FMO DATABASE

FMODB ID: MN2LZ

Calculation Name: 1VKU-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 1VKU

Chain ID: A

ChEMBL ID:
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UniProt ID: Q9WY19

Base Structure: X-ray

Registration Date: 2023-09-23

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	OptH
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	85
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-628691.924213
FMO2-HF: Nuclear repulsion	593347.89161
FMO2-HF: Total energy	-35344.032602
FMO2-MP2: Total energy	-35447.051226

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:-2:HIS)

Summations of interaction energy for fragment #1(A:-2:HIS)

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.
7.341	10.17	0.173	-0.907	-2.094	0.001

Interaction energy analysis for fragmet #1(A:-2:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.009 / q_NPA : -0.014

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	0	HIS	0	0.019	-0.008	3.399	-1.337	1.441	0.174	-0.901	-2.050	0.001
4	A	1	MET	0	-0.056	-0.045	4.681	0.163	0.214	-0.001	-0.006	-0.044	0.000
5	A	2	GLU	-1	-0.860	-0.919	7.384	1.860	1.860	0.000	0.000	0.000	0.000
6	A	3	ARG	1	0.853	0.903	9.199	-0.741	-0.741	0.000	0.000	0.000	0.000
7	A	4	LYS	1	0.931	0.959	11.604	-0.102	-0.102	0.000	0.000	0.000	0.000
8	A	5	LYS	1	0.922	0.966	8.975	-0.073	-0.073	0.000	0.000	0.000	0.000
9	A	6	LEU	0	0.059	0.046	12.705	-0.031	-0.031	0.000	0.000	0.000	0.000
10	A	7	ILE	0	0.013	0.010	15.425	-0.031	-0.031	0.000	0.000	0.000	0.000
11	A	8	ALA	0	-0.026	-0.011	16.688	-0.028	-0.028	0.000	0.000	0.000	0.000
12	A	9	LYS	1	0.855	0.931	17.517	-0.292	-0.292	0.000	0.000	0.000	0.000
13	A	10	PHE	0	0.000	-0.004	19.338	-0.015	-0.015	0.000	0.000	0.000	0.000
14	A	11	VAL	0	-0.008	-0.011	21.241	-0.017	-0.017	0.000	0.000	0.000	0.000
15	A	12	GLU	-1	-0.838	-0.903	21.406	0.192	0.192	0.000	0.000	0.000	0.000
16	A	13	ILE	0	0.010	0.009	21.833	-0.013	-0.013	0.000	0.000	0.000	0.000
17	A	14	ALA	0	0.006	-0.006	25.171	-0.011	-0.011	0.000	0.000	0.000	0.000
18	A	15	SER	0	-0.015	0.000	26.888	-0.013	-0.013	0.000	0.000	0.000	0.000
19	A	16	GLU	-1	-0.986	-1.005	26.590	0.133	0.133	0.000	0.000	0.000	0.000
20	A	17	LYS	1	0.859	0.935	26.908	-0.200	-0.200	0.000	0.000	0.000	0.000
21	A	18	MET	0	-0.043	-0.015	28.800	0.002	0.002	0.000	0.000	0.000	0.000
22	A	19	GLY	0	-0.020	0.017	31.514	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	20	LYS	1	0.835	0.921	30.130	-0.138	-0.138	0.000	0.000	0.000	0.000
24	A	21	ASP	-1	-0.922	-0.963	29.648	0.086	0.086	0.000	0.000	0.000	0.000
25	A	22	LEU	0	-0.046	-0.035	25.540	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	23	GLU	-1	-0.929	-0.954	25.839	0.050	0.050	0.000	0.000	0.000	0.000
27	A	24	THR	0	-0.067	-0.042	23.007	0.000	0.000	0.000	0.000	0.000	0.000
28	A	25	VAL	0	-0.007	0.002	21.181	0.001	0.001	0.000	0.000	0.000	0.000
29	A	26	ASP	-1	-0.870	-0.916	21.148	0.171	0.171	0.000	0.000	0.000	0.000
30	A	27	GLU	-1	-0.758	-0.895	15.583	0.464	0.464	0.000	0.000	0.000	0.000
31	A	28	GLU	-1	-0.934	-0.980	20.377	0.271	0.271	0.000	0.000	0.000	0.000
32	A	29	ASN	0	-0.020	0.000	23.132	-0.010	-0.010	0.000	0.000	0.000	0.000
33	A	30	THR	0	-0.057	-0.047	25.249	0.021	0.021	0.000	0.000	0.000	0.000
34	A	31	PHE	0	0.100	0.031	23.252	-0.013	-0.013	0.000	0.000	0.000	0.000
35	A	32	LYS	1	0.960	0.992	28.444	-0.137	-0.137	0.000	0.000	0.000	0.000
36	A	33	GLU	-1	-0.932	-0.962	28.862	0.127	0.127	0.000	0.000	0.000	0.000
37	A	34	LEU	0	-0.005	0.019	25.632	-0.010	-0.010	0.000	0.000	0.000	0.000
38	A	35	GLY	0	-0.066	-0.041	30.222	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	36	PHE	0	-0.008	0.000	27.805	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	37	ASP	-1	-0.896	-0.956	31.781	0.152	0.152	0.000	0.000	0.000	0.000
41	A	38	SER	0	-0.022	-0.039	32.176	0.008	0.008	0.000	0.000	0.000	0.000
42	A	39	ILE	0	-0.026	-0.014	32.115	0.013	0.013	0.000	0.000	0.000	0.000
43	A	40	ASP	-1	-0.757	-0.870	30.991	0.164	0.164	0.000	0.000	0.000	0.000
44	A	41	VAL	0	-0.061	-0.036	26.721	0.014	0.014	0.000	0.000	0.000	0.000
45	A	42	ILE	0	-0.010	-0.007	27.487	0.021	0.021	0.000	0.000	0.000	0.000
46	A	43	ASP	-1	-0.897	-0.941	28.623	0.200	0.200	0.000	0.000	0.000	0.000
47	A	44	LEU	0	-0.041	-0.019	23.964	0.012	0.012	0.000	0.000	0.000	0.000
48	A	45	VAL	0	-0.019	-0.017	23.820	0.026	0.026	0.000	0.000	0.000	0.000
49	A	46	MET	0	0.008	0.009	24.033	0.019	0.019	0.000	0.000	0.000	0.000
50	A	47	PHE	0	-0.008	-0.010	25.079	0.002	0.002	0.000	0.000	0.000	0.000
51	A	48	PHE	0	-0.007	-0.015	17.896	0.013	0.013	0.000	0.000	0.000	0.000
52	A	49	GLU	-1	-0.812	-0.898	20.599	0.393	0.393	0.000	0.000	0.000	0.000
53	A	50	ASP	-1	-0.949	-0.967	22.157	0.312	0.312	0.000	0.000	0.000	0.000
54	A	51	GLU	-1	-0.959	-0.977	19.877	0.308	0.308	0.000	0.000	0.000	0.000
55	A	52	PHE	0	-0.091	-0.055	15.026	0.025	0.025	0.000	0.000	0.000	0.000
56	A	53	ALA	0	-0.037	-0.001	17.994	0.059	0.059	0.000	0.000	0.000	0.000
57	A	54	LEU	0	-0.047	-0.020	16.327	0.049	0.049	0.000	0.000	0.000	0.000
58	A	55	ARG	1	0.814	0.900	20.328	-0.388	-0.388	0.000	0.000	0.000	0.000
59	A	56	ILE	0	-0.057	-0.040	20.159	0.045	0.045	0.000	0.000	0.000	0.000
60	A	57	GLU	-1	-0.934	-0.972	23.437	0.352	0.352	0.000	0.000	0.000	0.000
61	A	58	ASP	-1	-0.833	-0.939	26.385	0.260	0.260	0.000	0.000	0.000	0.000
62	A	59	GLU	-1	-0.917	-0.945	28.262	0.239	0.239	0.000	0.000	0.000	0.000
63	A	60	GLU	-1	-0.820	-0.915	22.862	0.460	0.460	0.000	0.000	0.000	0.000
64	A	61	ILE	0	0.045	0.032	25.578	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	62	SER	0	-0.090	-0.044	26.891	-0.015	-0.015	0.000	0.000	0.000	0.000
66	A	63	LYS	1	0.789	0.876	26.250	-0.290	-0.290	0.000	0.000	0.000	0.000
67	A	64	ILE	0	-0.012	0.025	23.421	0.001	0.001	0.000	0.000	0.000	0.000
68	A	65	ARG	1	0.828	0.909	25.495	-0.247	-0.247	0.000	0.000	0.000	0.000
69	A	66	LYS	1	0.839	0.927	23.488	-0.249	-0.249	0.000	0.000	0.000	0.000
70	A	67	VAL	0	0.066	0.036	20.125	0.027	0.027	0.000	0.000	0.000	0.000
71	A	68	LYS	1	0.847	0.906	16.738	-0.468	-0.468	0.000	0.000	0.000	0.000
72	A	69	ASP	-1	-0.804	-0.902	18.421	0.389	0.389	0.000	0.000	0.000	0.000
73	A	70	LEU	0	0.010	0.007	19.816	0.035	0.035	0.000	0.000	0.000	0.000
74	A	71	ILE	0	-0.039	-0.020	14.435	0.046	0.046	0.000	0.000	0.000	0.000
75	A	72	ASP	-1	-0.791	-0.880	14.954	0.741	0.741	0.000	0.000	0.000	0.000
76	A	73	ILE	0	-0.047	-0.013	15.409	0.089	0.089	0.000	0.000	0.000	0.000
77	A	74	VAL	0	0.025	0.010	14.552	0.052	0.052	0.000	0.000	0.000	0.000
78	A	75	ILE	0	0.013	0.004	9.985	0.010	0.010	0.000	0.000	0.000	0.000
79	A	76	LYS	1	0.850	0.929	11.983	-0.558	-0.558	0.000	0.000	0.000	0.000
80	A	77	LYS	1	0.840	0.908	14.196	-0.526	-0.526	0.000	0.000	0.000	0.000
81	A	78	LEU	0	-0.026	-0.021	11.589	-0.020	-0.020	0.000	0.000	0.000	0.000
82	A	79	GLU	-1	-0.968	-0.979	8.880	2.168	2.168	0.000	0.000	0.000	0.000
83	A	80	GLU	-1	-0.919	-0.943	11.241	0.783	0.783	0.000	0.000	0.000	0.000
84	A	81	ILE	0	-0.084	-0.017	14.682	-0.041	-0.041	0.000	0.000	0.000	0.000
85	A	82	ASP	-1	-1.004	-1.005	9.685	2.342	2.342	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-2:HIS)