FMO DATABASE

FMODB ID: MNVJZ

Calculation Name: 2YZT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YZT

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SHH4

Base Structure: X-ray

Registration Date: 2023-09-21

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	67
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-377380.413322
FMO2-HF: Nuclear repulsion	350492.378571
FMO2-HF: Total energy	-26888.03475
FMO2-MP2: Total energy	-26967.316884

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.
-45.8	-40.203	15.997	-7.572	-14.025	-0.048

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 : 0.030 / q_NPA : 0.015

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	ARG	1	0.943	0.973	2.626	-10.317	-12.164	10.214	-2.248	-6.120	0.009
4	A	4	ARG	1	0.970	0.985	5.679	-1.460	-1.460	0.000	0.000	0.000	0.000
5	A	5	TYR	0	0.046	0.025	5.289	0.353	0.353	0.000	0.000	0.000	0.000
6	A	6	ARG	1	0.955	0.980	11.035	-0.525	-0.525	0.000	0.000	0.000	0.000
7	A	7	VAL	0	0.022	0.004	14.366	-0.015	-0.015	0.000	0.000	0.000	0.000
8	A	8	VAL	0	0.004	0.007	16.180	0.023	0.023	0.000	0.000	0.000	0.000
9	A	9	VAL	0	-0.011	-0.014	18.973	-0.036	-0.036	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.937	-0.958	21.340	0.042	0.042	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.874	0.942	24.960	0.023	0.023	0.000	0.000	0.000	0.000
12	A	12	ASP	-1	-0.782	-0.892	27.456	-0.072	-0.072	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.954	-0.997	30.173	-0.054	-0.054	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.942	-0.943	31.893	-0.097	-0.097	0.000	0.000	0.000	0.000
15	A	15	GLY	0	-0.097	-0.050	30.701	-0.003	-0.003	0.000	0.000	0.000	0.000
16	A	16	TYR	0	-0.036	-0.037	27.341	-0.012	-0.012	0.000	0.000	0.000	0.000
17	A	17	PHE	0	-0.018	-0.018	22.738	0.019	0.019	0.000	0.000	0.000	0.000
18	A	18	VAL	0	0.046	0.017	22.121	-0.033	-0.033	0.000	0.000	0.000	0.000
19	A	19	ALA	0	-0.030	-0.013	17.362	0.032	0.032	0.000	0.000	0.000	0.000
20	A	20	HIS	0	0.007	0.001	17.927	-0.004	-0.004	0.000	0.000	0.000	0.000
21	A	21	VAL	0	0.020	0.004	11.316	0.063	0.063	0.000	0.000	0.000	0.000
22	A	22	PRO	0	-0.042	-0.030	14.447	0.011	0.011	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.967	-0.987	9.876	1.352	1.352	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.002	-0.004	7.786	0.074	0.074	0.000	0.000	0.000	0.000
25	A	25	HIS	0	-0.052	-0.016	11.740	-0.172	-0.172	0.000	0.000	0.000	0.000
26	A	26	ALA	0	0.027	0.028	13.648	-0.082	-0.082	0.000	0.000	0.000	0.000
27	A	27	HIS	0	0.002	-0.009	15.535	0.060	0.060	0.000	0.000	0.000	0.000
28	A	28	THR	0	-0.019	-0.006	15.309	-0.070	-0.070	0.000	0.000	0.000	0.000
29	A	29	GLN	0	0.009	0.011	18.597	0.049	0.049	0.000	0.000	0.000	0.000
30	A	30	ALA	0	-0.023	-0.013	21.486	-0.043	-0.043	0.000	0.000	0.000	0.000
31	A	31	GLN	0	0.002	0.022	23.299	0.023	0.023	0.000	0.000	0.000	0.000
32	A	32	SER	0	-0.006	0.003	24.637	0.019	0.019	0.000	0.000	0.000	0.000
33	A	33	PHE	0	0.053	0.011	20.889	-0.020	-0.020	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.936	-0.961	19.877	-0.207	-0.207	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.886	-0.951	19.742	-0.311	-0.311	0.000	0.000	0.000	0.000
36	A	36	LEU	0	0.014	0.000	18.343	-0.053	-0.053	0.000	0.000	0.000	0.000
37	A	37	LEU	0	0.038	0.026	14.436	-0.042	-0.042	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.911	0.960	14.795	0.419	0.419	0.000	0.000	0.000	0.000
39	A	39	ARG	1	0.915	0.946	14.909	0.306	0.306	0.000	0.000	0.000	0.000
40	A	40	LEU	0	0.000	0.017	12.910	-0.080	-0.080	0.000	0.000	0.000	0.000
41	A	41	GLN	0	0.029	0.013	10.475	0.060	0.060	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.906	-0.960	10.008	-1.093	-1.093	0.000	0.000	0.000	0.000
43	A	43	ALA	0	0.012	0.003	10.973	-0.216	-0.216	0.000	0.000	0.000	0.000
44	A	44	ILE	0	-0.032	-0.018	6.310	0.003	0.003	0.000	0.000	0.000	0.000
45	A	45	ALA	0	-0.010	-0.003	6.366	-0.122	-0.122	0.000	0.000	0.000	0.000
46	A	46	VAL	0	0.030	0.016	6.205	-0.721	-0.721	0.000	0.000	0.000	0.000
47	A	47	SER	0	-0.069	-0.030	7.929	-0.041	-0.041	0.000	0.000	0.000	0.000
48	A	48	LEU	0	-0.097	-0.061	2.638	-0.038	0.866	2.354	-0.647	-2.612	-0.004
49	A	49	GLU	-1	-0.975	-0.971	3.117	-7.289	-6.154	0.125	-0.624	-0.637	-0.006
50	A	50	GLU	-1	-0.964	-0.978	2.205	-25.870	-20.531	3.305	-4.042	-4.602	-0.047
51	A	51	GLU	-1	-0.958	-0.985	4.768	-1.030	-0.964	-0.001	-0.011	-0.054	0.000
52	A	52	ARG	1	0.890	0.939	7.190	2.176	2.176	0.000	0.000	0.000	0.000
53	A	53	ALA	0	-0.008	0.001	5.967	-1.134	-1.134	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.908	-0.967	6.919	-0.527	-0.527	0.000	0.000	0.000	0.000
55	A	55	VAL	0	-0.027	-0.008	8.361	0.119	0.119	0.000	0.000	0.000	0.000
56	A	56	VAL	0	-0.065	-0.042	9.068	0.115	0.115	0.000	0.000	0.000	0.000
57	A	57	GLY	0	-0.028	-0.023	11.541	0.068	0.068	0.000	0.000	0.000	0.000
58	A	58	LEU	0	0.002	-0.001	13.440	-0.029	-0.029	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.962	-0.965	15.603	0.483	0.483	0.000	0.000	0.000	0.000
60	A	60	GLY	0	-0.018	-0.024	18.319	0.017	0.017	0.000	0.000	0.000	0.000
61	A	61	ALA	0	-0.037	-0.011	20.812	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.016	-0.003	23.710	-0.010	-0.010	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.893	-0.937	25.799	0.108	0.108	0.000	0.000	0.000	0.000
64	A	64	ILE	0	-0.080	-0.051	28.602	-0.011	-0.011	0.000	0.000	0.000	0.000
65	A	65	GLU	-1	-0.906	-0.950	31.366	0.027	0.027	0.000	0.000	0.000	0.000
66	A	66	ALA	0	-0.053	-0.024	34.430	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	67	ALA	0	-0.011	0.000	37.092	0.000	0.000	0.000	0.000	0.000	0.000

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