FMO DATABASE

FMODB ID: NNJ1Q

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

Total energy (hartree)

FMO2-HF: Electronic energy	-281488.550336
FMO2-HF: Nuclear repulsion	259845.86307
FMO2-HF: Total energy	-21642.687266
FMO2-MP2: Total energy	-21706.536346

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.
-11.503	-4.736	1.512	-2.586	-5.691	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 : 0.006 / q_NPA : -0.015

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	0.033	0.018	3.426	-1.960	0.312	0.020	-0.922	-1.369	0.002
4	A	4	VAL	0	0.020	0.009	2.657	-2.014	-0.161	0.855	-0.543	-2.165	-0.001
5	A	5	TYR	0	-0.004	-0.013	2.638	-1.852	-0.233	0.463	-0.610	-1.472	-0.004
6	A	6	ALA	0	0.013	0.022	6.204	0.448	0.448	0.000	0.000	0.000	0.000
7	A	7	ALA	0	0.035	0.013	7.748	0.075	0.075	0.000	0.000	0.000	0.000
8	A	8	LEU	0	0.006	-0.004	6.262	0.011	0.011	0.000	0.000	0.000	0.000
9	A	9	LEU	0	-0.022	0.007	9.549	0.094	0.094	0.000	0.000	0.000	0.000
10	A	10	LEU	0	-0.027	-0.014	11.925	0.087	0.087	0.000	0.000	0.000	0.000
11	A	11	HIS	0	-0.004	-0.006	12.590	-0.019	-0.019	0.000	0.000	0.000	0.000
12	A	12	SER	0	-0.076	-0.044	13.588	0.018	0.018	0.000	0.000	0.000	0.000
13	A	13	VAL	0	-0.056	-0.028	15.334	0.019	0.019	0.000	0.000	0.000	0.000
14	A	14	GLY	0	-0.005	0.003	17.662	0.036	0.036	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.767	0.883	17.093	0.025	0.025	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.856	-0.926	16.835	0.132	0.132	0.000	0.000	0.000	0.000
17	A	17	ILE	0	-0.008	0.003	11.614	-0.007	-0.007	0.000	0.000	0.000	0.000
18	A	18	ASN	0	0.016	-0.002	14.401	0.111	0.111	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.740	-0.873	14.701	0.560	0.560	0.000	0.000	0.000	0.000
20	A	20	GLU	-1	-0.842	-0.900	15.681	0.069	0.069	0.000	0.000	0.000	0.000
21	A	21	ASN	0	-0.025	-0.029	15.677	-0.025	-0.025	0.000	0.000	0.000	0.000
22	A	22	LEU	0	0.036	0.027	9.420	-0.067	-0.067	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.814	0.869	11.929	-0.511	-0.511	0.000	0.000	0.000	0.000
24	A	24	ALA	0	0.000	0.006	13.768	-0.053	-0.053	0.000	0.000	0.000	0.000
25	A	25	VAL	0	-0.011	-0.007	10.625	-0.058	-0.058	0.000	0.000	0.000	0.000
26	A	26	LEU	0	-0.015	-0.009	6.516	-0.132	-0.132	0.000	0.000	0.000	0.000
27	A	27	GLN	0	0.002	-0.003	10.479	-0.142	-0.142	0.000	0.000	0.000	0.000
28	A	28	ALA	0	-0.062	-0.021	13.751	-0.046	-0.046	0.000	0.000	0.000	0.000
29	A	29	ALA	0	-0.056	-0.020	9.765	-0.062	-0.062	0.000	0.000	0.000	0.000
30	A	30	GLY	0	-0.023	-0.008	11.138	-0.097	-0.097	0.000	0.000	0.000	0.000
31	A	31	VAL	0	-0.097	-0.049	7.034	0.008	0.008	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.838	-0.925	10.299	0.271	0.271	0.000	0.000	0.000	0.000
33	A	33	PRO	0	-0.066	-0.034	10.383	0.161	0.161	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.847	-0.928	9.623	1.501	1.501	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.776	-0.872	11.252	0.746	0.746	0.000	0.000	0.000	0.000
36	A	36	ALA	0	-0.018	-0.005	13.009	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	37	ARG	1	0.850	0.918	3.023	-7.453	-6.430	0.174	-0.511	-0.685	0.005
38	A	38	ILE	0	-0.051	-0.016	9.440	0.155	0.155	0.000	0.000	0.000	0.000
39	A	39	LYS	1	0.825	0.877	11.133	-0.640	-0.640	0.000	0.000	0.000	0.000
40	A	40	ALA	0	-0.024	-0.017	10.931	-0.096	-0.096	0.000	0.000	0.000	0.000
41	A	41	LEU	0	-0.032	-0.003	6.927	-0.006	-0.006	0.000	0.000	0.000	0.000
42	A	42	VAL	0	0.017	0.003	9.971	-0.200	-0.200	0.000	0.000	0.000	0.000
43	A	43	ALA	0	0.025	0.016	13.238	-0.085	-0.085	0.000	0.000	0.000	0.000
44	A	44	ALA	0	-0.073	-0.033	10.852	-0.068	-0.068	0.000	0.000	0.000	0.000
45	A	45	LEU	0	-0.050	-0.038	8.907	-0.089	-0.089	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.914	-0.939	13.026	0.278	0.278	0.000	0.000	0.000	0.000
47	A	47	GLY	0	-0.059	-0.022	16.621	0.012	0.012	0.000	0.000	0.000	0.000
48	A	48	VAL	0	-0.046	-0.018	12.069	-0.048	-0.048	0.000	0.000	0.000	0.000
49	A	49	ASN	0	-0.035	-0.033	15.334	-0.049	-0.049	0.000	0.000	0.000	0.000
50	A	50	ILE	0	0.043	0.012	10.402	-0.012	-0.012	0.000	0.000	0.000	0.000
51	A	51	ASP	-1	-0.842	-0.916	12.903	-0.263	-0.263	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.801	-0.880	15.400	-0.086	-0.086	0.000	0.000	0.000	0.000
53	A	53	VAL	0	-0.019	-0.013	8.900	-0.009	-0.009	0.000	0.000	0.000	0.000
54	A	54	ILE	0	-0.029	-0.021	10.308	-0.099	-0.099	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.907	-0.955	12.691	-0.189	-0.189	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.751	0.864	14.144	0.120	0.120	0.000	0.000	0.000	0.000
57	A	57	ALA	0	-0.033	-0.003	10.015	0.013	0.013	0.000	0.000	0.000	0.000
58	A	58	ALA	0	-0.101	-0.031	11.842	-0.012	-0.012	0.000	0.000	0.000	0.000

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