FMO DATABASE

FMODB ID: 6Y5QZ

Calculation Name: 1B34-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1B34

Chain ID: B

ChEMBL ID:

UniProt ID: P62314

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	74
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-467336.408388
FMO2-HF: Nuclear repulsion	437253.97387
FMO2-HF: Total energy	-30082.434518
FMO2-MP2: Total energy	-30167.646894

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:26:THR)

Summations of interaction energy for fragment #1(B:26: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.
-3.255	0.853	9.145	-5.073	-8.181	-0.003

Interaction energy analysis for fragmet #1(B:26:THR)

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 : -0.034

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	28	PRO	0	0.048	0.029	3.564	-1.565	-0.163	0.015	-0.586	-0.831	0.002
4	B	29	LEU	0	0.027	0.003	2.228	-1.150	0.092	1.876	-0.871	-2.248	-0.001
5	B	30	SER	0	-0.005	-0.006	1.992	0.562	1.596	7.226	-3.630	-4.630	-0.004
6	B	31	VAL	0	0.032	0.013	3.515	0.121	0.383	0.030	0.022	-0.314	0.000
7	B	32	LEU	0	0.038	0.032	5.959	0.325	0.325	0.000	0.000	0.000	0.000
8	B	33	THR	0	-0.031	-0.004	5.113	-0.214	-0.140	-0.001	-0.001	-0.072	0.000
9	B	34	GLN	0	0.017	0.006	7.095	0.096	0.096	0.000	0.000	0.000	0.000
10	B	35	SER	0	-0.026	-0.030	9.290	0.040	0.040	0.000	0.000	0.000	0.000
11	B	36	VAL	0	-0.033	-0.014	10.950	0.022	0.022	0.000	0.000	0.000	0.000
12	B	37	LYS	1	0.933	0.982	11.687	0.124	0.124	0.000	0.000	0.000	0.000
13	B	38	ASN	0	-0.011	-0.013	12.576	0.043	0.043	0.000	0.000	0.000	0.000
14	B	39	ASN	0	0.028	0.023	15.333	0.000	0.000	0.000	0.000	0.000	0.000
15	B	40	THR	0	0.008	0.027	13.894	-0.007	-0.007	0.000	0.000	0.000	0.000
16	B	41	GLN	0	-0.061	-0.024	15.167	0.010	0.010	0.000	0.000	0.000	0.000
17	B	42	VAL	0	0.025	0.015	11.373	-0.057	-0.057	0.000	0.000	0.000	0.000
18	B	43	LEU	0	0.021	0.008	14.469	0.056	0.056	0.000	0.000	0.000	0.000
19	B	44	ILE	0	0.006	-0.003	13.181	-0.085	-0.085	0.000	0.000	0.000	0.000
20	B	45	ASN	0	-0.005	0.007	14.249	0.087	0.087	0.000	0.000	0.000	0.000
21	B	46	CYS	0	-0.028	-0.031	15.003	-0.022	-0.022	0.000	0.000	0.000	0.000
22	B	47	ARG	1	0.983	0.991	15.026	0.091	0.091	0.000	0.000	0.000	0.000
23	B	48	ASN	0	0.020	0.019	18.686	-0.008	-0.008	0.000	0.000	0.000	0.000
24	B	49	ASN	0	0.038	0.032	21.019	-0.003	-0.003	0.000	0.000	0.000	0.000
25	B	50	LYS	1	0.919	0.965	20.834	0.071	0.071	0.000	0.000	0.000	0.000
26	B	51	LYS	1	0.925	0.950	19.010	0.202	0.202	0.000	0.000	0.000	0.000
27	B	52	LEU	0	0.016	0.020	17.805	0.024	0.024	0.000	0.000	0.000	0.000
28	B	53	LEU	0	0.001	0.014	17.534	-0.034	-0.034	0.000	0.000	0.000	0.000
29	B	54	GLY	0	0.061	0.023	17.656	0.027	0.027	0.000	0.000	0.000	0.000
30	B	55	ARG	1	0.848	0.926	16.718	0.072	0.072	0.000	0.000	0.000	0.000
31	B	56	VAL	0	0.051	0.018	11.573	0.016	0.016	0.000	0.000	0.000	0.000
32	B	57	LYS	1	0.925	0.984	14.767	-0.063	-0.063	0.000	0.000	0.000	0.000
33	B	58	ALA	0	0.030	0.011	14.061	0.036	0.036	0.000	0.000	0.000	0.000
34	B	59	PHE	0	-0.001	-0.006	6.511	-0.076	-0.076	0.000	0.000	0.000	0.000
35	B	60	ASP	-1	-0.729	-0.848	10.294	0.500	0.500	0.000	0.000	0.000	0.000
36	B	61	ARG	1	0.949	0.954	4.370	-2.796	-2.702	-0.001	-0.007	-0.086	0.000
37	B	62	HIS	0	0.021	0.019	7.451	-0.006	-0.006	0.000	0.000	0.000	0.000
38	B	63	CYS	0	-0.064	-0.024	7.726	-0.172	-0.172	0.000	0.000	0.000	0.000
39	B	64	ASN	0	-0.003	-0.010	10.203	-0.146	-0.146	0.000	0.000	0.000	0.000
40	B	65	MET	0	-0.035	-0.017	10.602	0.051	0.051	0.000	0.000	0.000	0.000
41	B	66	VAL	0	-0.007	0.016	14.533	-0.027	-0.027	0.000	0.000	0.000	0.000
42	B	67	LEU	0	-0.022	-0.025	14.778	-0.006	-0.006	0.000	0.000	0.000	0.000
43	B	68	GLU	-1	-0.827	-0.918	18.318	0.032	0.032	0.000	0.000	0.000	0.000
44	B	69	ASN	0	-0.093	-0.050	20.764	-0.019	-0.019	0.000	0.000	0.000	0.000
45	B	70	VAL	0	-0.008	-0.022	20.097	-0.017	-0.017	0.000	0.000	0.000	0.000
46	B	71	LYS	1	0.928	0.977	22.186	0.122	0.122	0.000	0.000	0.000	0.000
47	B	72	GLU	-1	-0.858	-0.926	22.443	-0.070	-0.070	0.000	0.000	0.000	0.000
48	B	73	MET	0	0.023	0.005	21.838	-0.002	-0.002	0.000	0.000	0.000	0.000
49	B	93	ASP	-1	-0.918	-0.970	28.160	-0.071	-0.071	0.000	0.000	0.000	0.000
50	B	94	ARG	1	0.853	0.916	26.946	0.042	0.042	0.000	0.000	0.000	0.000
51	B	95	TYR	0	-0.002	-0.005	26.146	-0.005	-0.005	0.000	0.000	0.000	0.000
52	B	96	ILE	0	-0.004	-0.016	24.492	0.009	0.009	0.000	0.000	0.000	0.000
53	B	97	SER	0	0.001	0.025	24.582	0.000	0.000	0.000	0.000	0.000	0.000
54	B	98	LYS	1	0.926	0.940	23.048	-0.019	-0.019	0.000	0.000	0.000	0.000
55	B	99	MET	0	0.005	0.016	20.385	-0.003	-0.003	0.000	0.000	0.000	0.000
56	B	100	PHE	0	0.016	0.013	17.387	0.011	0.011	0.000	0.000	0.000	0.000
57	B	101	LEU	0	-0.004	-0.004	15.062	-0.017	-0.017	0.000	0.000	0.000	0.000
58	B	102	ARG	1	0.895	0.905	16.422	-0.041	-0.041	0.000	0.000	0.000	0.000
59	B	103	GLY	0	0.058	0.022	12.840	-0.034	-0.034	0.000	0.000	0.000	0.000
60	B	104	ASP	-1	-0.839	-0.881	13.071	-0.012	-0.012	0.000	0.000	0.000	0.000
61	B	105	SER	0	-0.034	-0.034	14.892	-0.032	-0.032	0.000	0.000	0.000	0.000
62	B	106	VAL	0	-0.031	-0.026	10.994	-0.035	-0.035	0.000	0.000	0.000	0.000
63	B	107	ILE	0	-0.025	0.004	12.257	-0.006	-0.006	0.000	0.000	0.000	0.000
64	B	108	VAL	0	0.013	0.000	10.491	-0.118	-0.118	0.000	0.000	0.000	0.000
65	B	109	VAL	0	0.000	0.010	8.837	0.126	0.126	0.000	0.000	0.000	0.000
66	B	110	LEU	0	0.005	0.000	9.927	-0.201	-0.201	0.000	0.000	0.000	0.000
67	B	111	ARG	1	0.943	0.959	9.401	0.808	0.808	0.000	0.000	0.000	0.000
68	B	112	ASN	0	-0.018	-0.005	13.066	0.010	0.010	0.000	0.000	0.000	0.000
69	B	113	PRO	0	-0.014	-0.010	15.005	0.042	0.042	0.000	0.000	0.000	0.000
70	B	114	LEU	0	0.018	0.007	17.673	0.009	0.009	0.000	0.000	0.000	0.000
71	B	115	ILE	0	-0.005	-0.007	17.740	-0.007	-0.007	0.000	0.000	0.000	0.000
72	B	116	ALA	0	0.019	0.023	21.867	0.011	0.011	0.000	0.000	0.000	0.000
73	B	117	GLY	0	0.014	0.001	24.638	-0.006	-0.006	0.000	0.000	0.000	0.000
74	B	118	LYS	1	0.997	1.004	24.505	0.099	0.099	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:26:THR)