FMO DATABASE

FMODB ID: 2NR4R

Calculation Name: 1B8Z-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1B8Z

Chain ID: B

ChEMBL ID:

UniProt ID: P36206

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	67
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-341113.481319
FMO2-HF: Nuclear repulsion	315782.19592
FMO2-HF: Total energy	-25331.285399
FMO2-MP2: Total energy	-25406.780432

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:MET)

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

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.
-15.992	-9.279	11.845	-6.372	-12.187	-0.043

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.023 / q_NPA : -0.004

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	B	3	LYS	1	0.895	0.909	2.653	-1.619	0.415	0.960	-1.370	-1.624	-0.006
4	B	4	LYS	1	0.988	0.998	5.093	1.257	1.436	-0.001	-0.006	-0.172	0.000
5	B	5	GLU	-1	-0.821	-0.922	1.970	-7.510	-5.905	7.044	-4.093	-4.557	-0.041
6	B	6	LEU	0	-0.001	0.002	2.764	1.241	3.623	2.029	-1.378	-3.033	0.000
7	B	7	ILE	0	0.002	-0.007	3.888	0.581	-0.176	0.038	1.095	-0.376	-0.001
8	B	8	ASP	-1	-0.852	-0.914	6.429	0.449	0.449	0.000	0.000	0.000	0.000
9	B	9	ARG	1	0.910	0.941	2.497	-4.980	-3.710	1.775	-0.620	-2.425	0.005
10	B	10	VAL	0	-0.001	0.004	6.217	-0.587	-0.587	0.000	0.000	0.000	0.000
11	B	11	ALA	0	-0.007	0.001	8.391	-0.397	-0.397	0.000	0.000	0.000	0.000
12	B	12	LYS	1	0.961	0.982	10.051	-0.845	-0.845	0.000	0.000	0.000	0.000
13	B	13	LYS	1	0.892	0.934	6.038	-2.019	-2.019	0.000	0.000	0.000	0.000
14	B	14	ALA	0	0.015	0.012	11.345	-0.130	-0.130	0.000	0.000	0.000	0.000
15	B	15	GLY	0	0.023	0.038	13.916	-0.102	-0.102	0.000	0.000	0.000	0.000
16	B	16	ALA	0	-0.012	0.006	14.203	-0.080	-0.080	0.000	0.000	0.000	0.000
17	B	17	LYS	1	0.962	0.967	14.934	-0.198	-0.198	0.000	0.000	0.000	0.000
18	B	18	LYS	1	0.946	0.951	10.485	-0.417	-0.417	0.000	0.000	0.000	0.000
19	B	19	LYS	1	0.925	0.959	13.429	-0.169	-0.169	0.000	0.000	0.000	0.000
20	B	20	ASP	-1	-0.817	-0.902	16.011	0.248	0.248	0.000	0.000	0.000	0.000
21	B	21	VAL	0	-0.016	-0.004	9.942	0.006	0.006	0.000	0.000	0.000	0.000
22	B	22	LYS	1	0.849	0.924	11.772	0.109	0.109	0.000	0.000	0.000	0.000
23	B	23	LEU	0	0.044	0.024	12.758	-0.049	-0.049	0.000	0.000	0.000	0.000
24	B	24	ILE	0	0.053	0.036	14.583	-0.028	-0.028	0.000	0.000	0.000	0.000
25	B	25	LEU	0	-0.038	-0.029	7.943	-0.014	-0.014	0.000	0.000	0.000	0.000
26	B	26	ASP	-1	-0.751	-0.859	12.259	-0.190	-0.190	0.000	0.000	0.000	0.000
27	B	27	THR	0	0.075	0.028	14.007	-0.048	-0.048	0.000	0.000	0.000	0.000
28	B	28	ILE	0	-0.041	-0.003	13.398	-0.009	-0.009	0.000	0.000	0.000	0.000
29	B	29	LEU	0	-0.076	-0.052	10.027	-0.055	-0.055	0.000	0.000	0.000	0.000
30	B	30	GLU	-1	-0.909	-0.940	14.415	-0.090	-0.090	0.000	0.000	0.000	0.000
31	B	31	THR	0	0.051	0.014	17.833	-0.009	-0.009	0.000	0.000	0.000	0.000
32	B	32	ILE	0	-0.059	-0.031	14.610	-0.002	-0.002	0.000	0.000	0.000	0.000
33	B	33	THR	0	-0.062	-0.040	16.685	-0.035	-0.035	0.000	0.000	0.000	0.000
34	B	34	GLU	-1	-0.924	-0.964	19.092	-0.025	-0.025	0.000	0.000	0.000	0.000
35	B	35	ALA	0	-0.010	-0.005	21.749	-0.002	-0.002	0.000	0.000	0.000	0.000
36	B	36	LEU	0	-0.057	-0.028	18.474	-0.008	-0.008	0.000	0.000	0.000	0.000
37	B	37	ALA	0	-0.018	0.001	22.667	-0.006	-0.006	0.000	0.000	0.000	0.000
38	B	38	LYS	1	0.924	0.967	24.692	0.009	0.009	0.000	0.000	0.000	0.000
39	B	39	GLY	0	-0.010	0.003	26.231	0.007	0.007	0.000	0.000	0.000	0.000
40	B	40	GLU	-1	-0.966	-0.970	25.272	0.008	0.008	0.000	0.000	0.000	0.000
41	B	41	LYS	1	0.908	0.948	23.515	0.002	0.002	0.000	0.000	0.000	0.000
42	B	42	VAL	0	0.037	0.028	18.799	0.016	0.016	0.000	0.000	0.000	0.000
43	B	43	GLN	0	-0.032	-0.033	20.054	-0.013	-0.013	0.000	0.000	0.000	0.000
44	B	44	ILE	0	0.031	0.024	15.525	0.016	0.016	0.000	0.000	0.000	0.000
45	B	45	VAL	0	0.040	-0.001	18.437	-0.003	-0.003	0.000	0.000	0.000	0.000
46	B	46	GLY	0	-0.004	0.000	17.637	0.032	0.032	0.000	0.000	0.000	0.000
47	B	47	PHE	0	-0.021	-0.008	10.378	0.050	0.050	0.000	0.000	0.000	0.000
48	B	48	GLY	0	0.017	-0.007	15.479	-0.055	-0.055	0.000	0.000	0.000	0.000
49	B	49	SER	0	-0.089	-0.025	17.777	0.024	0.024	0.000	0.000	0.000	0.000
50	B	50	PHE	0	0.042	0.016	13.194	-0.030	-0.030	0.000	0.000	0.000	0.000
51	B	51	GLU	-1	-0.816	-0.920	19.154	-0.040	-0.040	0.000	0.000	0.000	0.000
52	B	52	VAL	0	0.045	0.035	21.726	-0.022	-0.022	0.000	0.000	0.000	0.000
53	B	76	VAL	0	0.015	-0.010	21.642	0.001	0.001	0.000	0.000	0.000	0.000
54	B	77	PRO	0	0.022	0.045	18.352	0.020	0.020	0.000	0.000	0.000	0.000
55	B	78	LYS	1	0.958	0.968	18.863	0.108	0.108	0.000	0.000	0.000	0.000
56	B	79	PHE	0	0.030	0.015	14.170	0.021	0.021	0.000	0.000	0.000	0.000
57	B	80	LYS	1	0.809	0.900	17.607	0.056	0.056	0.000	0.000	0.000	0.000
58	B	81	PRO	0	0.018	0.034	15.790	0.035	0.035	0.000	0.000	0.000	0.000
59	B	82	GLY	0	0.045	-0.008	17.072	-0.004	-0.004	0.000	0.000	0.000	0.000
60	B	83	LYS	1	0.934	0.952	18.115	-0.034	-0.034	0.000	0.000	0.000	0.000
61	B	84	ALA	0	0.069	0.034	17.200	-0.012	-0.012	0.000	0.000	0.000	0.000
62	B	85	LEU	0	0.010	0.020	11.116	0.011	0.011	0.000	0.000	0.000	0.000
63	B	86	LYS	1	0.922	0.950	14.406	0.026	0.026	0.000	0.000	0.000	0.000
64	B	87	GLU	-1	-0.904	-0.950	16.640	0.006	0.006	0.000	0.000	0.000	0.000
65	B	88	LYS	1	0.915	0.963	9.536	-0.468	-0.468	0.000	0.000	0.000	0.000
66	B	89	VAL	0	-0.049	-0.027	10.645	-0.006	-0.006	0.000	0.000	0.000	0.000
67	B	90	LYS	1	0.954	1.002	13.271	-0.021	-0.021	0.000	0.000	0.000	0.000

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