FMO DATABASE

FMODB ID: 1NJYZ

Calculation Name: 3M21-B-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: 3M21

Chain ID: B

ChEMBL ID:
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UniProt ID: O25581

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	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	66
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-330050.477918
FMO2-HF: Nuclear repulsion	304841.883031
FMO2-HF: Total energy	-25208.594888
FMO2-MP2: Total energy	-25283.10735

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(B:1:PRO)

Summations of interaction energy for fragment #1(B:1:PRO)

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.
-13.183	-5.687	6.973	-4.737	-9.732	-0.01

Interaction energy analysis for fragmet #1(B:1:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.002 / q_NPA : -0.024

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	B	3	ILE	0	0.002	0.006	3.093	-0.519	1.975	0.075	-1.137	-1.433	0.000
4	B	4	ASN	0	-0.076	-0.037	5.965	0.133	0.133	0.000	0.000	0.000	0.000
5	B	5	ILE	0	0.011	0.000	9.720	0.152	0.152	0.000	0.000	0.000	0.000
6	B	6	LYS	1	0.914	0.973	12.295	0.369	0.369	0.000	0.000	0.000	0.000
7	B	7	LEU	0	-0.008	-0.001	15.863	0.038	0.038	0.000	0.000	0.000	0.000
8	B	8	VAL	0	-0.001	0.012	18.771	0.000	0.000	0.000	0.000	0.000	0.000
9	B	9	PRO	0	-0.004	0.013	22.462	0.004	0.004	0.000	0.000	0.000	0.000
10	B	10	GLU	-1	-0.912	-0.974	23.997	-0.155	-0.155	0.000	0.000	0.000	0.000
11	B	11	ASN	0	-0.005	0.003	26.152	-0.002	-0.002	0.000	0.000	0.000	0.000
12	B	12	GLY	0	-0.019	-0.007	27.973	-0.002	-0.002	0.000	0.000	0.000	0.000
13	B	13	GLY	0	-0.011	0.026	24.260	-0.012	-0.012	0.000	0.000	0.000	0.000
14	B	14	PRO	0	0.002	-0.013	18.974	0.010	0.010	0.000	0.000	0.000	0.000
15	B	15	THR	0	0.075	0.006	21.645	-0.015	-0.015	0.000	0.000	0.000	0.000
16	B	16	ASN	0	0.005	-0.027	20.158	-0.049	-0.049	0.000	0.000	0.000	0.000
17	B	17	GLU	-1	-0.908	-0.940	19.111	-0.417	-0.417	0.000	0.000	0.000	0.000
18	B	18	GLN	0	0.076	0.053	18.880	-0.030	-0.030	0.000	0.000	0.000	0.000
19	B	19	LYS	1	0.901	0.955	16.025	0.392	0.392	0.000	0.000	0.000	0.000
20	B	20	GLN	0	0.032	0.017	14.428	-0.134	-0.134	0.000	0.000	0.000	0.000
21	B	21	GLN	0	0.065	0.024	14.383	-0.046	-0.046	0.000	0.000	0.000	0.000
22	B	22	LEU	0	-0.048	-0.012	12.797	-0.016	-0.016	0.000	0.000	0.000	0.000
23	B	23	ILE	0	-0.012	-0.004	9.955	-0.103	-0.103	0.000	0.000	0.000	0.000
24	B	24	GLU	-1	-0.929	-0.937	9.481	-0.788	-0.788	0.000	0.000	0.000	0.000
25	B	25	GLY	0	0.063	0.036	10.827	-0.009	-0.009	0.000	0.000	0.000	0.000
26	B	26	VAL	0	-0.037	-0.034	6.056	0.074	0.074	0.000	0.000	0.000	0.000
27	B	27	SER	0	-0.051	-0.062	6.008	-0.286	-0.286	0.000	0.000	0.000	0.000
28	B	28	ASP	-1	-0.864	-0.941	6.792	-0.516	-0.516	0.000	0.000	0.000	0.000
29	B	29	LEU	0	-0.063	-0.020	8.437	0.204	0.204	0.000	0.000	0.000	0.000
30	B	30	MET	0	-0.019	-0.010	3.341	-0.088	0.569	0.034	-0.126	-0.565	0.000
31	B	31	VAL	0	-0.031	-0.019	5.493	0.426	0.426	0.000	0.000	0.000	0.000
32	B	32	LYS	1	0.978	1.005	7.174	0.229	0.229	0.000	0.000	0.000	0.000
33	B	33	VAL	0	-0.040	-0.021	8.568	0.062	0.062	0.000	0.000	0.000	0.000
34	B	34	LEU	0	-0.033	-0.025	5.292	0.196	0.196	0.000	0.000	0.000	0.000
35	B	35	ASN	0	-0.025	-0.003	7.477	0.103	0.103	0.000	0.000	0.000	0.000
36	B	36	LYS	1	0.900	0.960	2.148	-4.119	-4.728	3.845	-0.783	-2.453	0.010
37	B	37	ASN	0	0.046	0.010	3.823	-0.622	-0.477	0.000	-0.033	-0.111	0.000
38	B	38	LYS	1	1.043	0.986	3.969	-0.593	-0.314	0.003	-0.061	-0.221	0.000
39	B	39	ALA	0	-0.030	0.004	5.543	-0.476	-0.476	0.000	0.000	0.000	0.000
40	B	40	SER	0	-0.065	-0.032	3.052	-0.513	0.696	0.227	-0.573	-0.863	-0.004
41	B	41	ILE	0	-0.044	0.007	2.130	-7.271	-4.336	2.745	-2.196	-3.484	-0.015
42	B	42	VAL	0	0.020	0.024	3.236	2.089	2.475	0.044	0.172	-0.602	-0.001
43	B	43	VAL	0	-0.003	-0.008	5.350	-0.444	-0.444	0.000	0.000	0.000	0.000
44	B	44	ILE	0	-0.003	0.002	7.831	0.256	0.256	0.000	0.000	0.000	0.000
45	B	45	ILE	0	-0.009	0.003	11.056	0.057	0.057	0.000	0.000	0.000	0.000
46	B	46	ASP	-1	-0.851	-0.926	13.756	-0.532	-0.532	0.000	0.000	0.000	0.000
47	B	47	GLU	-1	-0.917	-0.983	16.589	-0.353	-0.353	0.000	0.000	0.000	0.000
48	B	48	VAL	0	-0.050	-0.034	19.523	0.019	0.019	0.000	0.000	0.000	0.000
49	B	49	ASP	-1	-0.734	-0.873	22.095	-0.156	-0.156	0.000	0.000	0.000	0.000
50	B	50	SER	0	-0.004	-0.008	25.865	0.009	0.009	0.000	0.000	0.000	0.000
51	B	51	ASN	0	-0.063	-0.055	27.411	0.019	0.019	0.000	0.000	0.000	0.000
52	B	52	ASN	0	-0.051	-0.027	25.089	0.014	0.014	0.000	0.000	0.000	0.000
53	B	53	TYR	0	0.011	0.009	19.099	0.004	0.004	0.000	0.000	0.000	0.000
54	B	54	GLY	0	0.010	0.005	24.537	0.010	0.010	0.000	0.000	0.000	0.000
55	B	55	LEU	0	-0.009	-0.013	23.439	-0.003	-0.003	0.000	0.000	0.000	0.000
56	B	56	GLY	0	0.003	-0.004	26.093	0.004	0.004	0.000	0.000	0.000	0.000
57	B	57	GLY	0	-0.018	-0.004	28.342	0.007	0.007	0.000	0.000	0.000	0.000
58	B	58	GLU	-1	-0.818	-0.901	29.747	-0.066	-0.066	0.000	0.000	0.000	0.000
59	B	59	SER	0	0.057	0.031	28.777	-0.006	-0.006	0.000	0.000	0.000	0.000
60	B	60	VAL	0	0.037	0.007	24.853	0.005	0.005	0.000	0.000	0.000	0.000
61	B	61	HIS	0	-0.036	-0.016	28.300	0.009	0.009	0.000	0.000	0.000	0.000
62	B	62	HIS	0	-0.020	-0.019	31.199	0.007	0.007	0.000	0.000	0.000	0.000
63	B	63	LEU	0	-0.026	-0.012	28.789	0.005	0.005	0.000	0.000	0.000	0.000
64	B	64	ARG	1	0.843	0.919	25.257	0.174	0.174	0.000	0.000	0.000	0.000
65	B	65	GLN	0	-0.070	-0.013	32.394	0.006	0.006	0.000	0.000	0.000	0.000
66	B	66	LYS	1	0.828	0.935	34.708	0.072	0.072	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:1:PRO)