FMO DATABASE

FMODB ID: 6YNKZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1471551.580719
FMO2-HF: Nuclear repulsion	1412572.269513
FMO2-HF: Total energy	-58979.311206
FMO2-MP2: Total energy	-59153.680436

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.
-4.535	0.0030000000000007	2.081	-2.85	-3.767	-0.012

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 : 0.019 / q_NPA : -0.007

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	0.026	0.004	2.988	-1.052	0.367	0.021	-0.575	-0.865	-0.001
4	A	-1	MET	0	0.016	0.016	3.020	0.189	0.799	0.094	-0.162	-0.542	0.000
5	A	369	LEU	0	0.014	0.001	4.104	0.908	1.172	-0.001	-0.108	-0.154	0.000
6	A	370	GLY	0	0.032	0.010	6.018	0.665	0.665	0.000	0.000	0.000	0.000
7	A	371	GLU	-1	-0.880	-0.917	7.714	-0.759	-0.759	0.000	0.000	0.000	0.000
8	A	372	ARG	1	0.736	0.842	7.878	1.270	1.270	0.000	0.000	0.000	0.000
9	A	373	LEU	0	-0.025	-0.017	9.959	0.177	0.177	0.000	0.000	0.000	0.000
10	A	374	GLY	0	-0.007	0.025	11.885	0.114	0.114	0.000	0.000	0.000	0.000
11	A	375	ILE	0	-0.051	-0.027	10.865	0.098	0.098	0.000	0.000	0.000	0.000
12	A	376	PRO	0	0.005	0.001	11.281	-0.154	-0.154	0.000	0.000	0.000	0.000
13	A	377	ALA	0	0.004	-0.010	6.683	-0.048	-0.048	0.000	0.000	0.000	0.000
14	A	378	PRO	0	-0.016	-0.001	7.277	0.209	0.209	0.000	0.000	0.000	0.000
15	A	379	ARG	1	0.814	0.870	8.485	-0.097	-0.097	0.000	0.000	0.000	0.000
16	A	380	ARG	1	0.778	0.860	10.216	-0.003	-0.003	0.000	0.000	0.000	0.000
17	A	381	ILE	0	0.001	0.008	6.998	-0.101	-0.101	0.000	0.000	0.000	0.000
18	A	382	GLU	-1	-0.773	-0.837	11.484	0.251	0.251	0.000	0.000	0.000	0.000
19	A	383	ALA	0	0.012	0.005	12.715	-0.057	-0.057	0.000	0.000	0.000	0.000
20	A	384	PHE	0	-0.025	-0.026	14.799	0.036	0.036	0.000	0.000	0.000	0.000
21	A	385	ASP	-1	-0.828	-0.891	17.910	0.073	0.073	0.000	0.000	0.000	0.000
22	A	386	ASN	0	0.031	-0.011	19.550	0.019	0.019	0.000	0.000	0.000	0.000
23	A	387	SER	0	0.032	-0.002	21.143	-0.012	-0.012	0.000	0.000	0.000	0.000
24	A	388	ASN	0	-0.067	-0.033	23.849	-0.009	-0.009	0.000	0.000	0.000	0.000
25	A	389	ILE	0	-0.022	0.001	26.045	0.002	0.002	0.000	0.000	0.000	0.000
26	A	390	TYR	0	0.015	-0.007	27.269	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	391	GLY	0	-0.017	0.010	30.589	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	392	ALA	0	0.009	-0.010	32.258	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	393	ASP	-1	-0.875	-0.921	31.872	0.064	0.064	0.000	0.000	0.000	0.000
30	A	394	PRO	0	-0.020	0.007	30.408	0.006	0.006	0.000	0.000	0.000	0.000
31	A	395	VAL	0	-0.034	-0.043	25.234	0.004	0.004	0.000	0.000	0.000	0.000
32	A	396	SER	0	0.001	0.004	23.145	0.001	0.001	0.000	0.000	0.000	0.000
33	A	397	ALA	0	-0.030	-0.021	20.428	0.008	0.008	0.000	0.000	0.000	0.000
34	A	398	LEU	0	0.003	0.015	17.901	-0.008	-0.008	0.000	0.000	0.000	0.000
35	A	399	VAL	0	-0.006	0.000	13.564	0.021	0.021	0.000	0.000	0.000	0.000
36	A	400	VAL	0	0.024	0.004	13.975	-0.025	-0.025	0.000	0.000	0.000	0.000
37	A	401	PHE	0	-0.006	-0.020	7.565	0.069	0.069	0.000	0.000	0.000	0.000
38	A	402	LEU	0	0.020	0.012	10.874	-0.109	-0.109	0.000	0.000	0.000	0.000
39	A	403	ASP	-1	-0.802	-0.867	7.787	0.851	0.851	0.000	0.000	0.000	0.000
40	A	404	GLY	0	-0.011	-0.007	4.983	0.727	0.777	-0.001	-0.007	-0.042	0.000
41	A	405	LYS	1	0.867	0.930	5.941	-1.910	-1.852	-0.001	0.000	-0.056	0.000
42	A	406	PRO	0	0.000	0.016	8.976	-0.219	-0.219	0.000	0.000	0.000	0.000
43	A	407	ALA	0	0.028	0.026	12.242	-0.024	-0.024	0.000	0.000	0.000	0.000
44	A	408	LYS	1	0.905	0.918	15.067	-0.543	-0.543	0.000	0.000	0.000	0.000
45	A	409	LYS	1	0.955	0.991	17.729	-0.271	-0.271	0.000	0.000	0.000	0.000
46	A	410	GLU	-1	-0.859	-0.911	17.883	0.229	0.229	0.000	0.000	0.000	0.000
47	A	411	TYR	0	-0.034	-0.010	14.375	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	412	ARG	1	0.823	0.902	19.571	-0.194	-0.194	0.000	0.000	0.000	0.000
49	A	413	LYS	1	0.948	0.992	22.209	-0.098	-0.098	0.000	0.000	0.000	0.000
50	A	414	TYR	0	0.003	-0.009	22.224	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	415	LYS	1	0.871	0.926	26.626	-0.067	-0.067	0.000	0.000	0.000	0.000
52	A	416	VAL	0	-0.008	0.007	28.141	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	417	LYS	1	0.951	0.966	30.980	-0.030	-0.030	0.000	0.000	0.000	0.000
54	A	418	THR	0	0.035	0.011	33.389	0.001	0.001	0.000	0.000	0.000	0.000
55	A	419	VAL	0	0.028	0.028	31.116	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	420	ALA	0	0.006	0.008	34.078	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	421	GLY	0	0.006	0.003	36.448	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	422	PRO	0	0.002	-0.011	34.422	0.002	0.002	0.000	0.000	0.000	0.000
59	A	423	ASN	0	-0.001	0.001	32.784	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	424	ASP	-1	-0.807	-0.898	27.703	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	425	TYR	0	0.027	0.011	27.596	0.000	0.000	0.000	0.000	0.000	0.000
62	A	426	GLU	-1	-0.798	-0.902	28.592	-0.006	-0.006	0.000	0.000	0.000	0.000
63	A	427	THR	0	-0.049	-0.008	28.104	0.005	0.005	0.000	0.000	0.000	0.000
64	A	428	MET	0	-0.009	0.001	21.604	0.010	0.010	0.000	0.000	0.000	0.000
65	A	429	ARG	1	0.758	0.855	25.510	0.024	0.024	0.000	0.000	0.000	0.000
66	A	430	GLU	-1	-0.883	-0.937	27.645	0.020	0.020	0.000	0.000	0.000	0.000
67	A	431	VAL	0	-0.062	-0.036	23.618	0.007	0.007	0.000	0.000	0.000	0.000
68	A	432	VAL	0	0.011	0.008	22.094	0.010	0.010	0.000	0.000	0.000	0.000
69	A	433	ARG	1	0.796	0.868	24.555	0.005	0.005	0.000	0.000	0.000	0.000
70	A	434	ARG	1	0.841	0.925	27.612	-0.054	-0.054	0.000	0.000	0.000	0.000
71	A	435	ARG	1	0.782	0.873	19.212	-0.134	-0.134	0.000	0.000	0.000	0.000
72	A	436	TYR	0	0.059	-0.028	18.664	0.001	0.001	0.000	0.000	0.000	0.000
73	A	437	THR	0	0.028	0.021	25.026	0.000	0.000	0.000	0.000	0.000	0.000
74	A	438	ARG	1	0.781	0.885	27.509	-0.063	-0.063	0.000	0.000	0.000	0.000
75	A	439	VAL	0	0.001	-0.003	22.329	0.002	0.002	0.000	0.000	0.000	0.000
76	A	440	LEU	0	0.036	0.022	25.578	0.003	0.003	0.000	0.000	0.000	0.000
77	A	441	LYS	1	0.894	0.955	27.444	-0.038	-0.038	0.000	0.000	0.000	0.000
78	A	442	GLU	-1	-0.913	-0.964	28.233	0.075	0.075	0.000	0.000	0.000	0.000
79	A	443	GLY	0	0.000	0.024	27.037	0.004	0.004	0.000	0.000	0.000	0.000
80	A	444	LEU	0	-0.074	-0.031	23.257	0.010	0.010	0.000	0.000	0.000	0.000
81	A	445	PRO	0	-0.028	-0.032	18.788	-0.009	-0.009	0.000	0.000	0.000	0.000
82	A	446	LEU	0	0.053	0.037	19.795	0.012	0.012	0.000	0.000	0.000	0.000
83	A	447	PRO	0	-0.049	-0.033	15.637	0.022	0.022	0.000	0.000	0.000	0.000
84	A	448	ASP	-1	-0.819	-0.891	12.371	0.027	0.027	0.000	0.000	0.000	0.000
85	A	449	LEU	0	-0.036	-0.031	9.446	-0.093	-0.093	0.000	0.000	0.000	0.000
86	A	450	ILE	0	-0.004	0.011	13.366	0.082	0.082	0.000	0.000	0.000	0.000
87	A	451	ILE	0	-0.016	-0.013	9.819	-0.047	-0.047	0.000	0.000	0.000	0.000
88	A	452	ILE	0	0.033	0.016	14.495	0.049	0.049	0.000	0.000	0.000	0.000
89	A	453	ASP	-1	-0.811	-0.885	17.122	0.003	0.003	0.000	0.000	0.000	0.000
90	A	454	GLY	0	0.052	0.017	18.902	0.009	0.009	0.000	0.000	0.000	0.000
91	A	455	GLY	0	-0.008	-0.002	20.492	-0.015	-0.015	0.000	0.000	0.000	0.000
92	A	456	LYS	1	0.871	0.910	22.516	0.129	0.129	0.000	0.000	0.000	0.000
93	A	457	GLY	0	0.018	0.021	23.928	0.000	0.000	0.000	0.000	0.000	0.000
94	A	458	HIS	0	0.017	-0.019	22.971	-0.005	-0.005	0.000	0.000	0.000	0.000
95	A	459	LEU	0	0.020	0.006	18.442	0.004	0.004	0.000	0.000	0.000	0.000
96	A	460	SER	0	-0.020	0.005	22.455	0.002	0.002	0.000	0.000	0.000	0.000
97	A	461	ALA	0	0.004	0.000	25.768	0.003	0.003	0.000	0.000	0.000	0.000
98	A	462	VAL	0	0.025	0.005	21.222	0.007	0.007	0.000	0.000	0.000	0.000
99	A	463	ARG	1	0.864	0.925	19.647	0.136	0.136	0.000	0.000	0.000	0.000
100	A	464	ASP	-1	-0.808	-0.863	24.096	-0.032	-0.032	0.000	0.000	0.000	0.000
101	A	465	VAL	0	-0.032	-0.007	26.286	0.004	0.004	0.000	0.000	0.000	0.000
102	A	466	LEU	0	-0.031	-0.029	20.728	0.006	0.006	0.000	0.000	0.000	0.000
103	A	467	GLU	-1	-0.832	-0.907	23.942	-0.094	-0.094	0.000	0.000	0.000	0.000
104	A	468	ASN	0	-0.060	-0.046	26.783	0.001	0.001	0.000	0.000	0.000	0.000
105	A	469	GLU	-1	-0.869	-0.904	29.283	-0.003	-0.003	0.000	0.000	0.000	0.000
106	A	470	LEU	0	-0.101	-0.061	25.058	0.007	0.007	0.000	0.000	0.000	0.000
107	A	471	GLY	0	0.005	0.024	27.576	0.004	0.004	0.000	0.000	0.000	0.000
108	A	472	LEU	0	-0.085	-0.049	22.230	0.003	0.003	0.000	0.000	0.000	0.000
109	A	473	ASP	-1	-0.907	-0.949	22.167	-0.094	-0.094	0.000	0.000	0.000	0.000
110	A	474	VAL	0	-0.009	-0.009	16.774	-0.016	-0.016	0.000	0.000	0.000	0.000
111	A	475	PRO	0	-0.022	-0.005	14.286	-0.005	-0.005	0.000	0.000	0.000	0.000
112	A	476	LEU	0	0.002	0.000	15.967	0.026	0.026	0.000	0.000	0.000	0.000
113	A	477	ALA	0	-0.024	-0.014	13.181	-0.033	-0.033	0.000	0.000	0.000	0.000
114	A	478	GLY	0	0.008	0.015	15.277	0.046	0.046	0.000	0.000	0.000	0.000
115	A	479	LEU	0	-0.079	-0.056	13.277	-0.033	-0.033	0.000	0.000	0.000	0.000
116	A	488	SER	0	0.009	-0.014	13.798	0.014	0.014	0.000	0.000	0.000	0.000
117	A	489	GLU	-1	-0.939	-0.971	15.522	-0.142	-0.142	0.000	0.000	0.000	0.000
118	A	490	LEU	0	0.040	0.031	10.302	0.005	0.005	0.000	0.000	0.000	0.000
119	A	491	LEU	0	-0.028	0.000	14.254	-0.009	-0.009	0.000	0.000	0.000	0.000
120	A	492	ALA	0	0.038	0.005	14.462	-0.009	-0.009	0.000	0.000	0.000	0.000
121	A	493	GLY	0	0.049	0.026	16.594	0.012	0.012	0.000	0.000	0.000	0.000
122	A	494	ASP	-1	-0.875	-0.932	19.222	-0.101	-0.101	0.000	0.000	0.000	0.000
123	A	495	PRO	0	0.020	-0.014	22.767	0.003	0.003	0.000	0.000	0.000	0.000
124	A	496	PRO	0	-0.028	0.008	20.190	-0.012	-0.012	0.000	0.000	0.000	0.000
125	A	497	ASP	-1	-0.840	-0.938	19.686	-0.123	-0.123	0.000	0.000	0.000	0.000
126	A	498	VAL	0	-0.024	0.001	17.186	-0.027	-0.027	0.000	0.000	0.000	0.000
127	A	499	VAL	0	-0.002	0.013	12.156	-0.015	-0.015	0.000	0.000	0.000	0.000
128	A	500	PRO	0	-0.028	-0.025	14.323	-0.001	-0.001	0.000	0.000	0.000	0.000
129	A	501	LEU	0	-0.017	-0.005	8.650	-0.041	-0.041	0.000	0.000	0.000	0.000
130	A	502	ASP	-1	-0.823	-0.918	10.913	-0.159	-0.159	0.000	0.000	0.000	0.000
131	A	503	ARG	1	0.850	0.925	10.464	0.078	0.078	0.000	0.000	0.000	0.000
132	A	504	GLN	0	-0.036	-0.011	10.510	0.086	0.086	0.000	0.000	0.000	0.000
133	A	505	SER	0	-0.001	0.006	7.216	-0.045	-0.045	0.000	0.000	0.000	0.000
134	A	506	GLN	0	0.028	-0.015	2.371	-0.036	0.213	0.953	-0.684	-0.518	-0.003
135	A	507	GLU	-1	-0.816	-0.905	3.149	-2.033	-0.891	0.200	-0.727	-0.614	-0.006
136	A	508	PHE	0	0.047	0.025	4.375	0.323	0.317	-0.001	-0.002	0.008	0.000
137	A	509	TYR	0	0.014	0.001	5.125	0.184	0.184	0.000	0.000	0.000	0.000
138	A	510	LEU	0	-0.083	-0.036	2.415	-0.089	0.430	0.809	-0.500	-0.828	-0.002
139	A	511	LEU	0	0.059	0.027	4.478	0.123	0.162	-0.001	-0.023	-0.015	0.000
140	A	512	GLN	0	0.017	0.011	7.672	0.035	0.035	0.000	0.000	0.000	0.000
141	A	513	ARG	1	0.929	0.971	3.211	-2.880	-2.686	0.009	-0.062	-0.141	0.000
142	A	514	ILE	0	-0.006	-0.001	7.552	-0.019	-0.019	0.000	0.000	0.000	0.000
143	A	515	GLN	0	0.019	0.003	10.328	-0.066	-0.066	0.000	0.000	0.000	0.000
144	A	516	ASP	-1	-0.863	-0.924	12.297	0.333	0.333	0.000	0.000	0.000	0.000
145	A	517	GLU	-1	-0.848	-0.895	12.434	0.459	0.459	0.000	0.000	0.000	0.000
146	A	518	VAL	0	0.010	0.015	14.623	-0.025	-0.025	0.000	0.000	0.000	0.000
147	A	519	HIS	0	0.021	0.012	16.692	-0.025	-0.025	0.000	0.000	0.000	0.000
148	A	520	ARG	1	0.784	0.878	13.062	-0.426	-0.426	0.000	0.000	0.000	0.000
149	A	521	PHE	0	-0.027	-0.018	18.663	-0.012	-0.012	0.000	0.000	0.000	0.000
150	A	522	ALA	0	0.054	0.041	20.357	-0.018	-0.018	0.000	0.000	0.000	0.000
151	A	523	VAL	0	-0.014	0.025	22.911	-0.016	-0.016	0.000	0.000	0.000	0.000
152	A	524	MET	0	-0.100	-0.058	24.159	-0.023	-0.023	0.000	0.000	0.000	0.000

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