FMO DATABASE

FMODB ID: 1N59Z

Calculation Name: 2VXQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2VXQ

Chain ID: A

ChEMBL ID:

UniProt ID: P01857

Base Structure: X-ray

Registration Date: 2023-09-22

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	-662242.178874
FMO2-HF: Nuclear repulsion	625785.705281
FMO2-HF: Total energy	-36456.473593
FMO2-MP2: Total energy	-36562.714003

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:3:LYS)

Summations of interaction energy for fragment #1(A:3:LYS)

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.
-167.143	-166.229	23.877	-11.968	-12.822	-0.128

Interaction energy analysis for fragmet #1(A:3:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.841 / q_NPA : 0.893

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	5	THR	0	-0.053	-0.012	3.880	6.546	8.434	-0.017	-0.957	-0.914	-0.001
4	A	6	PHE	0	0.083	0.026	6.300	-1.307	-1.307	0.000	0.000	0.000	0.000
5	A	7	THR	0	0.018	0.020	10.116	0.858	0.858	0.000	0.000	0.000	0.000
6	A	8	VAL	0	0.023	0.029	12.598	0.139	0.139	0.000	0.000	0.000	0.000
7	A	9	GLU	-1	-0.838	-0.930	15.983	-15.960	-15.960	0.000	0.000	0.000	0.000
8	A	10	LYS	1	0.903	0.939	18.491	12.139	12.139	0.000	0.000	0.000	0.000
9	A	11	GLY	0	0.005	-0.002	22.117	0.149	0.149	0.000	0.000	0.000	0.000
10	A	12	SER	0	-0.030	0.000	20.353	0.258	0.258	0.000	0.000	0.000	0.000
11	A	13	ASN	0	-0.056	-0.042	22.895	0.547	0.547	0.000	0.000	0.000	0.000
12	A	14	GLU	-1	-0.852	-0.933	24.953	-10.102	-10.102	0.000	0.000	0.000	0.000
13	A	15	LYS	1	0.809	0.910	27.253	9.411	9.411	0.000	0.000	0.000	0.000
14	A	16	HIS	0	-0.057	-0.042	23.543	-0.407	-0.407	0.000	0.000	0.000	0.000
15	A	17	LEU	0	-0.014	0.003	18.175	0.035	0.035	0.000	0.000	0.000	0.000
16	A	18	ALA	0	0.039	0.021	19.208	-0.353	-0.353	0.000	0.000	0.000	0.000
17	A	19	VAL	0	-0.011	-0.014	13.519	-0.120	-0.120	0.000	0.000	0.000	0.000
18	A	20	LEU	0	0.001	0.015	11.964	-0.523	-0.523	0.000	0.000	0.000	0.000
19	A	21	VAL	0	-0.022	-0.002	8.772	-1.256	-1.256	0.000	0.000	0.000	0.000
20	A	22	LYS	1	0.831	0.912	6.371	39.475	39.475	0.000	0.000	0.000	0.000
21	A	23	TYR	0	0.077	0.026	2.066	-27.566	-28.717	11.870	-4.732	-5.988	-0.053
22	A	24	GLU	-1	-0.845	-0.912	2.606	-41.715	-39.376	0.701	-1.005	-2.035	-0.003
23	A	25	GLY	0	0.018	0.008	1.790	-37.658	-40.116	11.325	-5.261	-3.605	-0.071
24	A	26	ASP	-1	-0.850	-0.928	4.572	-35.708	-35.564	-0.001	-0.008	-0.134	0.000
25	A	27	THR	0	0.021	0.016	6.046	-0.355	-0.355	0.000	0.000	0.000	0.000
26	A	28	MET	0	-0.028	0.001	6.414	-1.145	-1.145	0.000	0.000	0.000	0.000
27	A	29	ALA	0	0.024	0.013	9.995	2.135	2.135	0.000	0.000	0.000	0.000
28	A	30	GLU	-1	-0.912	-0.975	12.380	-16.816	-16.816	0.000	0.000	0.000	0.000
29	A	31	VAL	0	-0.017	-0.020	11.285	-2.602	-2.602	0.000	0.000	0.000	0.000
30	A	32	GLU	-1	-0.799	-0.872	13.821	-15.449	-15.449	0.000	0.000	0.000	0.000
31	A	33	LEU	0	-0.004	-0.008	15.148	-1.468	-1.468	0.000	0.000	0.000	0.000
32	A	34	ARG	1	0.855	0.927	17.421	15.491	15.491	0.000	0.000	0.000	0.000
33	A	35	GLU	-1	-0.803	-0.898	19.074	-12.877	-12.877	0.000	0.000	0.000	0.000
34	A	36	HIS	0	-0.090	-0.057	20.000	0.727	0.727	0.000	0.000	0.000	0.000
35	A	37	GLY	0	-0.004	-0.011	21.647	0.096	0.096	0.000	0.000	0.000	0.000
36	A	38	SER	0	-0.058	-0.015	23.188	0.649	0.649	0.000	0.000	0.000	0.000
37	A	39	ASP	-1	-0.902	-0.954	23.433	-11.671	-11.671	0.000	0.000	0.000	0.000
38	A	40	GLU	-1	-0.969	-0.982	23.623	-11.941	-11.941	0.000	0.000	0.000	0.000
39	A	41	TRP	0	-0.056	-0.036	15.503	-0.733	-0.733	0.000	0.000	0.000	0.000
40	A	42	VAL	0	0.026	0.014	20.432	0.461	0.461	0.000	0.000	0.000	0.000
41	A	43	ALA	0	0.018	0.005	18.855	-0.868	-0.868	0.000	0.000	0.000	0.000
42	A	44	MET	0	-0.054	-0.010	16.815	0.090	0.090	0.000	0.000	0.000	0.000
43	A	45	THR	0	-0.014	-0.008	18.564	-0.302	-0.302	0.000	0.000	0.000	0.000
44	A	46	LYS	1	0.801	0.918	14.425	20.298	20.298	0.000	0.000	0.000	0.000
45	A	47	GLY	0	0.035	0.011	17.629	1.123	1.123	0.000	0.000	0.000	0.000
46	A	48	GLU	-1	-0.911	-0.968	17.783	-16.231	-16.231	0.000	0.000	0.000	0.000
47	A	49	GLY	0	-0.041	-0.016	16.852	-0.361	-0.361	0.000	0.000	0.000	0.000
48	A	50	GLY	0	-0.009	-0.002	13.330	-1.100	-1.100	0.000	0.000	0.000	0.000
49	A	51	VAL	0	-0.026	-0.018	13.655	-1.265	-1.265	0.000	0.000	0.000	0.000
50	A	52	TRP	0	-0.024	-0.005	12.673	0.295	0.295	0.000	0.000	0.000	0.000
51	A	53	THR	0	-0.023	-0.023	17.022	-0.049	-0.049	0.000	0.000	0.000	0.000
52	A	54	PHE	0	0.020	0.010	20.274	-0.356	-0.356	0.000	0.000	0.000	0.000
53	A	55	ASP	-1	-0.836	-0.902	22.262	-12.474	-12.474	0.000	0.000	0.000	0.000
54	A	56	SER	0	-0.016	-0.019	26.045	0.003	0.003	0.000	0.000	0.000	0.000
55	A	57	GLU	-1	-0.891	-0.947	28.156	-9.541	-9.541	0.000	0.000	0.000	0.000
56	A	58	GLU	-1	-0.876	-0.944	30.302	-8.729	-8.729	0.000	0.000	0.000	0.000
57	A	59	PRO	0	-0.079	-0.031	29.132	-0.412	-0.412	0.000	0.000	0.000	0.000
58	A	60	LEU	0	0.013	0.026	23.128	-0.128	-0.128	0.000	0.000	0.000	0.000
59	A	61	GLN	0	-0.096	-0.063	25.163	0.169	0.169	0.000	0.000	0.000	0.000
60	A	62	GLY	0	-0.003	0.007	21.082	-0.256	-0.256	0.000	0.000	0.000	0.000
61	A	63	PRO	0	-0.065	-0.064	17.990	0.597	0.597	0.000	0.000	0.000	0.000
62	A	64	PHE	0	-0.005	0.007	16.835	0.311	0.311	0.000	0.000	0.000	0.000
63	A	65	ASN	0	-0.017	0.018	14.742	-1.316	-1.316	0.000	0.000	0.000	0.000
64	A	66	PHE	0	0.025	-0.002	11.739	0.399	0.399	0.000	0.000	0.000	0.000
65	A	67	ARG	1	0.793	0.878	11.650	16.195	16.195	0.000	0.000	0.000	0.000
66	A	68	PHE	0	0.036	0.009	5.661	-1.093	-1.093	0.000	0.000	0.000	0.000
67	A	69	LEU	0	0.002	0.012	10.599	-1.021	-1.021	0.000	0.000	0.000	0.000
68	A	70	THR	0	-0.047	-0.042	5.477	1.125	1.125	0.000	0.000	0.000	0.000
69	A	71	GLU	-1	-0.836	-0.930	8.853	-20.144	-20.144	0.000	0.000	0.000	0.000
70	A	72	LYS	1	0.816	0.916	7.259	39.351	39.351	0.000	0.000	0.000	0.000
71	A	73	GLY	0	0.019	0.018	10.597	0.949	0.949	0.000	0.000	0.000	0.000
72	A	74	MET	0	-0.049	-0.008	5.428	3.126	3.126	0.000	0.000	0.000	0.000
73	A	75	LYS	1	0.927	0.950	8.572	23.796	23.796	0.000	0.000	0.000	0.000
74	A	76	ASN	0	-0.074	-0.045	5.919	-6.915	-6.915	0.000	0.000	0.000	0.000
75	A	77	VAL	0	0.048	0.021	9.336	1.140	1.140	0.000	0.000	0.000	0.000
76	A	78	PHE	0	-0.069	-0.038	5.302	-2.077	-2.077	0.000	0.000	0.000	0.000
77	A	79	ASP	-1	-0.764	-0.897	10.579	-17.543	-17.543	0.000	0.000	0.000	0.000
78	A	80	ASP	-1	-0.870	-0.935	13.155	-15.808	-15.808	0.000	0.000	0.000	0.000
79	A	81	VAL	0	-0.048	-0.006	9.724	-0.023	-0.023	0.000	0.000	0.000	0.000
80	A	82	VAL	0	-0.016	0.003	12.539	-0.093	-0.093	0.000	0.000	0.000	0.000
81	A	83	PRO	0	0.020	0.008	14.846	0.579	0.579	0.000	0.000	0.000	0.000
82	A	84	GLU	-1	-0.757	-0.859	18.122	-11.115	-11.115	0.000	0.000	0.000	0.000
83	A	85	LYS	1	0.785	0.880	21.663	11.062	11.062	0.000	0.000	0.000	0.000
84	A	86	TYR	0	0.004	0.024	17.940	-0.246	-0.246	0.000	0.000	0.000	0.000
85	A	87	THR	0	-0.042	-0.040	18.098	0.834	0.834	0.000	0.000	0.000	0.000
86	A	88	ILE	0	-0.019	-0.001	17.819	-0.658	-0.658	0.000	0.000	0.000	0.000
87	A	89	GLY	0	-0.010	-0.005	17.146	0.518	0.518	0.000	0.000	0.000	0.000
88	A	90	ALA	0	-0.035	-0.010	15.013	-0.478	-0.478	0.000	0.000	0.000	0.000
89	A	91	THR	0	-0.039	-0.036	8.500	-0.211	-0.211	0.000	0.000	0.000	0.000
90	A	92	TYR	0	0.021	0.016	10.180	1.041	1.041	0.000	0.000	0.000	0.000
91	A	93	ALA	0	0.014	-0.011	5.145	-2.370	-2.370	0.000	0.000	0.000	0.000
92	A	94	PRO	0	-0.013	0.019	5.247	1.655	1.807	-0.001	-0.005	-0.146	0.000

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Overview

Highlights

Manual

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:LYS)