FMO DATABASE

FMODB ID: 8942Y

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	OptHSide
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	-280603.600352
FMO2-HF: Nuclear repulsion	258961.06689
FMO2-HF: Total energy	-21642.533461
FMO2-MP2: Total energy	-21706.395426

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.
-9.324	-4.246	1.635	-1.724	-4.988	-0.003

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	0.014	0.013	3.654	-2.187	-0.348	0.007	-0.652	-1.193	0.001
4	A	4	VAL	0	0.034	0.015	2.449	-1.631	-0.246	1.035	-0.429	-1.991	-0.001
5	A	5	TYR	0	0.012	-0.006	2.712	-1.435	0.209	0.593	-0.584	-1.653	-0.003
6	A	6	ALA	0	-0.014	0.007	5.694	0.573	0.573	0.000	0.000	0.000	0.000
7	A	7	ALA	0	0.028	0.001	7.695	0.160	0.160	0.000	0.000	0.000	0.000
8	A	8	LEU	0	0.001	-0.003	6.298	0.115	0.115	0.000	0.000	0.000	0.000
9	A	9	LEU	0	-0.008	0.011	9.497	0.155	0.155	0.000	0.000	0.000	0.000
10	A	10	LEU	0	-0.024	-0.013	11.770	0.124	0.124	0.000	0.000	0.000	0.000
11	A	11	HIS	0	0.002	-0.004	12.377	-0.008	-0.008	0.000	0.000	0.000	0.000
12	A	12	SER	0	-0.084	-0.043	13.582	0.057	0.057	0.000	0.000	0.000	0.000
13	A	13	VAL	0	-0.058	-0.034	15.332	0.049	0.049	0.000	0.000	0.000	0.000
14	A	14	GLY	0	-0.012	-0.003	17.700	0.047	0.047	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.852	0.929	17.002	0.163	0.163	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.865	-0.930	16.691	-0.038	-0.038	0.000	0.000	0.000	0.000
17	A	17	ILE	0	-0.020	-0.006	11.568	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	18	ASN	0	0.013	-0.001	14.750	0.076	0.076	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.770	-0.892	14.877	0.383	0.383	0.000	0.000	0.000	0.000
20	A	20	GLU	-1	-0.917	-0.953	15.429	0.031	0.031	0.000	0.000	0.000	0.000
21	A	21	ASN	0	-0.025	-0.022	16.195	-0.028	-0.028	0.000	0.000	0.000	0.000
22	A	22	LEU	0	0.048	0.028	9.519	-0.059	-0.059	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.820	0.883	12.107	-0.373	-0.373	0.000	0.000	0.000	0.000
24	A	24	ALA	0	0.008	0.017	14.018	-0.015	-0.015	0.000	0.000	0.000	0.000
25	A	25	VAL	0	-0.004	-0.002	10.921	-0.034	-0.034	0.000	0.000	0.000	0.000
26	A	26	LEU	0	-0.016	-0.016	6.824	-0.080	-0.080	0.000	0.000	0.000	0.000
27	A	27	GLN	0	-0.005	-0.012	10.557	-0.071	-0.071	0.000	0.000	0.000	0.000
28	A	28	ALA	0	-0.061	-0.014	13.660	-0.017	-0.017	0.000	0.000	0.000	0.000
29	A	29	ALA	0	-0.070	-0.028	9.420	-0.058	-0.058	0.000	0.000	0.000	0.000
30	A	30	GLY	0	-0.019	-0.008	10.566	-0.040	-0.040	0.000	0.000	0.000	0.000
31	A	31	VAL	0	-0.072	-0.030	7.067	0.099	0.099	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.856	-0.924	10.259	0.292	0.292	0.000	0.000	0.000	0.000
33	A	33	PRO	0	-0.079	-0.041	10.646	0.190	0.190	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.867	-0.941	10.696	1.477	1.477	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.770	-0.861	12.180	0.549	0.549	0.000	0.000	0.000	0.000
36	A	36	ALA	0	-0.010	-0.009	13.981	-0.020	-0.020	0.000	0.000	0.000	0.000
37	A	37	ARG	1	0.882	0.948	4.209	-5.949	-5.739	0.000	-0.059	-0.151	0.000
38	A	38	ILE	0	-0.037	-0.012	9.922	0.019	0.019	0.000	0.000	0.000	0.000
39	A	39	LYS	1	0.828	0.872	11.550	-0.542	-0.542	0.000	0.000	0.000	0.000
40	A	40	ALA	0	-0.014	-0.004	10.921	-0.073	-0.073	0.000	0.000	0.000	0.000
41	A	41	LEU	0	-0.013	0.003	7.112	-0.074	-0.074	0.000	0.000	0.000	0.000
42	A	42	VAL	0	0.013	0.001	10.210	-0.177	-0.177	0.000	0.000	0.000	0.000
43	A	43	ALA	0	0.008	0.006	13.360	-0.074	-0.074	0.000	0.000	0.000	0.000
44	A	44	ALA	0	-0.065	-0.032	10.148	-0.054	-0.054	0.000	0.000	0.000	0.000
45	A	45	LEU	0	-0.037	-0.035	8.269	-0.108	-0.108	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.925	-0.943	12.291	0.099	0.099	0.000	0.000	0.000	0.000
47	A	47	GLY	0	-0.056	-0.019	16.071	0.018	0.018	0.000	0.000	0.000	0.000
48	A	48	VAL	0	-0.055	-0.021	11.297	-0.037	-0.037	0.000	0.000	0.000	0.000
49	A	49	ASN	0	-0.032	-0.043	14.780	-0.054	-0.054	0.000	0.000	0.000	0.000
50	A	50	ILE	0	0.040	0.007	10.499	-0.032	-0.032	0.000	0.000	0.000	0.000
51	A	51	ASP	-1	-0.842	-0.902	13.300	-0.419	-0.419	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.778	-0.861	15.871	-0.224	-0.224	0.000	0.000	0.000	0.000
53	A	53	VAL	0	-0.045	-0.021	9.237	-0.015	-0.015	0.000	0.000	0.000	0.000
54	A	54	ILE	0	-0.027	-0.024	10.363	-0.085	-0.085	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.939	-0.971	12.855	-0.310	-0.310	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.783	0.870	14.272	0.287	0.287	0.000	0.000	0.000	0.000
57	A	57	ALA	0	-0.047	-0.004	10.143	0.021	0.021	0.000	0.000	0.000	0.000
58	A	58	ALA	0	-0.084	-0.022	12.133	0.015	0.015	0.000	0.000	0.000	0.000

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