FMO DATABASE

FMODB ID: 39J4L

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	OptAll
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	-544219.923962
FMO2-HF: Nuclear repulsion	506549.928379
FMO2-HF: Total energy	-37669.995583
FMO2-MP2: Total energy	-37778.097597

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.
-24.951	-37.135	34.854	-11.533	-11.137	-0.09

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 : -0.061 / q_NPA : -0.037

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	6	THR	0	-0.010	-0.009	3.872	-1.788	-0.177	-0.014	-0.856	-0.741	0.004
4	B	7	LEU	0	-0.025	0.016	6.602	0.043	0.043	0.000	0.000	0.000	0.000
5	B	8	THR	0	0.034	0.015	8.200	0.151	0.151	0.000	0.000	0.000	0.000
6	B	9	VAL	0	-0.014	0.006	11.768	0.053	0.053	0.000	0.000	0.000	0.000
7	B	10	GLN	0	-0.010	-0.037	14.342	0.081	0.081	0.000	0.000	0.000	0.000
8	B	11	ILE	0	-0.028	-0.016	15.830	0.018	0.018	0.000	0.000	0.000	0.000
9	B	12	LEU	0	-0.016	-0.029	19.982	0.019	0.019	0.000	0.000	0.000	0.000
10	B	13	ASP	-1	-0.806	-0.880	23.382	-0.266	-0.266	0.000	0.000	0.000	0.000
11	B	14	LYS	1	0.919	0.979	21.329	0.326	0.326	0.000	0.000	0.000	0.000
12	B	15	GLU	-1	-0.814	-0.895	16.511	-0.693	-0.693	0.000	0.000	0.000	0.000
13	B	16	TYR	0	-0.074	-0.036	14.781	0.062	0.062	0.000	0.000	0.000	0.000
14	B	17	CYS	0	-0.026	-0.008	11.621	-0.061	-0.061	0.000	0.000	0.000	0.000
15	B	18	ILE	0	-0.008	-0.013	8.224	0.195	0.195	0.000	0.000	0.000	0.000
16	B	19	ASN	0	0.009	0.004	4.673	-0.555	-0.552	-0.001	-0.006	0.004	0.000
17	B	20	CYS	0	-0.016	0.000	4.104	1.334	2.053	0.001	-0.350	-0.370	-0.001
18	B	21	PRO	0	0.076	0.043	1.885	-9.696	-14.578	14.702	-5.860	-3.960	-0.035
19	B	22	ASP	-1	-0.754	-0.884	1.779	-21.570	-31.528	20.127	-4.411	-5.758	-0.058
20	B	23	ASP	-1	-0.910	-0.952	3.590	1.272	1.502	0.040	-0.031	-0.239	0.000
21	B	24	GLU	-1	-0.852	-0.917	5.631	-0.276	-0.276	0.000	0.000	0.000	0.000
22	B	25	ARG	1	0.738	0.854	4.087	5.314	5.407	-0.001	-0.019	-0.073	0.000
23	B	26	ALA	0	0.079	0.033	7.434	0.178	0.178	0.000	0.000	0.000	0.000
24	B	27	ASN	0	-0.019	-0.009	10.295	0.093	0.093	0.000	0.000	0.000	0.000
25	B	28	LEU	0	0.021	0.004	7.858	0.095	0.095	0.000	0.000	0.000	0.000
26	B	29	GLU	-1	-0.853	-0.922	10.842	-0.856	-0.856	0.000	0.000	0.000	0.000
27	B	30	SER	0	-0.049	-0.034	12.737	0.121	0.121	0.000	0.000	0.000	0.000
28	B	31	ALA	0	-0.013	0.001	14.022	0.074	0.074	0.000	0.000	0.000	0.000
29	B	32	ALA	0	0.003	0.000	14.252	0.061	0.061	0.000	0.000	0.000	0.000
30	B	33	ARG	1	0.865	0.921	15.101	0.660	0.660	0.000	0.000	0.000	0.000
31	B	34	TYR	0	-0.066	-0.041	18.520	0.050	0.050	0.000	0.000	0.000	0.000
32	B	35	LEU	0	0.022	-0.003	17.444	0.040	0.040	0.000	0.000	0.000	0.000
33	B	36	ASP	-1	-0.788	-0.866	20.141	-0.344	-0.344	0.000	0.000	0.000	0.000
34	B	37	GLY	0	0.008	0.007	21.861	0.029	0.029	0.000	0.000	0.000	0.000
35	B	38	LYS	1	0.791	0.909	23.857	0.204	0.204	0.000	0.000	0.000	0.000
36	B	39	MET	0	-0.007	-0.008	21.028	0.023	0.023	0.000	0.000	0.000	0.000
37	B	40	ARG	1	0.762	0.857	23.510	0.339	0.339	0.000	0.000	0.000	0.000
38	B	41	GLU	-1	-0.853	-0.915	28.030	-0.162	-0.162	0.000	0.000	0.000	0.000
39	B	42	ILE	0	-0.005	0.002	27.625	0.016	0.016	0.000	0.000	0.000	0.000
40	B	43	ARG	1	0.823	0.900	28.035	0.244	0.244	0.000	0.000	0.000	0.000
41	B	44	SER	0	-0.030	-0.016	31.431	0.008	0.008	0.000	0.000	0.000	0.000
42	B	45	SER	0	-0.052	-0.031	33.741	0.012	0.012	0.000	0.000	0.000	0.000
43	B	46	GLY	0	-0.003	0.005	35.307	0.009	0.009	0.000	0.000	0.000	0.000
44	B	47	LYS	1	0.907	0.960	35.652	0.099	0.099	0.000	0.000	0.000	0.000
45	B	48	VAL	0	-0.026	-0.018	31.688	0.006	0.006	0.000	0.000	0.000	0.000
46	B	49	ILE	0	0.044	0.019	34.177	-0.006	-0.006	0.000	0.000	0.000	0.000
47	B	50	GLY	0	0.032	0.019	31.625	0.006	0.006	0.000	0.000	0.000	0.000
48	B	51	ALA	0	-0.008	-0.014	26.701	-0.003	-0.003	0.000	0.000	0.000	0.000
49	B	52	ASP	-1	-0.814	-0.917	25.772	-0.178	-0.178	0.000	0.000	0.000	0.000
50	B	53	ARG	1	0.933	0.970	26.561	0.119	0.119	0.000	0.000	0.000	0.000
51	B	54	VAL	0	0.006	0.009	26.501	0.004	0.004	0.000	0.000	0.000	0.000
52	B	55	ALA	0	0.034	0.016	22.773	-0.004	-0.004	0.000	0.000	0.000	0.000
53	B	56	VAL	0	-0.009	-0.006	24.083	-0.002	-0.002	0.000	0.000	0.000	0.000
54	B	57	MET	0	-0.010	-0.012	25.903	0.010	0.010	0.000	0.000	0.000	0.000
55	B	58	ALA	0	0.016	0.006	24.001	0.006	0.006	0.000	0.000	0.000	0.000
56	B	59	ALA	0	0.029	0.015	22.229	0.001	0.001	0.000	0.000	0.000	0.000
57	B	60	LEU	0	0.003	0.004	23.535	0.014	0.014	0.000	0.000	0.000	0.000
58	B	61	ASN	0	0.005	-0.006	26.984	0.017	0.017	0.000	0.000	0.000	0.000
59	B	62	ILE	0	0.018	0.018	21.148	0.007	0.007	0.000	0.000	0.000	0.000
60	B	63	THR	0	-0.031	-0.024	24.481	0.012	0.012	0.000	0.000	0.000	0.000
61	B	64	HIS	0	-0.007	-0.002	25.579	0.023	0.023	0.000	0.000	0.000	0.000
62	B	65	ASP	-1	-0.808	-0.901	26.243	-0.144	-0.144	0.000	0.000	0.000	0.000
63	B	66	LEU	0	-0.042	-0.010	23.258	0.006	0.006	0.000	0.000	0.000	0.000
64	B	67	LEU	0	0.020	-0.003	26.238	0.013	0.013	0.000	0.000	0.000	0.000
65	B	68	HIS	0	-0.016	-0.004	29.098	0.013	0.013	0.000	0.000	0.000	0.000
66	B	69	ARG	1	0.927	0.967	26.281	0.125	0.125	0.000	0.000	0.000	0.000
67	B	70	LYS	1	0.844	0.905	28.929	0.022	0.022	0.000	0.000	0.000	0.000
68	B	71	GLU	-1	-0.829	-0.892	30.634	-0.030	-0.030	0.000	0.000	0.000	0.000
69	B	72	ARG	1	0.826	0.890	33.369	0.061	0.061	0.000	0.000	0.000	0.000
70	B	73	LEU	0	0.015	0.013	30.332	0.002	0.002	0.000	0.000	0.000	0.000
71	B	74	ASP	-1	-0.796	-0.882	33.478	-0.016	-0.016	0.000	0.000	0.000	0.000
72	B	75	GLN	0	-0.048	-0.038	35.789	0.001	0.001	0.000	0.000	0.000	0.000
73	B	76	GLU	-1	-0.905	-0.919	36.921	-0.029	-0.029	0.000	0.000	0.000	0.000
74	B	77	SER	0	0.070	0.047	36.327	0.005	0.005	0.000	0.000	0.000	0.000
75	B	78	SER	0	-0.081	-0.055	38.461	0.006	0.006	0.000	0.000	0.000	0.000
76	B	79	SER	0	0.003	0.001	41.273	0.001	0.001	0.000	0.000	0.000	0.000
77	B	80	THR	0	-0.019	-0.035	40.750	0.002	0.002	0.000	0.000	0.000	0.000
78	B	81	ARG	1	0.891	0.924	40.284	0.007	0.007	0.000	0.000	0.000	0.000
79	B	82	GLU	-1	-0.897	-0.931	43.781	-0.015	-0.015	0.000	0.000	0.000	0.000
80	B	83	ARG	1	0.988	0.991	45.553	0.026	0.026	0.000	0.000	0.000	0.000
81	B	84	VAL	0	0.004	0.007	44.240	0.001	0.001	0.000	0.000	0.000	0.000
82	B	85	ARG	1	0.932	0.960	47.058	0.000	0.000	0.000	0.000	0.000	0.000
83	B	86	GLU	-1	-0.829	-0.890	49.835	-0.015	-0.015	0.000	0.000	0.000	0.000
84	B	87	LEU	0	-0.038	-0.008	49.396	0.000	0.000	0.000	0.000	0.000	0.000
85	B	88	LEU	0	-0.015	-0.024	48.614	0.001	0.001	0.000	0.000	0.000	0.000
86	B	89	ASP	-1	-0.820	-0.886	52.672	-0.003	-0.003	0.000	0.000	0.000	0.000
87	B	90	ARG	1	0.817	0.878	54.444	0.012	0.012	0.000	0.000	0.000	0.000
88	B	91	VAL	0	-0.043	-0.020	54.279	0.000	0.000	0.000	0.000	0.000	0.000
89	B	92	ASP	-1	-0.917	-0.940	56.742	0.004	0.004	0.000	0.000	0.000	0.000
90	B	93	ARG	1	0.778	0.857	58.432	0.004	0.004	0.000	0.000	0.000	0.000
91	B	94	ALA	0	-0.038	-0.012	60.928	0.000	0.000	0.000	0.000	0.000	0.000
92	B	95	LEU	0	-0.029	0.002	61.849	0.001	0.001	0.000	0.000	0.000	0.000
93	B	96	ALA	0	-0.030	-0.012	63.093	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:4:SER)