FMO DATABASE

FMODB ID: G6LR1

Calculation Name: 3TNU-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3TNU

Chain ID: B

ChEMBL ID:

UniProt ID: P02533

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	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	95
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-455496.213819
FMO2-HF: Nuclear repulsion	416304.952108
FMO2-HF: Total energy	-39191.261711
FMO2-MP2: Total energy	-39303.27372

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(B:382:THR)

Summations of interaction energy for fragment #1(B:382:THR)

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.
-22.5	-18.306	13.922	-8.57	-9.548	-0.058

Interaction energy analysis for fragmet #1(B:382:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.067 / q_NPA : 0.030

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	B	384	HIS	0	-0.008	-0.004	3.353	-4.008	-1.796	0.027	-0.969	-1.271	0.004
4	B	385	GLU	-1	-0.817	-0.921	2.109	-18.885	-17.944	13.854	-7.349	-7.447	-0.062
5	B	386	ILE	0	0.031	0.014	3.049	0.276	1.167	0.043	-0.247	-0.687	0.000
6	B	387	SER	0	-0.046	-0.016	5.305	0.271	0.337	-0.001	-0.002	-0.063	0.000
7	B	388	GLU	-1	-0.938	-0.979	7.022	-1.308	-1.308	0.000	0.000	0.000	0.000
8	B	389	MET	0	0.017	0.013	4.779	0.252	0.336	-0.001	-0.003	-0.080	0.000
9	B	390	ASN	0	-0.014	-0.014	9.072	0.113	0.113	0.000	0.000	0.000	0.000
10	B	391	ARG	1	0.955	0.978	10.744	0.141	0.141	0.000	0.000	0.000	0.000
11	B	392	MET	0	0.031	0.028	11.957	0.080	0.080	0.000	0.000	0.000	0.000
12	B	393	ILE	0	0.042	0.020	11.581	0.066	0.066	0.000	0.000	0.000	0.000
13	B	394	GLN	0	-0.033	-0.010	14.819	0.009	0.009	0.000	0.000	0.000	0.000
14	B	395	ARG	1	0.950	0.960	15.306	0.411	0.411	0.000	0.000	0.000	0.000
15	B	396	LEU	0	0.024	0.015	15.249	0.018	0.018	0.000	0.000	0.000	0.000
16	B	397	ARG	1	0.887	0.951	18.892	0.116	0.116	0.000	0.000	0.000	0.000
17	B	398	ALA	0	-0.004	0.004	20.744	0.019	0.019	0.000	0.000	0.000	0.000
18	B	399	GLU	-1	-0.906	-0.954	22.292	-0.219	-0.219	0.000	0.000	0.000	0.000
19	B	400	ILE	0	-0.031	-0.009	21.150	0.018	0.018	0.000	0.000	0.000	0.000
20	B	401	ASP	-1	-0.873	-0.959	24.649	-0.055	-0.055	0.000	0.000	0.000	0.000
21	B	402	ASN	0	-0.064	-0.021	26.473	0.024	0.024	0.000	0.000	0.000	0.000
22	B	403	VAL	0	0.073	0.026	27.549	0.011	0.011	0.000	0.000	0.000	0.000
23	B	404	LYS	1	0.906	0.957	26.635	0.095	0.095	0.000	0.000	0.000	0.000
24	B	405	LYS	1	0.974	0.992	30.080	0.060	0.060	0.000	0.000	0.000	0.000
25	B	406	GLN	0	0.004	-0.004	30.739	-0.003	-0.003	0.000	0.000	0.000	0.000
26	B	407	CYS	0	-0.016	-0.009	32.386	0.002	0.002	0.000	0.000	0.000	0.000
27	B	408	ALA	0	0.021	0.008	35.037	0.004	0.004	0.000	0.000	0.000	0.000
28	B	409	ASN	0	-0.011	-0.005	36.989	0.009	0.009	0.000	0.000	0.000	0.000
29	B	410	LEU	0	-0.024	-0.006	36.148	0.003	0.003	0.000	0.000	0.000	0.000
30	B	411	GLN	0	0.007	0.000	38.672	0.005	0.005	0.000	0.000	0.000	0.000
31	B	412	ASN	0	0.015	0.014	41.010	0.004	0.004	0.000	0.000	0.000	0.000
32	B	413	ALA	0	-0.013	-0.012	42.657	0.002	0.002	0.000	0.000	0.000	0.000
33	B	414	ILE	0	-0.027	-0.012	42.061	0.001	0.001	0.000	0.000	0.000	0.000
34	B	415	ALA	0	0.072	0.043	45.518	0.002	0.002	0.000	0.000	0.000	0.000
35	B	416	ASP	-1	-0.906	-0.956	47.144	-0.040	-0.040	0.000	0.000	0.000	0.000
36	B	417	ALA	0	-0.093	-0.046	48.510	0.002	0.002	0.000	0.000	0.000	0.000
37	B	418	GLU	-1	-0.910	-0.948	48.885	-0.050	-0.050	0.000	0.000	0.000	0.000
38	B	419	GLN	0	-0.012	0.002	51.571	0.001	0.001	0.000	0.000	0.000	0.000
39	B	420	ARG	1	0.921	0.951	49.198	0.048	0.048	0.000	0.000	0.000	0.000
40	B	421	GLY	0	-0.003	-0.007	54.094	0.001	0.001	0.000	0.000	0.000	0.000
41	B	422	GLU	-1	-0.906	-0.975	55.226	-0.038	-0.038	0.000	0.000	0.000	0.000
42	B	423	LEU	0	-0.073	-0.023	57.481	0.002	0.002	0.000	0.000	0.000	0.000
43	B	424	ALA	0	0.039	0.028	58.882	0.001	0.001	0.000	0.000	0.000	0.000
44	B	425	LEU	0	-0.026	-0.014	58.128	0.001	0.001	0.000	0.000	0.000	0.000
45	B	426	LYS	1	0.900	0.950	58.944	0.031	0.031	0.000	0.000	0.000	0.000
46	B	427	ASP	-1	-0.867	-0.928	63.153	-0.027	-0.027	0.000	0.000	0.000	0.000
47	B	428	ALA	0	-0.048	-0.034	64.575	0.001	0.001	0.000	0.000	0.000	0.000
48	B	429	ARG	1	0.931	0.948	61.419	0.034	0.034	0.000	0.000	0.000	0.000
49	B	430	ASN	0	0.032	0.032	67.591	0.000	0.000	0.000	0.000	0.000	0.000
50	B	431	LYS	1	1.003	1.010	69.512	0.029	0.029	0.000	0.000	0.000	0.000
51	B	432	LEU	0	-0.039	-0.009	69.504	0.000	0.000	0.000	0.000	0.000	0.000
52	B	433	ALA	0	0.038	0.015	71.906	0.001	0.001	0.000	0.000	0.000	0.000
53	B	434	GLU	-1	-0.913	-0.954	73.753	-0.021	-0.021	0.000	0.000	0.000	0.000
54	B	435	LEU	0	-0.052	-0.035	73.312	0.001	0.001	0.000	0.000	0.000	0.000
55	B	436	GLU	-1	-0.952	-0.983	75.206	-0.027	-0.027	0.000	0.000	0.000	0.000
56	B	437	GLU	-1	-0.941	-0.962	77.448	-0.019	-0.019	0.000	0.000	0.000	0.000
57	B	438	ALA	0	-0.008	-0.009	79.653	0.001	0.001	0.000	0.000	0.000	0.000
58	B	439	LEU	0	-0.040	-0.023	79.375	0.001	0.001	0.000	0.000	0.000	0.000
59	B	440	GLN	0	-0.039	-0.024	79.740	0.001	0.001	0.000	0.000	0.000	0.000
60	B	441	LYS	1	1.009	1.013	83.835	0.017	0.017	0.000	0.000	0.000	0.000
61	B	442	ALA	0	0.005	0.008	85.136	0.000	0.000	0.000	0.000	0.000	0.000
62	B	443	LYS	1	0.930	0.955	81.733	0.025	0.025	0.000	0.000	0.000	0.000
63	B	444	GLN	0	-0.008	0.000	86.922	0.001	0.001	0.000	0.000	0.000	0.000
64	B	445	ASP	-1	-0.885	-0.951	89.873	-0.017	-0.017	0.000	0.000	0.000	0.000
65	B	446	MET	0	-0.011	-0.004	90.411	0.000	0.000	0.000	0.000	0.000	0.000
66	B	447	ALA	0	-0.003	-0.007	91.895	0.000	0.000	0.000	0.000	0.000	0.000
67	B	448	ARG	1	0.850	0.908	93.275	0.016	0.016	0.000	0.000	0.000	0.000
68	B	449	LEU	0	0.006	0.011	93.924	0.000	0.000	0.000	0.000	0.000	0.000
69	B	450	LEU	0	-0.012	-0.004	94.205	0.000	0.000	0.000	0.000	0.000	0.000
70	B	451	ARG	1	0.908	0.968	95.405	0.016	0.016	0.000	0.000	0.000	0.000
71	B	452	GLU	-1	-0.822	-0.919	99.434	-0.015	-0.015	0.000	0.000	0.000	0.000
72	B	453	TYR	0	-0.036	-0.009	100.633	0.000	0.000	0.000	0.000	0.000	0.000
73	B	454	GLN	0	0.013	-0.002	101.765	0.001	0.001	0.000	0.000	0.000	0.000
74	B	455	GLU	-1	-0.946	-0.958	104.230	-0.014	-0.014	0.000	0.000	0.000	0.000
75	B	456	LEU	0	0.019	0.011	105.668	0.000	0.000	0.000	0.000	0.000	0.000
76	B	457	MET	0	-0.002	-0.010	106.176	0.000	0.000	0.000	0.000	0.000	0.000
77	B	458	ASN	0	-0.004	-0.012	108.000	0.000	0.000	0.000	0.000	0.000	0.000
78	B	459	THR	0	-0.048	-0.018	110.322	0.000	0.000	0.000	0.000	0.000	0.000
79	B	460	LYS	1	0.898	0.955	110.717	0.014	0.014	0.000	0.000	0.000	0.000
80	B	461	LEU	0	-0.014	-0.014	110.297	0.000	0.000	0.000	0.000	0.000	0.000
81	B	462	ALA	0	-0.031	-0.017	114.219	0.000	0.000	0.000	0.000	0.000	0.000
82	B	463	LEU	0	0.037	0.012	115.458	0.000	0.000	0.000	0.000	0.000	0.000
83	B	464	ASP	-1	-0.826	-0.906	114.751	-0.013	-0.013	0.000	0.000	0.000	0.000
84	B	465	VAL	0	-0.065	-0.024	118.112	0.000	0.000	0.000	0.000	0.000	0.000
85	B	466	GLU	-1	-0.908	-0.952	120.708	-0.011	-0.011	0.000	0.000	0.000	0.000
86	B	467	ILE	0	0.021	0.018	119.060	0.000	0.000	0.000	0.000	0.000	0.000
87	B	468	ALA	0	0.004	-0.005	122.355	0.000	0.000	0.000	0.000	0.000	0.000
88	B	469	THR	0	-0.125	-0.075	124.064	0.000	0.000	0.000	0.000	0.000	0.000
89	B	470	TYR	0	0.062	0.007	124.381	0.000	0.000	0.000	0.000	0.000	0.000
90	B	471	ARG	1	0.915	0.976	120.581	0.012	0.012	0.000	0.000	0.000	0.000
91	B	472	LYS	1	0.982	0.999	125.947	0.011	0.011	0.000	0.000	0.000	0.000
92	B	473	LEU	0	-0.051	-0.021	130.658	0.000	0.000	0.000	0.000	0.000	0.000
93	B	474	LEU	0	-0.060	-0.032	129.959	0.000	0.000	0.000	0.000	0.000	0.000
94	B	475	GLU	-1	-1.008	-0.983	129.589	-0.011	-0.011	0.000	0.000	0.000	0.000
95	B	476	GLY	0	-0.031	-0.009	134.069	0.000	0.000	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(B:382:THR)