FMO DATABASE

FMODB ID: 66JQZ

Calculation Name: 3B09-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3B09

Chain ID: A

ChEMBL ID:

UniProt ID: Q765B0

Base Structure: X-ray

Registration Date: 2023-06-21

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	65
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-285837.110652
FMO2-HF: Nuclear repulsion	260893.554423
FMO2-HF: Total energy	-24943.556229
FMO2-MP2: Total energy	-25014.543381

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:3:ASP)

Summations of interaction energy for fragment #1(A:3:ASP)

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.
18.801	20.991	8.073	-4.885	-5.377	-0.007

Interaction energy analysis for fragmet #1(A:3:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.919 / q_NPA : -0.982

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

Sort

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	5	PHE	0	-0.014	0.007	2.479	-18.628	-14.510	0.652	-2.152	-2.617	0.016
4	A	6	SER	0	0.060	0.042	1.960	-1.922	-4.686	7.400	-2.414	-2.222	-0.024
5	A	7	THR	0	-0.018	-0.027	2.996	-4.420	-3.665	0.022	-0.317	-0.460	0.001
6	A	8	MET	0	-0.013	-0.004	5.050	-3.580	-3.499	-0.001	-0.002	-0.078	0.000
7	A	9	GLU	-1	-0.824	-0.919	5.696	31.218	31.218	0.000	0.000	0.000	0.000
8	A	10	GLN	0	-0.016	0.008	7.814	-3.330	-3.330	0.000	0.000	0.000	0.000
9	A	11	HIS	0	0.018	0.006	9.096	-2.281	-2.281	0.000	0.000	0.000	0.000
10	A	12	ALA	0	0.003	0.006	10.830	-1.542	-1.542	0.000	0.000	0.000	0.000
11	A	13	SER	0	-0.022	-0.025	12.110	-1.462	-1.462	0.000	0.000	0.000	0.000
12	A	14	TYR	0	-0.005	-0.001	13.571	-1.300	-1.300	0.000	0.000	0.000	0.000
13	A	15	GLY	0	0.010	0.007	15.068	-0.891	-0.891	0.000	0.000	0.000	0.000
14	A	16	VAL	0	0.016	0.002	16.824	-0.829	-0.829	0.000	0.000	0.000	0.000
15	A	17	GLY	0	0.021	0.009	18.056	-0.713	-0.713	0.000	0.000	0.000	0.000
16	A	18	ARG	1	0.787	0.877	19.071	-12.850	-12.850	0.000	0.000	0.000	0.000
17	A	19	GLN	0	0.002	0.009	21.203	-0.180	-0.180	0.000	0.000	0.000	0.000
18	A	20	MET	0	-0.027	-0.017	22.246	-0.493	-0.493	0.000	0.000	0.000	0.000
19	A	21	GLY	0	0.034	0.019	23.872	-0.450	-0.450	0.000	0.000	0.000	0.000
20	A	22	GLU	-1	-0.847	-0.918	24.072	11.101	11.101	0.000	0.000	0.000	0.000
21	A	23	GLN	0	-0.012	-0.012	26.944	-0.182	-0.182	0.000	0.000	0.000	0.000
22	A	24	LEU	0	-0.008	0.001	27.405	-0.365	-0.365	0.000	0.000	0.000	0.000
23	A	25	ALA	0	-0.032	-0.017	29.608	-0.325	-0.325	0.000	0.000	0.000	0.000
24	A	26	ALA	0	-0.024	0.001	31.447	-0.276	-0.276	0.000	0.000	0.000	0.000
25	A	27	ASN	0	-0.113	-0.067	33.311	-0.369	-0.369	0.000	0.000	0.000	0.000
26	A	28	SER	0	-0.010	0.025	32.993	-0.065	-0.065	0.000	0.000	0.000	0.000
27	A	29	PHE	0	-0.016	-0.028	34.989	-0.179	-0.179	0.000	0.000	0.000	0.000
28	A	30	GLU	-1	-0.927	-0.966	37.206	7.048	7.048	0.000	0.000	0.000	0.000
29	A	31	GLY	0	0.020	0.005	38.305	-0.098	-0.098	0.000	0.000	0.000	0.000
30	A	32	ILE	0	-0.059	-0.021	32.017	0.072	0.072	0.000	0.000	0.000	0.000
31	A	33	ASP	-1	-0.817	-0.912	32.251	9.084	9.084	0.000	0.000	0.000	0.000
32	A	34	ILE	0	0.000	-0.008	26.785	0.186	0.186	0.000	0.000	0.000	0.000
33	A	35	PRO	0	0.018	0.008	27.417	0.330	0.330	0.000	0.000	0.000	0.000
34	A	36	ALA	0	0.026	0.016	28.032	0.265	0.265	0.000	0.000	0.000	0.000
35	A	37	VAL	0	-0.024	-0.005	27.249	0.096	0.096	0.000	0.000	0.000	0.000
36	A	38	GLN	0	-0.038	-0.029	22.470	0.052	0.052	0.000	0.000	0.000	0.000
37	A	39	ALA	0	-0.002	0.004	24.737	0.375	0.375	0.000	0.000	0.000	0.000
38	A	40	GLY	0	0.039	0.022	26.914	0.107	0.107	0.000	0.000	0.000	0.000
39	A	41	LEU	0	-0.030	-0.012	21.465	0.101	0.101	0.000	0.000	0.000	0.000
40	A	42	ALA	0	-0.009	-0.011	22.600	0.332	0.332	0.000	0.000	0.000	0.000
41	A	43	ASP	-1	-0.827	-0.919	23.570	10.506	10.506	0.000	0.000	0.000	0.000
42	A	44	ALA	0	-0.005	-0.003	26.689	0.038	0.038	0.000	0.000	0.000	0.000
43	A	45	PHE	0	-0.063	-0.030	17.581	0.196	0.196	0.000	0.000	0.000	0.000
44	A	46	ALA	0	-0.043	-0.023	22.782	0.363	0.363	0.000	0.000	0.000	0.000
45	A	47	GLY	0	-0.028	-0.005	23.664	-0.080	-0.080	0.000	0.000	0.000	0.000
46	A	48	LYS	1	0.748	0.874	27.014	-10.442	-10.442	0.000	0.000	0.000	0.000
47	A	49	GLU	-1	-0.941	-0.970	28.829	8.398	8.398	0.000	0.000	0.000	0.000
48	A	50	SER	0	-0.031	-0.033	31.579	0.267	0.267	0.000	0.000	0.000	0.000
49	A	51	ALA	0	-0.006	-0.005	32.208	-0.215	-0.215	0.000	0.000	0.000	0.000
50	A	52	VAL	0	-0.010	0.009	33.992	-0.203	-0.203	0.000	0.000	0.000	0.000
51	A	53	SER	0	0.007	-0.017	36.618	0.121	0.121	0.000	0.000	0.000	0.000
52	A	54	MET	0	0.017	-0.019	35.191	0.012	0.012	0.000	0.000	0.000	0.000
53	A	55	GLU	-1	-0.950	-0.959	39.667	6.519	6.519	0.000	0.000	0.000	0.000
54	A	56	GLU	-1	-0.809	-0.874	40.666	7.331	7.331	0.000	0.000	0.000	0.000
55	A	57	LEU	0	-0.010	0.000	35.317	-0.025	-0.025	0.000	0.000	0.000	0.000
56	A	58	GLN	0	0.029	0.016	39.379	-0.021	-0.021	0.000	0.000	0.000	0.000
57	A	59	VAL	0	0.000	0.011	42.041	-0.124	-0.124	0.000	0.000	0.000	0.000
58	A	60	ALA	0	0.056	0.027	39.948	-0.082	-0.082	0.000	0.000	0.000	0.000
59	A	61	PHE	0	-0.011	-0.016	35.882	0.000	0.000	0.000	0.000	0.000	0.000
60	A	62	THR	0	-0.017	-0.010	41.116	-0.135	-0.135	0.000	0.000	0.000	0.000
61	A	63	GLU	-1	-0.956	-0.970	44.549	6.338	6.338	0.000	0.000	0.000	0.000
62	A	64	ILE	0	0.037	0.024	39.133	-0.080	-0.080	0.000	0.000	0.000	0.000
63	A	65	SER	0	-0.037	-0.028	42.597	0.073	0.073	0.000	0.000	0.000	0.000
64	A	66	ARG	1	0.770	0.896	43.759	-6.275	-6.275	0.000	0.000	0.000	0.000
65	A	67	ARG	1	0.897	0.951	39.697	-7.316	-7.316	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:ASP)