FMO DATABASE

FMODB ID: JQV69

Calculation Name: 2FD4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2FD4

Chain ID: A

ChEMBL ID:

UniProt ID: Q8RSY1

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	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	120
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-949228.619407
FMO2-HF: Nuclear repulsion	902866.968117
FMO2-HF: Total energy	-46361.65129
FMO2-MP2: Total energy	-46496.213723

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:435:LYS)

Summations of interaction energy for fragment #1(A:435:LYS)

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.
-46.235	-43.61	0.032	-1.373	-1.285	0.004

Interaction energy analysis for fragmet #1(A:435:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.990 / q_NPA : 0.988

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

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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	436	ALA	0	0.027	0.008	3.407	-6.212	-3.587	0.032	-1.373	-1.285	0.004
4	A	437	ALA	0	-0.018	0.000	5.937	2.619	2.619	0.000	0.000	0.000	0.000
5	A	438	LEU	0	0.018	0.009	9.529	-0.363	-0.363	0.000	0.000	0.000	0.000
6	A	439	ASP	-1	-0.786	-0.897	12.353	-16.375	-16.375	0.000	0.000	0.000	0.000
7	A	440	PRO	0	0.055	0.030	14.984	0.371	0.371	0.000	0.000	0.000	0.000
8	A	441	ILE	0	0.032	0.025	18.479	0.806	0.806	0.000	0.000	0.000	0.000
9	A	442	ALA	0	0.021	0.002	16.035	0.265	0.265	0.000	0.000	0.000	0.000
10	A	443	SER	0	-0.100	-0.071	15.855	0.320	0.320	0.000	0.000	0.000	0.000
11	A	444	GLN	0	-0.010	-0.021	17.403	0.713	0.713	0.000	0.000	0.000	0.000
12	A	445	PHE	0	0.018	0.017	19.395	0.584	0.584	0.000	0.000	0.000	0.000
13	A	446	SER	0	-0.016	-0.044	19.002	0.468	0.468	0.000	0.000	0.000	0.000
14	A	447	GLN	0	-0.045	-0.017	21.781	0.148	0.148	0.000	0.000	0.000	0.000
15	A	448	LEU	0	-0.054	0.008	24.303	0.402	0.402	0.000	0.000	0.000	0.000
16	A	449	ARG	1	0.832	0.941	26.606	9.266	9.266	0.000	0.000	0.000	0.000
17	A	450	THR	0	-0.028	-0.021	27.642	-0.306	-0.306	0.000	0.000	0.000	0.000
18	A	451	ILE	0	-0.001	0.012	30.212	0.310	0.310	0.000	0.000	0.000	0.000
19	A	452	SER	0	-0.017	-0.011	31.136	-0.237	-0.237	0.000	0.000	0.000	0.000
20	A	453	LYS	1	0.861	0.924	29.414	10.503	10.503	0.000	0.000	0.000	0.000
21	A	454	ALA	0	-0.052	-0.025	32.848	0.108	0.108	0.000	0.000	0.000	0.000
22	A	455	ASP	-1	-0.878	-0.943	36.575	-7.575	-7.575	0.000	0.000	0.000	0.000
23	A	456	ALA	0	0.028	0.008	36.710	-0.062	-0.062	0.000	0.000	0.000	0.000
24	A	457	GLH	0	-0.020	0.011	38.679	-0.121	-0.121	0.000	0.000	0.000	0.000
25	A	458	SER	0	-0.061	-0.033	40.881	0.246	0.246	0.000	0.000	0.000	0.000
26	A	459	GLU	-1	-0.767	-0.898	39.657	-7.520	-7.520	0.000	0.000	0.000	0.000
27	A	460	GLU	-1	-0.872	-0.925	40.227	-7.853	-7.853	0.000	0.000	0.000	0.000
28	A	461	LEU	0	-0.063	-0.040	35.328	-0.263	-0.263	0.000	0.000	0.000	0.000
29	A	462	GLY	0	0.062	0.028	36.238	0.094	0.094	0.000	0.000	0.000	0.000
30	A	463	PHE	0	-0.088	-0.036	27.817	-0.147	-0.147	0.000	0.000	0.000	0.000
31	A	464	LYS	1	0.917	0.962	32.935	8.641	8.641	0.000	0.000	0.000	0.000
32	A	465	ASP	-1	-0.768	-0.863	28.431	-11.542	-11.542	0.000	0.000	0.000	0.000
33	A	466	ALA	0	0.064	0.024	27.221	0.286	0.286	0.000	0.000	0.000	0.000
34	A	467	ALA	0	0.069	-0.003	27.638	0.351	0.351	0.000	0.000	0.000	0.000
35	A	468	ASH	0	-0.070	-0.042	29.657	0.538	0.538	0.000	0.000	0.000	0.000
36	A	469	HIS	1	0.841	0.936	30.293	9.392	9.392	0.000	0.000	0.000	0.000
37	A	470	HIS	1	0.843	0.945	30.612	9.689	9.689	0.000	0.000	0.000	0.000
38	A	471	THR	0	0.103	-0.002	29.507	-0.214	-0.214	0.000	0.000	0.000	0.000
39	A	472	ASP	-1	-0.883	-0.924	31.663	-9.258	-9.258	0.000	0.000	0.000	0.000
40	A	473	ASH	0	-0.040	-0.035	35.098	0.084	0.084	0.000	0.000	0.000	0.000
41	A	474	VAL	0	-0.047	0.017	29.506	0.076	0.076	0.000	0.000	0.000	0.000
42	A	475	THR	0	0.012	0.008	30.290	0.110	0.110	0.000	0.000	0.000	0.000
43	A	476	HIS	0	-0.009	-0.013	28.486	-0.550	-0.550	0.000	0.000	0.000	0.000
44	A	477	CYM	-1	-0.855	-0.835	24.628	-12.819	-12.819	0.000	0.000	0.000	0.000
45	A	478	LEU	0	0.044	0.020	27.021	0.172	0.172	0.000	0.000	0.000	0.000
46	A	479	PHE	0	-0.026	-0.052	23.695	0.058	0.058	0.000	0.000	0.000	0.000
47	A	480	GLY	0	-0.017	-0.006	24.440	-0.416	-0.416	0.000	0.000	0.000	0.000
48	A	481	GLY	0	-0.003	-0.005	24.197	-0.613	-0.613	0.000	0.000	0.000	0.000
49	A	482	GLU	-1	-0.836	-0.871	25.355	-11.282	-11.282	0.000	0.000	0.000	0.000
50	A	483	LEU	0	0.007	0.011	24.286	-0.621	-0.621	0.000	0.000	0.000	0.000
51	A	484	SER	0	-0.049	-0.065	24.398	0.385	0.385	0.000	0.000	0.000	0.000
52	A	485	LEU	0	-0.020	-0.011	23.604	-0.485	-0.485	0.000	0.000	0.000	0.000
53	A	486	SER	0	-0.060	-0.030	23.433	-0.031	-0.031	0.000	0.000	0.000	0.000
54	A	487	ASN	0	-0.025	-0.005	19.244	-0.978	-0.978	0.000	0.000	0.000	0.000
55	A	488	PRO	0	-0.011	-0.005	16.200	0.102	0.102	0.000	0.000	0.000	0.000
56	A	489	ASP	-1	-0.920	-0.965	13.426	-22.608	-22.608	0.000	0.000	0.000	0.000
57	A	490	GLN	0	-0.085	-0.034	16.296	0.305	0.305	0.000	0.000	0.000	0.000
58	A	491	GLN	0	-0.019	-0.014	17.347	-0.097	-0.097	0.000	0.000	0.000	0.000
59	A	492	VAL	0	0.004	0.005	20.229	0.265	0.265	0.000	0.000	0.000	0.000
60	A	493	ILE	0	0.007	-0.012	23.629	0.210	0.210	0.000	0.000	0.000	0.000
61	A	494	GLY	0	0.006	0.013	26.177	0.061	0.061	0.000	0.000	0.000	0.000
62	A	495	LEU	0	-0.040	-0.038	27.479	-0.088	-0.088	0.000	0.000	0.000	0.000
63	A	496	ALA	0	0.076	0.033	30.121	0.170	0.170	0.000	0.000	0.000	0.000
64	A	497	GLY	0	0.025	0.025	33.198	-0.217	-0.217	0.000	0.000	0.000	0.000
65	A	498	ASN	0	-0.063	-0.048	35.735	0.135	0.135	0.000	0.000	0.000	0.000
66	A	499	PRO	0	-0.039	0.007	34.170	-0.125	-0.125	0.000	0.000	0.000	0.000
67	A	500	THR	0	0.019	0.002	35.076	0.331	0.331	0.000	0.000	0.000	0.000
68	A	501	ASP	-1	-0.872	-0.937	34.901	-8.219	-8.219	0.000	0.000	0.000	0.000
69	A	502	THR	0	-0.013	-0.029	30.434	-0.069	-0.069	0.000	0.000	0.000	0.000
70	A	503	SER	0	-0.057	-0.052	33.282	0.009	0.009	0.000	0.000	0.000	0.000
71	A	504	GLN	0	0.043	0.077	34.964	0.274	0.274	0.000	0.000	0.000	0.000
72	A	505	PRO	0	-0.036	-0.056	35.860	-0.276	-0.276	0.000	0.000	0.000	0.000
73	A	506	TYR	0	0.032	0.016	35.002	0.076	0.076	0.000	0.000	0.000	0.000
74	A	507	SER	0	0.006	-0.004	36.876	0.222	0.222	0.000	0.000	0.000	0.000
75	A	508	GLN	0	-0.026	-0.009	39.789	-0.075	-0.075	0.000	0.000	0.000	0.000
76	A	509	GLU	-1	-0.849	-0.912	42.181	-6.941	-6.941	0.000	0.000	0.000	0.000
77	A	510	GLY	0	-0.044	-0.024	38.976	0.051	0.051	0.000	0.000	0.000	0.000
78	A	511	ASN	0	-0.113	-0.058	37.994	-0.306	-0.306	0.000	0.000	0.000	0.000
79	A	512	LYS	1	0.785	0.862	38.736	7.316	7.316	0.000	0.000	0.000	0.000
80	A	513	ASP	-1	-0.858	-0.911	37.785	-8.191	-8.191	0.000	0.000	0.000	0.000
81	A	514	LEU	0	-0.070	-0.008	32.513	-0.225	-0.225	0.000	0.000	0.000	0.000
82	A	515	ALA	0	0.026	0.017	31.389	0.076	0.076	0.000	0.000	0.000	0.000
83	A	516	PHE	0	0.017	-0.007	29.074	-0.279	-0.279	0.000	0.000	0.000	0.000
84	A	517	MET	0	-0.001	-0.016	25.093	-0.158	-0.158	0.000	0.000	0.000	0.000
85	A	518	ASP	-1	-0.751	-0.900	19.162	-16.098	-16.098	0.000	0.000	0.000	0.000
86	A	519	MET	0	-0.036	-0.017	20.292	-0.111	-0.111	0.000	0.000	0.000	0.000
87	A	520	LYS	1	0.903	0.956	13.645	19.257	19.257	0.000	0.000	0.000	0.000
88	A	521	LYS	1	0.839	0.904	17.772	13.910	13.910	0.000	0.000	0.000	0.000
89	A	522	LEU	0	0.008	0.007	19.899	0.142	0.142	0.000	0.000	0.000	0.000
90	A	523	ALA	0	-0.002	-0.006	17.967	0.309	0.309	0.000	0.000	0.000	0.000
91	A	524	GLN	0	-0.021	-0.006	16.976	-0.417	-0.417	0.000	0.000	0.000	0.000
92	A	525	PHE	0	-0.034	-0.015	18.730	0.197	0.197	0.000	0.000	0.000	0.000
93	A	526	LEU	0	-0.013	-0.018	22.388	0.247	0.247	0.000	0.000	0.000	0.000
94	A	527	ALA	0	-0.062	-0.023	18.880	0.323	0.323	0.000	0.000	0.000	0.000
95	A	528	GLY	0	-0.042	-0.011	20.832	0.069	0.069	0.000	0.000	0.000	0.000
96	A	529	LYS	1	0.829	0.899	22.749	10.951	10.951	0.000	0.000	0.000	0.000
97	A	530	PRO	0	0.022	0.038	25.704	-0.014	-0.014	0.000	0.000	0.000	0.000
98	A	531	GLU	-1	-0.756	-0.847	26.907	-9.460	-9.460	0.000	0.000	0.000	0.000
99	A	532	HIS	0	0.028	-0.010	28.707	-0.470	-0.470	0.000	0.000	0.000	0.000
100	A	533	PRO	0	-0.017	-0.014	27.785	0.191	0.191	0.000	0.000	0.000	0.000
101	A	534	MET	0	-0.068	-0.037	30.035	0.050	0.050	0.000	0.000	0.000	0.000
102	A	535	THR	0	0.047	0.019	33.664	0.124	0.124	0.000	0.000	0.000	0.000
103	A	536	ARG	1	0.775	0.856	32.925	9.441	9.441	0.000	0.000	0.000	0.000
104	A	537	GLU	-1	-0.873	-0.918	33.996	-8.322	-8.322	0.000	0.000	0.000	0.000
105	A	538	THR	0	-0.037	-0.017	30.506	-0.255	-0.255	0.000	0.000	0.000	0.000
106	A	539	LEU	0	-0.041	-0.002	27.152	0.132	0.132	0.000	0.000	0.000	0.000
107	A	540	ASN	0	0.048	0.010	25.193	-0.220	-0.220	0.000	0.000	0.000	0.000
108	A	541	ALA	0	0.009	0.001	22.302	0.060	0.060	0.000	0.000	0.000	0.000
109	A	542	GLU	-1	-0.874	-0.930	24.162	-11.410	-11.410	0.000	0.000	0.000	0.000
110	A	543	ASN	0	-0.038	-0.032	27.529	0.006	0.006	0.000	0.000	0.000	0.000
111	A	544	ILE	0	0.070	0.051	23.726	0.221	0.221	0.000	0.000	0.000	0.000
112	A	545	ALA	0	0.027	0.010	26.868	0.178	0.178	0.000	0.000	0.000	0.000
113	A	546	LYS	1	0.933	0.962	28.175	9.439	9.439	0.000	0.000	0.000	0.000
114	A	547	TYR	0	0.025	-0.001	29.726	0.278	0.278	0.000	0.000	0.000	0.000
115	A	548	ALA	0	-0.020	0.011	26.335	0.068	0.068	0.000	0.000	0.000	0.000
116	A	549	PHE	0	0.006	0.002	28.416	0.120	0.120	0.000	0.000	0.000	0.000
117	A	550	ARG	1	0.937	0.974	23.051	11.655	11.655	0.000	0.000	0.000	0.000
118	A	551	ILE	0	-0.013	0.000	26.564	0.382	0.382	0.000	0.000	0.000	0.000
119	A	552	VAL	0	-0.025	-0.008	26.317	-0.495	-0.495	0.000	0.000	0.000	0.000
120	A	553	PRO	0	0.048	0.018	26.920	0.396	0.396	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:435:LYS)