FMO DATABASE

FMODB ID: ZV61N

Calculation Name: 2YZ8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YZ8

Chain ID: A

ChEMBL ID:

UniProt ID: Q5VST9

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	90
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-592420.282314
FMO2-HF: Nuclear repulsion	557692.83291
FMO2-HF: Total energy	-34727.449404
FMO2-MP2: Total energy	-34827.260279

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:459:PRO)

Summations of interaction energy for fragment #1(A:459:PRO)

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.
0.238	2.987	1.017	-1.15	-2.616	-0.001

Interaction energy analysis for fragmet #1(A:459:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.037 / q_NPA : -0.005

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	461	ARG	1	0.842	0.902	2.851	0.224	2.938	1.018	-1.140	-2.592	-0.001
4	A	462	PHE	0	-0.031	-0.021	6.003	0.366	0.366	0.000	0.000	0.000	0.000
5	A	463	GLN	0	-0.008	0.005	9.690	-0.151	-0.151	0.000	0.000	0.000	0.000
6	A	464	GLU	-1	-0.853	-0.904	10.968	-0.195	-0.195	0.000	0.000	0.000	0.000
7	A	465	ALA	0	0.019	0.005	14.558	0.013	0.013	0.000	0.000	0.000	0.000
8	A	466	LEU	0	-0.024	-0.013	15.446	0.044	0.044	0.000	0.000	0.000	0.000
9	A	467	LYS	1	0.817	0.884	18.234	0.239	0.239	0.000	0.000	0.000	0.000
10	A	468	ASP	-1	-0.833	-0.893	21.632	-0.163	-0.163	0.000	0.000	0.000	0.000
11	A	469	LEU	0	-0.033	-0.022	24.643	0.006	0.006	0.000	0.000	0.000	0.000
12	A	470	GLU	-1	-0.851	-0.899	27.431	-0.074	-0.074	0.000	0.000	0.000	0.000
13	A	471	VAL	0	-0.065	-0.031	30.005	0.002	0.002	0.000	0.000	0.000	0.000
14	A	472	LEU	0	0.033	0.017	32.897	0.001	0.001	0.000	0.000	0.000	0.000
15	A	473	GLU	-1	-0.866	-0.955	35.606	-0.037	-0.037	0.000	0.000	0.000	0.000
16	A	474	GLY	0	-0.019	-0.018	37.141	0.002	0.002	0.000	0.000	0.000	0.000
17	A	475	GLY	0	-0.027	0.000	35.381	0.003	0.003	0.000	0.000	0.000	0.000
18	A	476	ALA	0	-0.039	-0.037	31.146	0.003	0.003	0.000	0.000	0.000	0.000
19	A	477	ALA	0	0.027	0.033	27.896	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	478	THR	0	-0.039	-0.023	24.518	0.006	0.006	0.000	0.000	0.000	0.000
21	A	479	LEU	0	-0.003	0.011	21.488	-0.010	-0.010	0.000	0.000	0.000	0.000
22	A	480	ARG	1	0.895	0.929	19.998	0.079	0.079	0.000	0.000	0.000	0.000
23	A	481	CYS	0	-0.065	-0.017	14.993	-0.012	-0.012	0.000	0.000	0.000	0.000
24	A	482	VAL	0	0.040	0.021	12.940	0.050	0.050	0.000	0.000	0.000	0.000
25	A	483	LEU	0	-0.002	0.008	8.902	-0.139	-0.139	0.000	0.000	0.000	0.000
26	A	484	SER	0	0.023	0.006	4.758	0.195	0.230	-0.001	-0.010	-0.024	0.000
27	A	485	SER	0	-0.016	-0.013	6.091	0.525	0.525	0.000	0.000	0.000	0.000
28	A	486	VAL	0	-0.019	-0.009	8.570	-0.118	-0.118	0.000	0.000	0.000	0.000
29	A	487	ALA	0	0.005	0.020	7.498	0.199	0.199	0.000	0.000	0.000	0.000
30	A	488	ALA	0	0.032	0.034	9.571	-0.160	-0.160	0.000	0.000	0.000	0.000
31	A	489	PRO	0	0.032	0.014	11.356	0.088	0.088	0.000	0.000	0.000	0.000
32	A	490	VAL	0	0.044	0.020	11.601	0.000	0.000	0.000	0.000	0.000	0.000
33	A	491	LYS	1	0.822	0.906	12.113	-0.050	-0.050	0.000	0.000	0.000	0.000
34	A	492	TRP	0	0.102	0.032	15.983	-0.049	-0.049	0.000	0.000	0.000	0.000
35	A	493	CYS	0	-0.039	-0.023	18.713	0.021	0.021	0.000	0.000	0.000	0.000
36	A	494	TYR	0	0.005	0.002	20.770	-0.012	-0.012	0.000	0.000	0.000	0.000
37	A	495	GLY	0	0.024	0.007	23.739	0.009	0.009	0.000	0.000	0.000	0.000
38	A	496	ASN	0	-0.030	-0.026	21.875	-0.019	-0.019	0.000	0.000	0.000	0.000
39	A	497	ASN	0	-0.033	-0.005	22.821	0.013	0.013	0.000	0.000	0.000	0.000
40	A	498	VAL	0	0.021	0.007	19.785	-0.006	-0.006	0.000	0.000	0.000	0.000
41	A	499	LEU	0	-0.054	-0.021	21.877	0.009	0.009	0.000	0.000	0.000	0.000
42	A	500	ARG	1	0.954	0.969	22.766	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	501	PRO	0	-0.003	-0.005	22.923	-0.007	-0.007	0.000	0.000	0.000	0.000
44	A	502	GLY	0	0.014	0.007	25.681	0.005	0.005	0.000	0.000	0.000	0.000
45	A	503	ASP	-1	-0.857	-0.925	29.471	0.009	0.009	0.000	0.000	0.000	0.000
46	A	504	LYS	1	0.717	0.863	30.133	0.028	0.028	0.000	0.000	0.000	0.000
47	A	505	TYR	0	0.048	0.015	25.535	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	506	SER	0	-0.016	-0.003	25.933	0.011	0.011	0.000	0.000	0.000	0.000
49	A	507	LEU	0	-0.001	-0.012	19.772	-0.011	-0.011	0.000	0.000	0.000	0.000
50	A	508	ARG	1	0.868	0.938	21.216	0.020	0.020	0.000	0.000	0.000	0.000
51	A	509	GLN	0	-0.027	-0.034	12.871	-0.013	-0.013	0.000	0.000	0.000	0.000
52	A	510	GLU	-1	-0.896	-0.941	18.033	0.025	0.025	0.000	0.000	0.000	0.000
53	A	511	GLY	0	0.020	0.009	15.696	-0.018	-0.018	0.000	0.000	0.000	0.000
54	A	512	ALA	0	0.028	0.002	12.053	0.032	0.032	0.000	0.000	0.000	0.000
55	A	513	MET	0	-0.021	0.009	13.520	-0.096	-0.096	0.000	0.000	0.000	0.000
56	A	514	LEU	0	0.011	-0.002	12.720	0.038	0.038	0.000	0.000	0.000	0.000
57	A	515	GLU	-1	-0.745	-0.872	17.049	-0.061	-0.061	0.000	0.000	0.000	0.000
58	A	516	LEU	0	-0.041	-0.004	20.610	0.019	0.019	0.000	0.000	0.000	0.000
59	A	517	VAL	0	-0.014	-0.009	22.694	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	518	VAL	0	0.000	0.001	26.324	0.008	0.008	0.000	0.000	0.000	0.000
61	A	519	ARG	1	0.916	0.952	28.603	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	520	ASN	0	0.036	0.006	32.102	0.000	0.000	0.000	0.000	0.000	0.000
63	A	521	LEU	0	-0.021	0.003	30.449	0.000	0.000	0.000	0.000	0.000	0.000
64	A	522	ARG	1	0.917	0.928	33.309	0.034	0.034	0.000	0.000	0.000	0.000
65	A	523	PRO	0	0.097	0.040	34.378	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	524	GLN	0	-0.001	0.002	34.243	-0.005	-0.005	0.000	0.000	0.000	0.000
67	A	525	ASP	-1	-0.765	-0.821	30.689	-0.038	-0.038	0.000	0.000	0.000	0.000
68	A	526	SER	0	0.008	0.017	29.469	-0.007	-0.007	0.000	0.000	0.000	0.000
69	A	527	GLY	0	0.038	0.028	28.171	0.004	0.004	0.000	0.000	0.000	0.000
70	A	528	ARG	1	0.903	0.949	20.711	0.177	0.177	0.000	0.000	0.000	0.000
71	A	529	TYR	0	-0.016	-0.021	21.702	0.014	0.014	0.000	0.000	0.000	0.000
72	A	530	SER	0	-0.014	-0.006	16.919	-0.025	-0.025	0.000	0.000	0.000	0.000
73	A	531	CYS	0	-0.035	0.009	14.891	0.036	0.036	0.000	0.000	0.000	0.000
74	A	532	SER	0	0.023	0.007	11.948	-0.049	-0.049	0.000	0.000	0.000	0.000
75	A	533	PHE	0	-0.003	-0.015	5.470	0.083	0.083	0.000	0.000	0.000	0.000
76	A	534	GLY	0	0.009	0.008	7.661	-0.110	-0.110	0.000	0.000	0.000	0.000
77	A	535	ASP	-1	-0.769	-0.867	5.284	-0.738	-0.738	0.000	0.000	0.000	0.000
78	A	536	GLN	0	-0.071	-0.032	5.252	-0.179	-0.179	0.000	0.000	0.000	0.000
79	A	537	THR	0	0.015	-0.018	8.140	0.160	0.160	0.000	0.000	0.000	0.000
80	A	538	THR	0	0.015	0.020	11.700	-0.050	-0.050	0.000	0.000	0.000	0.000
81	A	539	SER	0	0.019	-0.013	14.186	0.055	0.055	0.000	0.000	0.000	0.000
82	A	540	ALA	0	-0.004	0.014	17.947	-0.017	-0.017	0.000	0.000	0.000	0.000
83	A	541	THR	0	-0.083	-0.071	21.366	0.017	0.017	0.000	0.000	0.000	0.000
84	A	542	LEU	0	-0.010	0.001	25.044	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	543	THR	0	0.017	0.001	27.539	0.005	0.005	0.000	0.000	0.000	0.000
86	A	544	VAL	0	-0.021	-0.018	31.103	0.001	0.001	0.000	0.000	0.000	0.000
87	A	545	THR	0	-0.037	-0.031	33.962	0.000	0.000	0.000	0.000	0.000	0.000
88	A	546	ALA	0	-0.001	-0.004	37.233	0.003	0.003	0.000	0.000	0.000	0.000
89	A	547	LEU	0	-0.007	-0.001	40.389	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	548	PRO	0	-0.030	0.000	42.437	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:459:PRO)