FMO DATABASE

FMODB ID: Q132Y

Calculation Name: 5DTC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5DTC

Chain ID: A

ChEMBL ID:

UniProt ID: Q12024

Base Structure: X-ray

Registration Date: 2023-06-20

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	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	87
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-616476.937819
FMO2-HF: Nuclear repulsion	581989.963024
FMO2-HF: Total energy	-34486.974795
FMO2-MP2: Total energy	-34589.693766

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:5:LYS)

Summations of interaction energy for fragment #1(A:5:LYS)

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.
-28.645	-24.519	0.844	-2.104	-2.864	-0.011

Interaction energy analysis for fragmet #1(A:5:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.997 / q_NPA : 0.977

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	7	GLN	0	-0.007	-0.003	3.044	3.599	5.852	-0.021	-0.958	-1.275	0.001
4	A	8	VAL	0	0.036	0.020	4.542	-4.700	-4.586	-0.001	-0.017	-0.096	0.000
5	A	9	LYS	1	0.939	0.989	7.258	22.352	22.352	0.000	0.000	0.000	0.000
6	A	10	ILE	0	-0.003	0.001	10.270	-0.226	-0.226	0.000	0.000	0.000	0.000
7	A	11	ARG	1	0.948	0.968	13.527	15.105	15.105	0.000	0.000	0.000	0.000
8	A	12	PHE	0	0.017	0.007	16.980	-0.216	-0.216	0.000	0.000	0.000	0.000
9	A	13	PHE	0	0.023	0.020	20.015	0.407	0.407	0.000	0.000	0.000	0.000
10	A	14	THR	0	0.033	-0.006	23.435	-0.012	-0.012	0.000	0.000	0.000	0.000
11	A	15	ARG	1	0.933	0.975	26.357	9.997	9.997	0.000	0.000	0.000	0.000
12	A	16	GLU	-1	-0.780	-0.853	29.368	-8.804	-8.804	0.000	0.000	0.000	0.000
13	A	17	LYS	1	0.942	0.955	31.389	7.791	7.791	0.000	0.000	0.000	0.000
14	A	18	ASP	-1	-0.902	-0.947	33.634	-8.217	-8.217	0.000	0.000	0.000	0.000
15	A	19	GLU	-1	-0.869	-0.929	32.620	-8.345	-8.345	0.000	0.000	0.000	0.000
16	A	20	LEU	0	-0.011	-0.004	32.074	-0.193	-0.193	0.000	0.000	0.000	0.000
17	A	21	LEU	0	-0.050	-0.026	29.459	-0.224	-0.224	0.000	0.000	0.000	0.000
18	A	22	HIS	0	-0.041	-0.005	27.915	-0.476	-0.476	0.000	0.000	0.000	0.000
19	A	23	VAL	0	-0.001	0.009	22.331	0.082	0.082	0.000	0.000	0.000	0.000
20	A	24	GLN	0	-0.017	-0.024	23.408	-0.035	-0.035	0.000	0.000	0.000	0.000
21	A	25	ASP	-1	-0.903	-0.954	22.367	-12.584	-12.584	0.000	0.000	0.000	0.000
22	A	26	THR	0	-0.041	-0.011	18.527	-0.489	-0.489	0.000	0.000	0.000	0.000
23	A	27	PRO	0	-0.047	-0.017	14.625	-0.368	-0.368	0.000	0.000	0.000	0.000
24	A	28	MET	0	0.006	0.007	13.821	0.530	0.530	0.000	0.000	0.000	0.000
25	A	29	TYR	0	-0.022	-0.019	7.226	-0.382	-0.382	0.000	0.000	0.000	0.000
26	A	30	ALA	0	0.032	0.026	9.557	1.283	1.283	0.000	0.000	0.000	0.000
27	A	31	PRO	0	0.045	0.014	7.931	-2.275	-2.275	0.000	0.000	0.000	0.000
28	A	32	ILE	0	0.024	0.006	4.435	1.774	1.941	-0.001	-0.024	-0.142	0.000
29	A	33	SER	0	-0.014	-0.005	8.235	0.982	0.982	0.000	0.000	0.000	0.000
30	A	34	LEU	0	-0.020	0.007	10.666	1.553	1.553	0.000	0.000	0.000	0.000
31	A	35	LYS	1	0.999	0.981	13.590	15.769	15.769	0.000	0.000	0.000	0.000
32	A	36	ARG	1	0.889	0.938	16.596	11.629	11.629	0.000	0.000	0.000	0.000
33	A	37	TYR	0	0.002	-0.009	19.868	0.283	0.283	0.000	0.000	0.000	0.000
34	A	38	GLY	0	0.080	0.050	17.287	0.245	0.245	0.000	0.000	0.000	0.000
35	A	39	LEU	0	-0.013	-0.008	14.549	0.024	0.024	0.000	0.000	0.000	0.000
36	A	40	SER	0	0.034	0.009	18.287	0.392	0.392	0.000	0.000	0.000	0.000
37	A	41	GLU	-1	-0.941	-0.961	20.056	-12.300	-12.300	0.000	0.000	0.000	0.000
38	A	42	ILE	0	-0.020	-0.014	15.134	0.161	0.161	0.000	0.000	0.000	0.000
39	A	43	VAL	0	0.014	0.008	19.598	0.277	0.277	0.000	0.000	0.000	0.000
40	A	44	ASN	0	-0.014	-0.013	22.163	0.749	0.749	0.000	0.000	0.000	0.000
41	A	45	HIS	0	-0.006	0.016	21.770	0.431	0.431	0.000	0.000	0.000	0.000
42	A	46	LEU	0	-0.062	-0.039	19.556	0.222	0.222	0.000	0.000	0.000	0.000
43	A	47	LEU	0	-0.043	-0.009	23.777	0.213	0.213	0.000	0.000	0.000	0.000
44	A	48	GLY	0	-0.028	0.009	26.754	0.336	0.336	0.000	0.000	0.000	0.000
45	A	49	SER	0	-0.061	-0.053	28.280	0.311	0.311	0.000	0.000	0.000	0.000
46	A	50	GLU	-1	-0.881	-0.923	30.187	-7.854	-7.854	0.000	0.000	0.000	0.000
47	A	51	LYS	1	0.854	0.915	32.525	7.825	7.825	0.000	0.000	0.000	0.000
48	A	52	PRO	0	-0.003	0.005	27.897	-0.059	-0.059	0.000	0.000	0.000	0.000
49	A	53	VAL	0	0.018	0.002	28.692	0.248	0.248	0.000	0.000	0.000	0.000
50	A	54	PRO	0	-0.036	-0.002	27.275	-0.396	-0.396	0.000	0.000	0.000	0.000
51	A	55	PHE	0	0.064	0.017	24.028	0.191	0.191	0.000	0.000	0.000	0.000
52	A	56	ASP	-1	-0.819	-0.897	23.620	-11.607	-11.607	0.000	0.000	0.000	0.000
53	A	57	PHE	0	0.012	-0.007	19.314	-0.054	-0.054	0.000	0.000	0.000	0.000
54	A	58	LEU	0	-0.033	-0.009	20.908	-0.070	-0.070	0.000	0.000	0.000	0.000
55	A	59	ILE	0	-0.007	0.000	14.674	-0.309	-0.309	0.000	0.000	0.000	0.000
56	A	60	GLU	-1	-0.853	-0.935	18.746	-14.197	-14.197	0.000	0.000	0.000	0.000
57	A	61	GLY	0	0.027	0.024	21.235	0.289	0.289	0.000	0.000	0.000	0.000
58	A	62	GLU	-1	-0.886	-0.913	19.835	-14.441	-14.441	0.000	0.000	0.000	0.000
59	A	63	LEU	0	-0.025	-0.016	20.831	-0.401	-0.401	0.000	0.000	0.000	0.000
60	A	64	LEU	0	-0.010	-0.010	15.239	-0.349	-0.349	0.000	0.000	0.000	0.000
61	A	65	ARG	1	0.934	0.963	19.301	12.309	12.309	0.000	0.000	0.000	0.000
62	A	66	THR	0	-0.073	-0.064	15.388	0.498	0.498	0.000	0.000	0.000	0.000
63	A	67	SER	0	-0.081	-0.047	12.030	-0.265	-0.265	0.000	0.000	0.000	0.000
64	A	68	LEU	0	0.048	0.020	10.410	-0.013	-0.013	0.000	0.000	0.000	0.000
65	A	69	HIS	0	0.037	0.012	7.110	-2.704	-2.704	0.000	0.000	0.000	0.000
66	A	70	ASP	-1	-0.782	-0.861	9.169	-20.918	-20.918	0.000	0.000	0.000	0.000
67	A	71	TYR	0	-0.008	0.004	12.236	0.077	0.077	0.000	0.000	0.000	0.000
68	A	72	LEU	0	-0.007	-0.015	6.836	0.414	0.414	0.000	0.000	0.000	0.000
69	A	73	THR	0	-0.010	-0.006	9.497	-1.121	-1.121	0.000	0.000	0.000	0.000
70	A	74	LYS	1	0.885	0.949	11.021	16.651	16.651	0.000	0.000	0.000	0.000
71	A	75	LYS	1	0.803	0.881	13.689	17.145	17.145	0.000	0.000	0.000	0.000
72	A	76	GLY	0	0.002	0.021	11.283	0.537	0.537	0.000	0.000	0.000	0.000
73	A	77	LEU	0	-0.042	-0.012	10.304	-0.432	-0.432	0.000	0.000	0.000	0.000
74	A	78	SER	0	0.017	-0.022	5.118	-0.046	-0.046	0.000	0.000	0.000	0.000
75	A	79	SER	0	-0.012	-0.025	2.650	-1.767	-0.277	0.868	-1.103	-1.254	-0.012
76	A	80	GLU	-1	-0.912	-0.933	5.032	-47.392	-47.290	-0.001	-0.002	-0.097	0.000
77	A	81	ALA	0	-0.039	-0.003	6.923	3.575	3.575	0.000	0.000	0.000	0.000
78	A	82	SER	0	-0.037	-0.030	9.387	0.033	0.033	0.000	0.000	0.000	0.000
79	A	83	LEU	0	-0.039	-0.023	10.715	0.849	0.849	0.000	0.000	0.000	0.000
80	A	84	ASN	0	-0.013	-0.006	13.786	0.507	0.507	0.000	0.000	0.000	0.000
81	A	85	VAL	0	-0.030	-0.028	15.208	0.036	0.036	0.000	0.000	0.000	0.000
82	A	86	GLU	-1	-0.862	-0.927	18.240	-11.033	-11.033	0.000	0.000	0.000	0.000
83	A	87	TYR	0	-0.048	-0.055	21.555	-0.475	-0.475	0.000	0.000	0.000	0.000
84	A	88	THR	0	0.009	0.015	23.562	0.468	0.468	0.000	0.000	0.000	0.000
85	A	89	ARG	1	0.839	0.893	26.740	8.535	8.535	0.000	0.000	0.000	0.000
86	A	90	ALA	0	-0.045	-0.027	27.773	-0.032	-0.032	0.000	0.000	0.000	0.000
87	A	91	ILE	0	-0.055	-0.024	27.543	0.452	0.452	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:LYS)