FMO DATABASE

FMODB ID: YY2R2

Calculation Name: 1YVW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YVW

Chain ID: A

ChEMBL ID:

UniProt ID: Q81G00

Base Structure: X-ray

Registration Date: 2023-06-21

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	92
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-645279.918409
FMO2-HF: Nuclear repulsion	607410.767159
FMO2-HF: Total energy	-37869.151251
FMO2-MP2: Total energy	-37977.802991

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:4:ALA)

Summations of interaction energy for fragment #1(A:4:ALA)

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.
-10.237	-6.519	0.979	-2.023	-2.675	0.007

Interaction energy analysis for fragmet #1(A:4:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : 0.002

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

Sort

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	6	LYS	1	0.984	0.974	3.310	-5.380	-3.104	0.058	-1.105	-1.228	0.007
4	A	7	LEU	0	0.006	0.007	2.477	-2.637	-1.571	0.921	-0.766	-1.222	0.000
5	A	8	LEU	0	0.057	0.046	3.956	-0.575	-0.199	0.000	-0.152	-0.225	0.000
6	A	9	TYR	0	0.029	-0.001	5.882	0.232	0.232	0.000	0.000	0.000	0.000
7	A	10	LYS	1	0.934	0.969	7.309	-1.338	-1.338	0.000	0.000	0.000	0.000
8	A	11	THR	0	0.032	0.013	7.333	-0.137	-0.137	0.000	0.000	0.000	0.000
9	A	12	ILE	0	-0.039	-0.017	9.864	-0.049	-0.049	0.000	0.000	0.000	0.000
10	A	13	GLU	-1	-0.903	-0.968	11.765	0.268	0.268	0.000	0.000	0.000	0.000
11	A	14	GLU	-1	-0.964	-0.988	11.253	0.340	0.340	0.000	0.000	0.000	0.000
12	A	15	ARG	1	0.917	0.962	14.339	0.042	0.042	0.000	0.000	0.000	0.000
13	A	16	LYS	1	0.878	0.960	16.234	-0.109	-0.109	0.000	0.000	0.000	0.000
14	A	17	GLY	0	-0.027	0.001	17.929	-0.005	-0.005	0.000	0.000	0.000	0.000
15	A	18	SER	0	-0.049	-0.019	18.646	-0.008	-0.008	0.000	0.000	0.000	0.000
16	A	19	PRO	0	-0.043	-0.026	19.412	-0.015	-0.015	0.000	0.000	0.000	0.000
17	A	20	LEU	0	0.021	0.012	18.610	0.000	0.000	0.000	0.000	0.000	0.000
18	A	21	PRO	0	-0.032	-0.022	21.522	-0.013	-0.013	0.000	0.000	0.000	0.000
19	A	22	GLU	-1	-0.862	-0.937	22.334	-0.045	-0.045	0.000	0.000	0.000	0.000
20	A	23	SER	0	-0.077	-0.038	17.737	-0.023	-0.023	0.000	0.000	0.000	0.000
21	A	24	TYR	0	0.044	-0.009	16.158	0.028	0.028	0.000	0.000	0.000	0.000
22	A	25	THR	0	0.021	-0.002	14.409	0.005	0.005	0.000	0.000	0.000	0.000
23	A	26	ASN	0	0.017	0.016	17.174	0.012	0.012	0.000	0.000	0.000	0.000
24	A	27	TYR	0	0.008	0.017	20.199	0.012	0.012	0.000	0.000	0.000	0.000
25	A	28	LEU	0	-0.009	-0.006	17.161	0.013	0.013	0.000	0.000	0.000	0.000
26	A	29	PHE	0	0.005	0.002	15.798	0.006	0.006	0.000	0.000	0.000	0.000
27	A	30	SER	0	-0.103	-0.041	21.508	0.007	0.007	0.000	0.000	0.000	0.000
28	A	31	LYS	1	0.878	0.931	24.461	0.036	0.036	0.000	0.000	0.000	0.000
29	A	32	GLY	0	0.065	0.045	24.032	0.003	0.003	0.000	0.000	0.000	0.000
30	A	33	GLU	-1	-0.785	-0.900	22.938	0.016	0.016	0.000	0.000	0.000	0.000
31	A	34	ASP	-1	-0.821	-0.915	23.637	-0.035	-0.035	0.000	0.000	0.000	0.000
32	A	35	LYS	1	0.914	0.969	22.933	0.070	0.070	0.000	0.000	0.000	0.000
33	A	36	ILE	0	0.026	0.007	18.298	-0.014	-0.014	0.000	0.000	0.000	0.000
34	A	37	LEU	0	0.001	0.002	20.388	-0.017	-0.017	0.000	0.000	0.000	0.000
35	A	38	LYS	1	0.808	0.899	22.493	0.029	0.029	0.000	0.000	0.000	0.000
36	A	39	LYS	1	0.780	0.886	19.054	0.158	0.158	0.000	0.000	0.000	0.000
37	A	40	ILE	0	0.011	0.014	17.238	-0.014	-0.014	0.000	0.000	0.000	0.000
38	A	41	GLY	0	-0.036	-0.013	19.464	-0.009	-0.009	0.000	0.000	0.000	0.000
39	A	42	GLU	-1	-0.877	-0.937	22.018	-0.128	-0.128	0.000	0.000	0.000	0.000
40	A	43	GLU	-1	-0.713	-0.864	16.535	-0.191	-0.191	0.000	0.000	0.000	0.000
41	A	44	CYS	0	-0.060	-0.025	19.053	-0.012	-0.012	0.000	0.000	0.000	0.000
42	A	45	ALA	0	-0.045	-0.026	20.154	0.000	0.000	0.000	0.000	0.000	0.000
43	A	46	GLU	-1	-0.855	-0.931	19.864	-0.159	-0.159	0.000	0.000	0.000	0.000
44	A	47	VAL	0	-0.027	-0.001	16.635	-0.009	-0.009	0.000	0.000	0.000	0.000
45	A	48	ILE	0	-0.071	-0.034	19.448	0.005	0.005	0.000	0.000	0.000	0.000
46	A	49	ILE	0	0.007	-0.004	22.752	0.005	0.005	0.000	0.000	0.000	0.000
47	A	50	ALA	0	0.056	0.036	19.942	0.006	0.006	0.000	0.000	0.000	0.000
48	A	51	CYS	0	-0.065	-0.038	20.522	0.005	0.005	0.000	0.000	0.000	0.000
49	A	52	LYS	1	0.884	0.936	21.970	0.115	0.115	0.000	0.000	0.000	0.000
50	A	53	ASN	0	0.000	0.009	24.340	0.018	0.018	0.000	0.000	0.000	0.000
51	A	54	ASN	0	-0.125	-0.060	23.373	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	55	ASP	-1	-0.829	-0.895	20.323	-0.230	-0.230	0.000	0.000	0.000	0.000
53	A	56	LYS	1	0.948	0.942	17.626	0.188	0.188	0.000	0.000	0.000	0.000
54	A	57	GLU	-1	-0.858	-0.918	15.718	-0.339	-0.339	0.000	0.000	0.000	0.000
55	A	58	GLU	-1	-0.811	-0.900	15.448	-0.309	-0.309	0.000	0.000	0.000	0.000
56	A	59	VAL	0	-0.040	-0.010	15.593	-0.014	-0.014	0.000	0.000	0.000	0.000
57	A	60	VAL	0	-0.056	-0.029	10.615	-0.030	-0.030	0.000	0.000	0.000	0.000
58	A	61	LYS	1	0.791	0.884	11.747	0.247	0.247	0.000	0.000	0.000	0.000
59	A	62	GLU	-1	-0.795	-0.904	13.068	-0.302	-0.302	0.000	0.000	0.000	0.000
60	A	63	MET	0	-0.055	-0.028	11.843	0.005	0.005	0.000	0.000	0.000	0.000
61	A	64	VAL	0	-0.057	-0.035	7.847	-0.058	-0.058	0.000	0.000	0.000	0.000
62	A	65	ASP	-1	-0.829	-0.914	10.180	-0.358	-0.358	0.000	0.000	0.000	0.000
63	A	66	VAL	0	0.014	0.013	13.005	0.045	0.045	0.000	0.000	0.000	0.000
64	A	67	PHE	0	-0.043	-0.030	8.461	0.052	0.052	0.000	0.000	0.000	0.000
65	A	68	TYR	0	0.001	0.010	10.107	0.077	0.077	0.000	0.000	0.000	0.000
66	A	69	HIS	0	0.082	0.045	11.020	0.124	0.124	0.000	0.000	0.000	0.000
67	A	70	CYS	0	-0.047	-0.021	13.160	0.067	0.067	0.000	0.000	0.000	0.000
68	A	71	PHE	0	-0.048	-0.041	6.539	0.103	0.103	0.000	0.000	0.000	0.000
69	A	72	VAL	0	0.025	0.014	12.344	0.075	0.075	0.000	0.000	0.000	0.000
70	A	73	LEU	0	0.011	0.009	14.915	0.037	0.037	0.000	0.000	0.000	0.000
71	A	74	LEU	0	-0.055	-0.026	12.571	0.031	0.031	0.000	0.000	0.000	0.000
72	A	75	ALA	0	0.034	0.023	14.506	0.020	0.020	0.000	0.000	0.000	0.000
73	A	76	GLU	-1	-0.905	-0.949	16.369	0.051	0.051	0.000	0.000	0.000	0.000
74	A	77	LYS	1	0.750	0.862	19.362	-0.050	-0.050	0.000	0.000	0.000	0.000
75	A	78	ASN	0	-0.054	-0.017	19.160	0.014	0.014	0.000	0.000	0.000	0.000
76	A	79	ILE	0	-0.004	0.010	16.901	0.010	0.010	0.000	0.000	0.000	0.000
77	A	80	ALA	0	0.058	0.028	15.390	0.029	0.029	0.000	0.000	0.000	0.000
78	A	81	LEU	0	0.035	0.012	7.522	0.077	0.077	0.000	0.000	0.000	0.000
79	A	82	GLU	-1	-0.908	-0.963	12.059	0.545	0.545	0.000	0.000	0.000	0.000
80	A	83	ASP	-1	-0.798	-0.895	13.095	0.266	0.266	0.000	0.000	0.000	0.000
81	A	84	VAL	0	0.016	0.017	12.191	-0.040	-0.040	0.000	0.000	0.000	0.000
82	A	85	MET	0	-0.038	-0.031	7.820	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	86	ARG	1	0.791	0.902	11.792	-0.366	-0.366	0.000	0.000	0.000	0.000
84	A	87	GLU	-1	-0.775	-0.878	15.369	0.077	0.077	0.000	0.000	0.000	0.000
85	A	88	VAL	0	-0.024	-0.014	10.824	-0.035	-0.035	0.000	0.000	0.000	0.000
86	A	89	LYS	1	0.880	0.925	12.066	-0.604	-0.604	0.000	0.000	0.000	0.000
87	A	90	GLU	-1	-0.853	-0.907	15.042	0.100	0.100	0.000	0.000	0.000	0.000
88	A	91	ARG	1	0.863	0.922	16.680	-0.065	-0.065	0.000	0.000	0.000	0.000
89	A	92	ASN	0	-0.050	-0.041	13.397	-0.040	-0.040	0.000	0.000	0.000	0.000
90	A	93	GLY	0	-0.001	0.012	17.165	-0.017	-0.017	0.000	0.000	0.000	0.000
91	A	94	LYS	1	0.818	0.903	20.123	-0.106	-0.106	0.000	0.000	0.000	0.000
92	A	95	LEU	0	-0.064	-0.011	18.567	-0.020	-0.020	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:4:ALA)