FMO DATABASE

FMODB ID: 98YR2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-842683.140651
FMO2-HF: Nuclear repulsion	800259.010789
FMO2-HF: Total energy	-42424.129862
FMO2-MP2: Total energy	-42546.859923

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.
0.34500000000003	8.576	1.933	-3.977	-6.187	-0.001

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 : 1.006 / q_NPA : 0.998

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	0.002	0.013	2.099	-4.950	1.121	1.578	-3.293	-4.357	0.001
4	A	5	LEU	0	0.054	0.034	2.566	6.894	8.625	0.356	-0.600	-1.487	-0.002
5	A	6	GLU	-1	-0.785	-0.874	5.219	-27.911	-27.720	-0.001	-0.014	-0.175	0.000
6	A	7	THR	0	-0.109	-0.059	7.078	3.272	3.272	0.000	0.000	0.000	0.000
7	A	8	ILE	0	-0.031	-0.006	7.847	2.104	2.104	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.819	-0.915	10.832	-19.870	-19.870	0.000	0.000	0.000	0.000
9	A	10	ASP	-1	-0.893	-0.947	13.337	-16.257	-16.257	0.000	0.000	0.000	0.000
10	A	11	MET	0	-0.051	-0.021	11.672	-1.319	-1.319	0.000	0.000	0.000	0.000
11	A	12	ILE	0	-0.028	-0.018	6.451	0.302	0.302	0.000	0.000	0.000	0.000
12	A	13	LEU	0	0.018	0.005	9.087	-0.216	-0.216	0.000	0.000	0.000	0.000
13	A	14	ILE	0	-0.034	-0.014	5.397	-0.724	-0.724	0.000	0.000	0.000	0.000
14	A	15	ILE	0	0.000	0.016	9.302	0.403	0.403	0.000	0.000	0.000	0.000
15	A	16	ASN	0	0.065	0.015	12.790	-0.032	-0.032	0.000	0.000	0.000	0.000
16	A	17	ARG	1	0.950	0.959	14.993	11.993	11.993	0.000	0.000	0.000	0.000
17	A	18	GLU	-1	-0.882	-0.929	18.469	-11.766	-11.766	0.000	0.000	0.000	0.000
18	A	19	GLY	0	0.020	0.010	17.839	0.438	0.438	0.000	0.000	0.000	0.000
19	A	20	ARG	1	0.820	0.903	15.863	13.531	13.531	0.000	0.000	0.000	0.000
20	A	21	LEU	0	-0.019	-0.014	12.107	-0.549	-0.549	0.000	0.000	0.000	0.000
21	A	22	LEU	0	-0.033	-0.018	9.287	0.225	0.225	0.000	0.000	0.000	0.000
22	A	23	TYR	0	-0.065	-0.066	4.484	-2.389	-2.151	0.000	-0.070	-0.168	0.000
23	A	24	ALA	0	0.022	0.002	7.447	1.412	1.412	0.000	0.000	0.000	0.000
24	A	25	ASN	0	0.014	0.030	7.060	0.792	0.792	0.000	0.000	0.000	0.000
25	A	26	THR	0	0.029	-0.006	8.256	2.813	2.813	0.000	0.000	0.000	0.000
26	A	27	ALA	0	-0.012	-0.002	11.337	1.715	1.715	0.000	0.000	0.000	0.000
27	A	28	VAL	0	0.004	0.005	11.137	1.539	1.539	0.000	0.000	0.000	0.000
28	A	29	PRO	0	0.026	0.006	12.563	1.076	1.076	0.000	0.000	0.000	0.000
29	A	30	LYS	1	0.795	0.911	14.528	20.670	20.670	0.000	0.000	0.000	0.000
30	A	31	LYS	1	0.846	0.905	16.806	15.214	15.214	0.000	0.000	0.000	0.000
31	A	32	LEU	0	0.021	0.010	17.345	0.690	0.690	0.000	0.000	0.000	0.000
32	A	33	GLY	0	0.018	0.026	19.441	0.665	0.665	0.000	0.000	0.000	0.000
33	A	34	TYR	0	-0.040	-0.019	18.294	0.482	0.482	0.000	0.000	0.000	0.000
34	A	35	THR	0	0.008	-0.034	17.067	-0.692	-0.692	0.000	0.000	0.000	0.000
35	A	36	HIS	0	0.023	0.008	8.934	0.399	0.399	0.000	0.000	0.000	0.000
36	A	37	GLU	-1	-0.848	-0.937	14.030	-16.698	-16.698	0.000	0.000	0.000	0.000
37	A	38	GLU	-1	-0.767	-0.832	16.069	-11.986	-11.986	0.000	0.000	0.000	0.000
38	A	39	LEU	0	0.029	-0.004	12.909	0.259	0.259	0.000	0.000	0.000	0.000
39	A	40	MET	0	-0.037	-0.003	10.219	-0.218	-0.218	0.000	0.000	0.000	0.000
40	A	41	SER	0	-0.028	-0.010	14.004	0.434	0.434	0.000	0.000	0.000	0.000
41	A	42	MET	0	-0.038	0.001	17.080	0.579	0.579	0.000	0.000	0.000	0.000
42	A	43	HIS	0	0.043	0.027	17.398	-0.600	-0.600	0.000	0.000	0.000	0.000
43	A	44	ILE	0	0.054	0.028	15.826	0.176	0.176	0.000	0.000	0.000	0.000
44	A	45	LEU	0	0.016	0.009	18.452	0.128	0.128	0.000	0.000	0.000	0.000
45	A	46	THR	0	-0.056	-0.053	21.172	0.471	0.471	0.000	0.000	0.000	0.000
46	A	47	ILE	0	-0.009	0.007	17.194	0.069	0.069	0.000	0.000	0.000	0.000
47	A	48	THR	0	-0.019	-0.016	19.679	0.020	0.020	0.000	0.000	0.000	0.000
48	A	49	SER	0	-0.071	-0.041	22.453	0.178	0.178	0.000	0.000	0.000	0.000
49	A	50	ALA	0	0.089	0.068	25.692	0.297	0.297	0.000	0.000	0.000	0.000
50	A	51	GLY	0	0.023	0.009	27.108	0.227	0.227	0.000	0.000	0.000	0.000
51	A	52	LYS	1	0.800	0.883	29.142	8.619	8.619	0.000	0.000	0.000	0.000
52	A	53	MET	0	0.060	0.044	25.808	-0.301	-0.301	0.000	0.000	0.000	0.000
53	A	54	ALA	0	0.056	0.038	27.310	-0.217	-0.217	0.000	0.000	0.000	0.000
54	A	55	GLU	-1	-0.829	-0.924	29.079	-8.717	-8.717	0.000	0.000	0.000	0.000
55	A	56	GLY	0	0.028	0.014	25.339	-0.203	-0.203	0.000	0.000	0.000	0.000
56	A	57	GLU	-1	-0.932	-0.961	24.265	-10.213	-10.213	0.000	0.000	0.000	0.000
57	A	58	LYS	1	0.881	0.925	25.264	8.999	8.999	0.000	0.000	0.000	0.000
58	A	59	ILE	0	-0.033	-0.026	22.813	-0.119	-0.119	0.000	0.000	0.000	0.000
59	A	60	LEU	0	0.044	0.023	18.645	-0.337	-0.337	0.000	0.000	0.000	0.000
60	A	61	ALA	0	0.014	0.000	21.479	-0.349	-0.349	0.000	0.000	0.000	0.000
61	A	62	GLU	-1	-0.858	-0.918	23.794	-9.761	-9.761	0.000	0.000	0.000	0.000
62	A	63	LEU	0	-0.043	-0.019	19.218	-0.107	-0.107	0.000	0.000	0.000	0.000
63	A	64	PHE	0	0.010	0.017	15.813	-0.354	-0.354	0.000	0.000	0.000	0.000
64	A	65	ALA	0	-0.078	-0.026	20.298	-0.099	-0.099	0.000	0.000	0.000	0.000
65	A	66	GLY	0	0.035	0.026	20.902	0.144	0.144	0.000	0.000	0.000	0.000
66	A	67	LYS	1	0.861	0.943	21.929	9.648	9.648	0.000	0.000	0.000	0.000
67	A	68	LYS	1	0.861	0.907	22.490	10.761	10.761	0.000	0.000	0.000	0.000
68	A	69	GLU	-1	-0.844	-0.903	19.233	-13.434	-13.434	0.000	0.000	0.000	0.000
69	A	70	SER	0	-0.089	-0.056	18.327	-0.628	-0.628	0.000	0.000	0.000	0.000
70	A	71	LEU	0	-0.008	-0.004	19.516	0.618	0.618	0.000	0.000	0.000	0.000
71	A	72	PRO	0	-0.013	0.000	21.231	-0.483	-0.483	0.000	0.000	0.000	0.000
72	A	73	LEU	0	-0.003	-0.014	18.860	0.049	0.049	0.000	0.000	0.000	0.000
73	A	74	SER	0	-0.020	-0.010	22.992	0.276	0.276	0.000	0.000	0.000	0.000
74	A	75	LEU	0	-0.027	-0.015	18.040	-0.141	-0.141	0.000	0.000	0.000	0.000
75	A	76	GLU	-1	-0.898	-0.954	21.940	-10.034	-10.034	0.000	0.000	0.000	0.000
76	A	77	LYS	1	0.820	0.900	22.142	10.509	10.509	0.000	0.000	0.000	0.000
77	A	78	LYS	1	0.782	0.879	22.025	12.302	12.302	0.000	0.000	0.000	0.000
78	A	79	GLU	-1	-0.821	-0.894	24.209	-10.119	-10.119	0.000	0.000	0.000	0.000
79	A	80	GLY	0	0.031	0.033	26.660	0.369	0.369	0.000	0.000	0.000	0.000
80	A	81	THR	0	-0.074	-0.058	27.834	0.177	0.177	0.000	0.000	0.000	0.000
81	A	82	SER	0	0.021	0.006	25.433	-0.489	-0.489	0.000	0.000	0.000	0.000
82	A	83	ILE	0	-0.026	-0.005	20.485	0.236	0.236	0.000	0.000	0.000	0.000
83	A	84	PRO	0	0.015	0.021	23.719	-0.182	-0.182	0.000	0.000	0.000	0.000
84	A	85	ALA	0	0.030	0.005	19.580	-0.410	-0.410	0.000	0.000	0.000	0.000
85	A	86	LYS	1	0.906	0.948	20.063	12.791	12.791	0.000	0.000	0.000	0.000
86	A	87	ALA	0	0.023	0.033	16.690	-0.749	-0.749	0.000	0.000	0.000	0.000
87	A	88	ARG	1	0.916	0.945	15.067	15.905	15.905	0.000	0.000	0.000	0.000
88	A	89	ILE	0	0.001	-0.005	13.909	-0.844	-0.844	0.000	0.000	0.000	0.000
89	A	90	TRP	0	0.019	0.008	12.050	0.075	0.075	0.000	0.000	0.000	0.000
90	A	91	GLN	0	-0.020	-0.007	12.967	-0.612	-0.612	0.000	0.000	0.000	0.000
91	A	92	GLY	0	0.025	0.014	11.762	-0.588	-0.588	0.000	0.000	0.000	0.000
92	A	93	LYS	1	0.890	0.923	11.790	15.934	15.934	0.000	0.000	0.000	0.000
93	A	94	TRP	0	0.027	0.014	5.443	-0.152	-0.152	0.000	0.000	0.000	0.000
94	A	95	HIS	0	0.004	0.011	8.458	-0.887	-0.887	0.000	0.000	0.000	0.000
95	A	96	ASN	0	0.041	0.013	11.807	0.329	0.329	0.000	0.000	0.000	0.000
96	A	97	GLU	-1	-0.881	-0.944	14.588	-12.574	-12.574	0.000	0.000	0.000	0.000
97	A	98	PRO	0	-0.088	-0.040	14.377	-0.927	-0.927	0.000	0.000	0.000	0.000
98	A	99	CYS	0	-0.039	-0.014	11.240	-0.054	-0.054	0.000	0.000	0.000	0.000
99	A	100	LEU	0	-0.004	0.000	13.223	0.105	0.105	0.000	0.000	0.000	0.000
100	A	101	PHE	0	-0.003	0.011	6.211	-0.613	-0.613	0.000	0.000	0.000	0.000
101	A	102	ALA	0	0.024	-0.001	9.965	1.164	1.164	0.000	0.000	0.000	0.000
102	A	103	ILE	0	0.006	0.007	9.697	-1.296	-1.296	0.000	0.000	0.000	0.000
103	A	104	ILE	0	-0.021	-0.019	12.075	1.332	1.332	0.000	0.000	0.000	0.000
104	A	105	LYS	1	0.966	1.003	15.150	14.286	14.286	0.000	0.000	0.000	0.000
105	A	106	ASP	-1	-0.749	-0.845	17.505	-12.308	-12.308	0.000	0.000	0.000	0.000
106	A	107	LEU	0	-0.071	-0.034	20.163	-0.075	-0.075	0.000	0.000	0.000	0.000
107	A	108	SER	0	-0.087	-0.059	23.703	0.803	0.803	0.000	0.000	0.000	0.000

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