FMO DATABASE

FMODB ID: G5ZN1

Calculation Name: 3A1Y-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3A1Y

Chain ID: A

ChEMBL ID:

UniProt ID: O74109

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

Total energy (hartree)

FMO2-HF: Electronic energy	-280249.087136
FMO2-HF: Nuclear repulsion	258607.10318
FMO2-HF: Total energy	-21641.983956
FMO2-MP2: Total energy	-21705.81498

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.
-9.758	-5.78	2.962	-1.865	-5.073	-0.002

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 : 0.016 / q_NPA : -0.006

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	TYR	0	0.027	0.020	3.641	-2.450	-0.618	0.004	-0.652	-1.184	0.001
4	A	4	VAL	0	0.024	0.012	2.295	-1.149	-0.766	2.771	-0.630	-2.524	-0.002
5	A	5	TYR	0	0.019	-0.002	3.215	-1.119	0.358	0.187	-0.471	-1.192	-0.002
6	A	6	ALA	0	-0.013	0.004	5.553	0.623	0.623	0.000	0.000	0.000	0.000
7	A	7	ALA	0	0.030	0.002	7.484	0.180	0.180	0.000	0.000	0.000	0.000
8	A	8	LEU	0	0.003	-0.006	6.199	0.111	0.111	0.000	0.000	0.000	0.000
9	A	9	LEU	0	-0.011	0.011	9.516	0.176	0.176	0.000	0.000	0.000	0.000
10	A	10	LEU	0	-0.017	-0.008	11.631	0.137	0.137	0.000	0.000	0.000	0.000
11	A	11	HIS	0	0.009	0.015	12.433	0.005	0.005	0.000	0.000	0.000	0.000
12	A	12	SER	0	-0.079	-0.041	13.608	0.069	0.069	0.000	0.000	0.000	0.000
13	A	13	VAL	0	-0.057	-0.032	15.375	0.057	0.057	0.000	0.000	0.000	0.000
14	A	14	GLY	0	-0.011	-0.003	17.697	0.054	0.054	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.860	0.947	16.807	0.207	0.207	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.926	-0.978	16.543	-0.075	-0.075	0.000	0.000	0.000	0.000
17	A	17	ILE	0	-0.013	0.003	11.224	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	18	ASN	0	0.064	0.034	14.480	0.060	0.060	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.871	-0.967	14.827	0.378	0.378	0.000	0.000	0.000	0.000
20	A	20	GLU	-1	-0.969	-0.982	15.382	0.059	0.059	0.000	0.000	0.000	0.000
21	A	21	ASN	0	-0.013	-0.022	16.051	-0.032	-0.032	0.000	0.000	0.000	0.000
22	A	22	LEU	0	0.045	0.024	9.452	-0.058	-0.058	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.920	0.965	12.083	-0.377	-0.377	0.000	0.000	0.000	0.000
24	A	24	ALA	0	0.006	0.016	14.057	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	25	VAL	0	0.004	0.003	10.717	-0.028	-0.028	0.000	0.000	0.000	0.000
26	A	26	LEU	0	-0.020	-0.017	6.989	-0.075	-0.075	0.000	0.000	0.000	0.000
27	A	27	GLN	0	0.000	-0.004	10.590	-0.047	-0.047	0.000	0.000	0.000	0.000
28	A	28	ALA	0	-0.061	-0.013	13.698	-0.016	-0.016	0.000	0.000	0.000	0.000
29	A	29	ALA	0	-0.073	-0.028	9.443	-0.065	-0.065	0.000	0.000	0.000	0.000
30	A	30	GLY	0	-0.022	-0.011	10.592	-0.020	-0.020	0.000	0.000	0.000	0.000
31	A	31	VAL	0	-0.059	-0.024	7.181	0.111	0.111	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.873	-0.938	10.305	0.356	0.356	0.000	0.000	0.000	0.000
33	A	33	PRO	0	-0.076	-0.038	10.701	0.218	0.218	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.884	-0.951	10.750	1.600	1.600	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.813	-0.922	12.161	0.592	0.592	0.000	0.000	0.000	0.000
36	A	36	ALA	0	-0.016	-0.008	13.967	-0.036	-0.036	0.000	0.000	0.000	0.000
37	A	37	ARG	1	0.942	0.975	4.060	-6.995	-6.709	0.000	-0.112	-0.173	0.001
38	A	38	ILE	0	-0.028	-0.005	9.901	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	39	LYS	1	0.929	0.948	11.519	-0.608	-0.608	0.000	0.000	0.000	0.000
40	A	40	ALA	0	-0.030	-0.008	10.537	-0.086	-0.086	0.000	0.000	0.000	0.000
41	A	41	LEU	0	-0.020	-0.001	6.334	-0.103	-0.103	0.000	0.000	0.000	0.000
42	A	42	VAL	0	0.025	0.010	9.566	-0.190	-0.190	0.000	0.000	0.000	0.000
43	A	43	ALA	0	0.007	0.009	12.779	-0.075	-0.075	0.000	0.000	0.000	0.000
44	A	44	ALA	0	-0.073	-0.038	9.501	-0.056	-0.056	0.000	0.000	0.000	0.000
45	A	45	LEU	0	-0.033	-0.040	8.166	-0.119	-0.119	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.921	-0.944	11.890	0.068	0.068	0.000	0.000	0.000	0.000
47	A	47	GLY	0	-0.060	-0.018	15.655	0.017	0.017	0.000	0.000	0.000	0.000
48	A	48	VAL	0	-0.048	-0.008	11.229	-0.032	-0.032	0.000	0.000	0.000	0.000
49	A	49	ASN	0	-0.054	-0.065	14.673	-0.042	-0.042	0.000	0.000	0.000	0.000
50	A	50	ILE	0	0.043	0.001	10.809	-0.038	-0.038	0.000	0.000	0.000	0.000
51	A	51	ASP	-1	-0.844	-0.913	13.289	-0.507	-0.507	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.850	-0.905	15.963	-0.291	-0.291	0.000	0.000	0.000	0.000
53	A	53	VAL	0	-0.057	-0.025	9.476	-0.017	-0.017	0.000	0.000	0.000	0.000
54	A	54	ILE	0	-0.037	-0.028	10.858	-0.098	-0.098	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.958	-0.979	12.981	-0.384	-0.384	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.881	0.932	14.317	0.342	0.342	0.000	0.000	0.000	0.000
57	A	57	ALA	0	-0.051	-0.007	10.467	0.020	0.020	0.000	0.000	0.000	0.000
58	A	58	ALA	0	-0.060	-0.011	12.387	-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:1:MET)