FMO DATABASE

FMODB ID: 52KNZ

Calculation Name: 3A01-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3A01

Chain ID: B

ChEMBL ID:

UniProt ID: Q06453

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	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	57
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-353124.032055
FMO2-HF: Nuclear repulsion	328573.445122
FMO2-HF: Total energy	-24550.586933
FMO2-MP2: Total energy	-24623.591816

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:86:ARG)

Summations of interaction energy for fragment #1(B:86:ARG)

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.
62.822	64.031	0.001	-0.561	-0.648	0.002

Interaction energy analysis for fragmet #1(B:86:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.019 / q_NPA : 0.997

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	88	TYR	0	0.060	0.031	3.785	0.210	1.419	0.001	-0.561	-0.648	0.002
4	B	89	ARG	1	0.910	0.941	5.569	23.230	23.230	0.000	0.000	0.000	0.000
5	B	90	THR	0	0.003	0.008	7.507	0.079	0.079	0.000	0.000	0.000	0.000
6	B	91	THR	0	-0.010	-0.007	10.167	-0.087	-0.087	0.000	0.000	0.000	0.000
7	B	92	PHE	0	-0.015	-0.005	12.787	0.048	0.048	0.000	0.000	0.000	0.000
8	B	93	THR	0	0.064	0.024	16.478	0.405	0.405	0.000	0.000	0.000	0.000
9	B	94	SER	0	0.053	0.012	19.047	0.252	0.252	0.000	0.000	0.000	0.000
10	B	95	PHE	0	0.060	0.038	21.981	0.220	0.220	0.000	0.000	0.000	0.000
11	B	96	GLN	0	0.061	0.031	18.308	-0.357	-0.357	0.000	0.000	0.000	0.000
12	B	97	LEU	0	-0.020	-0.011	19.025	-0.006	-0.006	0.000	0.000	0.000	0.000
13	B	98	GLU	-1	-0.853	-0.908	21.646	-9.620	-9.620	0.000	0.000	0.000	0.000
14	B	99	GLU	-1	-0.763	-0.878	25.375	-9.326	-9.326	0.000	0.000	0.000	0.000
15	B	100	LEU	0	-0.006	0.005	20.365	0.216	0.216	0.000	0.000	0.000	0.000
16	B	101	GLU	-1	-0.824	-0.881	23.330	-10.759	-10.759	0.000	0.000	0.000	0.000
17	B	102	LYS	1	0.816	0.890	25.935	9.809	9.809	0.000	0.000	0.000	0.000
18	B	103	ALA	0	-0.022	-0.005	26.968	0.336	0.336	0.000	0.000	0.000	0.000
19	B	104	PHE	0	-0.009	-0.017	25.925	0.202	0.202	0.000	0.000	0.000	0.000
20	B	105	SER	0	-0.081	-0.044	28.052	0.276	0.276	0.000	0.000	0.000	0.000
21	B	106	ARG	1	0.953	1.003	31.116	9.175	9.175	0.000	0.000	0.000	0.000
22	B	107	THR	0	0.050	0.013	31.399	0.127	0.127	0.000	0.000	0.000	0.000
23	B	108	HIS	0	0.000	-0.002	28.602	-0.181	-0.181	0.000	0.000	0.000	0.000
24	B	109	TYR	0	-0.010	-0.027	27.856	-0.554	-0.554	0.000	0.000	0.000	0.000
25	B	110	PRO	0	0.033	0.051	27.493	0.235	0.235	0.000	0.000	0.000	0.000
26	B	111	ASP	-1	-0.762	-0.856	29.008	-9.354	-9.354	0.000	0.000	0.000	0.000
27	B	112	VAL	0	0.004	-0.018	27.845	-0.245	-0.245	0.000	0.000	0.000	0.000
28	B	113	PHE	0	0.049	0.031	28.878	-0.293	-0.293	0.000	0.000	0.000	0.000
29	B	114	THR	0	0.002	-0.018	29.965	-0.057	-0.057	0.000	0.000	0.000	0.000
30	B	115	ARG	1	0.700	0.804	24.814	10.714	10.714	0.000	0.000	0.000	0.000
31	B	116	GLU	-1	-0.910	-0.957	26.108	-11.601	-11.601	0.000	0.000	0.000	0.000
32	B	117	GLU	-1	-0.947	-0.966	27.756	-9.143	-9.143	0.000	0.000	0.000	0.000
33	B	118	LEU	0	-0.024	-0.022	24.939	-0.158	-0.158	0.000	0.000	0.000	0.000
34	B	119	ALA	0	-0.027	-0.032	23.621	-0.251	-0.251	0.000	0.000	0.000	0.000
35	B	120	MET	0	0.016	0.008	24.389	-0.338	-0.338	0.000	0.000	0.000	0.000
36	B	121	LYS	1	0.835	0.928	26.914	9.546	9.546	0.000	0.000	0.000	0.000
37	B	122	ILE	0	-0.056	-0.033	22.167	-0.006	-0.006	0.000	0.000	0.000	0.000
38	B	123	GLY	0	0.028	0.034	22.196	-0.493	-0.493	0.000	0.000	0.000	0.000
39	B	124	LEU	0	-0.099	-0.053	17.701	-0.973	-0.973	0.000	0.000	0.000	0.000
40	B	125	THR	0	0.072	0.031	18.768	0.290	0.290	0.000	0.000	0.000	0.000
41	B	126	GLU	-1	-0.609	-0.775	20.596	-12.224	-12.224	0.000	0.000	0.000	0.000
42	B	127	ALA	0	-0.007	0.001	18.485	-0.089	-0.089	0.000	0.000	0.000	0.000
43	B	128	ARG	1	0.868	0.938	14.274	16.981	16.981	0.000	0.000	0.000	0.000
44	B	129	ILE	0	0.063	0.046	17.693	-0.099	-0.099	0.000	0.000	0.000	0.000
45	B	130	GLN	0	-0.027	-0.027	20.814	0.133	0.133	0.000	0.000	0.000	0.000
46	B	131	VAL	0	0.008	0.002	15.082	0.095	0.095	0.000	0.000	0.000	0.000
47	B	132	TRP	0	0.001	0.014	17.516	0.100	0.100	0.000	0.000	0.000	0.000
48	B	133	PHE	0	0.030	0.000	18.779	0.296	0.296	0.000	0.000	0.000	0.000
49	B	134	GLN	0	-0.058	-0.024	19.660	-0.048	-0.048	0.000	0.000	0.000	0.000
50	B	135	ASN	0	-0.023	-0.020	15.774	0.222	0.222	0.000	0.000	0.000	0.000
51	B	136	ARG	1	0.726	0.868	19.149	11.122	11.122	0.000	0.000	0.000	0.000
52	B	137	ARG	1	0.912	0.940	21.851	11.140	11.140	0.000	0.000	0.000	0.000
53	B	138	ALA	0	-0.020	-0.003	20.568	0.334	0.334	0.000	0.000	0.000	0.000
54	B	139	LYS	1	0.902	0.946	20.609	11.796	11.796	0.000	0.000	0.000	0.000
55	B	140	TRP	0	0.094	0.019	22.468	-0.047	-0.047	0.000	0.000	0.000	0.000
56	B	141	ARG	1	0.907	0.975	25.407	10.260	10.260	0.000	0.000	0.000	0.000
57	B	142	LYS	1	0.918	0.977	21.917	11.282	11.282	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:86:ARG)