FMO DATABASE

FMODB ID: G57J1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-922798.418654
FMO2-HF: Nuclear repulsion	877286.904983
FMO2-HF: Total energy	-45511.513671
FMO2-MP2: Total energy	-45647.316024

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.
-71.202	-88.375	43.446	-13.028	-13.243	-0.074

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 : 0.878 / q_NPA : 0.910

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	0.027	0.020	3.337	-8.408	-6.003	0.016	-1.156	-1.265	-0.002
4	D	362	ASP	-1	-0.930	-0.948	5.416	-22.502	-22.502	0.000	0.000	0.000	0.000
5	D	363	LEU	0	-0.031	-0.023	9.101	-1.299	-1.299	0.000	0.000	0.000	0.000
6	D	364	LEU	0	-0.017	-0.016	11.424	1.614	1.614	0.000	0.000	0.000	0.000
7	D	365	LEU	0	-0.031	-0.016	14.807	-0.280	-0.280	0.000	0.000	0.000	0.000
8	D	366	ASP	-1	-0.826	-0.914	17.753	-12.933	-12.933	0.000	0.000	0.000	0.000
9	D	367	HIS	0	-0.004	0.013	21.092	-0.323	-0.323	0.000	0.000	0.000	0.000
10	D	368	SER	0	0.063	0.001	24.206	0.547	0.547	0.000	0.000	0.000	0.000
11	D	369	GLY	0	-0.062	-0.020	27.005	0.366	0.366	0.000	0.000	0.000	0.000
12	D	370	ALA	0	-0.036	-0.020	28.663	0.098	0.098	0.000	0.000	0.000	0.000
13	D	371	TYR	0	-0.059	-0.047	26.512	0.182	0.182	0.000	0.000	0.000	0.000
14	D	372	VAL	0	0.042	0.026	29.892	-0.275	-0.275	0.000	0.000	0.000	0.000
15	D	373	ALA	0	-0.004	-0.005	24.894	-0.052	-0.052	0.000	0.000	0.000	0.000
16	D	374	GLN	0	0.048	0.061	25.147	-0.304	-0.304	0.000	0.000	0.000	0.000
17	D	375	TYR	0	0.012	0.002	18.941	-0.271	-0.271	0.000	0.000	0.000	0.000
18	D	376	TYR	0	-0.059	-0.076	19.910	0.318	0.318	0.000	0.000	0.000	0.000
19	D	377	ILE	0	-0.024	-0.010	13.941	-0.690	-0.690	0.000	0.000	0.000	0.000
20	D	378	THR	0	-0.023	-0.010	15.297	0.660	0.660	0.000	0.000	0.000	0.000
21	D	379	TRP	0	0.030	0.008	10.748	-1.488	-1.488	0.000	0.000	0.000	0.000
22	D	380	ASN	0	0.018	0.033	11.595	1.471	1.471	0.000	0.000	0.000	0.000
23	D	381	GLU	-1	-0.826	-0.912	9.973	-23.583	-23.583	0.000	0.000	0.000	0.000
24	D	382	LEU	0	-0.022	-0.010	9.266	1.067	1.067	0.000	0.000	0.000	0.000
25	D	383	SER	0	-0.070	-0.028	10.683	0.095	0.095	0.000	0.000	0.000	0.000
26	D	384	TYR	0	0.032	0.013	11.455	-0.568	-0.568	0.000	0.000	0.000	0.000
27	D	385	ASP	-1	-0.799	-0.895	15.720	-13.722	-13.722	0.000	0.000	0.000	0.000
28	D	386	HIS	0	-0.024	-0.011	19.176	0.087	0.087	0.000	0.000	0.000	0.000
29	D	387	GLN	0	-0.024	-0.018	21.640	0.080	0.080	0.000	0.000	0.000	0.000
30	D	388	GLY	0	-0.027	0.005	18.156	0.031	0.031	0.000	0.000	0.000	0.000
31	D	389	LYS	1	0.916	0.936	18.212	12.952	12.952	0.000	0.000	0.000	0.000
32	D	390	GLU	-1	-0.922	-0.976	13.417	-21.607	-21.607	0.000	0.000	0.000	0.000
33	D	391	VAL	0	-0.005	0.013	15.631	0.802	0.802	0.000	0.000	0.000	0.000
34	D	392	LEU	0	0.007	-0.003	12.169	-1.313	-1.313	0.000	0.000	0.000	0.000
35	D	393	THR	0	-0.003	-0.010	14.433	1.468	1.468	0.000	0.000	0.000	0.000
36	D	394	PRO	0	-0.032	-0.026	14.760	-1.225	-1.225	0.000	0.000	0.000	0.000
37	D	395	LYS	1	0.871	0.938	13.946	18.900	18.900	0.000	0.000	0.000	0.000
38	D	396	ALA	0	0.013	-0.010	16.072	-0.500	-0.500	0.000	0.000	0.000	0.000
39	D	397	TRP	0	0.027	0.022	16.695	0.165	0.165	0.000	0.000	0.000	0.000
40	D	398	ASP	-1	-0.868	-0.939	17.972	-13.736	-13.736	0.000	0.000	0.000	0.000
41	D	399	ARG	1	0.871	0.946	20.949	13.225	13.225	0.000	0.000	0.000	0.000
42	D	400	ASN	0	-0.006	-0.013	18.726	-0.166	-0.166	0.000	0.000	0.000	0.000
43	D	401	GLY	0	-0.005	-0.003	22.314	0.409	0.409	0.000	0.000	0.000	0.000
44	D	402	GLN	0	-0.019	0.011	25.019	0.185	0.185	0.000	0.000	0.000	0.000
45	D	403	ASP	-1	-0.871	-0.925	26.406	-10.525	-10.525	0.000	0.000	0.000	0.000
46	D	404	LEU	0	-0.063	-0.036	23.557	0.067	0.067	0.000	0.000	0.000	0.000
47	D	405	THR	0	-0.018	-0.018	27.643	0.085	0.085	0.000	0.000	0.000	0.000
48	D	406	ALA	0	-0.016	0.041	28.098	-0.199	-0.199	0.000	0.000	0.000	0.000
49	D	407	HIS	0	-0.089	-0.051	24.621	0.745	0.745	0.000	0.000	0.000	0.000
50	D	408	PHE	0	0.039	-0.005	21.169	-0.023	-0.023	0.000	0.000	0.000	0.000
51	D	409	THR	0	-0.013	0.001	20.768	-0.494	-0.494	0.000	0.000	0.000	0.000
52	D	410	THR	0	-0.004	-0.008	17.439	0.537	0.537	0.000	0.000	0.000	0.000
53	D	411	SER	0	-0.026	-0.015	13.936	-1.101	-1.101	0.000	0.000	0.000	0.000
54	D	412	ILE	0	-0.031	-0.006	12.479	0.812	0.812	0.000	0.000	0.000	0.000
55	D	413	PRO	0	0.054	0.042	10.512	-1.843	-1.843	0.000	0.000	0.000	0.000
56	D	414	LEU	0	-0.030	-0.019	7.213	0.470	0.470	0.000	0.000	0.000	0.000
57	D	415	LYS	1	0.944	0.970	5.842	18.897	18.897	0.000	0.000	0.000	0.000
58	D	416	GLY	0	0.091	0.040	2.631	-3.031	-2.709	2.580	-1.667	-1.236	0.007
59	D	417	ASN	0	-0.085	-0.047	3.388	-4.430	-6.165	-0.021	2.275	-0.518	0.000
60	D	418	VAL	0	0.030	0.034	5.559	2.519	2.519	0.000	0.000	0.000	0.000
61	D	419	ARG	1	0.863	0.914	5.047	32.693	32.693	0.000	0.000	0.000	0.000
62	D	420	ASN	0	0.029	-0.005	8.681	1.496	1.496	0.000	0.000	0.000	0.000
63	D	421	LEU	0	0.001	0.016	8.387	2.276	2.276	0.000	0.000	0.000	0.000
64	D	422	SER	0	-0.007	0.004	10.193	0.177	0.177	0.000	0.000	0.000	0.000
65	D	423	VAL	0	-0.005	0.004	12.743	0.645	0.645	0.000	0.000	0.000	0.000
66	D	424	LYS	1	0.903	0.960	15.196	15.374	15.374	0.000	0.000	0.000	0.000
67	D	425	ILE	0	0.029	0.010	18.025	0.129	0.129	0.000	0.000	0.000	0.000
68	D	426	ARG	1	0.941	0.986	21.297	12.459	12.459	0.000	0.000	0.000	0.000
69	D	427	GLU	-1	-0.746	-0.848	24.995	-10.498	-10.498	0.000	0.000	0.000	0.000
70	D	428	CYS	0	-0.061	-0.050	28.158	-0.019	-0.019	0.000	0.000	0.000	0.000
71	D	429	THR	0	-0.003	-0.012	31.239	0.264	0.264	0.000	0.000	0.000	0.000
72	D	430	GLY	0	0.019	0.038	35.030	-0.039	-0.039	0.000	0.000	0.000	0.000
73	D	431	LEU	0	-0.013	-0.021	37.582	-0.049	-0.049	0.000	0.000	0.000	0.000
74	D	432	ALA	0	-0.019	-0.001	38.232	-0.146	-0.146	0.000	0.000	0.000	0.000
75	D	433	TRP	0	-0.006	-0.005	35.524	-0.042	-0.042	0.000	0.000	0.000	0.000
76	D	434	GLU	-1	-0.768	-0.893	30.657	-10.208	-10.208	0.000	0.000	0.000	0.000
77	D	435	TRP	0	-0.078	-0.035	34.038	-0.107	-0.107	0.000	0.000	0.000	0.000
78	D	436	TRP	0	-0.001	0.001	26.713	-0.368	-0.368	0.000	0.000	0.000	0.000
79	D	437	ARG	1	0.738	0.846	28.550	10.215	10.215	0.000	0.000	0.000	0.000
80	D	438	THR	0	-0.037	-0.031	21.996	0.021	0.021	0.000	0.000	0.000	0.000
81	D	439	VAL	0	-0.007	0.008	22.827	0.151	0.151	0.000	0.000	0.000	0.000
82	D	440	TYR	0	-0.049	-0.068	13.740	-0.467	-0.467	0.000	0.000	0.000	0.000
83	D	441	GLU	-1	-0.891	-0.961	17.816	-14.709	-14.709	0.000	0.000	0.000	0.000
84	D	442	LYS	1	0.894	0.965	12.838	18.420	18.420	0.000	0.000	0.000	0.000
85	D	443	THR	0	0.015	-0.003	13.134	-0.276	-0.276	0.000	0.000	0.000	0.000
86	D	444	ASP	-1	-0.928	-0.957	8.486	-31.297	-31.297	0.000	0.000	0.000	0.000
87	D	445	LEU	0	-0.033	-0.018	8.326	-1.828	-1.828	0.000	0.000	0.000	0.000
88	D	446	PRO	0	0.014	0.001	4.097	-3.643	-3.538	-0.001	-0.012	-0.092	0.000
89	D	447	LEU	0	0.026	0.028	2.285	-1.930	1.347	1.955	-1.832	-3.399	-0.007
90	D	448	VAL	0	-0.061	-0.016	1.550	-33.032	-55.328	38.916	-10.433	-6.187	-0.071
91	D	449	ARG	1	0.949	0.969	3.971	33.280	33.562	-0.001	-0.074	-0.207	0.000
92	D	450	LYS	1	0.942	0.979	5.084	24.427	24.414	-0.001	-0.002	0.016	0.000
93	D	451	ARG	1	0.894	0.947	6.890	32.036	32.036	0.000	0.000	0.000	0.000
94	D	452	THR	0	-0.008	-0.006	10.453	1.092	1.092	0.000	0.000	0.000	0.000
95	D	453	ILE	0	-0.004	0.001	13.237	0.193	0.193	0.000	0.000	0.000	0.000
96	D	454	SER	0	0.007	0.008	16.243	0.574	0.574	0.000	0.000	0.000	0.000
97	D	455	ILE	0	-0.016	-0.005	19.918	-0.053	-0.053	0.000	0.000	0.000	0.000
98	D	456	TRP	0	0.046	0.013	21.745	0.286	0.286	0.000	0.000	0.000	0.000
99	D	457	GLY	0	0.047	0.038	26.559	-0.035	-0.035	0.000	0.000	0.000	0.000
100	D	458	THR	0	-0.003	-0.016	29.784	0.190	0.190	0.000	0.000	0.000	0.000
101	D	459	THR	0	0.078	0.023	31.097	-0.114	-0.114	0.000	0.000	0.000	0.000
102	D	460	LEU	0	-0.003	0.018	32.014	-0.133	-0.133	0.000	0.000	0.000	0.000
103	D	461	TYR	0	-0.022	-0.017	31.250	-0.025	-0.025	0.000	0.000	0.000	0.000
104	D	462	PRO	0	0.009	0.035	26.647	-0.069	-0.069	0.000	0.000	0.000	0.000
105	D	463	GLN	0	-0.049	-0.034	25.430	0.166	0.166	0.000	0.000	0.000	0.000
106	D	464	VAL	0	0.018	-0.002	19.071	-0.173	-0.173	0.000	0.000	0.000	0.000
107	D	465	GLU	-1	-0.948	-0.966	17.826	-15.709	-15.709	0.000	0.000	0.000	0.000
108	D	466	ASP	-1	-0.861	-0.909	12.626	-24.199	-24.199	0.000	0.000	0.000	0.000
109	D	467	LYS	1	0.963	0.996	14.032	17.837	17.837	0.000	0.000	0.000	0.000
110	D	468	VAL	0	-0.011	-0.020	7.951	-1.649	-1.649	0.000	0.000	0.000	0.000
111	D	469	GLU	-1	-0.865	-0.938	9.413	-20.534	-20.534	0.000	0.000	0.000	0.000
112	D	470	ASN	0	-0.040	-0.039	3.758	-7.768	-7.288	0.003	-0.127	-0.355	-0.001
113	D	471	ASP	-1	-0.904	-0.932	6.886	-28.447	-28.447	0.000	0.000	0.000	0.000

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