FMO DATABASE

FMODB ID: 2NJ9R

Calculation Name: 3C65-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3C65

Chain ID: A

ChEMBL ID:

UniProt ID: Q5KWH6

Base Structure: X-ray

Registration Date: 2023-09-21

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	152
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1471289.041084
FMO2-HF: Nuclear repulsion	1412310.523731
FMO2-HF: Total energy	-58978.517354
FMO2-MP2: Total energy	-59152.915428

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:-4:GLY)

Summations of interaction energy for fragment #1(A:-4:GLY)

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.
-4.845	-0.224	1.994	-2.851	-3.76	-0.011

Interaction energy analysis for fragmet #1(A:-4:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / q_NPA : -0.011

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	A	-2	HIS	0	0.038	0.010	2.990	-1.021	0.422	0.021	-0.582	-0.881	-0.001
4	A	-1	MET	0	0.030	0.019	3.047	0.238	0.837	0.083	-0.154	-0.528	0.000
5	A	369	LEU	0	0.012	0.000	4.111	0.943	1.199	-0.001	-0.104	-0.151	0.000
6	A	370	GLY	0	0.029	0.006	6.015	0.699	0.699	0.000	0.000	0.000	0.000
7	A	371	GLU	-1	-0.943	-0.959	7.723	-0.737	-0.737	0.000	0.000	0.000	0.000
8	A	372	ARG	1	0.856	0.927	8.187	1.196	1.196	0.000	0.000	0.000	0.000
9	A	373	LEU	0	-0.020	-0.014	10.083	0.184	0.184	0.000	0.000	0.000	0.000
10	A	374	GLY	0	-0.005	0.026	11.879	0.119	0.119	0.000	0.000	0.000	0.000
11	A	375	ILE	0	-0.050	-0.025	10.744	0.102	0.102	0.000	0.000	0.000	0.000
12	A	376	PRO	0	-0.003	0.002	11.281	-0.164	-0.164	0.000	0.000	0.000	0.000
13	A	377	ALA	0	0.012	-0.011	6.638	-0.053	-0.053	0.000	0.000	0.000	0.000
14	A	378	PRO	0	-0.031	-0.003	7.337	0.233	0.233	0.000	0.000	0.000	0.000
15	A	379	ARG	1	0.878	0.932	8.446	-0.052	-0.052	0.000	0.000	0.000	0.000
16	A	380	ARG	1	0.801	0.895	10.177	0.017	0.017	0.000	0.000	0.000	0.000
17	A	381	ILE	0	0.001	0.010	7.084	-0.103	-0.103	0.000	0.000	0.000	0.000
18	A	382	GLU	-1	-0.777	-0.857	11.484	0.243	0.243	0.000	0.000	0.000	0.000
19	A	383	ALA	0	0.012	0.007	12.730	-0.058	-0.058	0.000	0.000	0.000	0.000
20	A	384	PHE	0	-0.023	-0.023	14.799	0.039	0.039	0.000	0.000	0.000	0.000
21	A	385	ASP	-1	-0.837	-0.906	17.990	0.071	0.071	0.000	0.000	0.000	0.000
22	A	386	ASN	0	0.039	0.007	19.549	0.019	0.019	0.000	0.000	0.000	0.000
23	A	387	SER	0	0.037	0.014	21.092	-0.013	-0.013	0.000	0.000	0.000	0.000
24	A	388	ASN	0	-0.032	-0.014	23.847	-0.010	-0.010	0.000	0.000	0.000	0.000
25	A	389	ILE	0	-0.039	-0.010	26.045	0.002	0.002	0.000	0.000	0.000	0.000
26	A	390	TYR	0	0.042	0.006	27.590	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	391	GLY	0	-0.019	0.008	30.599	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	392	ALA	0	0.009	-0.010	32.257	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	393	ASP	-1	-0.919	-0.957	31.565	0.065	0.065	0.000	0.000	0.000	0.000
30	A	394	PRO	0	-0.018	0.010	30.411	0.006	0.006	0.000	0.000	0.000	0.000
31	A	395	VAL	0	-0.031	-0.045	25.279	0.003	0.003	0.000	0.000	0.000	0.000
32	A	396	SER	0	-0.010	-0.010	23.084	0.000	0.000	0.000	0.000	0.000	0.000
33	A	397	ALA	0	-0.028	-0.020	20.385	0.008	0.008	0.000	0.000	0.000	0.000
34	A	398	LEU	0	0.005	0.013	17.896	-0.009	-0.009	0.000	0.000	0.000	0.000
35	A	399	VAL	0	-0.017	-0.002	13.613	0.021	0.021	0.000	0.000	0.000	0.000
36	A	400	VAL	0	0.029	0.005	13.970	-0.027	-0.027	0.000	0.000	0.000	0.000
37	A	401	PHE	0	-0.011	-0.023	7.596	0.087	0.087	0.000	0.000	0.000	0.000
38	A	402	LEU	0	0.021	0.012	10.874	-0.116	-0.116	0.000	0.000	0.000	0.000
39	A	403	ASP	-1	-0.845	-0.920	7.786	0.854	0.854	0.000	0.000	0.000	0.000
40	A	404	GLY	0	-0.018	-0.010	4.983	0.751	0.800	-0.001	-0.006	-0.041	0.000
41	A	405	LYS	1	0.855	0.920	5.941	-1.827	-1.770	-0.001	0.000	-0.055	0.000
42	A	406	PRO	0	0.003	0.016	8.976	-0.221	-0.221	0.000	0.000	0.000	0.000
43	A	407	ALA	0	0.036	0.032	12.242	-0.021	-0.021	0.000	0.000	0.000	0.000
44	A	408	LYS	1	0.973	0.967	15.067	-0.545	-0.545	0.000	0.000	0.000	0.000
45	A	409	LYS	1	0.948	0.987	17.730	-0.262	-0.262	0.000	0.000	0.000	0.000
46	A	410	GLU	-1	-0.866	-0.934	17.839	0.232	0.232	0.000	0.000	0.000	0.000
47	A	411	TYR	0	-0.051	-0.021	14.366	0.000	0.000	0.000	0.000	0.000	0.000
48	A	412	ARG	1	0.826	0.907	19.571	-0.188	-0.188	0.000	0.000	0.000	0.000
49	A	413	LYS	1	0.976	1.016	22.208	-0.094	-0.094	0.000	0.000	0.000	0.000
50	A	414	TYR	0	-0.010	-0.012	22.263	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	415	LYS	1	0.924	0.963	26.625	-0.066	-0.066	0.000	0.000	0.000	0.000
52	A	416	VAL	0	0.007	0.011	28.120	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	417	LYS	1	0.939	0.958	30.979	-0.028	-0.028	0.000	0.000	0.000	0.000
54	A	418	THR	0	0.035	0.013	33.388	0.001	0.001	0.000	0.000	0.000	0.000
55	A	419	VAL	0	0.034	0.032	31.217	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	420	ALA	0	0.000	0.004	34.076	0.000	0.000	0.000	0.000	0.000	0.000
57	A	421	GLY	0	-0.001	0.000	36.446	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	422	PRO	0	0.004	-0.014	34.418	0.002	0.002	0.000	0.000	0.000	0.000
59	A	423	ASN	0	0.006	0.010	32.747	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	424	ASP	-1	-0.799	-0.885	27.740	-0.005	-0.005	0.000	0.000	0.000	0.000
61	A	425	TYR	0	0.011	-0.002	27.452	0.002	0.002	0.000	0.000	0.000	0.000
62	A	426	GLU	-1	-0.812	-0.915	28.591	-0.010	-0.010	0.000	0.000	0.000	0.000
63	A	427	THR	0	-0.040	-0.003	27.935	0.005	0.005	0.000	0.000	0.000	0.000
64	A	428	MET	0	-0.010	-0.002	21.656	0.009	0.009	0.000	0.000	0.000	0.000
65	A	429	ARG	1	0.772	0.877	25.523	0.029	0.029	0.000	0.000	0.000	0.000
66	A	430	GLU	-1	-0.905	-0.953	27.644	0.017	0.017	0.000	0.000	0.000	0.000
67	A	431	VAL	0	-0.048	-0.029	23.742	0.007	0.007	0.000	0.000	0.000	0.000
68	A	432	VAL	0	0.018	0.011	22.154	0.010	0.010	0.000	0.000	0.000	0.000
69	A	433	ARG	1	0.794	0.880	24.554	0.010	0.010	0.000	0.000	0.000	0.000
70	A	434	ARG	1	0.857	0.943	27.591	-0.053	-0.053	0.000	0.000	0.000	0.000
71	A	435	ARG	1	0.773	0.875	19.282	-0.124	-0.124	0.000	0.000	0.000	0.000
72	A	436	TYR	0	0.056	-0.036	18.590	0.000	0.000	0.000	0.000	0.000	0.000
73	A	437	THR	0	0.022	0.021	25.025	0.000	0.000	0.000	0.000	0.000	0.000
74	A	438	ARG	1	0.861	0.941	27.457	-0.057	-0.057	0.000	0.000	0.000	0.000
75	A	439	VAL	0	-0.008	-0.006	22.413	0.002	0.002	0.000	0.000	0.000	0.000
76	A	440	LEU	0	0.042	0.024	25.598	0.003	0.003	0.000	0.000	0.000	0.000
77	A	441	LYS	1	0.886	0.953	27.444	-0.034	-0.034	0.000	0.000	0.000	0.000
78	A	442	GLU	-1	-0.981	-1.016	28.071	0.074	0.074	0.000	0.000	0.000	0.000
79	A	443	GLY	0	0.004	0.025	26.997	0.004	0.004	0.000	0.000	0.000	0.000
80	A	444	LEU	0	-0.071	-0.030	23.174	0.010	0.010	0.000	0.000	0.000	0.000
81	A	445	PRO	0	-0.033	-0.034	18.738	-0.010	-0.010	0.000	0.000	0.000	0.000
82	A	446	LEU	0	0.056	0.036	19.755	0.013	0.013	0.000	0.000	0.000	0.000
83	A	447	PRO	0	-0.052	-0.029	15.610	0.021	0.021	0.000	0.000	0.000	0.000
84	A	448	ASP	-1	-0.817	-0.896	12.379	-0.011	-0.011	0.000	0.000	0.000	0.000
85	A	449	LEU	0	-0.032	-0.029	9.574	-0.095	-0.095	0.000	0.000	0.000	0.000
86	A	450	ILE	0	-0.003	0.013	13.365	0.082	0.082	0.000	0.000	0.000	0.000
87	A	451	ILE	0	-0.016	-0.011	9.848	-0.046	-0.046	0.000	0.000	0.000	0.000
88	A	452	ILE	0	0.023	0.012	14.493	0.051	0.051	0.000	0.000	0.000	0.000
89	A	453	ASP	-1	-0.827	-0.898	17.121	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	454	GLY	0	0.056	0.022	18.900	0.009	0.009	0.000	0.000	0.000	0.000
91	A	455	GLY	0	-0.005	-0.002	20.490	-0.016	-0.016	0.000	0.000	0.000	0.000
92	A	456	LYS	1	1.002	0.982	22.742	0.120	0.120	0.000	0.000	0.000	0.000
93	A	457	GLY	0	0.003	0.013	23.927	0.000	0.000	0.000	0.000	0.000	0.000
94	A	458	HIS	0	0.008	-0.029	23.022	-0.005	-0.005	0.000	0.000	0.000	0.000
95	A	459	LEU	0	0.020	0.006	18.486	0.004	0.004	0.000	0.000	0.000	0.000
96	A	460	SER	0	-0.025	0.000	22.454	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	461	ALA	0	0.005	0.002	25.767	0.003	0.003	0.000	0.000	0.000	0.000
98	A	462	VAL	0	0.019	0.001	21.265	0.007	0.007	0.000	0.000	0.000	0.000
99	A	463	ARG	1	0.972	0.990	19.132	0.157	0.157	0.000	0.000	0.000	0.000
100	A	464	ASP	-1	-0.795	-0.874	24.095	-0.039	-0.039	0.000	0.000	0.000	0.000
101	A	465	VAL	0	-0.014	0.000	26.260	0.004	0.004	0.000	0.000	0.000	0.000
102	A	466	LEU	0	-0.041	-0.036	20.687	0.006	0.006	0.000	0.000	0.000	0.000
103	A	467	GLU	-1	-0.904	-0.947	24.842	-0.098	-0.098	0.000	0.000	0.000	0.000
104	A	468	ASN	0	-0.055	-0.040	26.783	0.002	0.002	0.000	0.000	0.000	0.000
105	A	469	GLU	-1	-0.881	-0.902	29.287	-0.008	-0.008	0.000	0.000	0.000	0.000
106	A	470	LEU	0	-0.110	-0.066	25.132	0.007	0.007	0.000	0.000	0.000	0.000
107	A	471	GLY	0	0.008	0.026	27.576	0.003	0.003	0.000	0.000	0.000	0.000
108	A	472	LEU	0	-0.087	-0.052	22.273	0.002	0.002	0.000	0.000	0.000	0.000
109	A	473	ASP	-1	-0.908	-0.950	21.670	-0.115	-0.115	0.000	0.000	0.000	0.000
110	A	474	VAL	0	-0.018	-0.006	16.823	-0.018	-0.018	0.000	0.000	0.000	0.000
111	A	475	PRO	0	-0.016	-0.002	14.305	-0.004	-0.004	0.000	0.000	0.000	0.000
112	A	476	LEU	0	0.005	0.000	15.966	0.025	0.025	0.000	0.000	0.000	0.000
113	A	477	ALA	0	-0.025	-0.019	13.198	-0.033	-0.033	0.000	0.000	0.000	0.000
114	A	478	GLY	0	-0.010	-0.001	15.276	0.048	0.048	0.000	0.000	0.000	0.000
115	A	479	LEU	0	-0.036	-0.028	12.983	-0.032	-0.032	0.000	0.000	0.000	0.000
116	A	488	SER	0	0.000	-0.018	13.710	0.007	0.007	0.000	0.000	0.000	0.000
117	A	489	GLU	-1	-0.933	-0.974	15.520	-0.145	-0.145	0.000	0.000	0.000	0.000
118	A	490	LEU	0	0.031	0.029	10.315	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	491	LEU	0	-0.039	-0.005	14.253	-0.008	-0.008	0.000	0.000	0.000	0.000
120	A	492	ALA	0	0.031	0.002	14.467	-0.011	-0.011	0.000	0.000	0.000	0.000
121	A	493	GLY	0	0.046	0.025	16.593	0.013	0.013	0.000	0.000	0.000	0.000
122	A	494	ASP	-1	-0.929	-0.964	19.221	-0.111	-0.111	0.000	0.000	0.000	0.000
123	A	495	PRO	0	0.022	-0.014	22.765	0.003	0.003	0.000	0.000	0.000	0.000
124	A	496	PRO	0	-0.060	-0.015	20.271	-0.011	-0.011	0.000	0.000	0.000	0.000
125	A	497	ASP	-1	-0.912	-0.961	19.689	-0.141	-0.141	0.000	0.000	0.000	0.000
126	A	498	VAL	0	-0.035	-0.020	17.085	-0.030	-0.030	0.000	0.000	0.000	0.000
127	A	499	VAL	0	-0.013	0.008	12.174	-0.018	-0.018	0.000	0.000	0.000	0.000
128	A	500	PRO	0	-0.023	-0.022	14.321	0.001	0.001	0.000	0.000	0.000	0.000
129	A	501	LEU	0	-0.029	-0.015	8.939	-0.041	-0.041	0.000	0.000	0.000	0.000
130	A	502	ASP	-1	-0.843	-0.925	10.897	-0.144	-0.144	0.000	0.000	0.000	0.000
131	A	503	ARG	1	0.882	0.929	10.465	0.062	0.062	0.000	0.000	0.000	0.000
132	A	504	GLN	0	-0.038	-0.007	10.500	0.099	0.099	0.000	0.000	0.000	0.000
133	A	505	SER	0	0.009	0.026	7.246	-0.042	-0.042	0.000	0.000	0.000	0.000
134	A	506	GLN	0	0.014	-0.025	2.394	-0.118	0.228	0.951	-0.733	-0.564	-0.002
135	A	507	GLU	-1	-0.850	-0.934	3.147	-2.014	-0.872	0.200	-0.740	-0.601	-0.006
136	A	508	PHE	0	0.036	0.022	4.374	0.350	0.336	-0.001	-0.002	0.017	0.000
137	A	509	TYR	0	0.011	-0.002	5.027	0.186	0.186	0.000	0.000	0.000	0.000
138	A	510	LEU	0	-0.092	-0.035	2.451	-0.034	0.458	0.737	-0.435	-0.794	-0.002
139	A	511	LEU	0	0.064	0.027	4.477	0.129	0.161	-0.001	-0.021	-0.010	0.000
140	A	512	GLN	0	-0.004	0.003	7.671	0.021	0.021	0.000	0.000	0.000	0.000
141	A	513	ARG	1	0.941	0.970	3.225	-3.404	-3.185	0.007	-0.074	-0.152	0.000
142	A	514	ILE	0	-0.010	0.001	7.638	-0.023	-0.023	0.000	0.000	0.000	0.000
143	A	515	GLN	0	-0.005	-0.008	10.328	-0.075	-0.075	0.000	0.000	0.000	0.000
144	A	516	ASP	-1	-0.902	-0.949	12.310	0.331	0.331	0.000	0.000	0.000	0.000
145	A	517	GLU	-1	-0.876	-0.931	12.624	0.457	0.457	0.000	0.000	0.000	0.000
146	A	518	VAL	0	0.014	0.017	14.623	-0.028	-0.028	0.000	0.000	0.000	0.000
147	A	519	HIS	0	0.022	0.014	16.694	-0.026	-0.026	0.000	0.000	0.000	0.000
148	A	520	ARG	1	0.843	0.911	13.572	-0.439	-0.439	0.000	0.000	0.000	0.000
149	A	521	PHE	0	-0.045	-0.027	18.645	-0.015	-0.015	0.000	0.000	0.000	0.000
150	A	522	ALA	0	0.040	0.033	20.356	-0.019	-0.019	0.000	0.000	0.000	0.000
151	A	523	VAL	0	-0.045	0.000	22.910	-0.015	-0.015	0.000	0.000	0.000	0.000
152	A	524	MET	0	-0.086	-0.046	23.974	-0.017	-0.017	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-4:GLY)