FMO DATABASE

FMODB ID: 52KRZ

Calculation Name: 3B5N-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

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:

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	61
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-237888.180362
FMO2-HF: Nuclear repulsion	213960.500684
FMO2-HF: Total energy	-23927.679678
FMO2-MP2: Total energy	-23996.811216

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: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.
-1.938	0.451	0.034	-0.998	-1.424	0.002

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 : 0.022 / q_NPA : 0.003

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	1.007	1.011	3.468	-2.211	-0.505	0.005	-0.829	-0.882	0.002
4	A	29	THR	0	-0.014	-0.021	3.318	-0.507	-0.015	0.030	-0.110	-0.411	0.000
5	A	30	ALA	0	0.013	0.014	4.326	0.565	0.756	-0.001	-0.059	-0.131	0.000
6	A	31	GLU	-1	-0.910	-0.953	6.164	0.141	0.141	0.000	0.000	0.000	0.000
7	A	32	LEU	0	-0.022	-0.006	8.049	0.124	0.124	0.000	0.000	0.000	0.000
8	A	33	GLN	0	-0.061	-0.037	8.628	0.064	0.064	0.000	0.000	0.000	0.000
9	A	34	ALA	0	0.026	0.014	10.295	0.104	0.104	0.000	0.000	0.000	0.000
10	A	35	GLU	-1	-0.892	-0.936	12.283	-0.098	-0.098	0.000	0.000	0.000	0.000
11	A	36	ILE	0	-0.035	-0.023	12.207	0.055	0.055	0.000	0.000	0.000	0.000
12	A	37	ASP	-1	-0.894	-0.954	14.192	-0.331	-0.331	0.000	0.000	0.000	0.000
13	A	38	ASP	-1	-0.902	-0.944	16.314	-0.156	-0.156	0.000	0.000	0.000	0.000
14	A	39	THR	0	-0.081	-0.049	17.913	0.039	0.039	0.000	0.000	0.000	0.000
15	A	40	VAL	0	-0.037	-0.025	18.692	0.025	0.025	0.000	0.000	0.000	0.000
16	A	41	GLY	0	-0.004	0.002	20.638	0.018	0.018	0.000	0.000	0.000	0.000
17	A	42	ILE	0	0.046	0.028	21.898	0.016	0.016	0.000	0.000	0.000	0.000
18	A	43	MET	0	0.000	-0.003	23.706	0.017	0.017	0.000	0.000	0.000	0.000
19	A	44	ARG	1	0.918	0.963	23.343	0.146	0.146	0.000	0.000	0.000	0.000
20	A	45	ASP	-1	-0.893	-0.936	26.721	-0.081	-0.081	0.000	0.000	0.000	0.000
21	A	46	ASN	0	-0.073	-0.060	27.498	0.012	0.012	0.000	0.000	0.000	0.000
22	A	47	ILE	0	-0.019	-0.001	28.888	0.007	0.007	0.000	0.000	0.000	0.000
23	A	48	ASN	0	0.020	0.004	31.081	0.006	0.006	0.000	0.000	0.000	0.000
24	A	49	LYS	1	0.974	0.989	31.036	0.064	0.064	0.000	0.000	0.000	0.000
25	A	50	VAL	0	-0.047	-0.024	33.877	0.005	0.005	0.000	0.000	0.000	0.000
26	A	51	ALA	0	0.016	0.015	35.544	0.003	0.003	0.000	0.000	0.000	0.000
27	A	52	GLU	-1	-0.909	-0.942	37.367	-0.040	-0.040	0.000	0.000	0.000	0.000
28	A	53	ARG	1	0.906	0.946	38.054	0.043	0.043	0.000	0.000	0.000	0.000
29	A	54	GLY	0	0.004	-0.006	39.659	0.003	0.003	0.000	0.000	0.000	0.000
30	A	55	GLU	-1	-0.914	-0.947	41.451	-0.036	-0.036	0.000	0.000	0.000	0.000
31	A	56	ARG	1	0.913	0.949	43.175	0.035	0.035	0.000	0.000	0.000	0.000
32	A	57	LEU	0	-0.007	-0.021	42.175	0.002	0.002	0.000	0.000	0.000	0.000
33	A	58	THR	0	0.047	0.041	45.313	0.002	0.002	0.000	0.000	0.000	0.000
34	A	59	SER	0	-0.062	-0.018	47.592	0.002	0.002	0.000	0.000	0.000	0.000
35	A	60	ILE	0	-0.036	-0.039	46.906	0.002	0.002	0.000	0.000	0.000	0.000
36	A	61	GLU	-1	-0.933	-0.959	49.574	-0.027	-0.027	0.000	0.000	0.000	0.000
37	A	62	ASP	-1	-0.890	-0.934	51.362	-0.023	-0.023	0.000	0.000	0.000	0.000
38	A	63	LYS	1	0.911	0.945	52.749	0.025	0.025	0.000	0.000	0.000	0.000
39	A	64	ALA	0	-0.010	-0.005	53.528	0.001	0.001	0.000	0.000	0.000	0.000
40	A	65	ASP	-1	-0.893	-0.935	55.410	-0.020	-0.020	0.000	0.000	0.000	0.000
41	A	66	ASN	0	0.015	-0.003	57.417	0.001	0.001	0.000	0.000	0.000	0.000
42	A	67	LEU	0	-0.049	-0.020	57.539	0.001	0.001	0.000	0.000	0.000	0.000
43	A	68	ALA	0	0.034	0.018	59.326	0.001	0.001	0.000	0.000	0.000	0.000
44	A	69	VAL	0	0.014	0.012	61.050	0.001	0.001	0.000	0.000	0.000	0.000
45	A	70	SER	0	-0.017	-0.016	63.124	0.001	0.001	0.000	0.000	0.000	0.000
46	A	71	ALA	0	-0.006	0.007	63.242	0.001	0.001	0.000	0.000	0.000	0.000
47	A	72	GLN	0	-0.048	-0.029	65.143	0.001	0.001	0.000	0.000	0.000	0.000
48	A	73	GLY	0	-0.008	-0.016	67.159	0.001	0.001	0.000	0.000	0.000	0.000
49	A	74	PHE	0	0.036	0.023	68.098	0.001	0.001	0.000	0.000	0.000	0.000
50	A	75	LYS	1	0.980	0.998	68.154	0.013	0.013	0.000	0.000	0.000	0.000
51	A	76	ARG	1	0.907	0.941	70.390	0.014	0.014	0.000	0.000	0.000	0.000
52	A	77	GLY	0	0.019	0.013	72.958	0.000	0.000	0.000	0.000	0.000	0.000
53	A	78	ALA	0	0.064	0.032	73.564	0.000	0.000	0.000	0.000	0.000	0.000
54	A	79	ASN	0	-0.012	-0.002	75.096	0.001	0.001	0.000	0.000	0.000	0.000
55	A	80	ARG	1	0.937	0.956	75.566	0.011	0.011	0.000	0.000	0.000	0.000
56	A	81	VAL	0	0.076	0.049	78.539	0.000	0.000	0.000	0.000	0.000	0.000
57	A	82	ARG	1	0.909	0.960	78.250	0.009	0.009	0.000	0.000	0.000	0.000
58	A	83	LYS	1	0.880	0.921	80.787	0.009	0.009	0.000	0.000	0.000	0.000
59	A	84	ALA	0	-0.007	0.007	82.901	0.000	0.000	0.000	0.000	0.000	0.000
60	A	85	MET	0	-0.027	-0.019	83.053	0.000	0.000	0.000	0.000	0.000	0.000
61	A	86	TRP	0	-0.029	0.012	85.123	0.000	0.000	0.000	0.000	0.000	0.000

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