FMO DATABASE

FMODB ID: 3QVLL

Calculation Name: 4YVQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4YVQ

Chain ID: A

ChEMBL ID:

UniProt ID: Q940U6

Base Structure: X-ray

Registration Date: 2023-06-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	89
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-578927.093815
FMO2-HF: Nuclear repulsion	541520.032734
FMO2-HF: Total energy	-37407.061082
FMO2-MP2: Total energy	-37510.642429

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:439:MET)

Summations of interaction energy for fragment #1(A:439: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.
-38.454	-34.925	16.153	-7.54	-12.14	-0.003

Interaction energy analysis for fragmet #1(A:439:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.038 / q_NPA : 0.034

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	441	GLU	-1	-0.847	-0.932	2.423	-8.457	-4.970	2.432	-2.629	-3.290	-0.025
4	A	442	THR	0	0.004	-0.027	3.964	0.348	0.633	-0.001	-0.044	-0.240	0.000
5	A	443	VAL	0	-0.014	-0.001	5.497	0.486	0.486	0.000	0.000	0.000	0.000
6	A	444	PRO	0	-0.007	-0.018	7.773	-0.023	-0.023	0.000	0.000	0.000	0.000
7	A	445	THR	0	0.031	0.005	9.218	-0.016	-0.016	0.000	0.000	0.000	0.000
8	A	446	ILE	0	0.026	0.019	6.727	-0.032	-0.032	0.000	0.000	0.000	0.000
9	A	447	LYS	1	0.938	0.971	10.852	-0.566	-0.566	0.000	0.000	0.000	0.000
10	A	448	LYS	1	0.793	0.880	13.639	-0.193	-0.193	0.000	0.000	0.000	0.000
11	A	449	LEU	0	0.048	0.028	13.544	-0.046	-0.046	0.000	0.000	0.000	0.000
12	A	450	ARG	1	0.971	0.979	14.054	-0.834	-0.834	0.000	0.000	0.000	0.000
13	A	451	ALA	0	-0.021	0.000	16.798	-0.048	-0.048	0.000	0.000	0.000	0.000
14	A	452	TYR	0	-0.019	-0.011	18.828	-0.052	-0.052	0.000	0.000	0.000	0.000
15	A	453	ALA	0	0.026	0.006	19.364	-0.032	-0.032	0.000	0.000	0.000	0.000
16	A	454	GLU	-1	-0.796	-0.873	20.857	0.362	0.362	0.000	0.000	0.000	0.000
17	A	455	ARG	1	0.942	0.974	22.813	-0.228	-0.228	0.000	0.000	0.000	0.000
18	A	456	ILE	0	-0.022	-0.006	23.327	-0.024	-0.024	0.000	0.000	0.000	0.000
19	A	457	ARG	1	0.749	0.824	24.406	-0.349	-0.349	0.000	0.000	0.000	0.000
20	A	458	VAL	0	-0.003	0.004	26.603	-0.013	-0.013	0.000	0.000	0.000	0.000
21	A	459	ALA	0	0.064	0.044	28.801	-0.015	-0.015	0.000	0.000	0.000	0.000
22	A	460	GLU	-1	-0.826	-0.906	29.702	0.157	0.157	0.000	0.000	0.000	0.000
23	A	461	LEU	0	-0.021	0.001	30.388	-0.009	-0.009	0.000	0.000	0.000	0.000
24	A	462	GLU	-1	-0.899	-0.953	32.350	0.177	0.177	0.000	0.000	0.000	0.000
25	A	463	LYS	1	0.808	0.888	33.392	-0.168	-0.168	0.000	0.000	0.000	0.000
26	A	464	CYS	0	-0.058	-0.030	34.877	-0.010	-0.010	0.000	0.000	0.000	0.000
27	A	465	MET	0	0.009	-0.004	35.744	-0.008	-0.008	0.000	0.000	0.000	0.000
28	A	466	SER	0	-0.022	-0.025	38.367	-0.009	-0.009	0.000	0.000	0.000	0.000
29	A	467	LYS	1	0.856	0.935	37.620	-0.146	-0.146	0.000	0.000	0.000	0.000
30	A	468	MET	0	-0.045	-0.017	39.686	0.002	0.002	0.000	0.000	0.000	0.000
31	A	469	GLY	0	0.001	0.008	42.845	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	470	ASP	-1	-0.916	-0.959	45.208	0.107	0.107	0.000	0.000	0.000	0.000
33	A	471	ASP	-1	-0.897	-0.939	43.934	0.132	0.132	0.000	0.000	0.000	0.000
34	A	472	ILE	0	-0.032	-0.005	39.405	0.009	0.009	0.000	0.000	0.000	0.000
35	A	473	ASN	0	0.048	0.042	42.261	0.006	0.006	0.000	0.000	0.000	0.000
36	A	474	LYS	1	0.957	0.968	40.037	-0.149	-0.149	0.000	0.000	0.000	0.000
37	A	475	LYS	1	0.981	0.985	38.332	-0.149	-0.149	0.000	0.000	0.000	0.000
38	A	476	THR	0	0.024	0.001	37.475	0.011	0.011	0.000	0.000	0.000	0.000
39	A	477	THR	0	0.031	-0.007	35.805	0.006	0.006	0.000	0.000	0.000	0.000
40	A	478	ARG	1	0.793	0.863	28.827	-0.293	-0.293	0.000	0.000	0.000	0.000
41	A	479	ALA	0	0.024	0.015	32.665	0.017	0.017	0.000	0.000	0.000	0.000
42	A	480	VAL	0	0.037	0.020	32.790	0.011	0.011	0.000	0.000	0.000	0.000
43	A	481	ASP	-1	-0.785	-0.857	29.309	0.319	0.319	0.000	0.000	0.000	0.000
44	A	482	ASP	-1	-0.775	-0.865	28.393	0.338	0.338	0.000	0.000	0.000	0.000
45	A	483	LEU	0	-0.013	0.006	27.908	0.023	0.023	0.000	0.000	0.000	0.000
46	A	484	SER	0	-0.017	-0.005	27.931	0.019	0.019	0.000	0.000	0.000	0.000
47	A	485	ARG	1	0.853	0.901	23.920	-0.360	-0.360	0.000	0.000	0.000	0.000
48	A	486	GLY	0	0.009	0.009	23.260	0.045	0.045	0.000	0.000	0.000	0.000
49	A	487	ILE	0	-0.011	-0.014	23.700	0.026	0.026	0.000	0.000	0.000	0.000
50	A	488	VAL	0	0.030	0.015	20.711	0.025	0.025	0.000	0.000	0.000	0.000
51	A	489	ASN	0	-0.008	-0.015	19.036	0.073	0.073	0.000	0.000	0.000	0.000
52	A	490	ARG	1	0.934	0.969	18.368	-0.295	-0.295	0.000	0.000	0.000	0.000
53	A	491	PHE	0	-0.008	0.004	19.263	0.011	0.011	0.000	0.000	0.000	0.000
54	A	492	LEU	0	-0.018	-0.014	15.584	0.023	0.023	0.000	0.000	0.000	0.000
55	A	493	HIS	0	-0.014	-0.002	14.266	0.123	0.123	0.000	0.000	0.000	0.000
56	A	494	GLY	0	0.037	0.026	13.220	0.146	0.146	0.000	0.000	0.000	0.000
57	A	495	PRO	0	0.039	0.008	12.396	0.113	0.113	0.000	0.000	0.000	0.000
58	A	496	MET	0	-0.019	-0.015	9.909	0.131	0.131	0.000	0.000	0.000	0.000
59	A	497	GLN	0	0.021	0.019	8.454	0.431	0.431	0.000	0.000	0.000	0.000
60	A	498	HIS	0	-0.042	-0.024	8.200	0.322	0.322	0.000	0.000	0.000	0.000
61	A	499	LEU	0	0.000	0.024	6.419	-0.202	-0.202	0.000	0.000	0.000	0.000
62	A	500	ARG	1	0.830	0.910	2.041	-19.981	-23.693	10.150	-3.180	-3.258	0.025
63	A	501	CYS	0	-0.027	-0.011	3.506	-2.925	-2.100	0.036	-0.309	-0.552	0.002
64	A	502	ASP	-1	-0.736	-0.857	3.670	-3.175	-1.865	0.062	-0.549	-0.823	-0.004
65	A	503	GLY	0	-0.078	-0.053	5.974	0.550	0.550	0.000	0.000	0.000	0.000
66	A	504	SER	0	-0.094	-0.049	8.274	0.088	0.088	0.000	0.000	0.000	0.000
67	A	505	ASP	-1	-0.870	-0.909	9.205	-0.372	-0.372	0.000	0.000	0.000	0.000
68	A	506	SER	0	-0.077	-0.042	7.864	0.042	0.042	0.000	0.000	0.000	0.000
69	A	507	ARG	1	0.839	0.925	5.925	-1.753	-1.753	0.000	0.000	0.000	0.000
70	A	508	THR	0	0.004	-0.034	4.716	-1.114	-0.997	-0.001	-0.004	-0.111	0.000
71	A	509	LEU	0	0.040	-0.001	2.435	-0.969	-0.295	3.467	-0.751	-3.390	-0.001
72	A	510	SER	0	0.034	0.009	4.544	0.211	0.308	0.000	-0.005	-0.092	0.000
73	A	511	GLU	-1	-0.809	-0.872	8.315	-0.285	-0.285	0.000	0.000	0.000	0.000
74	A	512	THR	0	-0.035	-0.009	3.699	-0.044	0.325	0.009	-0.066	-0.312	0.000
75	A	513	LEU	0	-0.001	-0.006	4.791	-0.027	0.050	-0.001	-0.003	-0.072	0.000
76	A	514	GLU	-1	-0.756	-0.849	7.388	-0.135	-0.135	0.000	0.000	0.000	0.000
77	A	515	ASN	0	-0.024	-0.008	8.951	-0.073	-0.073	0.000	0.000	0.000	0.000
78	A	516	MET	0	-0.017	0.007	8.178	0.050	0.050	0.000	0.000	0.000	0.000
79	A	517	HIS	0	0.020	0.009	10.171	0.098	0.098	0.000	0.000	0.000	0.000
80	A	518	ALA	0	-0.056	-0.009	12.846	0.009	0.009	0.000	0.000	0.000	0.000
81	A	519	LEU	0	0.053	0.011	11.370	0.010	0.010	0.000	0.000	0.000	0.000
82	A	520	ASN	0	-0.006	-0.024	12.383	0.073	0.073	0.000	0.000	0.000	0.000
83	A	521	ARG	1	0.781	0.859	15.136	0.075	0.075	0.000	0.000	0.000	0.000
84	A	522	MET	0	-0.022	-0.011	18.140	0.013	0.013	0.000	0.000	0.000	0.000
85	A	523	TYR	0	0.000	0.003	17.074	0.018	0.018	0.000	0.000	0.000	0.000
86	A	524	GLY	0	0.028	0.016	20.035	0.003	0.003	0.000	0.000	0.000	0.000
87	A	525	LEU	0	-0.068	-0.025	14.363	0.005	0.005	0.000	0.000	0.000	0.000
88	A	526	GLU	-1	-0.794	-0.866	13.740	0.046	0.046	0.000	0.000	0.000	0.000
89	A	527	LYS	1	0.836	0.922	17.783	-0.162	-0.162	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:439:MET)