FMO DATABASE

FMODB ID: LNLV9

Calculation Name: 3MJQ-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: 3MJQ

Chain ID: A

ChEMBL ID:
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UniProt ID: Q24QT8

Base Structure: X-ray

Registration Date: 2023-09-20

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	OptHSide
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	107
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-841016.298761
FMO2-HF: Nuclear repulsion	798592.792741
FMO2-HF: Total energy	-42423.506021
FMO2-MP2: Total energy	-42546.274611

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:LYS)

Summations of interaction energy for fragment #1(A:2: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.
3.312	10.188	4.784	-4.131	-7.528	-0.007

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.956 / q_NPA : 0.983

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

Sort

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	4	PHE	0	0.006	-0.004	1.860	-2.073	2.523	4.393	-3.586	-5.403	-0.004
4	A	5	LEU	0	0.074	0.057	2.536	5.895	7.736	0.392	-0.458	-1.774	-0.003
5	A	6	GLU	-1	-0.763	-0.876	4.923	-25.544	-25.337	-0.001	-0.022	-0.184	0.000
6	A	7	THR	0	-0.135	-0.094	6.929	3.458	3.458	0.000	0.000	0.000	0.000
7	A	8	ILE	0	-0.034	0.000	7.373	1.796	1.796	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.906	-0.961	10.238	-19.585	-19.585	0.000	0.000	0.000	0.000
9	A	10	ASP	-1	-0.934	-0.962	12.969	-16.688	-16.688	0.000	0.000	0.000	0.000
10	A	11	MET	0	-0.044	-0.018	11.216	-1.362	-1.362	0.000	0.000	0.000	0.000
11	A	12	ILE	0	-0.028	-0.022	6.565	0.381	0.381	0.000	0.000	0.000	0.000
12	A	13	LEU	0	0.020	0.010	8.878	-0.392	-0.392	0.000	0.000	0.000	0.000
13	A	14	ILE	0	-0.040	-0.014	5.776	-0.336	-0.336	0.000	0.000	0.000	0.000
14	A	15	ILE	0	-0.009	-0.002	9.606	0.431	0.431	0.000	0.000	0.000	0.000
15	A	16	ASN	0	0.084	0.038	13.196	0.243	0.243	0.000	0.000	0.000	0.000
16	A	17	ARG	1	0.998	0.981	15.432	11.937	11.937	0.000	0.000	0.000	0.000
17	A	18	GLU	-1	-0.959	-0.967	18.779	-11.227	-11.227	0.000	0.000	0.000	0.000
18	A	19	GLY	0	0.014	0.012	18.168	0.337	0.337	0.000	0.000	0.000	0.000
19	A	20	ARG	1	0.855	0.923	16.260	13.251	13.251	0.000	0.000	0.000	0.000
20	A	21	LEU	0	0.015	-0.011	12.517	-0.546	-0.546	0.000	0.000	0.000	0.000
21	A	22	LEU	0	-0.037	-0.005	9.526	-0.119	-0.119	0.000	0.000	0.000	0.000
22	A	23	TYR	0	-0.043	-0.035	4.435	-2.641	-2.409	0.000	-0.065	-0.167	0.000
23	A	24	ALA	0	0.029	0.014	7.531	1.389	1.389	0.000	0.000	0.000	0.000
24	A	25	ASN	0	0.033	0.036	6.967	0.463	0.463	0.000	0.000	0.000	0.000
25	A	26	THR	0	0.058	0.015	8.584	2.913	2.913	0.000	0.000	0.000	0.000
26	A	27	ALA	0	-0.029	-0.013	11.165	1.754	1.754	0.000	0.000	0.000	0.000
27	A	28	VAL	0	0.013	0.005	11.249	1.474	1.474	0.000	0.000	0.000	0.000
28	A	29	PRO	0	0.002	0.007	12.904	1.014	1.014	0.000	0.000	0.000	0.000
29	A	30	LYS	1	0.864	0.933	14.312	19.981	19.981	0.000	0.000	0.000	0.000
30	A	31	LYS	1	0.844	0.904	16.733	15.279	15.279	0.000	0.000	0.000	0.000
31	A	32	LEU	0	0.011	-0.011	17.049	0.685	0.685	0.000	0.000	0.000	0.000
32	A	33	GLY	0	0.010	0.026	19.592	0.661	0.661	0.000	0.000	0.000	0.000
33	A	34	TYR	0	-0.028	-0.011	18.556	0.465	0.465	0.000	0.000	0.000	0.000
34	A	35	THR	0	0.008	-0.027	17.031	-0.609	-0.609	0.000	0.000	0.000	0.000
35	A	36	HIS	0	0.043	0.023	9.000	0.258	0.258	0.000	0.000	0.000	0.000
36	A	37	GLU	-1	-0.864	-0.938	14.114	-16.287	-16.287	0.000	0.000	0.000	0.000
37	A	38	GLU	-1	-0.783	-0.859	16.301	-12.202	-12.202	0.000	0.000	0.000	0.000
38	A	39	LEU	0	0.013	-0.013	13.111	0.256	0.256	0.000	0.000	0.000	0.000
39	A	40	MET	0	-0.056	-0.004	10.296	-0.308	-0.308	0.000	0.000	0.000	0.000
40	A	41	SER	0	-0.060	-0.022	14.423	0.442	0.442	0.000	0.000	0.000	0.000
41	A	42	MET	0	-0.008	0.000	18.025	0.464	0.464	0.000	0.000	0.000	0.000
42	A	43	HIS	0	0.060	0.049	17.918	-0.616	-0.616	0.000	0.000	0.000	0.000
43	A	44	ILE	0	0.045	0.016	15.906	0.185	0.185	0.000	0.000	0.000	0.000
44	A	45	LEU	0	0.014	-0.002	18.725	0.074	0.074	0.000	0.000	0.000	0.000
45	A	46	THR	0	-0.069	-0.040	21.828	0.469	0.469	0.000	0.000	0.000	0.000
46	A	47	ILE	0	-0.013	-0.003	17.639	0.144	0.144	0.000	0.000	0.000	0.000
47	A	48	THR	0	-0.024	-0.017	19.801	0.215	0.215	0.000	0.000	0.000	0.000
48	A	49	SER	0	-0.050	-0.034	22.571	0.312	0.312	0.000	0.000	0.000	0.000
49	A	50	ALA	0	0.081	0.067	25.910	0.319	0.319	0.000	0.000	0.000	0.000
50	A	51	GLY	0	0.028	0.013	27.474	0.225	0.225	0.000	0.000	0.000	0.000
51	A	52	LYS	1	0.780	0.875	29.267	8.582	8.582	0.000	0.000	0.000	0.000
52	A	53	MET	0	0.080	0.039	26.215	-0.300	-0.300	0.000	0.000	0.000	0.000
53	A	54	ALA	0	0.052	0.038	27.826	-0.190	-0.190	0.000	0.000	0.000	0.000
54	A	55	GLU	-1	-0.834	-0.932	29.540	-8.623	-8.623	0.000	0.000	0.000	0.000
55	A	56	GLY	0	0.014	0.006	25.887	-0.213	-0.213	0.000	0.000	0.000	0.000
56	A	57	GLU	-1	-0.963	-0.983	24.621	-10.084	-10.084	0.000	0.000	0.000	0.000
57	A	58	LYS	1	0.874	0.929	25.764	9.052	9.052	0.000	0.000	0.000	0.000
58	A	59	ILE	0	-0.003	-0.006	22.974	-0.175	-0.175	0.000	0.000	0.000	0.000
59	A	60	LEU	0	0.045	0.028	18.807	-0.319	-0.319	0.000	0.000	0.000	0.000
60	A	61	ALA	0	0.033	0.011	21.732	-0.317	-0.317	0.000	0.000	0.000	0.000
61	A	62	GLU	-1	-0.883	-0.941	23.944	-9.807	-9.807	0.000	0.000	0.000	0.000
62	A	63	LEU	0	-0.041	-0.029	19.110	-0.118	-0.118	0.000	0.000	0.000	0.000
63	A	64	PHE	0	-0.007	0.019	16.500	-0.410	-0.410	0.000	0.000	0.000	0.000
64	A	65	ALA	0	-0.073	-0.030	20.604	-0.067	-0.067	0.000	0.000	0.000	0.000
65	A	66	GLY	0	0.052	0.037	21.688	0.085	0.085	0.000	0.000	0.000	0.000
66	A	67	LYS	1	0.847	0.945	22.736	9.575	9.575	0.000	0.000	0.000	0.000
67	A	68	LYS	1	0.863	0.917	22.946	10.537	10.537	0.000	0.000	0.000	0.000
68	A	69	GLU	-1	-0.828	-0.906	19.730	-13.352	-13.352	0.000	0.000	0.000	0.000
69	A	70	SER	0	-0.092	-0.058	18.831	-0.646	-0.646	0.000	0.000	0.000	0.000
70	A	71	LEU	0	-0.024	-0.002	19.786	0.643	0.643	0.000	0.000	0.000	0.000
71	A	72	PRO	0	-0.011	-0.004	21.325	-0.501	-0.501	0.000	0.000	0.000	0.000
72	A	73	LEU	0	-0.013	-0.023	18.891	0.037	0.037	0.000	0.000	0.000	0.000
73	A	74	SER	0	0.010	0.007	22.985	0.213	0.213	0.000	0.000	0.000	0.000
74	A	75	LEU	0	-0.037	-0.014	17.995	-0.055	-0.055	0.000	0.000	0.000	0.000
75	A	76	GLU	-1	-0.879	-0.938	22.027	-9.891	-9.891	0.000	0.000	0.000	0.000
76	A	77	LYS	1	0.844	0.898	22.290	10.636	10.636	0.000	0.000	0.000	0.000
77	A	78	LYS	1	0.837	0.913	22.485	12.121	12.121	0.000	0.000	0.000	0.000
78	A	79	GLU	-1	-0.852	-0.928	24.550	-10.062	-10.062	0.000	0.000	0.000	0.000
79	A	80	GLY	0	0.037	0.032	26.851	0.349	0.349	0.000	0.000	0.000	0.000
80	A	81	THR	0	-0.078	-0.037	27.688	0.277	0.277	0.000	0.000	0.000	0.000
81	A	82	SER	0	0.001	-0.002	25.557	-0.456	-0.456	0.000	0.000	0.000	0.000
82	A	83	ILE	0	-0.031	-0.010	20.431	0.200	0.200	0.000	0.000	0.000	0.000
83	A	84	PRO	0	0.013	0.028	23.696	-0.178	-0.178	0.000	0.000	0.000	0.000
84	A	85	ALA	0	0.033	0.013	19.524	-0.435	-0.435	0.000	0.000	0.000	0.000
85	A	86	LYS	1	0.946	0.975	20.074	12.694	12.694	0.000	0.000	0.000	0.000
86	A	87	ALA	0	0.005	0.023	16.721	-0.725	-0.725	0.000	0.000	0.000	0.000
87	A	88	ARG	1	0.925	0.957	15.454	15.680	15.680	0.000	0.000	0.000	0.000
88	A	89	ILE	0	-0.008	-0.012	14.386	-0.867	-0.867	0.000	0.000	0.000	0.000
89	A	90	TRP	0	0.031	0.013	12.525	0.135	0.135	0.000	0.000	0.000	0.000
90	A	91	GLN	0	-0.010	0.000	13.421	-0.510	-0.510	0.000	0.000	0.000	0.000
91	A	92	GLY	0	0.032	0.023	11.682	-0.419	-0.419	0.000	0.000	0.000	0.000
92	A	93	LYS	1	0.891	0.909	11.605	16.390	16.390	0.000	0.000	0.000	0.000
93	A	94	TRP	0	0.001	0.010	5.741	-0.295	-0.295	0.000	0.000	0.000	0.000
94	A	95	HIS	0	0.039	0.035	8.189	-0.719	-0.719	0.000	0.000	0.000	0.000
95	A	96	ASN	0	0.033	-0.013	11.872	0.090	0.090	0.000	0.000	0.000	0.000
96	A	97	GLU	-1	-0.919	-0.942	14.897	-12.632	-12.632	0.000	0.000	0.000	0.000
97	A	98	PRO	0	-0.055	-0.032	14.806	-0.846	-0.846	0.000	0.000	0.000	0.000
98	A	99	CYS	0	-0.043	-0.015	11.681	0.075	0.075	0.000	0.000	0.000	0.000
99	A	100	LEU	0	0.002	-0.004	13.682	-0.029	-0.029	0.000	0.000	0.000	0.000
100	A	101	PHE	0	-0.033	-0.009	6.559	-0.723	-0.723	0.000	0.000	0.000	0.000
101	A	102	ALA	0	0.028	0.005	10.595	0.823	0.823	0.000	0.000	0.000	0.000
102	A	103	ILE	0	0.024	0.024	9.886	-1.056	-1.056	0.000	0.000	0.000	0.000
103	A	104	ILE	0	-0.047	-0.040	12.238	1.335	1.335	0.000	0.000	0.000	0.000
104	A	105	LYS	1	0.992	1.003	15.215	13.606	13.606	0.000	0.000	0.000	0.000
105	A	106	ASP	-1	-0.761	-0.846	17.812	-12.318	-12.318	0.000	0.000	0.000	0.000
106	A	107	LEU	0	-0.111	-0.064	20.177	0.002	0.002	0.000	0.000	0.000	0.000
107	A	108	SER	0	-0.048	-0.044	23.434	0.878	0.878	0.000	0.000	0.000	0.000

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