FMO DATABASE

FMODB ID: 7625K

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

Total energy (hartree)

FMO2-HF: Electronic energy	-376974.881461
FMO2-HF: Nuclear repulsion	350086.466312
FMO2-HF: Total energy	-26888.415149
FMO2-MP2: Total energy	-26967.673471

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.
-61.805	-60.459	29.132	-12.197	-18.28	-0.037

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 : 0.043 / q_NPA : 0.045

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	0.902	0.941	2.377	-18.632	-25.214	20.585	-5.489	-8.514	0.040
4	A	4	ARG	1	0.903	0.945	5.208	-1.414	-1.375	-0.001	-0.008	-0.029	0.000
5	A	5	TYR	0	0.052	0.028	5.750	0.490	0.490	0.000	0.000	0.000	0.000
6	A	6	ARG	1	0.954	0.981	10.650	-0.671	-0.671	0.000	0.000	0.000	0.000
7	A	7	VAL	0	0.018	-0.001	14.060	-0.021	-0.021	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.003	0.007	15.954	0.028	0.028	0.000	0.000	0.000	0.000
9	A	9	VAL	0	-0.011	-0.016	18.833	-0.042	-0.042	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.926	-0.951	21.270	0.032	0.032	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.833	0.904	24.908	0.058	0.058	0.000	0.000	0.000	0.000
12	A	12	ASP	-1	-0.802	-0.909	27.484	-0.097	-0.097	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.960	-0.985	30.202	-0.068	-0.068	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.872	-0.919	32.077	-0.124	-0.124	0.000	0.000	0.000	0.000
15	A	15	GLY	0	-0.074	-0.038	30.794	-0.005	-0.005	0.000	0.000	0.000	0.000
16	A	16	TYR	0	-0.073	-0.043	27.456	-0.020	-0.020	0.000	0.000	0.000	0.000
17	A	17	PHE	0	-0.009	-0.008	22.822	0.021	0.021	0.000	0.000	0.000	0.000
18	A	18	VAL	0	0.048	0.016	22.100	-0.038	-0.038	0.000	0.000	0.000	0.000
19	A	19	ALA	0	-0.026	-0.010	17.380	0.034	0.034	0.000	0.000	0.000	0.000
20	A	20	HIS	0	0.012	-0.002	17.769	0.014	0.014	0.000	0.000	0.000	0.000
21	A	21	VAL	0	0.021	0.007	11.115	0.069	0.069	0.000	0.000	0.000	0.000
22	A	22	PRO	0	-0.027	-0.024	14.287	0.025	0.025	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.975	-0.990	10.173	1.485	1.485	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.006	-0.006	7.788	0.126	0.126	0.000	0.000	0.000	0.000
25	A	25	HIS	0	-0.061	-0.019	11.777	-0.234	-0.234	0.000	0.000	0.000	0.000
26	A	26	ALA	0	0.030	0.030	13.434	-0.092	-0.092	0.000	0.000	0.000	0.000
27	A	27	HIS	0	0.007	-0.004	15.481	0.067	0.067	0.000	0.000	0.000	0.000
28	A	28	THR	0	-0.013	0.001	15.632	-0.082	-0.082	0.000	0.000	0.000	0.000
29	A	29	GLN	0	0.000	0.005	18.718	0.048	0.048	0.000	0.000	0.000	0.000
30	A	30	ALA	0	-0.041	-0.020	21.625	-0.052	-0.052	0.000	0.000	0.000	0.000
31	A	31	GLN	0	0.011	0.015	23.549	0.016	0.016	0.000	0.000	0.000	0.000
32	A	32	SER	0	-0.014	-0.001	24.929	0.021	0.021	0.000	0.000	0.000	0.000
33	A	33	PHE	0	0.047	0.009	20.575	-0.025	-0.025	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.926	-0.956	20.174	-0.294	-0.294	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.836	-0.908	19.757	-0.394	-0.394	0.000	0.000	0.000	0.000
36	A	36	LEU	0	0.004	-0.002	18.533	-0.062	-0.062	0.000	0.000	0.000	0.000
37	A	37	LEU	0	0.029	0.020	14.629	-0.053	-0.053	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.855	0.916	15.003	0.528	0.528	0.000	0.000	0.000	0.000
39	A	39	ARG	1	0.876	0.920	15.033	0.340	0.340	0.000	0.000	0.000	0.000
40	A	40	LEU	0	-0.007	0.011	12.744	-0.096	-0.096	0.000	0.000	0.000	0.000
41	A	41	GLN	0	0.015	0.000	10.715	0.059	0.059	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.837	-0.911	10.212	-1.273	-1.273	0.000	0.000	0.000	0.000
43	A	43	ALA	0	0.013	0.003	10.822	-0.252	-0.252	0.000	0.000	0.000	0.000
44	A	44	ILE	0	-0.030	-0.012	6.582	-0.011	-0.011	0.000	0.000	0.000	0.000
45	A	45	ALA	0	-0.010	-0.002	6.176	-0.334	-0.334	0.000	0.000	0.000	0.000
46	A	46	VAL	0	0.029	0.014	6.120	-0.812	-0.812	0.000	0.000	0.000	0.000
47	A	47	SER	0	-0.071	-0.036	7.869	0.030	0.030	0.000	0.000	0.000	0.000
48	A	48	LEU	0	-0.085	-0.057	2.403	0.358	0.678	3.451	-0.775	-2.995	-0.006
49	A	49	GLU	-1	-0.987	-0.977	3.199	-7.320	-6.211	0.120	-0.609	-0.621	-0.005
50	A	50	GLU	-1	-0.936	-0.970	2.193	-33.360	-26.962	4.978	-5.308	-6.068	-0.066
51	A	51	GLU	-1	-0.975	-0.988	4.853	-1.005	-0.943	-0.001	-0.008	-0.053	0.000
52	A	52	ARG	1	0.890	0.937	7.181	2.318	2.318	0.000	0.000	0.000	0.000
53	A	53	ALA	0	0.001	0.009	5.948	-1.234	-1.234	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.905	-0.969	6.996	-0.744	-0.744	0.000	0.000	0.000	0.000
55	A	55	VAL	0	-0.017	0.004	8.470	0.109	0.109	0.000	0.000	0.000	0.000
56	A	56	VAL	0	-0.060	-0.039	9.258	0.120	0.120	0.000	0.000	0.000	0.000
57	A	57	GLY	0	-0.036	-0.024	11.721	0.082	0.082	0.000	0.000	0.000	0.000
58	A	58	LEU	0	0.011	0.005	13.411	-0.036	-0.036	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.910	-0.940	15.065	0.503	0.503	0.000	0.000	0.000	0.000
60	A	60	GLY	0	-0.008	-0.016	18.051	0.023	0.023	0.000	0.000	0.000	0.000
61	A	61	ALA	0	-0.033	-0.009	20.568	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.019	-0.005	23.120	-0.012	-0.012	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.890	-0.936	25.672	0.102	0.102	0.000	0.000	0.000	0.000
64	A	64	ILE	0	-0.089	-0.059	28.468	-0.014	-0.014	0.000	0.000	0.000	0.000
65	A	65	GLU	-1	-0.885	-0.936	31.290	0.018	0.018	0.000	0.000	0.000	0.000
66	A	66	ALA	0	-0.065	-0.030	34.382	-0.006	-0.006	0.000	0.000	0.000	0.000
67	A	67	ALA	0	-0.009	0.000	37.074	0.001	0.001	0.000	0.000	0.000	0.000

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