	-0.020	31.322	-0.039	-0.039	0.000	0.000	0.000	0.000
104	D	462	PRO	0	0.001	0.035	26.731	-0.058	-0.058	0.000	0.000	0.000	0.000
105	D	463	GLN	0	-0.027	-0.022	25.540	0.102	0.102	0.000	0.000	0.000	0.000
106	D	464	VAL	0	0.017	-0.005	19.156	-0.179	-0.179	0.000	0.000	0.000	0.000
107	D	465	GLU	-1	-0.944	-0.960	17.959	-15.741	-15.741	0.000	0.000	0.000	0.000
108	D	466	ASP	-1	-0.844	-0.889	12.704	-23.922	-23.922	0.000	0.000	0.000	0.000
109	D	467	LYS	1	0.922	0.961	14.119	18.452	18.452	0.000	0.000	0.000	0.000
110	D	468	VAL	0	-0.010	-0.017	8.145	-1.606	-1.606	0.000	0.000	0.000	0.000
111	D	469	GLU	-1	-0.798	-0.880	9.292	-20.110	-20.110	0.000	0.000	0.000	0.000
112	D	470	ASN	0	-0.008	-0.012	3.699	-9.786	-9.214	0.005	-0.183	-0.395	-0.001
113	D	471	ASP	-1	-0.833	-0.899	6.884	-28.801	-28.801	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:359:ARG)