FMO DATABASE

FMODB ID: N9N7Q

Calculation Name: 1T3U-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1T3U

Chain ID: B

ChEMBL ID:

UniProt ID: Q9HTW3

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:

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	93
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-541775.145143
FMO2-HF: Nuclear repulsion	504106.225494
FMO2-HF: Total energy	-37668.919649
FMO2-MP2: Total energy	-37777.038661

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:4:SER)

Summations of interaction energy for fragment #1(B:4:SER)

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.
-14.008	-12.87	9.523	-4.159	-6.503	-0.025

Interaction energy analysis for fragmet #1(B:4:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.004 / q_NPA : 0.016

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	B	6	THR	0	0.027	0.007	3.827	-1.225	0.999	-0.025	-1.250	-0.949	0.007
4	B	7	LEU	0	-0.062	-0.026	6.915	0.032	0.032	0.000	0.000	0.000	0.000
5	B	8	THR	0	0.039	0.011	8.340	0.114	0.114	0.000	0.000	0.000	0.000
6	B	9	VAL	0	-0.044	-0.011	12.105	0.052	0.052	0.000	0.000	0.000	0.000
7	B	10	GLN	0	0.037	-0.002	14.597	0.051	0.051	0.000	0.000	0.000	0.000
8	B	11	ILE	0	-0.046	-0.026	16.118	0.018	0.018	0.000	0.000	0.000	0.000
9	B	12	LEU	0	-0.044	-0.040	20.101	0.016	0.016	0.000	0.000	0.000	0.000
10	B	13	ASP	-1	-0.942	-0.979	23.534	-0.227	-0.227	0.000	0.000	0.000	0.000
11	B	14	LYS	1	0.937	0.979	20.821	0.260	0.260	0.000	0.000	0.000	0.000
12	B	15	GLU	-1	-0.884	-0.938	16.245	-0.624	-0.624	0.000	0.000	0.000	0.000
13	B	16	TYR	0	-0.052	-0.025	14.189	0.059	0.059	0.000	0.000	0.000	0.000
14	B	17	CYS	0	-0.011	0.016	11.276	-0.095	-0.095	0.000	0.000	0.000	0.000
15	B	18	ILE	0	-0.002	-0.014	7.855	0.126	0.126	0.000	0.000	0.000	0.000
16	B	19	ASN	0	-0.004	0.003	4.735	-0.453	-0.487	-0.001	-0.007	0.042	0.000
17	B	20	CYS	0	-0.045	-0.029	4.342	1.012	1.369	0.000	-0.113	-0.244	0.000
18	B	21	PRO	0	0.063	0.020	2.064	-8.314	-8.170	8.404	-5.025	-3.524	-0.026
19	B	22	ASP	-1	-0.832	-0.927	2.590	-9.837	-11.536	1.140	2.274	-1.715	-0.006
20	B	23	ASP	-1	-0.973	-0.978	3.920	0.876	1.022	0.005	-0.038	-0.113	0.000
21	B	24	GLU	-1	-0.862	-0.936	5.879	0.337	0.337	0.000	0.000	0.000	0.000
22	B	25	ARG	1	0.873	0.945	4.851	3.265	3.265	0.000	0.000	0.000	0.000
23	B	26	ALA	0	0.063	0.032	7.646	0.151	0.151	0.000	0.000	0.000	0.000
24	B	27	ASN	0	0.019	0.024	10.436	0.033	0.033	0.000	0.000	0.000	0.000
25	B	28	LEU	0	0.037	0.006	8.071	0.063	0.063	0.000	0.000	0.000	0.000
26	B	29	GLU	-1	-0.948	-0.964	11.111	-0.799	-0.799	0.000	0.000	0.000	0.000
27	B	30	SER	0	-0.084	-0.066	13.165	0.091	0.091	0.000	0.000	0.000	0.000
28	B	31	ALA	0	-0.014	0.002	14.244	0.048	0.048	0.000	0.000	0.000	0.000
29	B	32	ALA	0	0.025	0.011	14.554	0.044	0.044	0.000	0.000	0.000	0.000
30	B	33	ARG	1	0.958	0.985	16.301	0.454	0.454	0.000	0.000	0.000	0.000
31	B	34	TYR	0	-0.042	-0.022	18.840	0.037	0.037	0.000	0.000	0.000	0.000
32	B	35	LEU	0	0.005	-0.010	18.238	0.028	0.028	0.000	0.000	0.000	0.000
33	B	36	ASP	-1	-0.802	-0.875	20.262	-0.258	-0.258	0.000	0.000	0.000	0.000
34	B	37	GLY	0	0.021	0.008	22.077	0.023	0.023	0.000	0.000	0.000	0.000
35	B	38	LYS	1	0.857	0.943	24.060	0.136	0.136	0.000	0.000	0.000	0.000
36	B	39	MET	0	0.006	-0.005	21.571	0.017	0.017	0.000	0.000	0.000	0.000
37	B	40	ARG	1	0.796	0.893	24.384	0.258	0.258	0.000	0.000	0.000	0.000
38	B	41	GLU	-1	-0.919	-0.964	27.979	-0.115	-0.115	0.000	0.000	0.000	0.000
39	B	42	ILE	0	-0.007	0.010	27.939	0.013	0.013	0.000	0.000	0.000	0.000
40	B	43	ARG	1	0.920	0.966	28.758	0.184	0.184	0.000	0.000	0.000	0.000
41	B	44	SER	0	-0.063	-0.029	31.764	0.008	0.008	0.000	0.000	0.000	0.000
42	B	45	SER	0	0.002	0.009	34.117	0.009	0.009	0.000	0.000	0.000	0.000
43	B	46	GLY	0	0.000	0.007	35.326	0.006	0.006	0.000	0.000	0.000	0.000
44	B	47	LYS	1	0.912	0.958	35.834	0.068	0.068	0.000	0.000	0.000	0.000
45	B	48	VAL	0	-0.024	-0.012	31.648	0.006	0.006	0.000	0.000	0.000	0.000
46	B	49	ILE	0	0.050	0.024	33.927	-0.007	-0.007	0.000	0.000	0.000	0.000
47	B	50	GLY	0	0.034	0.012	31.456	0.005	0.005	0.000	0.000	0.000	0.000
48	B	51	ALA	0	0.002	-0.007	26.461	0.000	0.000	0.000	0.000	0.000	0.000
49	B	52	ASP	-1	-0.829	-0.910	25.474	-0.125	-0.125	0.000	0.000	0.000	0.000
50	B	53	ARG	1	0.961	0.962	26.334	0.080	0.080	0.000	0.000	0.000	0.000
51	B	54	VAL	0	-0.040	-0.016	26.993	0.004	0.004	0.000	0.000	0.000	0.000
52	B	55	ALA	0	0.053	0.019	22.635	-0.001	-0.001	0.000	0.000	0.000	0.000
53	B	56	VAL	0	-0.005	0.002	24.200	0.003	0.003	0.000	0.000	0.000	0.000
54	B	57	MET	0	-0.008	-0.014	25.762	0.010	0.010	0.000	0.000	0.000	0.000
55	B	58	ALA	0	0.009	0.004	24.461	0.006	0.006	0.000	0.000	0.000	0.000
56	B	59	ALA	0	0.029	0.012	22.548	0.001	0.001	0.000	0.000	0.000	0.000
57	B	60	LEU	0	0.001	0.005	23.919	0.013	0.013	0.000	0.000	0.000	0.000
58	B	61	ASN	0	0.025	0.002	27.213	0.014	0.014	0.000	0.000	0.000	0.000
59	B	62	ILE	0	0.013	0.018	21.848	0.005	0.005	0.000	0.000	0.000	0.000
60	B	63	THR	0	-0.024	-0.015	24.612	0.011	0.011	0.000	0.000	0.000	0.000
61	B	64	HIS	0	-0.041	-0.032	25.797	0.015	0.015	0.000	0.000	0.000	0.000
62	B	65	ASP	-1	-0.835	-0.923	26.746	-0.084	-0.084	0.000	0.000	0.000	0.000
63	B	66	LEU	0	-0.035	-0.006	23.737	0.005	0.005	0.000	0.000	0.000	0.000
64	B	67	LEU	0	0.012	-0.004	26.744	0.008	0.008	0.000	0.000	0.000	0.000
65	B	68	HIS	0	0.027	0.017	29.603	0.005	0.005	0.000	0.000	0.000	0.000
66	B	69	ARG	1	0.921	0.972	27.111	0.061	0.061	0.000	0.000	0.000	0.000
67	B	70	LYS	1	0.914	0.945	28.714	-0.016	-0.016	0.000	0.000	0.000	0.000
68	B	71	GLU	-1	-0.914	-0.945	30.911	0.002	0.002	0.000	0.000	0.000	0.000
69	B	72	ARG	1	0.900	0.947	33.880	0.031	0.031	0.000	0.000	0.000	0.000
70	B	73	LEU	0	0.006	0.001	30.232	-0.001	-0.001	0.000	0.000	0.000	0.000
71	B	74	ASP	-1	-0.851	-0.928	33.949	0.014	0.014	0.000	0.000	0.000	0.000
72	B	75	GLN	0	-0.045	-0.032	36.076	-0.001	-0.001	0.000	0.000	0.000	0.000
73	B	76	GLU	-1	-0.944	-0.960	37.093	-0.012	-0.012	0.000	0.000	0.000	0.000
74	B	77	SER	0	0.028	0.010	36.579	0.002	0.002	0.000	0.000	0.000	0.000
75	B	78	SER	0	-0.028	-0.024	38.656	0.003	0.003	0.000	0.000	0.000	0.000
76	B	79	SER	0	-0.007	0.006	41.548	0.001	0.001	0.000	0.000	0.000	0.000
77	B	80	THR	0	-0.010	-0.001	40.618	0.000	0.000	0.000	0.000	0.000	0.000
78	B	81	ARG	1	0.943	0.957	41.329	-0.016	-0.016	0.000	0.000	0.000	0.000
79	B	82	GLU	-1	-0.960	-0.978	44.197	0.001	0.001	0.000	0.000	0.000	0.000
80	B	83	ARG	1	0.999	0.993	45.739	0.009	0.009	0.000	0.000	0.000	0.000
81	B	84	VAL	0	-0.006	0.008	44.490	0.000	0.000	0.000	0.000	0.000	0.000
82	B	85	ARG	1	0.932	0.961	46.531	-0.014	-0.014	0.000	0.000	0.000	0.000
83	B	86	GLU	-1	-0.947	-0.949	50.204	-0.002	-0.002	0.000	0.000	0.000	0.000
84	B	87	LEU	0	-0.031	-0.026	49.601	0.000	0.000	0.000	0.000	0.000	0.000
85	B	88	LEU	0	-0.020	-0.029	49.787	0.000	0.000	0.000	0.000	0.000	0.000
86	B	89	ASP	-1	-0.882	-0.948	53.057	0.007	0.007	0.000	0.000	0.000	0.000
87	B	90	ARG	1	0.952	0.973	55.511	0.001	0.001	0.000	0.000	0.000	0.000
88	B	91	VAL	0	-0.107	-0.043	54.627	0.000	0.000	0.000	0.000	0.000	0.000
89	B	92	ASP	-1	-0.887	-0.939	57.037	0.012	0.012	0.000	0.000	0.000	0.000
90	B	93	ARG	1	0.860	0.938	58.935	-0.005	-0.005	0.000	0.000	0.000	0.000
91	B	94	ALA	0	-0.071	-0.022	61.311	-0.001	-0.001	0.000	0.000	0.000	0.000
92	B	95	LEU	0	0.017	0.017	62.554	0.000	0.000	0.000	0.000	0.000	0.000
93	B	96	ALA	0	-0.028	-0.013	63.581	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:4:SER)