FMO DATABASE

FMODB ID: YZKN2

Calculation Name: 3B5N-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3B5N

Chain ID: A

ChEMBL ID:

UniProt ID: P40357

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:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	61
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-237898.519242
FMO2-HF: Nuclear repulsion	213970.466464
FMO2-HF: Total energy	-23928.052778
FMO2-MP2: Total energy	-23997.167989

3D Structure Molmil

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:26:GLY)

Summations of interaction energy for fragment #1(A:26:GLY)

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.
-1.37	1.069	0.027	-1.011	-1.456	0.001

Interaction energy analysis for fragmet #1(A:26:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : 0.001

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	A	28	ARG	1	1.004	1.006	3.314	-1.737	-0.070	0.006	-0.795	-0.878	0.001
4	A	29	THR	0	-0.014	-0.020	3.285	-0.537	0.049	0.022	-0.159	-0.449	0.000
5	A	30	ALA	0	0.014	0.015	4.331	0.694	0.880	-0.001	-0.057	-0.129	0.000
6	A	31	GLU	-1	-0.899	-0.946	6.165	0.064	0.064	0.000	0.000	0.000	0.000
7	A	32	LEU	0	-0.029	-0.012	7.953	0.161	0.161	0.000	0.000	0.000	0.000
8	A	33	GLN	0	-0.084	-0.059	8.629	0.105	0.105	0.000	0.000	0.000	0.000
9	A	34	ALA	0	0.033	0.019	10.294	0.124	0.124	0.000	0.000	0.000	0.000
10	A	35	GLU	-1	-0.906	-0.944	12.274	-0.171	-0.171	0.000	0.000	0.000	0.000
11	A	36	ILE	0	-0.023	-0.011	12.240	0.070	0.070	0.000	0.000	0.000	0.000
12	A	37	ASP	-1	-0.868	-0.931	13.900	-0.369	-0.369	0.000	0.000	0.000	0.000
13	A	38	ASP	-1	-0.897	-0.941	16.315	-0.175	-0.175	0.000	0.000	0.000	0.000
14	A	39	THR	0	-0.089	-0.054	17.864	0.045	0.045	0.000	0.000	0.000	0.000
15	A	40	VAL	0	-0.025	-0.022	18.753	0.031	0.031	0.000	0.000	0.000	0.000
16	A	41	GLY	0	-0.003	0.006	20.636	0.022	0.022	0.000	0.000	0.000	0.000
17	A	42	ILE	0	0.025	0.011	21.876	0.020	0.020	0.000	0.000	0.000	0.000
18	A	43	MET	0	0.007	0.003	23.706	0.019	0.019	0.000	0.000	0.000	0.000
19	A	44	ARG	1	0.918	0.962	23.051	0.166	0.166	0.000	0.000	0.000	0.000
20	A	45	ASP	-1	-0.845	-0.908	26.720	-0.080	-0.080	0.000	0.000	0.000	0.000
21	A	46	ASN	0	-0.042	-0.041	27.466	0.014	0.014	0.000	0.000	0.000	0.000
22	A	47	ILE	0	-0.016	-0.001	28.889	0.008	0.008	0.000	0.000	0.000	0.000
23	A	48	ASN	0	-0.001	-0.003	30.579	0.007	0.007	0.000	0.000	0.000	0.000
24	A	49	LYS	1	0.913	0.953	30.191	0.086	0.086	0.000	0.000	0.000	0.000
25	A	50	VAL	0	-0.049	-0.027	33.820	0.006	0.006	0.000	0.000	0.000	0.000
26	A	51	ALA	0	0.014	0.014	35.543	0.004	0.004	0.000	0.000	0.000	0.000
27	A	52	GLU	-1	-0.917	-0.948	37.365	-0.049	-0.049	0.000	0.000	0.000	0.000
28	A	53	ARG	1	0.922	0.953	38.079	0.054	0.054	0.000	0.000	0.000	0.000
29	A	54	GLY	0	0.013	0.002	39.657	0.003	0.003	0.000	0.000	0.000	0.000
30	A	55	GLU	-1	-0.827	-0.883	41.452	-0.041	-0.041	0.000	0.000	0.000	0.000
31	A	56	ARG	1	0.829	0.889	43.176	0.044	0.044	0.000	0.000	0.000	0.000
32	A	57	LEU	0	-0.012	-0.017	42.158	0.002	0.002	0.000	0.000	0.000	0.000
33	A	58	THR	0	0.026	0.018	45.177	0.002	0.002	0.000	0.000	0.000	0.000
34	A	59	SER	0	-0.026	-0.009	47.593	0.002	0.002	0.000	0.000	0.000	0.000
35	A	60	ILE	0	-0.033	-0.027	46.943	0.002	0.002	0.000	0.000	0.000	0.000
36	A	61	GLU	-1	-0.938	-0.959	49.238	-0.033	-0.033	0.000	0.000	0.000	0.000
37	A	62	ASP	-1	-0.797	-0.893	51.363	-0.027	-0.027	0.000	0.000	0.000	0.000
38	A	63	LYS	1	0.839	0.919	52.485	0.031	0.031	0.000	0.000	0.000	0.000
39	A	64	ALA	0	-0.015	-0.004	53.495	0.001	0.001	0.000	0.000	0.000	0.000
40	A	65	ASP	-1	-0.901	-0.941	55.411	-0.024	-0.024	0.000	0.000	0.000	0.000
41	A	66	ASN	0	-0.033	-0.037	57.418	0.002	0.002	0.000	0.000	0.000	0.000
42	A	67	LEU	0	-0.022	0.004	57.409	0.001	0.001	0.000	0.000	0.000	0.000
43	A	68	ALA	0	0.030	0.017	59.278	0.001	0.001	0.000	0.000	0.000	0.000
44	A	69	VAL	0	0.011	0.009	61.051	0.001	0.001	0.000	0.000	0.000	0.000
45	A	70	SER	0	-0.025	-0.025	62.934	0.001	0.001	0.000	0.000	0.000	0.000
46	A	71	ALA	0	-0.006	0.005	63.223	0.001	0.001	0.000	0.000	0.000	0.000
47	A	72	GLN	0	-0.012	-0.006	65.144	0.002	0.002	0.000	0.000	0.000	0.000
48	A	73	GLY	0	0.000	-0.012	67.160	0.001	0.001	0.000	0.000	0.000	0.000
49	A	74	PHE	0	0.032	0.022	68.123	0.001	0.001	0.000	0.000	0.000	0.000
50	A	75	LYS	1	0.979	0.993	67.789	0.017	0.017	0.000	0.000	0.000	0.000
51	A	76	ARG	1	0.877	0.923	69.762	0.017	0.017	0.000	0.000	0.000	0.000
52	A	77	GLY	0	0.016	0.012	72.958	0.001	0.001	0.000	0.000	0.000	0.000
53	A	78	ALA	0	0.063	0.031	73.550	0.001	0.001	0.000	0.000	0.000	0.000
54	A	79	ASN	0	0.001	0.003	75.103	0.001	0.001	0.000	0.000	0.000	0.000
55	A	80	ARG	1	0.940	0.965	76.099	0.014	0.014	0.000	0.000	0.000	0.000
56	A	81	VAL	0	0.061	0.039	78.539	0.000	0.000	0.000	0.000	0.000	0.000
57	A	82	ARG	1	0.894	0.948	78.071	0.012	0.012	0.000	0.000	0.000	0.000
58	A	83	LYS	1	0.917	0.944	80.729	0.011	0.011	0.000	0.000	0.000	0.000
59	A	84	ALA	0	0.001	0.006	82.898	0.000	0.000	0.000	0.000	0.000	0.000
60	A	85	MET	0	-0.024	-0.018	83.010	0.000	0.000	0.000	0.000	0.000	0.000
61	A	86	TRP	0	-0.063	-0.003	84.984	0.001	0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:26:GLY)