FMO DATABASE

FMODB ID: NNLVQ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-948699.82267
FMO2-HF: Nuclear repulsion	902338.993571
FMO2-HF: Total energy	-46360.829099
FMO2-MP2: Total energy	-46495.482322

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.
-44.573	-41.896	0.036	-1.417	-1.296	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 : 0.995 / q_NPA : 0.990

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	0.020	0.000	3.493	-6.530	-3.853	0.036	-1.417	-1.296	0.004
4	A	437	ALA	0	-0.015	0.004	5.712	2.697	2.697	0.000	0.000	0.000	0.000
5	A	438	LEU	0	0.010	0.007	9.413	-0.385	-0.385	0.000	0.000	0.000	0.000
6	A	439	ASP	-1	-0.836	-0.922	12.152	-16.352	-16.352	0.000	0.000	0.000	0.000
7	A	440	PRO	0	0.050	0.007	14.777	0.423	0.423	0.000	0.000	0.000	0.000
8	A	441	ILE	0	0.029	0.029	18.269	0.851	0.851	0.000	0.000	0.000	0.000
9	A	442	ALA	0	0.001	-0.011	15.857	0.229	0.229	0.000	0.000	0.000	0.000
10	A	443	SER	0	-0.105	-0.053	15.852	0.322	0.322	0.000	0.000	0.000	0.000
11	A	444	GLN	0	0.007	-0.010	17.328	0.724	0.724	0.000	0.000	0.000	0.000
12	A	445	PHE	0	0.007	0.010	19.434	0.587	0.587	0.000	0.000	0.000	0.000
13	A	446	SER	0	-0.033	-0.049	19.253	0.472	0.472	0.000	0.000	0.000	0.000
14	A	447	GLN	0	-0.045	-0.014	21.798	0.137	0.137	0.000	0.000	0.000	0.000
15	A	448	LEU	0	-0.061	0.003	24.211	0.404	0.404	0.000	0.000	0.000	0.000
16	A	449	ARG	1	0.832	0.936	26.623	9.287	9.287	0.000	0.000	0.000	0.000
17	A	450	THR	0	-0.063	-0.039	27.709	-0.197	-0.197	0.000	0.000	0.000	0.000
18	A	451	ILE	0	0.040	0.029	30.224	0.294	0.294	0.000	0.000	0.000	0.000
19	A	452	SER	0	-0.021	-0.011	31.144	-0.240	-0.240	0.000	0.000	0.000	0.000
20	A	453	LYS	1	0.929	0.967	30.173	10.207	10.207	0.000	0.000	0.000	0.000
21	A	454	ALA	0	-0.056	-0.026	32.827	0.107	0.107	0.000	0.000	0.000	0.000
22	A	455	ASP	-1	-0.884	-0.946	36.578	-7.569	-7.569	0.000	0.000	0.000	0.000
23	A	456	ALA	0	0.027	0.009	36.790	-0.029	-0.029	0.000	0.000	0.000	0.000
24	A	457	GLH	0	-0.028	0.007	38.787	-0.121	-0.121	0.000	0.000	0.000	0.000
25	A	458	SER	0	-0.065	-0.037	41.041	0.242	0.242	0.000	0.000	0.000	0.000
26	A	459	GLU	-1	-0.777	-0.909	39.420	-7.586	-7.586	0.000	0.000	0.000	0.000
27	A	460	GLU	-1	-0.921	-0.949	40.301	-7.858	-7.858	0.000	0.000	0.000	0.000
28	A	461	LEU	0	-0.031	-0.009	35.548	-0.249	-0.249	0.000	0.000	0.000	0.000
29	A	462	GLY	0	0.083	0.031	36.235	0.087	0.087	0.000	0.000	0.000	0.000
30	A	463	PHE	0	-0.095	-0.041	27.900	-0.127	-0.127	0.000	0.000	0.000	0.000
31	A	464	LYS	1	0.895	0.947	32.742	8.625	8.625	0.000	0.000	0.000	0.000
32	A	465	ASP	-1	-0.761	-0.818	28.245	-11.588	-11.588	0.000	0.000	0.000	0.000
33	A	466	ALA	0	0.062	0.029	27.235	0.286	0.286	0.000	0.000	0.000	0.000
34	A	467	ALA	0	0.083	0.008	27.779	0.353	0.353	0.000	0.000	0.000	0.000
35	A	468	ASH	0	-0.082	-0.058	29.719	0.534	0.534	0.000	0.000	0.000	0.000
36	A	469	HIS	1	0.842	0.939	30.376	9.394	9.394	0.000	0.000	0.000	0.000
37	A	470	HIS	1	0.803	0.904	30.624	9.657	9.657	0.000	0.000	0.000	0.000
38	A	471	THR	0	0.136	0.006	30.256	-0.227	-0.227	0.000	0.000	0.000	0.000
39	A	472	ASP	-1	-0.935	-0.960	32.196	-9.285	-9.285	0.000	0.000	0.000	0.000
40	A	473	ASH	0	-0.021	-0.027	35.396	0.061	0.061	0.000	0.000	0.000	0.000
41	A	474	VAL	0	-0.047	0.004	29.529	0.081	0.081	0.000	0.000	0.000	0.000
42	A	475	THR	0	0.017	0.018	30.242	0.100	0.100	0.000	0.000	0.000	0.000
43	A	476	HIS	0	-0.014	-0.017	28.323	-0.505	-0.505	0.000	0.000	0.000	0.000
44	A	477	CYM	-1	-0.851	-0.845	24.456	-12.702	-12.702	0.000	0.000	0.000	0.000
45	A	478	LEU	0	0.027	0.011	26.789	0.195	0.195	0.000	0.000	0.000	0.000
46	A	479	PHE	0	-0.052	-0.068	23.382	0.080	0.080	0.000	0.000	0.000	0.000
47	A	480	GLY	0	-0.025	-0.009	24.217	-0.403	-0.403	0.000	0.000	0.000	0.000
48	A	481	GLY	0	-0.025	-0.014	24.048	-0.559	-0.559	0.000	0.000	0.000	0.000
49	A	482	GLU	-1	-0.799	-0.811	25.407	-10.892	-10.892	0.000	0.000	0.000	0.000
50	A	483	LEU	0	0.003	0.010	24.098	-0.611	-0.611	0.000	0.000	0.000	0.000
51	A	484	SER	0	-0.100	-0.130	24.417	0.454	0.454	0.000	0.000	0.000	0.000
52	A	485	LEU	0	-0.025	-0.020	23.598	-0.515	-0.515	0.000	0.000	0.000	0.000
53	A	486	SER	0	-0.057	-0.025	23.442	-0.043	-0.043	0.000	0.000	0.000	0.000
54	A	487	ASN	0	-0.030	-0.011	19.171	-1.047	-1.047	0.000	0.000	0.000	0.000
55	A	488	PRO	0	-0.004	-0.009	16.249	0.028	0.028	0.000	0.000	0.000	0.000
56	A	489	ASP	-1	-0.926	-0.969	13.399	-22.895	-22.895	0.000	0.000	0.000	0.000
57	A	490	GLN	0	-0.084	-0.020	16.278	0.293	0.293	0.000	0.000	0.000	0.000
58	A	491	GLN	0	-0.021	-0.017	16.861	-0.166	-0.166	0.000	0.000	0.000	0.000
59	A	492	VAL	0	0.011	0.012	20.160	0.241	0.241	0.000	0.000	0.000	0.000
60	A	493	ILE	0	0.001	-0.016	23.526	0.215	0.215	0.000	0.000	0.000	0.000
61	A	494	GLY	0	0.011	0.015	26.082	0.066	0.066	0.000	0.000	0.000	0.000
62	A	495	LEU	0	-0.042	-0.035	27.278	-0.096	-0.096	0.000	0.000	0.000	0.000
63	A	496	ALA	0	0.074	0.032	29.987	0.176	0.176	0.000	0.000	0.000	0.000
64	A	497	GLY	0	0.020	0.018	33.042	-0.227	-0.227	0.000	0.000	0.000	0.000
65	A	498	ASN	0	-0.050	-0.037	35.578	0.096	0.096	0.000	0.000	0.000	0.000
66	A	499	PRO	0	-0.037	0.004	34.029	-0.118	-0.118	0.000	0.000	0.000	0.000
67	A	500	THR	0	0.024	-0.002	34.908	0.357	0.357	0.000	0.000	0.000	0.000
68	A	501	ASP	-1	-0.923	-0.970	34.742	-8.342	-8.342	0.000	0.000	0.000	0.000
69	A	502	THR	0	0.006	-0.016	30.254	-0.072	-0.072	0.000	0.000	0.000	0.000
70	A	503	SER	0	-0.065	-0.061	33.261	0.029	0.029	0.000	0.000	0.000	0.000
71	A	504	GLN	0	0.076	0.100	34.984	0.228	0.228	0.000	0.000	0.000	0.000
72	A	505	PRO	0	-0.037	-0.054	35.874	-0.273	-0.273	0.000	0.000	0.000	0.000
73	A	506	TYR	0	0.042	0.022	34.895	0.067	0.067	0.000	0.000	0.000	0.000
74	A	507	SER	0	0.003	0.002	36.765	0.222	0.222	0.000	0.000	0.000	0.000
75	A	508	GLN	0	-0.005	-0.002	39.665	-0.072	-0.072	0.000	0.000	0.000	0.000
76	A	509	GLU	-1	-0.844	-0.912	42.039	-6.944	-6.944	0.000	0.000	0.000	0.000
77	A	510	GLY	0	-0.047	-0.023	39.161	0.063	0.063	0.000	0.000	0.000	0.000
78	A	511	ASN	0	-0.128	-0.062	38.220	-0.294	-0.294	0.000	0.000	0.000	0.000
79	A	512	LYS	1	0.792	0.874	38.775	7.373	7.373	0.000	0.000	0.000	0.000
80	A	513	ASP	-1	-0.838	-0.913	37.672	-8.252	-8.252	0.000	0.000	0.000	0.000
81	A	514	LEU	0	-0.076	-0.015	32.441	-0.231	-0.231	0.000	0.000	0.000	0.000
82	A	515	ALA	0	0.034	0.021	31.186	0.080	0.080	0.000	0.000	0.000	0.000
83	A	516	PHE	0	-0.012	-0.015	28.960	-0.267	-0.267	0.000	0.000	0.000	0.000
84	A	517	MET	0	-0.004	-0.022	24.706	-0.159	-0.159	0.000	0.000	0.000	0.000
85	A	518	ASP	-1	-0.755	-0.913	19.245	-16.169	-16.169	0.000	0.000	0.000	0.000
86	A	519	MET	0	-0.024	-0.016	20.111	-0.163	-0.163	0.000	0.000	0.000	0.000
87	A	520	LYS	1	0.947	0.975	13.009	19.982	19.982	0.000	0.000	0.000	0.000
88	A	521	LYS	1	0.922	0.967	17.594	15.682	15.682	0.000	0.000	0.000	0.000
89	A	522	LEU	0	0.033	0.020	19.766	0.101	0.101	0.000	0.000	0.000	0.000
90	A	523	ALA	0	-0.006	-0.007	17.798	0.294	0.294	0.000	0.000	0.000	0.000
91	A	524	GLN	0	-0.013	-0.002	16.536	-0.482	-0.482	0.000	0.000	0.000	0.000
92	A	525	PHE	0	-0.042	-0.021	18.544	0.178	0.178	0.000	0.000	0.000	0.000
93	A	526	LEU	0	-0.013	-0.018	22.206	0.243	0.243	0.000	0.000	0.000	0.000
94	A	527	ALA	0	-0.051	-0.018	18.884	0.333	0.333	0.000	0.000	0.000	0.000
95	A	528	GLY	0	-0.048	-0.013	20.850	0.061	0.061	0.000	0.000	0.000	0.000
96	A	529	LYS	1	0.876	0.940	22.836	11.136	11.136	0.000	0.000	0.000	0.000
97	A	530	PRO	0	0.015	0.033	25.738	-0.029	-0.029	0.000	0.000	0.000	0.000
98	A	531	GLU	-1	-0.851	-0.945	26.847	-9.544	-9.544	0.000	0.000	0.000	0.000
99	A	532	HIS	0	0.022	-0.002	28.513	-0.482	-0.482	0.000	0.000	0.000	0.000
100	A	533	PRO	0	-0.008	-0.012	27.798	0.193	0.193	0.000	0.000	0.000	0.000
101	A	534	MET	0	-0.067	-0.044	29.863	0.050	0.050	0.000	0.000	0.000	0.000
102	A	535	THR	0	0.051	0.025	33.500	0.117	0.117	0.000	0.000	0.000	0.000
103	A	536	ARG	1	0.832	0.919	32.740	9.429	9.429	0.000	0.000	0.000	0.000
104	A	537	GLU	-1	-0.872	-0.919	33.800	-8.373	-8.373	0.000	0.000	0.000	0.000
105	A	538	THR	0	-0.026	-0.013	30.335	-0.308	-0.308	0.000	0.000	0.000	0.000
106	A	539	LEU	0	-0.048	-0.011	27.007	0.144	0.144	0.000	0.000	0.000	0.000
107	A	540	ASN	0	0.047	0.013	24.977	-0.264	-0.264	0.000	0.000	0.000	0.000
108	A	541	ALA	0	0.019	0.004	22.100	0.061	0.061	0.000	0.000	0.000	0.000
109	A	542	GLU	-1	-0.895	-0.940	23.953	-11.483	-11.483	0.000	0.000	0.000	0.000
110	A	543	ASN	0	-0.030	-0.026	27.318	0.013	0.013	0.000	0.000	0.000	0.000
111	A	544	ILE	0	0.062	0.047	23.618	0.235	0.235	0.000	0.000	0.000	0.000
112	A	545	ALA	0	0.037	0.013	26.783	0.184	0.184	0.000	0.000	0.000	0.000
113	A	546	LYS	1	0.929	0.965	28.015	9.370	9.370	0.000	0.000	0.000	0.000
114	A	547	TYR	0	0.017	-0.003	29.551	0.359	0.359	0.000	0.000	0.000	0.000
115	A	548	ALA	0	-0.018	0.010	26.254	0.069	0.069	0.000	0.000	0.000	0.000
116	A	549	PHE	0	0.009	0.008	28.277	0.111	0.111	0.000	0.000	0.000	0.000
117	A	550	ARG	1	0.976	0.990	23.152	11.686	11.686	0.000	0.000	0.000	0.000
118	A	551	ILE	0	-0.013	-0.001	26.495	0.381	0.381	0.000	0.000	0.000	0.000
119	A	552	VAL	0	-0.034	-0.011	26.484	-0.494	-0.494	0.000	0.000	0.000	0.000
120	A	553	PRO	0	0.044	0.015	26.913	0.410	0.410	0.000	0.000	0.000	0.000

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