FMO DATABASE

FMODB ID: LZV39

Calculation Name: 5TDQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5TDQ

Chain ID: A

ChEMBL ID:

UniProt ID: Q9H3P7

Base Structure: X-ray

Registration Date: 2023-06-22

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	130
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1213874.920151
FMO2-HF: Nuclear repulsion	1161274.489342
FMO2-HF: Total energy	-52600.430809
FMO2-MP2: Total energy	-52756.72141

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:367:PRO)

Summations of interaction energy for fragment #1(A:367:PRO)

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.
-4.221	-1.708	-0.019	-0.954	-1.54	0.001

Interaction energy analysis for fragmet #1(A:367:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.031 / q_NPA : -0.020

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	369	ILE	0	0.041	0.018	3.823	-1.830	0.164	-0.024	-0.845	-1.125	0.002
4	A	370	ALA	0	-0.026	0.002	6.498	0.220	0.220	0.000	0.000	0.000	0.000
5	A	371	ALA	0	0.042	0.007	10.077	-0.094	-0.094	0.000	0.000	0.000	0.000
6	A	372	PRO	0	-0.011	0.007	12.472	0.050	0.050	0.000	0.000	0.000	0.000
7	A	373	SER	0	-0.040	-0.010	14.957	0.016	0.016	0.000	0.000	0.000	0.000
8	A	374	MET	0	-0.004	-0.024	17.641	-0.017	-0.017	0.000	0.000	0.000	0.000
9	A	375	TRP	0	-0.064	-0.014	21.351	0.009	0.009	0.000	0.000	0.000	0.000
10	A	376	THR	0	0.000	-0.017	25.144	-0.008	-0.008	0.000	0.000	0.000	0.000
11	A	377	ARG	1	0.848	0.904	28.372	0.056	0.056	0.000	0.000	0.000	0.000
12	A	378	PRO	0	0.104	0.053	31.512	-0.002	-0.002	0.000	0.000	0.000	0.000
13	A	379	GLN	0	-0.041	-0.011	34.394	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	380	ILE	0	0.038	0.008	33.551	0.001	0.001	0.000	0.000	0.000	0.000
15	A	381	LYS	1	0.902	0.940	35.527	0.039	0.039	0.000	0.000	0.000	0.000
16	A	382	ASP	-1	-0.846	-0.905	37.935	-0.033	-0.033	0.000	0.000	0.000	0.000
17	A	383	PHE	0	-0.026	-0.006	28.888	0.001	0.001	0.000	0.000	0.000	0.000
18	A	384	LYS	1	0.837	0.895	34.700	0.059	0.059	0.000	0.000	0.000	0.000
19	A	385	GLU	-1	-0.864	-0.916	35.815	-0.033	-0.033	0.000	0.000	0.000	0.000
20	A	386	LYS	1	0.842	0.887	36.463	0.033	0.033	0.000	0.000	0.000	0.000
21	A	387	ILE	0	-0.117	-0.028	30.623	0.000	0.000	0.000	0.000	0.000	0.000
22	A	388	GLN	0	-0.004	-0.011	34.541	0.000	0.000	0.000	0.000	0.000	0.000
23	A	389	GLN	0	-0.054	-0.006	37.385	0.001	0.001	0.000	0.000	0.000	0.000
24	A	390	ASP	-1	-0.885	-0.956	37.326	-0.038	-0.038	0.000	0.000	0.000	0.000
25	A	391	ALA	0	-0.108	-0.036	34.508	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	392	ASP	-1	-0.826	-0.906	33.779	-0.064	-0.064	0.000	0.000	0.000	0.000
27	A	393	SER	0	-0.069	-0.047	29.179	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	394	VAL	0	-0.043	-0.025	30.182	-0.008	-0.008	0.000	0.000	0.000	0.000
29	A	395	ILE	0	-0.013	-0.002	26.973	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	396	THR	0	-0.020	-0.012	31.166	0.003	0.003	0.000	0.000	0.000	0.000
31	A	397	VAL	0	-0.003	-0.003	28.202	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	398	GLY	0	0.095	0.053	30.958	0.006	0.006	0.000	0.000	0.000	0.000
33	A	399	ARG	1	0.874	0.934	32.452	0.066	0.066	0.000	0.000	0.000	0.000
34	A	400	GLY	0	0.067	0.037	31.699	0.001	0.001	0.000	0.000	0.000	0.000
35	A	401	GLU	-1	-0.959	-0.967	28.902	-0.108	-0.108	0.000	0.000	0.000	0.000
36	A	402	VAL	0	0.020	-0.007	22.614	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	403	VAL	0	0.005	0.017	25.076	0.000	0.000	0.000	0.000	0.000	0.000
38	A	404	THR	0	-0.050	-0.027	18.884	-0.019	-0.019	0.000	0.000	0.000	0.000
39	A	405	VAL	0	0.027	0.017	21.327	0.008	0.008	0.000	0.000	0.000	0.000
40	A	406	ARG	1	0.808	0.890	16.592	0.201	0.201	0.000	0.000	0.000	0.000
41	A	407	VAL	0	0.008	-0.007	17.552	0.024	0.024	0.000	0.000	0.000	0.000
42	A	408	PRO	0	0.018	0.016	15.969	-0.022	-0.022	0.000	0.000	0.000	0.000
43	A	409	THR	0	-0.028	-0.011	12.057	0.009	0.009	0.000	0.000	0.000	0.000
44	A	410	HIS	0	-0.106	-0.044	15.509	0.002	0.002	0.000	0.000	0.000	0.000
45	A	411	GLU	-1	-0.863	-0.915	15.206	0.002	0.002	0.000	0.000	0.000	0.000
46	A	412	GLU	-1	-0.864	-0.928	16.725	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	413	GLY	0	-0.017	-0.007	18.601	0.010	0.010	0.000	0.000	0.000	0.000
48	A	414	SER	0	0.011	-0.004	15.039	0.000	0.000	0.000	0.000	0.000	0.000
49	A	415	TYR	0	-0.033	-0.032	14.367	-0.016	-0.016	0.000	0.000	0.000	0.000
50	A	416	LEU	0	-0.004	0.025	15.700	0.003	0.003	0.000	0.000	0.000	0.000
51	A	417	PHE	0	0.007	-0.009	17.462	0.000	0.000	0.000	0.000	0.000	0.000
52	A	418	TRP	0	0.028	0.010	16.734	-0.007	-0.007	0.000	0.000	0.000	0.000
53	A	419	GLU	-1	-0.783	-0.860	22.428	-0.052	-0.052	0.000	0.000	0.000	0.000
54	A	420	PHE	0	-0.014	-0.023	23.291	-0.004	-0.004	0.000	0.000	0.000	0.000
55	A	421	ALA	0	0.026	0.016	27.400	0.003	0.003	0.000	0.000	0.000	0.000
56	A	422	THR	0	0.021	-0.009	29.954	-0.003	-0.003	0.000	0.000	0.000	0.000
57	A	423	ASP	-1	-0.784	-0.848	32.576	-0.054	-0.054	0.000	0.000	0.000	0.000
58	A	424	ASN	0	-0.067	-0.029	36.077	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	425	TYR	0	-0.022	-0.028	34.679	0.001	0.001	0.000	0.000	0.000	0.000
60	A	426	ASP	-1	-0.694	-0.758	30.177	-0.099	-0.099	0.000	0.000	0.000	0.000
61	A	427	ILE	0	-0.016	-0.028	26.666	0.002	0.002	0.000	0.000	0.000	0.000
62	A	428	GLY	0	0.011	0.011	24.755	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	429	PHE	0	0.004	0.000	19.768	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	430	GLY	0	0.047	0.018	18.370	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	431	VAL	0	-0.038	-0.008	13.919	0.019	0.019	0.000	0.000	0.000	0.000
66	A	432	TYR	0	-0.017	-0.021	11.772	-0.011	-0.011	0.000	0.000	0.000	0.000
67	A	433	PHE	0	-0.016	-0.018	7.377	0.077	0.077	0.000	0.000	0.000	0.000
68	A	434	GLU	-1	-0.805	-0.905	8.804	-0.421	-0.421	0.000	0.000	0.000	0.000
69	A	435	TRP	0	0.022	0.010	3.702	-0.309	0.131	0.006	-0.103	-0.343	-0.001
70	A	436	THR	0	-0.041	-0.031	9.103	0.047	0.047	0.000	0.000	0.000	0.000
71	A	437	ASP	-1	-0.796	-0.857	12.704	-0.158	-0.158	0.000	0.000	0.000	0.000
72	A	438	SER	0	-0.050	-0.035	15.360	0.024	0.024	0.000	0.000	0.000	0.000
73	A	439	PRO	0	0.015	0.008	17.818	-0.006	-0.006	0.000	0.000	0.000	0.000
74	A	440	ASN	0	0.001	-0.019	20.361	-0.010	-0.010	0.000	0.000	0.000	0.000
75	A	441	THR	0	-0.016	0.012	21.749	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	442	ALA	0	0.002	0.019	21.329	0.008	0.008	0.000	0.000	0.000	0.000
77	A	443	VAL	0	0.017	0.005	22.617	-0.010	-0.010	0.000	0.000	0.000	0.000
78	A	444	SER	0	-0.029	-0.015	22.924	0.005	0.005	0.000	0.000	0.000	0.000
79	A	445	VAL	0	0.031	0.020	24.734	-0.003	-0.003	0.000	0.000	0.000	0.000
80	A	476	LEU	0	-0.075	-0.051	9.039	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	477	ASP	-1	-0.856	-0.926	4.596	-2.238	-2.159	-0.001	-0.006	-0.072	0.000
82	A	478	GLU	-1	-0.859	-0.923	7.913	-0.256	-0.256	0.000	0.000	0.000	0.000
83	A	479	ILE	0	-0.058	-0.017	9.012	-0.047	-0.047	0.000	0.000	0.000	0.000
84	A	480	VAL	0	-0.049	-0.035	11.552	0.051	0.051	0.000	0.000	0.000	0.000
85	A	481	PRO	0	0.067	0.045	14.968	0.000	0.000	0.000	0.000	0.000	0.000
86	A	482	VAL	0	-0.004	-0.018	16.511	0.033	0.033	0.000	0.000	0.000	0.000
87	A	483	TYR	0	-0.023	-0.008	19.356	0.006	0.006	0.000	0.000	0.000	0.000
88	A	484	ARG	1	0.815	0.872	22.716	0.105	0.105	0.000	0.000	0.000	0.000
89	A	485	ARG	1	0.896	0.959	19.747	0.176	0.176	0.000	0.000	0.000	0.000
90	A	486	ASP	-1	-0.834	-0.908	27.045	-0.083	-0.083	0.000	0.000	0.000	0.000
91	A	487	CYS	0	-0.063	-0.038	27.926	0.003	0.003	0.000	0.000	0.000	0.000
92	A	488	HIS	0	-0.048	-0.012	30.050	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	489	GLU	-1	-0.931	-0.956	33.276	-0.055	-0.055	0.000	0.000	0.000	0.000
94	A	490	GLU	-1	-0.901	-0.938	31.494	-0.050	-0.050	0.000	0.000	0.000	0.000
95	A	491	VAL	0	-0.053	-0.023	28.765	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	492	TYR	0	0.031	0.010	24.567	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	493	ALA	0	-0.012	-0.009	24.577	-0.003	-0.003	0.000	0.000	0.000	0.000
98	A	494	GLY	0	0.017	0.000	20.564	-0.004	-0.004	0.000	0.000	0.000	0.000
99	A	495	SER	0	-0.036	-0.014	18.705	0.004	0.004	0.000	0.000	0.000	0.000
100	A	496	HIS	0	0.057	0.033	9.895	0.029	0.029	0.000	0.000	0.000	0.000
101	A	497	GLN	0	0.027	0.036	10.901	0.005	0.005	0.000	0.000	0.000	0.000
102	A	498	TYR	0	0.022	-0.004	11.021	-0.065	-0.065	0.000	0.000	0.000	0.000
103	A	499	PRO	0	-0.047	-0.006	5.721	0.082	0.082	0.000	0.000	0.000	0.000
104	A	500	GLY	0	0.021	-0.006	6.205	0.171	0.171	0.000	0.000	0.000	0.000
105	A	501	ARG	1	0.791	0.867	8.015	0.081	0.081	0.000	0.000	0.000	0.000
106	A	502	GLY	0	-0.008	-0.016	9.696	-0.084	-0.084	0.000	0.000	0.000	0.000
107	A	503	VAL	0	-0.025	0.007	11.760	0.060	0.060	0.000	0.000	0.000	0.000
108	A	504	TYR	0	-0.020	-0.016	12.210	-0.049	-0.049	0.000	0.000	0.000	0.000
109	A	505	LEU	0	-0.049	-0.029	13.943	0.042	0.042	0.000	0.000	0.000	0.000
110	A	506	LEU	0	0.010	0.013	15.994	-0.017	-0.017	0.000	0.000	0.000	0.000
111	A	507	LYS	1	0.918	0.941	17.404	0.267	0.267	0.000	0.000	0.000	0.000
112	A	508	PHE	0	0.021	0.014	20.485	0.003	0.003	0.000	0.000	0.000	0.000
113	A	509	ASP	-1	-0.839	-0.899	23.012	-0.168	-0.168	0.000	0.000	0.000	0.000
114	A	510	ASN	0	0.020	-0.018	25.061	0.008	0.008	0.000	0.000	0.000	0.000
115	A	511	SER	0	-0.016	-0.032	26.064	0.009	0.009	0.000	0.000	0.000	0.000
116	A	512	TYR	0	-0.100	-0.064	27.832	0.006	0.006	0.000	0.000	0.000	0.000
117	A	513	SER	0	-0.100	-0.039	30.185	0.010	0.010	0.000	0.000	0.000	0.000
118	A	514	LEU	0	0.075	0.031	33.153	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	515	TRP	0	-0.012	-0.020	36.164	0.003	0.003	0.000	0.000	0.000	0.000
120	A	516	ARG	1	0.889	0.957	36.144	0.064	0.064	0.000	0.000	0.000	0.000
121	A	517	SER	0	0.045	0.025	34.484	-0.004	-0.004	0.000	0.000	0.000	0.000
122	A	518	LYS	1	0.782	0.889	31.126	0.097	0.097	0.000	0.000	0.000	0.000
123	A	519	SER	0	0.033	0.024	32.956	-0.003	-0.003	0.000	0.000	0.000	0.000
124	A	520	VAL	0	-0.004	-0.008	27.047	0.001	0.001	0.000	0.000	0.000	0.000
125	A	521	TYR	0	-0.021	-0.029	30.508	0.001	0.001	0.000	0.000	0.000	0.000
126	A	522	TYR	0	0.018	-0.009	23.919	-0.006	-0.006	0.000	0.000	0.000	0.000
127	A	523	ARG	1	0.937	0.964	26.238	0.061	0.061	0.000	0.000	0.000	0.000
128	A	524	VAL	0	0.001	0.003	20.603	-0.009	-0.009	0.000	0.000	0.000	0.000
129	A	525	TYR	0	-0.091	-0.073	22.551	0.011	0.011	0.000	0.000	0.000	0.000
130	A	526	TYR	0	0.021	0.022	19.677	-0.004	-0.004	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:367:PRO)