FMO DATABASE

FMODB ID: LN979

Calculation Name: 3BID-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BID

Chain ID: A

ChEMBL ID:

UniProt ID: Q7DDI1

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	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	58
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-290416.765313
FMO2-HF: Nuclear repulsion	267049.231817
FMO2-HF: Total energy	-23367.533495
FMO2-MP2: Total energy	-23435.44957

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:1:MET)

Summations of interaction energy for fragment #1(A: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.
-9.074	-2.279	7.514	-5.829	-8.481	-0.04

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / q_NPA : 0.009

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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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	3	PHE	0	0.057	0.023	3.879	-0.822	1.908	-0.020	-1.469	-1.241	0.005
4	A	4	GLU	-1	-0.807	-0.876	6.395	-0.777	-0.777	0.000	0.000	0.000	0.000
5	A	5	ILE	0	-0.012	-0.025	9.673	0.211	0.211	0.000	0.000	0.000	0.000
6	A	6	TYR	0	-0.006	0.004	13.150	0.029	0.029	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.873	0.929	16.289	0.263	0.263	0.000	0.000	0.000	0.000
8	A	8	ASP	-1	-0.793	-0.906	19.768	-0.138	-0.138	0.000	0.000	0.000	0.000
9	A	9	ALA	0	0.011	-0.012	21.394	-0.005	-0.005	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.839	0.926	23.241	0.098	0.098	0.000	0.000	0.000	0.000
11	A	11	GLY	0	0.007	0.014	24.576	0.001	0.001	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.813	-0.872	21.392	-0.145	-0.145	0.000	0.000	0.000	0.000
13	A	13	TYR	0	-0.006	-0.012	18.562	-0.013	-0.013	0.000	0.000	0.000	0.000
14	A	14	ARG	1	0.826	0.901	15.834	0.185	0.185	0.000	0.000	0.000	0.000
15	A	15	TRP	0	0.042	0.025	9.011	-0.111	-0.111	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.824	0.904	8.645	0.514	0.514	0.000	0.000	0.000	0.000
17	A	17	LEU	0	-0.010	-0.005	2.340	-1.049	-0.670	1.664	-0.371	-1.672	-0.002
18	A	18	LYS	1	0.810	0.901	4.345	1.069	1.457	-0.001	-0.095	-0.293	0.000
19	A	19	ALA	0	0.057	0.018	2.350	-6.722	-4.248	4.247	-3.493	-3.228	-0.041
20	A	20	ALA	0	0.008	-0.007	3.632	-0.887	-0.617	0.006	0.002	-0.278	0.000
21	A	21	ASN	0	-0.016	-0.008	4.885	-0.803	-0.773	-0.001	-0.007	-0.021	0.000
22	A	22	HIS	0	0.027	-0.003	6.800	-0.290	-0.290	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.854	-0.911	7.843	0.634	0.634	0.000	0.000	0.000	0.000
24	A	24	ILE	0	-0.053	-0.027	6.434	-0.183	-0.183	0.000	0.000	0.000	0.000
25	A	25	ILE	0	-0.008	0.009	2.381	-0.793	-0.269	1.619	-0.396	-1.748	-0.002
26	A	26	ALA	0	0.015	0.006	6.559	-0.008	-0.008	0.000	0.000	0.000	0.000
27	A	27	GLN	0	0.017	-0.005	8.727	-0.283	-0.283	0.000	0.000	0.000	0.000
28	A	28	GLY	0	0.025	0.010	11.593	0.039	0.039	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.836	-0.913	13.813	-0.047	-0.047	0.000	0.000	0.000	0.000
30	A	30	GLY	0	-0.043	-0.032	17.302	-0.055	-0.055	0.000	0.000	0.000	0.000
31	A	31	TYR	0	-0.002	-0.010	15.936	-0.007	-0.007	0.000	0.000	0.000	0.000
32	A	32	THR	0	0.037	0.003	21.023	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	33	SER	0	-0.009	-0.010	22.380	-0.006	-0.006	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.940	0.975	17.863	0.572	0.572	0.000	0.000	0.000	0.000
35	A	35	GLN	0	0.033	0.020	18.462	-0.077	-0.077	0.000	0.000	0.000	0.000
36	A	36	ASN	0	-0.002	-0.014	19.171	-0.025	-0.025	0.000	0.000	0.000	0.000
37	A	37	CYS	0	0.010	0.029	14.659	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	38	GLN	0	-0.049	-0.017	14.482	-0.020	-0.020	0.000	0.000	0.000	0.000
39	A	39	HIS	0	0.050	0.024	14.584	-0.088	-0.088	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.004	0.009	15.032	-0.005	-0.005	0.000	0.000	0.000	0.000
41	A	41	VAL	0	0.017	0.011	9.203	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	42	ASP	-1	-0.855	-0.930	10.468	-1.107	-1.107	0.000	0.000	0.000	0.000
43	A	43	LEU	0	-0.003	0.002	12.612	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	44	LEU	0	0.010	0.024	9.230	0.015	0.015	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.842	0.926	7.510	1.346	1.346	0.000	0.000	0.000	0.000
46	A	46	SER	0	-0.078	-0.044	8.536	-0.042	-0.042	0.000	0.000	0.000	0.000
47	A	47	THR	0	-0.062	-0.030	9.499	0.123	0.123	0.000	0.000	0.000	0.000
48	A	48	THR	0	0.023	-0.006	9.456	-0.127	-0.127	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.020	0.008	9.933	0.089	0.089	0.000	0.000	0.000	0.000
50	A	50	ALA	0	-0.005	0.004	11.103	0.064	0.064	0.000	0.000	0.000	0.000
51	A	51	THR	0	-0.024	-0.012	12.645	-0.022	-0.022	0.000	0.000	0.000	0.000
52	A	52	PRO	0	-0.013	0.004	14.261	0.042	0.042	0.000	0.000	0.000	0.000
53	A	53	VAL	0	0.031	0.008	13.554	-0.013	-0.013	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.900	0.943	16.740	-0.052	-0.052	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.915	-0.942	18.271	0.252	0.252	0.000	0.000	0.000	0.000
56	A	56	VAL	0	-0.051	-0.040	20.383	-0.020	-0.020	0.000	0.000	0.000	0.000
57	A	57	LEU	0	-0.006	0.000	23.049	0.012	0.012	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.957	-0.966	25.777	0.121	0.121	0.000	0.000	0.000	0.000

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