FMO DATABASE

FMODB ID: NN6KQ

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	OptAll
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	-921783.421661
FMO2-HF: Nuclear repulsion	876271.064196
FMO2-HF: Total energy	-45512.357465
FMO2-MP2: Total energy	-45648.189977

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.
-73.262	-70.115	14.894	-6.621	-11.418	-0.071

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 : 0.888 / q_NPA : 0.927

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	0.011	0.010	3.255	-7.981	-5.658	0.050	-1.151	-1.221	-0.003
4	D	362	ASP	-1	-0.860	-0.903	5.042	-19.680	-19.641	-0.001	-0.003	-0.035	0.000
5	D	363	LEU	0	-0.026	-0.006	8.763	-1.197	-1.197	0.000	0.000	0.000	0.000
6	D	364	LEU	0	0.008	0.009	11.357	1.583	1.583	0.000	0.000	0.000	0.000
7	D	365	LEU	0	-0.038	-0.025	14.513	-0.460	-0.460	0.000	0.000	0.000	0.000
8	D	366	ASP	-1	-0.816	-0.888	17.712	-12.742	-12.742	0.000	0.000	0.000	0.000
9	D	367	HIS	0	-0.001	0.017	21.186	-0.437	-0.437	0.000	0.000	0.000	0.000
10	D	368	SER	0	0.048	-0.021	24.507	0.560	0.560	0.000	0.000	0.000	0.000
11	D	369	GLY	0	-0.054	-0.016	27.164	0.309	0.309	0.000	0.000	0.000	0.000
12	D	370	ALA	0	-0.029	-0.016	28.964	0.105	0.105	0.000	0.000	0.000	0.000
13	D	371	TYR	0	-0.055	-0.065	26.339	0.152	0.152	0.000	0.000	0.000	0.000
14	D	372	VAL	0	0.033	0.033	30.315	-0.225	-0.225	0.000	0.000	0.000	0.000
15	D	373	ALA	0	0.003	-0.002	25.305	-0.047	-0.047	0.000	0.000	0.000	0.000
16	D	374	GLN	0	0.001	0.003	25.228	-0.305	-0.305	0.000	0.000	0.000	0.000
17	D	375	TYR	0	0.037	0.011	18.822	-0.196	-0.196	0.000	0.000	0.000	0.000
18	D	376	TYR	0	-0.049	-0.045	19.915	0.393	0.393	0.000	0.000	0.000	0.000
19	D	377	ILE	0	0.000	0.002	13.970	-0.688	-0.688	0.000	0.000	0.000	0.000
20	D	378	THR	0	0.014	0.006	15.317	0.994	0.994	0.000	0.000	0.000	0.000
21	D	379	TRP	0	-0.017	-0.006	10.944	-1.352	-1.352	0.000	0.000	0.000	0.000
22	D	380	ASN	0	0.000	-0.001	11.893	1.554	1.554	0.000	0.000	0.000	0.000
23	D	381	GLU	-1	-0.802	-0.887	10.433	-23.348	-23.348	0.000	0.000	0.000	0.000
24	D	382	LEU	0	-0.026	-0.001	8.736	1.290	1.290	0.000	0.000	0.000	0.000
25	D	383	SER	0	-0.045	-0.025	10.833	0.099	0.099	0.000	0.000	0.000	0.000
26	D	384	TYR	0	-0.001	-0.039	11.207	-0.480	-0.480	0.000	0.000	0.000	0.000
27	D	385	ASP	-1	-0.803	-0.891	15.928	-12.962	-12.962	0.000	0.000	0.000	0.000
28	D	386	HIS	0	-0.038	-0.023	19.423	-0.058	-0.058	0.000	0.000	0.000	0.000
29	D	387	GLN	0	-0.064	-0.030	21.920	0.583	0.583	0.000	0.000	0.000	0.000
30	D	388	GLY	0	-0.002	0.014	18.557	0.021	0.021	0.000	0.000	0.000	0.000
31	D	389	LYS	1	0.912	0.940	18.224	12.314	12.314	0.000	0.000	0.000	0.000
32	D	390	GLU	-1	-0.843	-0.909	13.951	-21.443	-21.443	0.000	0.000	0.000	0.000
33	D	391	VAL	0	-0.005	0.002	15.840	0.835	0.835	0.000	0.000	0.000	0.000
34	D	392	LEU	0	0.030	0.022	12.242	-1.058	-1.058	0.000	0.000	0.000	0.000
35	D	393	THR	0	0.013	0.015	14.945	1.080	1.080	0.000	0.000	0.000	0.000
36	D	394	PRO	0	0.001	-0.003	15.033	-1.162	-1.162	0.000	0.000	0.000	0.000
37	D	395	LYS	1	0.831	0.915	14.195	18.545	18.545	0.000	0.000	0.000	0.000
38	D	396	ALA	0	0.030	0.006	16.384	-0.420	-0.420	0.000	0.000	0.000	0.000
39	D	397	TRP	0	0.046	0.026	16.630	0.069	0.069	0.000	0.000	0.000	0.000
40	D	398	ASP	-1	-0.898	-0.954	18.151	-14.307	-14.307	0.000	0.000	0.000	0.000
41	D	399	ARG	1	0.853	0.923	21.114	12.935	12.935	0.000	0.000	0.000	0.000
42	D	400	ASN	0	-0.021	-0.014	18.681	-0.154	-0.154	0.000	0.000	0.000	0.000
43	D	401	GLY	0	-0.005	-0.002	22.333	0.416	0.416	0.000	0.000	0.000	0.000
44	D	402	GLN	0	-0.022	-0.003	25.068	0.344	0.344	0.000	0.000	0.000	0.000
45	D	403	ASP	-1	-0.854	-0.917	26.243	-10.582	-10.582	0.000	0.000	0.000	0.000
46	D	404	LEU	0	-0.059	-0.020	23.779	0.016	0.016	0.000	0.000	0.000	0.000
47	D	405	THR	0	0.005	-0.009	27.896	0.138	0.138	0.000	0.000	0.000	0.000
48	D	406	ALA	0	-0.023	0.026	28.254	-0.201	-0.201	0.000	0.000	0.000	0.000
49	D	407	HIS	0	-0.114	-0.063	24.455	0.760	0.760	0.000	0.000	0.000	0.000
50	D	408	PHE	0	0.039	-0.001	21.667	0.067	0.067	0.000	0.000	0.000	0.000
51	D	409	THR	0	-0.007	-0.003	20.553	-0.389	-0.389	0.000	0.000	0.000	0.000
52	D	410	THR	0	-0.033	-0.011	17.769	0.616	0.616	0.000	0.000	0.000	0.000
53	D	411	SER	0	-0.032	-0.048	12.770	-0.403	-0.403	0.000	0.000	0.000	0.000
54	D	412	ILE	0	-0.018	0.004	12.550	0.988	0.988	0.000	0.000	0.000	0.000
55	D	413	PRO	0	0.047	0.040	9.983	-2.024	-2.024	0.000	0.000	0.000	0.000
56	D	414	LEU	0	-0.026	-0.017	6.838	0.351	0.351	0.000	0.000	0.000	0.000
57	D	415	LYS	1	0.898	0.931	5.965	18.768	18.768	0.000	0.000	0.000	0.000
58	D	416	GLY	0	0.056	0.026	2.666	-2.313	-2.158	2.556	-1.471	-1.240	0.006
59	D	417	ASN	0	-0.059	-0.040	3.371	-2.751	-4.559	-0.021	2.384	-0.555	0.000
60	D	418	VAL	0	-0.003	0.014	6.036	1.912	1.912	0.000	0.000	0.000	0.000
61	D	419	ARG	1	0.861	0.912	4.482	32.647	32.783	-0.001	-0.005	-0.130	0.000
62	D	420	ASN	0	0.049	0.012	8.898	1.085	1.085	0.000	0.000	0.000	0.000
63	D	421	LEU	0	-0.022	0.013	7.671	2.383	2.383	0.000	0.000	0.000	0.000
64	D	422	SER	0	-0.028	-0.018	10.290	-0.222	-0.222	0.000	0.000	0.000	0.000
65	D	423	VAL	0	-0.009	0.001	12.689	0.593	0.593	0.000	0.000	0.000	0.000
66	D	424	LYS	1	0.825	0.892	15.315	14.490	14.490	0.000	0.000	0.000	0.000
67	D	425	ILE	0	0.011	0.004	17.614	0.114	0.114	0.000	0.000	0.000	0.000
68	D	426	ARG	1	0.860	0.949	21.234	11.969	11.969	0.000	0.000	0.000	0.000
69	D	427	GLU	-1	-0.737	-0.846	25.020	-10.593	-10.593	0.000	0.000	0.000	0.000
70	D	428	CYS	0	-0.058	-0.048	28.133	-0.053	-0.053	0.000	0.000	0.000	0.000
71	D	429	THR	0	-0.012	-0.016	31.058	0.225	0.225	0.000	0.000	0.000	0.000
72	D	430	GLY	0	0.020	0.017	34.901	-0.011	-0.011	0.000	0.000	0.000	0.000
73	D	431	LEU	0	-0.025	-0.026	37.876	0.084	0.084	0.000	0.000	0.000	0.000
74	D	432	ALA	0	-0.011	0.003	38.424	-0.137	-0.137	0.000	0.000	0.000	0.000
75	D	433	TRP	0	-0.025	-0.001	35.736	0.012	0.012	0.000	0.000	0.000	0.000
76	D	434	GLU	-1	-0.787	-0.885	30.434	-10.215	-10.215	0.000	0.000	0.000	0.000
77	D	435	TRP	0	0.001	0.007	34.187	-0.107	-0.107	0.000	0.000	0.000	0.000
78	D	436	TRP	0	0.034	0.010	26.469	-0.399	-0.399	0.000	0.000	0.000	0.000
79	D	437	ARG	1	0.742	0.845	28.445	10.278	10.278	0.000	0.000	0.000	0.000
80	D	438	THR	0	-0.013	-0.013	22.010	0.054	0.054	0.000	0.000	0.000	0.000
81	D	439	VAL	0	0.000	0.015	22.847	0.132	0.132	0.000	0.000	0.000	0.000
82	D	440	TYR	0	-0.028	-0.059	13.419	-0.282	-0.282	0.000	0.000	0.000	0.000
83	D	441	GLU	-1	-0.801	-0.887	17.880	-14.632	-14.632	0.000	0.000	0.000	0.000
84	D	442	LYS	1	0.850	0.933	13.124	18.140	18.140	0.000	0.000	0.000	0.000
85	D	443	THR	0	0.040	0.009	13.582	0.550	0.550	0.000	0.000	0.000	0.000
86	D	444	ASP	-1	-0.910	-0.957	8.615	-32.208	-32.208	0.000	0.000	0.000	0.000
87	D	445	LEU	0	-0.012	0.005	8.485	-1.758	-1.758	0.000	0.000	0.000	0.000
88	D	446	PRO	0	-0.001	-0.012	4.012	-3.575	-3.461	-0.001	-0.012	-0.100	0.000
89	D	447	LEU	0	0.031	0.030	2.326	-0.414	1.610	0.898	-0.747	-2.176	-0.003
90	D	448	VAL	0	-0.045	-0.025	1.785	-39.155	-40.122	11.396	-5.261	-5.168	-0.069
91	D	449	ARG	1	0.853	0.896	3.721	34.226	34.512	0.000	-0.023	-0.262	0.000
92	D	450	LYS	1	0.821	0.906	4.834	25.353	25.352	-0.001	-0.004	0.006	0.000
93	D	451	ARG	1	0.862	0.922	6.979	30.281	30.281	0.000	0.000	0.000	0.000
94	D	452	THR	0	-0.014	-0.020	10.228	1.250	1.250	0.000	0.000	0.000	0.000
95	D	453	ILE	0	-0.003	0.018	12.829	0.174	0.174	0.000	0.000	0.000	0.000
96	D	454	SER	0	0.017	0.009	16.280	0.220	0.220	0.000	0.000	0.000	0.000
97	D	455	ILE	0	-0.022	-0.006	20.001	-0.005	-0.005	0.000	0.000	0.000	0.000
98	D	456	TRP	0	0.057	0.014	21.850	0.307	0.307	0.000	0.000	0.000	0.000
99	D	457	GLY	0	0.034	0.038	26.595	-0.059	-0.059	0.000	0.000	0.000	0.000
100	D	458	THR	0	-0.022	-0.036	29.800	0.243	0.243	0.000	0.000	0.000	0.000
101	D	459	THR	0	0.068	0.019	31.549	-0.066	-0.066	0.000	0.000	0.000	0.000
102	D	460	LEU	0	-0.034	0.010	32.990	-0.001	-0.001	0.000	0.000	0.000	0.000
103	D	461	TYR	0	-0.026	-0.015	31.378	-0.039	-0.039	0.000	0.000	0.000	0.000
104	D	462	PRO	0	0.022	0.040	26.619	-0.023	-0.023	0.000	0.000	0.000	0.000
105	D	463	GLN	0	-0.031	-0.023	25.367	0.113	0.113	0.000	0.000	0.000	0.000
106	D	464	VAL	0	0.004	-0.004	19.006	-0.128	-0.128	0.000	0.000	0.000	0.000
107	D	465	GLU	-1	-0.918	-0.945	17.474	-16.127	-16.127	0.000	0.000	0.000	0.000
108	D	466	ASP	-1	-0.811	-0.882	12.525	-24.124	-24.124	0.000	0.000	0.000	0.000
109	D	467	LYS	1	0.897	0.954	13.743	18.008	18.008	0.000	0.000	0.000	0.000
110	D	468	VAL	0	-0.008	-0.015	7.854	-1.612	-1.612	0.000	0.000	0.000	0.000
111	D	469	GLU	-1	-0.797	-0.869	8.827	-19.812	-19.812	0.000	0.000	0.000	0.000
112	D	470	ASN	0	-0.016	-0.022	3.448	-10.516	-9.670	0.019	-0.328	-0.537	-0.002
113	D	471	ASP	-1	-0.805	-0.864	6.799	-28.352	-28.352	0.000	0.000	0.000	0.000

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