FMO DATABASE

FMODB ID: M3K8Z

Calculation Name: 1T4A-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1T4A

Chain ID: A

ChEMBL ID:

UniProt ID: P12049

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	80
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-491882.345612
FMO2-HF: Nuclear repulsion	458311.483056
FMO2-HF: Total energy	-33570.862556
FMO2-MP2: Total energy	-33665.961383

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:1:MET)

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

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.
-19.244	-11.119	5.939	-5.498	-8.567	-0.027

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.034 / q_NPA : -0.033

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	3	LYS	1	0.951	0.996	3.552	0.403	2.548	0.007	-1.019	-1.133	-0.001
4	A	4	VAL	0	-0.009	-0.024	5.603	0.155	0.155	0.000	0.000	0.000	0.000
5	A	5	LYS	1	0.914	0.982	8.857	0.833	0.833	0.000	0.000	0.000	0.000
6	A	6	VAL	0	0.007	-0.009	12.032	0.008	0.008	0.000	0.000	0.000	0.000
7	A	7	TYR	0	-0.046	-0.033	14.993	0.055	0.055	0.000	0.000	0.000	0.000
8	A	8	VAL	0	0.010	0.006	18.582	0.003	0.003	0.000	0.000	0.000	0.000
9	A	9	SER	0	0.021	0.010	21.226	0.007	0.007	0.000	0.000	0.000	0.000
10	A	10	LEU	0	0.011	0.013	24.839	-0.001	-0.001	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.932	0.978	27.627	0.103	0.103	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.922	-0.956	29.748	-0.089	-0.089	0.000	0.000	0.000	0.000
13	A	13	SER	0	-0.057	-0.027	32.330	0.003	0.003	0.000	0.000	0.000	0.000
14	A	14	VAL	0	-0.039	-0.007	31.604	0.007	0.007	0.000	0.000	0.000	0.000
15	A	15	LEU	0	0.012	-0.003	33.775	-0.003	-0.003	0.000	0.000	0.000	0.000
16	A	16	ASP	-1	-0.749	-0.880	31.037	-0.089	-0.089	0.000	0.000	0.000	0.000
17	A	17	PRO	0	-0.012	-0.012	33.821	0.002	0.002	0.000	0.000	0.000	0.000
18	A	18	GLN	0	0.003	0.007	28.718	0.005	0.005	0.000	0.000	0.000	0.000
19	A	19	GLY	0	0.064	0.024	32.951	0.002	0.002	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.005	-0.001	33.477	0.003	0.003	0.000	0.000	0.000	0.000
21	A	21	ALA	0	-0.012	-0.003	36.521	0.003	0.003	0.000	0.000	0.000	0.000
22	A	22	VAL	0	0.000	-0.005	32.513	0.003	0.003	0.000	0.000	0.000	0.000
23	A	23	GLN	0	0.011	0.010	35.841	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	24	HIS	0	0.011	0.016	37.565	0.001	0.001	0.000	0.000	0.000	0.000
25	A	25	ALA	0	-0.005	-0.005	38.247	0.002	0.002	0.000	0.000	0.000	0.000
26	A	26	LEU	0	0.003	-0.007	34.424	0.002	0.002	0.000	0.000	0.000	0.000
27	A	27	HIS	0	-0.024	-0.018	39.042	0.003	0.003	0.000	0.000	0.000	0.000
28	A	28	SER	0	-0.045	-0.015	42.247	0.003	0.003	0.000	0.000	0.000	0.000
29	A	29	MET	0	-0.115	-0.045	38.439	0.002	0.002	0.000	0.000	0.000	0.000
30	A	30	THR	0	-0.078	-0.049	42.203	0.000	0.000	0.000	0.000	0.000	0.000
31	A	31	TYR	0	0.023	0.024	38.716	0.000	0.000	0.000	0.000	0.000	0.000
32	A	32	ASN	0	0.000	-0.018	40.120	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.912	-0.952	38.989	-0.056	-0.056	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.044	-0.019	35.472	-0.004	-0.004	0.000	0.000	0.000	0.000
35	A	35	GLN	0	-0.046	-0.016	37.457	0.004	0.004	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.888	-0.959	34.064	-0.083	-0.083	0.000	0.000	0.000	0.000
37	A	37	VAL	0	-0.043	-0.006	31.601	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.840	0.931	29.222	0.099	0.099	0.000	0.000	0.000	0.000
39	A	39	ILE	0	-0.040	-0.032	26.963	-0.007	-0.007	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.012	0.003	24.427	0.002	0.002	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.886	0.939	20.243	0.133	0.133	0.000	0.000	0.000	0.000
42	A	42	TYR	0	-0.035	-0.042	13.453	-0.028	-0.028	0.000	0.000	0.000	0.000
43	A	43	MET	0	-0.040	-0.021	14.209	0.035	0.035	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.842	-0.884	9.838	-0.431	-0.431	0.000	0.000	0.000	0.000
45	A	45	LEU	0	-0.010	-0.006	8.604	0.135	0.135	0.000	0.000	0.000	0.000
46	A	46	THR	0	-0.009	0.002	3.033	-0.781	-0.423	1.259	-0.324	-1.294	0.001
47	A	47	ILE	0	-0.030	-0.019	3.575	-0.336	0.354	0.007	-0.160	-0.537	0.000
48	A	48	GLU	-1	-0.914	-0.950	2.374	-6.985	-4.536	4.448	-3.208	-3.689	-0.035
49	A	49	LYS	1	0.929	0.955	3.256	-7.108	-5.273	0.218	-0.696	-1.356	0.008
50	A	50	SER	0	-0.021	-0.020	4.946	-0.567	-0.508	-0.001	-0.004	-0.054	0.000
51	A	51	ASP	-1	-0.941	-0.976	8.633	0.417	0.417	0.000	0.000	0.000	0.000
52	A	52	ARG	1	0.949	0.991	10.927	-0.139	-0.139	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.850	-0.904	10.563	0.284	0.284	0.000	0.000	0.000	0.000
54	A	54	LEU	0	-0.042	-0.039	7.370	-0.067	-0.067	0.000	0.000	0.000	0.000
55	A	55	ASP	-1	-0.868	-0.944	10.230	-0.192	-0.192	0.000	0.000	0.000	0.000
56	A	56	VAL	0	-0.001	-0.006	13.685	-0.024	-0.024	0.000	0.000	0.000	0.000
57	A	57	LEU	0	-0.004	-0.003	8.531	-0.007	-0.007	0.000	0.000	0.000	0.000
58	A	58	VAL	0	-0.005	-0.010	10.527	-0.039	-0.039	0.000	0.000	0.000	0.000
59	A	59	LYS	1	1.000	1.000	12.884	0.167	0.167	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.897	-0.937	15.766	-0.030	-0.030	0.000	0.000	0.000	0.000
61	A	61	MET	0	-0.030	-0.010	9.922	0.014	0.014	0.000	0.000	0.000	0.000
62	A	62	CYS	0	-0.042	-0.025	15.292	0.005	0.005	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.979	-0.987	17.560	-0.097	-0.097	0.000	0.000	0.000	0.000
64	A	64	LYS	1	0.849	0.928	18.878	0.088	0.088	0.000	0.000	0.000	0.000
65	A	65	LEU	0	-0.068	-0.028	16.114	0.013	0.013	0.000	0.000	0.000	0.000
66	A	66	LEU	0	-0.042	-0.028	13.798	0.006	0.006	0.000	0.000	0.000	0.000
67	A	67	ALA	0	0.022	0.015	18.357	0.003	0.003	0.000	0.000	0.000	0.000
68	A	68	ASN	0	0.027	0.037	21.600	0.009	0.009	0.000	0.000	0.000	0.000
69	A	69	THR	0	0.042	0.002	23.118	0.007	0.007	0.000	0.000	0.000	0.000
70	A	70	VAL	0	-0.052	-0.019	25.654	0.003	0.003	0.000	0.000	0.000	0.000
71	A	71	ILE	0	-0.043	-0.032	28.099	0.004	0.004	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.915	-0.954	24.053	-0.131	-0.131	0.000	0.000	0.000	0.000
73	A	73	ASP	-1	-0.848	-0.934	24.573	-0.133	-0.133	0.000	0.000	0.000	0.000
74	A	74	TYR	0	-0.008	-0.029	17.856	-0.012	-0.012	0.000	0.000	0.000	0.000
75	A	75	ARG	1	0.889	0.957	18.218	0.321	0.321	0.000	0.000	0.000	0.000
76	A	76	TYR	0	0.008	-0.012	12.618	0.024	0.024	0.000	0.000	0.000	0.000
77	A	77	GLU	-1	-0.887	-0.933	13.381	-0.439	-0.439	0.000	0.000	0.000	0.000
78	A	78	VAL	0	-0.037	-0.024	7.613	-0.046	-0.046	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.858	-0.929	8.040	-0.747	-0.747	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.966	-0.982	3.609	-3.945	-3.356	0.001	-0.087	-0.504	0.000

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