FMO DATABASE

FMODB ID: 43M4N

Calculation Name: 3A4C-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3A4C

Chain ID: A

ChEMBL ID:

UniProt ID: Q8R4E9

Base Structure: X-ray

Registration Date: 2023-06-21

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	106
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-829359.881633
FMO2-HF: Nuclear repulsion	786444.498999
FMO2-HF: Total energy	-42915.382634
FMO2-MP2: Total energy	-43038.35844

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:452:ARG)

Summations of interaction energy for fragment #1(A:452: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.
-151.881	-149.704	29.321	-12.2	-19.3	-0.111

Interaction energy analysis for fragmet #1(A:452:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.934 / q_NPA : 0.971

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	454	PRO	0	0.089	0.020	2.831	-9.433	-5.472	0.274	-2.078	-2.157	0.000
4	A	455	GLU	-1	-0.921	-0.952	5.318	-26.702	-26.569	-0.001	-0.005	-0.127	0.000
5	A	456	GLN	0	0.030	-0.003	2.707	-5.073	-2.669	0.812	-1.106	-2.110	-0.012
6	A	457	GLU	-1	-0.812	-0.892	1.706	-110.861	-113.168	17.286	-7.448	-7.532	-0.090
7	A	458	LEU	0	-0.033	-0.009	3.096	4.851	4.414	0.067	0.622	-0.252	-0.001
8	A	459	ARG	1	0.803	0.860	6.420	28.947	28.947	0.000	0.000	0.000	0.000
9	A	460	LEU	0	0.025	0.016	2.456	1.604	1.196	3.116	-0.578	-2.130	-0.003
10	A	461	GLN	0	-0.021	-0.025	5.404	9.455	9.455	0.000	0.000	0.000	0.000
11	A	462	ARG	1	0.897	0.946	7.507	27.330	27.330	0.000	0.000	0.000	0.000
12	A	463	LEU	0	-0.023	-0.019	8.626	2.689	2.689	0.000	0.000	0.000	0.000
13	A	464	GLU	-1	-0.926	-0.958	5.674	-41.446	-41.446	0.000	0.000	0.000	0.000
14	A	465	ARG	1	0.909	0.953	10.097	27.741	27.741	0.000	0.000	0.000	0.000
15	A	466	LEU	0	-0.028	-0.001	13.353	2.034	2.034	0.000	0.000	0.000	0.000
16	A	467	PRO	0	0.015	0.010	14.056	1.674	1.674	0.000	0.000	0.000	0.000
17	A	468	GLU	-1	-0.939	-0.967	16.373	-16.289	-16.289	0.000	0.000	0.000	0.000
18	A	469	LEU	0	0.016	-0.010	16.599	1.126	1.126	0.000	0.000	0.000	0.000
19	A	470	ALA	0	0.018	0.018	19.184	0.971	0.971	0.000	0.000	0.000	0.000
20	A	471	ARG	1	0.961	0.974	21.132	14.442	14.442	0.000	0.000	0.000	0.000
21	A	472	VAL	0	0.001	0.008	22.036	0.768	0.768	0.000	0.000	0.000	0.000
22	A	473	LEU	0	0.036	0.012	23.275	0.674	0.674	0.000	0.000	0.000	0.000
23	A	474	ARG	1	0.891	0.932	25.120	11.729	11.729	0.000	0.000	0.000	0.000
24	A	475	ASN	0	0.005	-0.008	26.896	0.546	0.546	0.000	0.000	0.000	0.000
25	A	476	VAL	0	0.038	0.032	27.653	0.501	0.501	0.000	0.000	0.000	0.000
26	A	477	PHE	0	0.002	-0.016	28.375	0.459	0.459	0.000	0.000	0.000	0.000
27	A	478	VAL	0	-0.091	-0.032	31.190	0.374	0.374	0.000	0.000	0.000	0.000
28	A	479	SER	0	-0.007	0.007	32.866	0.332	0.332	0.000	0.000	0.000	0.000
29	A	480	GLU	-1	-0.813	-0.883	34.244	-8.485	-8.485	0.000	0.000	0.000	0.000
30	A	481	ARG	1	0.967	0.979	35.925	7.516	7.516	0.000	0.000	0.000	0.000
31	A	482	LYS	1	0.867	0.939	37.132	8.603	8.603	0.000	0.000	0.000	0.000
32	A	483	PRO	0	0.032	0.004	35.855	-0.209	-0.209	0.000	0.000	0.000	0.000
33	A	484	ALA	0	-0.017	-0.009	33.044	-0.259	-0.259	0.000	0.000	0.000	0.000
34	A	485	LEU	0	-0.041	-0.005	31.177	0.305	0.305	0.000	0.000	0.000	0.000
35	A	486	THR	0	0.058	0.033	31.028	-0.296	-0.296	0.000	0.000	0.000	0.000
36	A	487	MET	0	0.041	0.001	22.544	-0.060	-0.060	0.000	0.000	0.000	0.000
37	A	488	GLU	-1	-0.905	-0.930	27.113	-10.370	-10.370	0.000	0.000	0.000	0.000
38	A	489	VAL	0	-0.007	-0.004	28.837	-0.078	-0.078	0.000	0.000	0.000	0.000
39	A	490	VAL	0	-0.029	-0.018	25.830	-0.077	-0.077	0.000	0.000	0.000	0.000
40	A	491	CYS	0	-0.020	-0.005	24.125	-0.437	-0.437	0.000	0.000	0.000	0.000
41	A	492	ALA	0	0.030	0.018	25.522	-0.293	-0.293	0.000	0.000	0.000	0.000
42	A	493	ARG	1	0.894	0.928	28.138	9.622	9.622	0.000	0.000	0.000	0.000
43	A	494	MET	0	-0.045	0.002	21.848	0.032	0.032	0.000	0.000	0.000	0.000
44	A	495	VAL	0	-0.035	-0.023	22.128	-0.344	-0.344	0.000	0.000	0.000	0.000
45	A	496	ASP	-1	-0.893	-0.933	24.263	-10.970	-10.970	0.000	0.000	0.000	0.000
46	A	497	SER	0	-0.108	-0.063	26.113	0.402	0.402	0.000	0.000	0.000	0.000
47	A	498	CYS	0	-0.109	-0.048	22.177	-0.335	-0.335	0.000	0.000	0.000	0.000
48	A	499	GLN	0	0.008	-0.002	22.051	0.109	0.109	0.000	0.000	0.000	0.000
49	A	500	THR	0	0.005	0.005	18.578	-0.863	-0.863	0.000	0.000	0.000	0.000
50	A	501	ALA	0	0.011	0.007	16.268	0.515	0.515	0.000	0.000	0.000	0.000
51	A	502	LEU	0	-0.063	-0.019	14.893	-0.255	-0.255	0.000	0.000	0.000	0.000
52	A	503	SER	0	0.033	-0.019	18.788	1.025	1.025	0.000	0.000	0.000	0.000
53	A	504	PRO	0	0.062	0.010	21.037	-0.478	-0.478	0.000	0.000	0.000	0.000
54	A	505	GLY	0	0.043	0.024	21.831	-0.086	-0.086	0.000	0.000	0.000	0.000
55	A	506	GLU	-1	-0.836	-0.893	16.465	-18.118	-18.118	0.000	0.000	0.000	0.000
56	A	507	MET	0	-0.006	0.022	17.490	-1.094	-1.094	0.000	0.000	0.000	0.000
57	A	508	GLU	-1	-0.842	-0.929	19.656	-14.045	-14.045	0.000	0.000	0.000	0.000
58	A	509	LYS	1	0.848	0.914	15.957	15.202	15.202	0.000	0.000	0.000	0.000
59	A	510	HIS	0	0.016	0.000	13.760	-2.047	-2.047	0.000	0.000	0.000	0.000
60	A	511	LEU	0	0.000	-0.020	16.646	-0.047	-0.047	0.000	0.000	0.000	0.000
61	A	512	VAL	0	-0.024	-0.009	18.576	0.409	0.409	0.000	0.000	0.000	0.000
62	A	513	LEU	0	0.009	0.013	12.495	-0.225	-0.225	0.000	0.000	0.000	0.000
63	A	514	LEU	0	-0.003	0.001	16.429	0.066	0.066	0.000	0.000	0.000	0.000
64	A	515	ALA	0	-0.030	-0.024	18.650	0.428	0.428	0.000	0.000	0.000	0.000
65	A	516	GLU	-1	-0.947	-0.970	16.338	-17.343	-17.343	0.000	0.000	0.000	0.000
66	A	517	LEU	0	-0.024	-0.015	13.895	0.065	0.065	0.000	0.000	0.000	0.000
67	A	518	LEU	0	-0.068	-0.038	18.303	0.413	0.413	0.000	0.000	0.000	0.000
68	A	519	PRO	0	0.053	0.036	21.625	0.556	0.556	0.000	0.000	0.000	0.000
69	A	520	ASP	-1	-0.956	-0.972	24.272	-11.545	-11.545	0.000	0.000	0.000	0.000
70	A	521	TRP	0	-0.102	-0.046	22.440	0.242	0.242	0.000	0.000	0.000	0.000
71	A	522	LEU	0	-0.012	-0.010	22.029	0.532	0.532	0.000	0.000	0.000	0.000
72	A	523	SER	0	0.023	0.020	25.322	-0.068	-0.068	0.000	0.000	0.000	0.000
73	A	524	LEU	0	0.021	-0.008	23.298	0.108	0.108	0.000	0.000	0.000	0.000
74	A	525	HIS	0	0.005	-0.004	27.852	-0.058	-0.058	0.000	0.000	0.000	0.000
75	A	526	ARG	1	0.957	0.990	25.992	11.237	11.237	0.000	0.000	0.000	0.000
76	A	527	ILE	0	-0.006	-0.003	32.175	0.282	0.282	0.000	0.000	0.000	0.000
77	A	528	ARG	1	0.954	0.969	35.717	7.553	7.553	0.000	0.000	0.000	0.000
78	A	529	THR	0	0.034	0.013	33.858	-0.081	-0.081	0.000	0.000	0.000	0.000
79	A	530	ASP	-1	-0.848	-0.873	32.581	-9.165	-9.165	0.000	0.000	0.000	0.000
80	A	531	THR	0	-0.024	-0.035	27.214	-0.073	-0.073	0.000	0.000	0.000	0.000
81	A	532	TYR	0	-0.101	-0.071	30.070	-0.125	-0.125	0.000	0.000	0.000	0.000
82	A	533	VAL	0	0.044	0.023	26.611	-0.191	-0.191	0.000	0.000	0.000	0.000
83	A	534	LYS	1	0.960	0.964	29.072	9.680	9.680	0.000	0.000	0.000	0.000
84	A	535	LEU	0	0.000	0.010	26.730	-0.285	-0.285	0.000	0.000	0.000	0.000
85	A	536	ASP	-1	-0.855	-0.920	29.515	-9.364	-9.364	0.000	0.000	0.000	0.000
86	A	537	LYS	1	0.850	0.893	30.833	9.238	9.238	0.000	0.000	0.000	0.000
87	A	538	ALA	0	-0.016	0.013	32.865	0.125	0.125	0.000	0.000	0.000	0.000
88	A	539	VAL	0	-0.033	-0.014	28.355	-0.101	-0.101	0.000	0.000	0.000	0.000
89	A	540	ASP	-1	-0.810	-0.910	29.047	-11.029	-11.029	0.000	0.000	0.000	0.000
90	A	541	LEU	0	-0.004	-0.011	22.974	-0.328	-0.328	0.000	0.000	0.000	0.000
91	A	542	ALA	0	-0.021	0.012	24.033	-0.718	-0.718	0.000	0.000	0.000	0.000
92	A	543	GLY	0	0.039	0.011	23.917	-0.428	-0.428	0.000	0.000	0.000	0.000
93	A	544	LEU	0	-0.023	-0.017	23.017	-0.464	-0.464	0.000	0.000	0.000	0.000
94	A	545	THR	0	-0.028	-0.022	19.161	-0.852	-0.852	0.000	0.000	0.000	0.000
95	A	546	ALA	0	-0.001	0.008	18.951	-0.892	-0.892	0.000	0.000	0.000	0.000
96	A	547	ARG	1	0.952	0.971	19.036	12.138	12.138	0.000	0.000	0.000	0.000
97	A	548	LEU	0	0.010	0.013	15.962	-0.500	-0.500	0.000	0.000	0.000	0.000
98	A	549	ALA	0	0.010	0.002	14.636	-1.253	-1.253	0.000	0.000	0.000	0.000
99	A	550	HIS	0	-0.041	-0.021	14.156	-1.027	-1.027	0.000	0.000	0.000	0.000
100	A	551	HIS	0	0.014	0.003	15.147	-0.978	-0.978	0.000	0.000	0.000	0.000
101	A	552	VAL	0	0.021	0.009	10.144	-0.902	-0.902	0.000	0.000	0.000	0.000
102	A	553	HIS	0	-0.027	-0.015	10.510	-3.179	-3.179	0.000	0.000	0.000	0.000
103	A	554	ALA	0	-0.026	-0.019	10.849	-1.086	-1.086	0.000	0.000	0.000	0.000
104	A	555	GLU	-1	-0.820	-0.866	9.589	-27.419	-27.419	0.000	0.000	0.000	0.000
105	A	556	GLY	0	-0.025	0.007	8.224	-0.786	-0.786	0.000	0.000	0.000	0.000
106	A	557	LEU	0	-0.052	-0.027	1.744	-7.016	-8.185	7.767	-1.607	-4.992	-0.005

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:452:ARG)