FMO DATABASE

FMODB ID: VR4Y1

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	OptAll
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	-646535.086045
FMO2-HF: Nuclear repulsion	608665.530731
FMO2-HF: Total energy	-37869.555314
FMO2-MP2: Total energy	-37978.194768

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.
-7.371	-4.395	0.198	-1.271	-1.903	0.002

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 : 0.020 / 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	6	LYS	1	0.994	0.984	3.610	-4.576	-2.702	0.010	-0.882	-1.002	0.003
4	A	7	LEU	0	0.020	0.017	2.903	-1.587	-0.811	0.189	-0.253	-0.712	-0.001
5	A	8	LEU	0	0.043	0.038	4.159	-0.292	0.034	-0.001	-0.136	-0.189	0.000
6	A	9	TYR	0	0.001	-0.038	6.132	0.274	0.274	0.000	0.000	0.000	0.000
7	A	10	LYS	1	0.859	0.924	7.784	-0.713	-0.713	0.000	0.000	0.000	0.000
8	A	11	THR	0	0.007	-0.003	7.566	-0.069	-0.069	0.000	0.000	0.000	0.000
9	A	12	ILE	0	-0.032	-0.010	10.069	-0.017	-0.017	0.000	0.000	0.000	0.000
10	A	13	GLU	-1	-0.808	-0.894	12.165	0.201	0.201	0.000	0.000	0.000	0.000
11	A	14	GLU	-1	-0.908	-0.958	11.499	0.330	0.330	0.000	0.000	0.000	0.000
12	A	15	ARG	1	0.918	0.966	14.405	0.081	0.081	0.000	0.000	0.000	0.000
13	A	16	LYS	1	0.828	0.926	16.308	-0.055	-0.055	0.000	0.000	0.000	0.000
14	A	17	GLY	0	-0.031	-0.002	17.786	0.001	0.001	0.000	0.000	0.000	0.000
15	A	18	SER	0	-0.054	-0.030	18.240	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	19	PRO	0	-0.045	-0.019	19.223	-0.017	-0.017	0.000	0.000	0.000	0.000
17	A	20	LEU	0	0.017	0.005	18.492	0.001	0.001	0.000	0.000	0.000	0.000
18	A	21	PRO	0	-0.006	-0.010	21.167	-0.016	-0.016	0.000	0.000	0.000	0.000
19	A	22	GLU	-1	-0.870	-0.935	22.254	-0.061	-0.061	0.000	0.000	0.000	0.000
20	A	23	SER	0	-0.074	-0.033	17.584	-0.021	-0.021	0.000	0.000	0.000	0.000
21	A	24	TYR	0	0.021	-0.027	16.043	0.026	0.026	0.000	0.000	0.000	0.000
22	A	25	THR	0	0.023	0.005	14.523	0.003	0.003	0.000	0.000	0.000	0.000
23	A	26	ASN	0	0.020	0.011	17.041	0.012	0.012	0.000	0.000	0.000	0.000
24	A	27	TYR	0	-0.001	0.014	20.422	0.013	0.013	0.000	0.000	0.000	0.000
25	A	28	LEU	0	0.010	0.018	16.919	0.015	0.015	0.000	0.000	0.000	0.000
26	A	29	PHE	0	0.056	0.021	15.985	0.009	0.009	0.000	0.000	0.000	0.000
27	A	30	SER	0	-0.097	-0.037	21.703	0.010	0.010	0.000	0.000	0.000	0.000
28	A	31	LYS	1	0.803	0.879	24.156	0.047	0.047	0.000	0.000	0.000	0.000
29	A	32	GLY	0	0.048	0.040	23.858	0.003	0.003	0.000	0.000	0.000	0.000
30	A	33	GLU	-1	-0.778	-0.891	22.681	-0.005	-0.005	0.000	0.000	0.000	0.000
31	A	34	ASP	-1	-0.816	-0.886	23.404	-0.051	-0.051	0.000	0.000	0.000	0.000
32	A	35	LYS	1	0.961	0.986	22.724	0.092	0.092	0.000	0.000	0.000	0.000
33	A	36	ILE	0	0.012	0.004	18.145	-0.013	-0.013	0.000	0.000	0.000	0.000
34	A	37	LEU	0	-0.018	-0.011	20.231	-0.016	-0.016	0.000	0.000	0.000	0.000
35	A	38	LYS	1	0.803	0.883	22.302	0.041	0.041	0.000	0.000	0.000	0.000
36	A	39	LYS	1	0.755	0.874	18.950	0.173	0.173	0.000	0.000	0.000	0.000
37	A	40	ILE	0	0.020	0.009	16.988	-0.011	-0.011	0.000	0.000	0.000	0.000
38	A	41	GLY	0	-0.033	-0.015	19.174	-0.007	-0.007	0.000	0.000	0.000	0.000
39	A	42	GLU	-1	-0.881	-0.932	21.405	-0.134	-0.134	0.000	0.000	0.000	0.000
40	A	43	GLU	-1	-0.716	-0.865	16.056	-0.196	-0.196	0.000	0.000	0.000	0.000
41	A	44	CYS	0	-0.067	-0.035	18.904	-0.008	-0.008	0.000	0.000	0.000	0.000
42	A	45	ALA	0	-0.031	-0.009	19.856	0.004	0.004	0.000	0.000	0.000	0.000
43	A	46	GLU	-1	-0.837	-0.919	19.786	-0.152	-0.152	0.000	0.000	0.000	0.000
44	A	47	VAL	0	-0.032	-0.012	16.234	-0.005	-0.005	0.000	0.000	0.000	0.000
45	A	48	ILE	0	-0.047	-0.023	19.023	0.005	0.005	0.000	0.000	0.000	0.000
46	A	49	ILE	0	0.010	0.006	22.342	0.008	0.008	0.000	0.000	0.000	0.000
47	A	50	ALA	0	0.038	0.024	19.770	0.007	0.007	0.000	0.000	0.000	0.000
48	A	51	CYS	0	-0.056	-0.031	20.361	0.008	0.008	0.000	0.000	0.000	0.000
49	A	52	LYS	1	0.871	0.926	21.808	0.113	0.113	0.000	0.000	0.000	0.000
50	A	53	ASN	0	0.000	0.003	24.245	0.017	0.017	0.000	0.000	0.000	0.000
51	A	54	ASN	0	-0.049	-0.027	23.300	-0.006	-0.006	0.000	0.000	0.000	0.000
52	A	55	ASP	-1	-0.813	-0.884	19.937	-0.225	-0.225	0.000	0.000	0.000	0.000
53	A	56	LYS	1	0.880	0.915	17.455	0.166	0.166	0.000	0.000	0.000	0.000
54	A	57	GLU	-1	-0.866	-0.913	15.471	-0.326	-0.326	0.000	0.000	0.000	0.000
55	A	58	GLU	-1	-0.842	-0.915	15.271	-0.288	-0.288	0.000	0.000	0.000	0.000
56	A	59	VAL	0	-0.030	-0.015	15.252	-0.019	-0.019	0.000	0.000	0.000	0.000
57	A	60	VAL	0	-0.053	-0.025	10.462	-0.031	-0.031	0.000	0.000	0.000	0.000
58	A	61	LYS	1	0.772	0.873	11.453	0.227	0.227	0.000	0.000	0.000	0.000
59	A	62	GLU	-1	-0.820	-0.918	12.505	-0.319	-0.319	0.000	0.000	0.000	0.000
60	A	63	MET	0	-0.045	-0.025	11.532	0.002	0.002	0.000	0.000	0.000	0.000
61	A	64	VAL	0	-0.036	-0.021	7.466	-0.061	-0.061	0.000	0.000	0.000	0.000
62	A	65	ASP	-1	-0.825	-0.917	9.832	-0.378	-0.378	0.000	0.000	0.000	0.000
63	A	66	VAL	0	0.025	0.017	12.524	0.041	0.041	0.000	0.000	0.000	0.000
64	A	67	PHE	0	-0.037	-0.022	8.349	0.050	0.050	0.000	0.000	0.000	0.000
65	A	68	TYR	0	-0.002	0.013	9.753	0.061	0.061	0.000	0.000	0.000	0.000
66	A	69	HIS	0	0.083	0.046	10.865	0.116	0.116	0.000	0.000	0.000	0.000
67	A	70	CYS	0	-0.045	-0.023	12.971	0.065	0.065	0.000	0.000	0.000	0.000
68	A	71	PHE	0	-0.038	-0.031	6.573	0.082	0.082	0.000	0.000	0.000	0.000
69	A	72	VAL	0	0.016	0.006	12.386	0.068	0.068	0.000	0.000	0.000	0.000
70	A	73	LEU	0	0.001	0.010	15.166	0.036	0.036	0.000	0.000	0.000	0.000
71	A	74	LEU	0	-0.059	-0.027	12.366	0.028	0.028	0.000	0.000	0.000	0.000
72	A	75	ALA	0	0.053	0.034	14.672	0.024	0.024	0.000	0.000	0.000	0.000
73	A	76	GLU	-1	-0.875	-0.932	16.465	0.023	0.023	0.000	0.000	0.000	0.000
74	A	77	LYS	1	0.764	0.859	19.476	-0.020	-0.020	0.000	0.000	0.000	0.000
75	A	78	ASN	0	-0.047	-0.016	19.172	0.013	0.013	0.000	0.000	0.000	0.000
76	A	79	ILE	0	-0.034	-0.006	17.023	0.016	0.016	0.000	0.000	0.000	0.000
77	A	80	ALA	0	0.064	0.029	15.484	0.013	0.013	0.000	0.000	0.000	0.000
78	A	81	LEU	0	0.020	0.005	7.620	0.060	0.060	0.000	0.000	0.000	0.000
79	A	82	GLU	-1	-0.912	-0.960	12.144	0.480	0.480	0.000	0.000	0.000	0.000
80	A	83	ASP	-1	-0.778	-0.885	13.068	0.235	0.235	0.000	0.000	0.000	0.000
81	A	84	VAL	0	0.015	0.017	12.466	-0.030	-0.030	0.000	0.000	0.000	0.000
82	A	85	MET	0	-0.043	-0.026	8.136	-0.007	-0.007	0.000	0.000	0.000	0.000
83	A	86	ARG	1	0.774	0.895	12.110	-0.307	-0.307	0.000	0.000	0.000	0.000
84	A	87	GLU	-1	-0.689	-0.836	15.760	0.071	0.071	0.000	0.000	0.000	0.000
85	A	88	VAL	0	-0.024	-0.011	10.553	-0.023	-0.023	0.000	0.000	0.000	0.000
86	A	89	LYS	1	0.870	0.928	12.447	-0.539	-0.539	0.000	0.000	0.000	0.000
87	A	90	GLU	-1	-0.831	-0.906	15.182	0.093	0.093	0.000	0.000	0.000	0.000
88	A	91	ARG	1	0.857	0.920	16.479	-0.052	-0.052	0.000	0.000	0.000	0.000
89	A	92	ASN	0	-0.026	-0.029	13.360	-0.041	-0.041	0.000	0.000	0.000	0.000
90	A	93	GLY	0	-0.014	0.011	17.236	-0.016	-0.016	0.000	0.000	0.000	0.000
91	A	94	LYS	1	0.743	0.859	20.307	-0.102	-0.102	0.000	0.000	0.000	0.000
92	A	95	LEU	0	-0.084	-0.032	18.726	-0.021	-0.021	0.000	0.000	0.000	0.000

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