FMO DATABASE

FMODB ID: 53LKZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-831933.536571
FMO2-HF: Nuclear repulsion	789017.880845
FMO2-HF: Total energy	-42915.655726
FMO2-MP2: Total energy	-43038.624013

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.
-153.802	-152.118	29.699	-12.212	-19.17	-0.115

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 : 0.938 / q_NPA : 0.970

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	0.065	0.007	2.811	-9.048	-5.693	0.315	-1.775	-1.894	-0.004
4	A	455	GLU	-1	-0.916	-0.955	5.125	-25.591	-25.453	-0.001	-0.006	-0.131	0.000
5	A	456	GLN	0	0.027	-0.010	2.682	-5.717	-2.712	1.126	-1.543	-2.587	-0.017
6	A	457	GLU	-1	-0.802	-0.878	1.681	-110.514	-114.652	20.573	-8.276	-8.159	-0.092
7	A	458	LEU	0	-0.037	-0.010	2.950	5.308	4.363	0.108	1.120	-0.284	-0.001
8	A	459	ARG	1	0.753	0.843	6.447	27.813	27.813	0.000	0.000	0.000	0.000
9	A	460	LEU	0	0.023	0.016	2.549	1.493	1.495	2.465	-0.515	-1.952	-0.002
10	A	461	GLN	0	-0.017	-0.032	5.150	10.398	10.398	0.000	0.000	0.000	0.000
11	A	462	ARG	1	0.880	0.944	7.232	28.016	28.016	0.000	0.000	0.000	0.000
12	A	463	LEU	0	0.003	-0.007	8.802	2.789	2.789	0.000	0.000	0.000	0.000
13	A	464	GLU	-1	-0.918	-0.968	5.340	-43.411	-43.411	0.000	0.000	0.000	0.000
14	A	465	ARG	1	0.920	0.968	9.901	29.071	29.071	0.000	0.000	0.000	0.000
15	A	466	LEU	0	-0.019	0.004	13.024	2.140	2.140	0.000	0.000	0.000	0.000
16	A	467	PRO	0	-0.013	-0.008	13.948	1.675	1.675	0.000	0.000	0.000	0.000
17	A	468	GLU	-1	-0.948	-0.959	16.147	-16.422	-16.422	0.000	0.000	0.000	0.000
18	A	469	LEU	0	0.010	-0.008	16.325	1.149	1.149	0.000	0.000	0.000	0.000
19	A	470	ALA	0	0.045	0.018	19.040	0.957	0.957	0.000	0.000	0.000	0.000
20	A	471	ARG	1	0.939	0.969	20.933	14.769	14.769	0.000	0.000	0.000	0.000
21	A	472	VAL	0	0.010	0.009	21.725	0.785	0.785	0.000	0.000	0.000	0.000
22	A	473	LEU	0	0.030	0.015	22.877	0.693	0.693	0.000	0.000	0.000	0.000
23	A	474	ARG	1	0.917	0.944	24.841	11.691	11.691	0.000	0.000	0.000	0.000
24	A	475	ASN	0	0.009	-0.001	26.638	0.627	0.627	0.000	0.000	0.000	0.000
25	A	476	VAL	0	0.020	0.015	27.172	0.540	0.540	0.000	0.000	0.000	0.000
26	A	477	PHE	0	0.002	-0.011	28.228	0.446	0.446	0.000	0.000	0.000	0.000
27	A	478	VAL	0	-0.071	-0.020	30.943	0.360	0.360	0.000	0.000	0.000	0.000
28	A	479	SER	0	-0.032	-0.011	32.389	0.354	0.354	0.000	0.000	0.000	0.000
29	A	480	GLU	-1	-0.791	-0.886	33.906	-8.602	-8.602	0.000	0.000	0.000	0.000
30	A	481	ARG	1	0.968	0.982	35.670	7.509	7.509	0.000	0.000	0.000	0.000
31	A	482	LYS	1	0.868	0.945	36.659	8.797	8.797	0.000	0.000	0.000	0.000
32	A	483	PRO	0	0.016	-0.005	35.709	-0.214	-0.214	0.000	0.000	0.000	0.000
33	A	484	ALA	0	-0.010	-0.003	32.882	-0.273	-0.273	0.000	0.000	0.000	0.000
34	A	485	LEU	0	-0.043	-0.011	30.999	0.327	0.327	0.000	0.000	0.000	0.000
35	A	486	THR	0	0.056	0.031	31.032	-0.261	-0.261	0.000	0.000	0.000	0.000
36	A	487	MET	0	0.026	-0.004	22.401	-0.061	-0.061	0.000	0.000	0.000	0.000
37	A	488	GLU	-1	-0.906	-0.930	26.789	-10.491	-10.491	0.000	0.000	0.000	0.000
38	A	489	VAL	0	0.006	0.003	28.402	-0.094	-0.094	0.000	0.000	0.000	0.000
39	A	490	VAL	0	-0.034	-0.018	25.584	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	491	CYS	0	-0.032	-0.012	23.827	-0.401	-0.401	0.000	0.000	0.000	0.000
41	A	492	ALA	0	0.020	0.015	25.038	-0.302	-0.302	0.000	0.000	0.000	0.000
42	A	493	ARG	1	0.916	0.944	27.326	9.571	9.571	0.000	0.000	0.000	0.000
43	A	494	MET	0	-0.046	-0.005	21.502	0.061	0.061	0.000	0.000	0.000	0.000
44	A	495	VAL	0	-0.021	-0.013	21.823	-0.389	-0.389	0.000	0.000	0.000	0.000
45	A	496	ASP	-1	-0.898	-0.941	24.050	-10.943	-10.943	0.000	0.000	0.000	0.000
46	A	497	SER	0	-0.102	-0.060	25.850	0.350	0.350	0.000	0.000	0.000	0.000
47	A	498	CYS	0	-0.103	-0.052	21.655	-0.411	-0.411	0.000	0.000	0.000	0.000
48	A	499	GLN	0	0.014	0.017	21.722	0.103	0.103	0.000	0.000	0.000	0.000
49	A	500	THR	0	-0.002	-0.003	18.348	-1.040	-1.040	0.000	0.000	0.000	0.000
50	A	501	ALA	0	0.017	0.004	16.147	0.573	0.573	0.000	0.000	0.000	0.000
51	A	502	LEU	0	-0.071	-0.018	14.345	-0.088	-0.088	0.000	0.000	0.000	0.000
52	A	503	SER	0	0.029	-0.021	18.242	1.105	1.105	0.000	0.000	0.000	0.000
53	A	504	PRO	0	0.038	-0.003	20.655	-0.501	-0.501	0.000	0.000	0.000	0.000
54	A	505	GLY	0	0.042	0.020	21.710	-0.029	-0.029	0.000	0.000	0.000	0.000
55	A	506	GLU	-1	-0.821	-0.885	15.955	-18.603	-18.603	0.000	0.000	0.000	0.000
56	A	507	MET	0	-0.002	0.027	17.430	-0.997	-0.997	0.000	0.000	0.000	0.000
57	A	508	GLU	-1	-0.790	-0.898	19.501	-14.597	-14.597	0.000	0.000	0.000	0.000
58	A	509	LYS	1	0.814	0.888	16.181	15.099	15.099	0.000	0.000	0.000	0.000
59	A	510	HIS	0	-0.004	-0.009	13.667	-2.185	-2.185	0.000	0.000	0.000	0.000
60	A	511	LEU	0	0.000	-0.016	16.347	0.004	0.004	0.000	0.000	0.000	0.000
61	A	512	VAL	0	-0.032	-0.012	18.111	0.385	0.385	0.000	0.000	0.000	0.000
62	A	513	LEU	0	0.022	0.014	12.213	-0.065	-0.065	0.000	0.000	0.000	0.000
63	A	514	LEU	0	-0.006	-0.003	16.047	-0.020	-0.020	0.000	0.000	0.000	0.000
64	A	515	ALA	0	-0.022	-0.018	18.322	0.484	0.484	0.000	0.000	0.000	0.000
65	A	516	GLU	-1	-0.896	-0.945	15.283	-18.862	-18.862	0.000	0.000	0.000	0.000
66	A	517	LEU	0	-0.017	-0.001	14.031	0.228	0.228	0.000	0.000	0.000	0.000
67	A	518	LEU	0	-0.047	-0.020	18.444	0.453	0.453	0.000	0.000	0.000	0.000
68	A	519	PRO	0	0.054	0.038	21.735	0.582	0.582	0.000	0.000	0.000	0.000
69	A	520	ASP	-1	-0.908	-0.944	24.438	-12.148	-12.148	0.000	0.000	0.000	0.000
70	A	521	TRP	0	-0.024	-0.022	22.392	0.081	0.081	0.000	0.000	0.000	0.000
71	A	522	LEU	0	-0.010	-0.002	21.664	0.523	0.523	0.000	0.000	0.000	0.000
72	A	523	SER	0	-0.003	0.007	25.144	-0.050	-0.050	0.000	0.000	0.000	0.000
73	A	524	LEU	0	0.023	-0.002	23.133	0.070	0.070	0.000	0.000	0.000	0.000
74	A	525	HIS	0	0.019	0.012	27.734	-0.086	-0.086	0.000	0.000	0.000	0.000
75	A	526	ARG	1	0.946	0.974	25.790	11.143	11.143	0.000	0.000	0.000	0.000
76	A	527	ILE	0	-0.013	-0.010	32.429	0.286	0.286	0.000	0.000	0.000	0.000
77	A	528	ARG	1	0.946	0.969	35.855	7.573	7.573	0.000	0.000	0.000	0.000
78	A	529	THR	0	0.036	0.013	34.103	-0.068	-0.068	0.000	0.000	0.000	0.000
79	A	530	ASP	-1	-0.850	-0.874	32.319	-9.245	-9.245	0.000	0.000	0.000	0.000
80	A	531	THR	0	-0.023	-0.037	26.900	-0.109	-0.109	0.000	0.000	0.000	0.000
81	A	532	TYR	0	-0.090	-0.063	29.597	-0.161	-0.161	0.000	0.000	0.000	0.000
82	A	533	VAL	0	0.042	0.022	26.435	-0.131	-0.131	0.000	0.000	0.000	0.000
83	A	534	LYS	1	0.952	0.956	28.848	9.878	9.878	0.000	0.000	0.000	0.000
84	A	535	LEU	0	-0.006	0.016	26.392	-0.235	-0.235	0.000	0.000	0.000	0.000
85	A	536	ASP	-1	-0.880	-0.936	29.466	-9.352	-9.352	0.000	0.000	0.000	0.000
86	A	537	LYS	1	0.858	0.900	30.730	9.169	9.169	0.000	0.000	0.000	0.000
87	A	538	ALA	0	-0.010	0.012	32.928	0.143	0.143	0.000	0.000	0.000	0.000
88	A	539	VAL	0	-0.030	-0.011	28.666	-0.002	-0.002	0.000	0.000	0.000	0.000
89	A	540	ASP	-1	-0.801	-0.908	28.549	-11.314	-11.314	0.000	0.000	0.000	0.000
90	A	541	LEU	0	0.001	-0.005	22.710	-0.313	-0.313	0.000	0.000	0.000	0.000
91	A	542	ALA	0	-0.014	0.016	23.788	-0.740	-0.740	0.000	0.000	0.000	0.000
92	A	543	GLY	0	0.036	0.013	23.574	-0.485	-0.485	0.000	0.000	0.000	0.000
93	A	544	LEU	0	-0.028	-0.011	22.897	-0.381	-0.381	0.000	0.000	0.000	0.000
94	A	545	THR	0	-0.030	-0.039	18.834	-0.791	-0.791	0.000	0.000	0.000	0.000
95	A	546	ALA	0	-0.006	0.004	18.829	-0.906	-0.906	0.000	0.000	0.000	0.000
96	A	547	ARG	1	0.849	0.916	19.232	12.156	12.156	0.000	0.000	0.000	0.000
97	A	548	LEU	0	0.017	0.012	15.833	-0.513	-0.513	0.000	0.000	0.000	0.000
98	A	549	ALA	0	0.011	0.001	14.634	-1.237	-1.237	0.000	0.000	0.000	0.000
99	A	550	HIS	0	-0.047	-0.026	14.325	-0.878	-0.878	0.000	0.000	0.000	0.000
100	A	551	HIS	0	0.020	0.012	15.425	-0.978	-0.978	0.000	0.000	0.000	0.000
101	A	552	VAL	0	0.014	0.001	10.044	-0.859	-0.859	0.000	0.000	0.000	0.000
102	A	553	HIS	0	-0.027	-0.008	10.561	-3.338	-3.338	0.000	0.000	0.000	0.000
103	A	554	ALA	0	-0.020	-0.016	11.295	-0.855	-0.855	0.000	0.000	0.000	0.000
104	A	555	GLU	-1	-0.835	-0.895	9.369	-27.025	-27.025	0.000	0.000	0.000	0.000
105	A	556	GLY	0	-0.033	-0.001	9.072	-0.839	-0.839	0.000	0.000	0.000	0.000
106	A	557	LEU	0	-0.062	-0.018	1.866	-8.355	-8.088	5.113	-1.217	-4.163	0.001

Top

Graph

Manual

About

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