FMO DATABASE

FMODB ID: YQ2R2

Calculation Name: 4YVQ-A-Xray313

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	90
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-576563.645629
FMO2-HF: Nuclear repulsion	539138.15182
FMO2-HF: Total energy	-37425.493809
FMO2-MP2: Total energy	-37529.203489

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.
-23.859	-16.101	6.381	-4.364	-9.774	-0.019

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 : 0.018 / q_NPA : 0.006

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	-0.865	-0.926	2.772	-7.276	-3.251	0.395	-1.921	-2.500	-0.010
4	A	442	THR	0	-0.028	-0.032	3.897	0.244	0.597	0.001	-0.063	-0.292	0.000
5	A	443	VAL	0	-0.017	-0.010	5.226	0.680	0.680	0.000	0.000	0.000	0.000
6	A	444	PRO	0	0.014	-0.007	7.274	0.135	0.135	0.000	0.000	0.000	0.000
7	A	445	THR	0	0.061	0.026	9.274	0.049	0.049	0.000	0.000	0.000	0.000
8	A	446	ILE	0	0.032	0.023	6.586	0.052	0.052	0.000	0.000	0.000	0.000
9	A	447	LYS	1	0.924	0.969	10.667	-0.265	-0.265	0.000	0.000	0.000	0.000
10	A	448	LYS	1	0.777	0.863	13.423	0.002	0.002	0.000	0.000	0.000	0.000
11	A	449	LEU	0	0.046	0.032	13.508	-0.020	-0.020	0.000	0.000	0.000	0.000
12	A	450	ARG	1	0.957	0.975	13.891	-0.521	-0.521	0.000	0.000	0.000	0.000
13	A	451	ALA	0	-0.010	-0.001	16.644	-0.024	-0.024	0.000	0.000	0.000	0.000
14	A	452	TYR	0	-0.017	-0.002	18.606	-0.029	-0.029	0.000	0.000	0.000	0.000
15	A	453	ALA	0	0.017	0.000	18.991	-0.017	-0.017	0.000	0.000	0.000	0.000
16	A	454	GLU	-1	-0.801	-0.877	20.810	0.238	0.238	0.000	0.000	0.000	0.000
17	A	455	ARG	1	0.966	0.975	22.764	-0.123	-0.123	0.000	0.000	0.000	0.000
18	A	456	ILE	0	-0.026	0.000	23.495	-0.013	-0.013	0.000	0.000	0.000	0.000
19	A	457	ARG	1	0.791	0.872	24.185	-0.232	-0.232	0.000	0.000	0.000	0.000
20	A	458	VAL	0	-0.003	0.000	26.489	-0.007	-0.007	0.000	0.000	0.000	0.000
21	A	459	ALA	0	0.036	0.026	28.656	-0.010	-0.010	0.000	0.000	0.000	0.000
22	A	460	GLU	-1	-0.893	-0.957	29.879	0.092	0.092	0.000	0.000	0.000	0.000
23	A	461	LEU	0	-0.031	-0.009	30.123	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	462	GLU	-1	-0.909	-0.959	32.204	0.115	0.115	0.000	0.000	0.000	0.000
25	A	463	LYS	1	0.866	0.932	33.972	-0.095	-0.095	0.000	0.000	0.000	0.000
26	A	464	CYS	0	-0.050	-0.026	35.116	-0.006	-0.006	0.000	0.000	0.000	0.000
27	A	465	MET	0	-0.008	-0.010	35.727	-0.003	-0.003	0.000	0.000	0.000	0.000
28	A	466	SER	0	0.004	0.002	38.272	-0.005	-0.005	0.000	0.000	0.000	0.000
29	A	467	LYS	1	0.852	0.933	38.282	-0.087	-0.087	0.000	0.000	0.000	0.000
30	A	468	MET	0	-0.022	-0.008	39.403	0.001	0.001	0.000	0.000	0.000	0.000
31	A	469	GLY	0	0.028	0.028	42.839	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	470	ASP	-1	-0.915	-0.957	44.881	0.074	0.074	0.000	0.000	0.000	0.000
33	A	471	ASP	-1	-0.880	-0.937	43.970	0.082	0.082	0.000	0.000	0.000	0.000
34	A	472	ILE	0	-0.109	-0.033	39.866	0.007	0.007	0.000	0.000	0.000	0.000
35	A	473	ASN	0	0.031	-0.001	41.715	0.002	0.002	0.000	0.000	0.000	0.000
36	A	474	LYS	1	0.969	0.981	39.588	-0.110	-0.110	0.000	0.000	0.000	0.000
37	A	475	LYS	1	1.012	0.997	38.130	-0.110	-0.110	0.000	0.000	0.000	0.000
38	A	476	THR	0	0.036	0.034	37.743	0.008	0.008	0.000	0.000	0.000	0.000
39	A	477	THR	0	0.023	-0.010	35.629	0.003	0.003	0.000	0.000	0.000	0.000
40	A	478	ARG	1	0.891	0.945	29.831	-0.206	-0.206	0.000	0.000	0.000	0.000
41	A	479	ALA	0	0.012	0.016	32.799	0.011	0.011	0.000	0.000	0.000	0.000
42	A	480	VAL	0	0.039	0.013	32.814	0.007	0.007	0.000	0.000	0.000	0.000
43	A	481	ASP	-1	-0.861	-0.922	29.447	0.216	0.216	0.000	0.000	0.000	0.000
44	A	482	ASP	-1	-0.838	-0.930	28.521	0.227	0.227	0.000	0.000	0.000	0.000
45	A	483	LEU	0	-0.020	0.003	27.980	0.014	0.014	0.000	0.000	0.000	0.000
46	A	484	SER	0	-0.042	-0.029	27.994	0.011	0.011	0.000	0.000	0.000	0.000
47	A	485	ARG	1	0.896	0.932	23.794	-0.253	-0.253	0.000	0.000	0.000	0.000
48	A	486	GLY	0	0.005	0.010	23.320	0.029	0.029	0.000	0.000	0.000	0.000
49	A	487	ILE	0	-0.016	-0.019	23.959	0.014	0.014	0.000	0.000	0.000	0.000
50	A	488	VAL	0	0.037	0.018	20.464	0.009	0.009	0.000	0.000	0.000	0.000
51	A	489	ASN	0	0.000	-0.013	19.179	0.022	0.022	0.000	0.000	0.000	0.000
52	A	490	ARG	1	0.928	0.963	18.582	-0.197	-0.197	0.000	0.000	0.000	0.000
53	A	491	PHE	0	-0.009	0.008	19.794	0.000	0.000	0.000	0.000	0.000	0.000
54	A	492	LEU	0	-0.030	-0.022	15.608	0.006	0.006	0.000	0.000	0.000	0.000
55	A	493	HIS	0	0.007	0.013	14.413	0.092	0.092	0.000	0.000	0.000	0.000
56	A	494	GLY	0	0.047	0.028	13.430	0.089	0.089	0.000	0.000	0.000	0.000
57	A	495	PRO	0	0.050	0.008	12.567	0.069	0.069	0.000	0.000	0.000	0.000
58	A	496	MET	0	-0.011	-0.010	10.019	0.065	0.065	0.000	0.000	0.000	0.000
59	A	497	GLN	0	-0.012	0.014	8.755	0.231	0.231	0.000	0.000	0.000	0.000
60	A	498	HIS	0	-0.056	-0.033	8.449	0.237	0.237	0.000	0.000	0.000	0.000
61	A	499	LEU	0	-0.006	0.010	6.526	-0.084	-0.084	0.000	0.000	0.000	0.000
62	A	500	ARG	1	0.940	0.981	3.421	-6.634	-6.236	0.008	-0.109	-0.296	0.000
63	A	501	CYS	0	-0.051	0.028	3.643	-2.240	-1.756	0.008	-0.148	-0.343	0.001
64	A	502	ASP	-1	-0.669	-0.869	2.447	-7.182	-4.811	0.588	-1.102	-1.857	-0.010
65	A	503	GLY	0	-0.109	-0.079	4.449	1.169	1.300	0.000	-0.011	-0.120	0.000
66	A	504	SER	0	-0.054	-0.017	4.809	0.465	0.465	0.000	0.000	0.000	0.000
67	A	505	ASP	-1	-0.902	-0.926	6.576	-0.660	-0.660	0.000	0.000	0.000	0.000
68	A	506	SER	0	-0.113	-0.045	7.037	0.296	0.296	0.000	0.000	0.000	0.000
69	A	507	ARG	1	0.871	0.898	6.102	-0.773	-0.773	0.000	0.000	0.000	0.000
70	A	508	THR	0	0.067	0.054	4.629	-0.956	-0.819	0.000	-0.006	-0.131	0.000
71	A	509	LEU	0	0.068	0.005	2.172	-0.596	-1.062	5.378	-0.989	-3.922	0.000
72	A	510	SER	0	-0.007	-0.015	4.470	0.185	0.281	0.002	0.009	-0.107	0.000
73	A	511	GLU	-1	-0.844	-0.923	8.042	-0.166	-0.166	0.000	0.000	0.000	0.000
74	A	512	THR	0	-0.039	-0.002	4.261	0.023	0.252	0.001	-0.024	-0.206	0.000
75	A	513	LEU	0	-0.001	-0.012	4.985	-0.115	-0.115	0.000	0.000	0.000	0.000
76	A	514	GLU	-1	-0.881	-0.936	7.441	-0.328	-0.328	0.000	0.000	0.000	0.000
77	A	515	ASN	0	-0.043	-0.018	9.371	-0.034	-0.034	0.000	0.000	0.000	0.000
78	A	516	MET	0	-0.029	-0.011	8.073	-0.009	-0.009	0.000	0.000	0.000	0.000
79	A	517	HIS	0	0.006	0.003	10.083	0.086	0.086	0.000	0.000	0.000	0.000
80	A	518	ALA	0	-0.011	-0.007	12.729	0.026	0.026	0.000	0.000	0.000	0.000
81	A	519	LEU	0	0.009	0.003	11.496	0.027	0.027	0.000	0.000	0.000	0.000
82	A	520	ASN	0	0.001	-0.010	11.974	0.064	0.064	0.000	0.000	0.000	0.000
83	A	521	ARG	1	0.933	0.969	15.589	0.155	0.155	0.000	0.000	0.000	0.000
84	A	522	MET	0	-0.045	-0.016	18.123	0.015	0.015	0.000	0.000	0.000	0.000
85	A	523	TYR	0	0.005	0.001	17.098	0.011	0.011	0.000	0.000	0.000	0.000
86	A	524	GLY	0	0.003	0.016	19.676	0.008	0.008	0.000	0.000	0.000	0.000
87	A	525	LEU	0	-0.048	-0.021	14.390	0.012	0.012	0.000	0.000	0.000	0.000
88	A	526	GLU	-1	-0.845	-0.908	13.863	-0.098	-0.098	0.000	0.000	0.000	0.000
89	A	527	LYS	1	0.826	0.904	17.781	-0.041	-0.041	0.000	0.000	0.000	0.000
90	A	1	NME	0	0.062	0.051	21.571	-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:439:MET )