FMO DATABASE

FMODB ID: 1496Z

Calculation Name: 3D3R-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3D3R

Chain ID: A

ChEMBL ID:

UniProt ID: Q8EF93

Base Structure: X-ray

Registration Date: 2023-03-14

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	83
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-455497.559965
FMO2-HF: Nuclear repulsion	422199.534996
FMO2-HF: Total energy	-33298.024969
FMO2-MP2: Total energy	-33393.241984

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:-6:GLU)

Summations of interaction energy for fragment #1(A:-6:GLU)

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.
42.522	46.753	0.207	-1.687	-2.751	0.005

Interaction energy analysis for fragmet #1(A:-6:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.945 / q_NPA : -0.981

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	-4	LEU	0	0.000	0.008	2.918	-9.623	-6.533	0.140	-1.387	-1.843	0.005
4	A	-3	TYR	0	-0.053	-0.011	2.940	-6.341	-5.295	0.068	-0.293	-0.822	0.000
5	A	-2	PHE	0	0.018	0.011	5.661	2.124	2.124	0.000	0.000	0.000	0.000
6	A	-1	GLN	0	0.064	0.014	7.832	0.531	0.531	0.000	0.000	0.000	0.000
7	A	0	GLY	0	0.024	0.006	6.761	-0.037	-0.037	0.000	0.000	0.000	0.000
8	A	1	MET	0	-0.055	-0.019	7.829	-0.530	-0.530	0.000	0.000	0.000	0.000
9	A	2	CYS	0	-0.031	-0.014	9.297	-2.184	-2.184	0.000	0.000	0.000	0.000
10	A	3	LEU	0	0.017	0.011	6.679	1.740	1.740	0.000	0.000	0.000	0.000
11	A	4	SER	0	-0.039	-0.042	7.663	-2.097	-2.097	0.000	0.000	0.000	0.000
12	A	5	ILE	0	-0.014	-0.012	9.403	-0.623	-0.623	0.000	0.000	0.000	0.000
13	A	6	PRO	0	-0.018	-0.007	11.218	-0.096	-0.096	0.000	0.000	0.000	0.000
14	A	7	SER	0	-0.017	0.004	13.404	-1.466	-1.466	0.000	0.000	0.000	0.000
15	A	8	GLN	0	0.012	0.034	16.392	0.348	0.348	0.000	0.000	0.000	0.000
16	A	9	VAL	0	0.035	0.014	18.113	-0.314	-0.314	0.000	0.000	0.000	0.000
17	A	10	VAL	0	-0.063	-0.051	20.565	-0.556	-0.556	0.000	0.000	0.000	0.000
18	A	11	ALA	0	-0.011	-0.010	23.679	-0.624	-0.624	0.000	0.000	0.000	0.000
19	A	12	VAL	0	0.015	0.005	22.288	0.582	0.582	0.000	0.000	0.000	0.000
20	A	13	ASP	-1	-0.826	-0.897	24.385	10.421	10.421	0.000	0.000	0.000	0.000
21	A	14	ASN	0	0.042	-0.008	22.796	0.757	0.757	0.000	0.000	0.000	0.000
22	A	15	GLU	-1	-0.981	-0.973	25.031	10.058	10.058	0.000	0.000	0.000	0.000
23	A	16	ARG	1	0.836	0.910	26.505	-10.241	-10.241	0.000	0.000	0.000	0.000
24	A	17	GLN	0	-0.032	-0.003	21.304	0.816	0.816	0.000	0.000	0.000	0.000
25	A	18	SER	0	-0.020	0.006	21.025	0.393	0.393	0.000	0.000	0.000	0.000
26	A	19	VAL	0	0.028	0.004	18.058	-0.244	-0.244	0.000	0.000	0.000	0.000
27	A	20	THR	0	-0.024	-0.016	20.809	0.177	0.177	0.000	0.000	0.000	0.000
28	A	21	VAL	0	-0.006	-0.013	17.240	0.143	0.143	0.000	0.000	0.000	0.000
29	A	22	ASP	-1	-0.829	-0.902	20.411	11.908	11.908	0.000	0.000	0.000	0.000
30	A	23	THR	0	0.021	-0.007	16.185	0.494	0.494	0.000	0.000	0.000	0.000
31	A	24	LEU	0	-0.017	-0.015	17.712	-0.400	-0.400	0.000	0.000	0.000	0.000
32	A	25	GLY	0	0.036	0.029	20.884	-0.493	-0.493	0.000	0.000	0.000	0.000
33	A	26	VAL	0	-0.075	-0.043	21.737	-0.359	-0.359	0.000	0.000	0.000	0.000
34	A	27	ARG	1	0.841	0.905	21.988	-10.981	-10.981	0.000	0.000	0.000	0.000
35	A	28	ARG	1	0.919	0.954	18.636	-14.812	-14.812	0.000	0.000	0.000	0.000
36	A	29	ASP	-1	-0.835	-0.873	21.630	12.259	12.259	0.000	0.000	0.000	0.000
37	A	30	VAL	0	-0.042	-0.027	16.673	0.236	0.236	0.000	0.000	0.000	0.000
38	A	31	SER	0	0.015	0.007	18.076	-0.353	-0.353	0.000	0.000	0.000	0.000
39	A	32	SER	0	0.038	-0.006	16.963	0.660	0.660	0.000	0.000	0.000	0.000
40	A	33	HIS	0	-0.043	-0.030	17.074	0.253	0.253	0.000	0.000	0.000	0.000
41	A	34	LEU	0	-0.037	-0.015	11.982	0.253	0.253	0.000	0.000	0.000	0.000
42	A	35	MET	0	-0.055	0.003	12.097	1.600	1.600	0.000	0.000	0.000	0.000
43	A	36	THR	0	-0.029	-0.042	9.263	-0.044	-0.044	0.000	0.000	0.000	0.000
44	A	37	GLU	-1	-0.910	-0.924	12.552	22.262	22.262	0.000	0.000	0.000	0.000
45	A	38	PRO	0	-0.042	-0.043	16.024	-0.095	-0.095	0.000	0.000	0.000	0.000
46	A	39	LEU	0	0.022	0.026	15.530	0.211	0.211	0.000	0.000	0.000	0.000
47	A	40	ALA	0	-0.030	-0.024	19.700	-0.794	-0.794	0.000	0.000	0.000	0.000
48	A	41	ILE	0	-0.041	-0.022	21.960	0.376	0.376	0.000	0.000	0.000	0.000
49	A	42	GLY	0	-0.012	-0.006	23.083	-0.369	-0.369	0.000	0.000	0.000	0.000
50	A	43	ASP	-1	-0.830	-0.899	17.923	15.578	15.578	0.000	0.000	0.000	0.000
51	A	44	TYR	0	-0.085	-0.064	15.733	-0.263	-0.263	0.000	0.000	0.000	0.000
52	A	45	VAL	0	0.015	0.013	12.907	0.850	0.850	0.000	0.000	0.000	0.000
53	A	46	LEU	0	-0.013	-0.003	6.810	-0.757	-0.757	0.000	0.000	0.000	0.000
54	A	47	ILE	0	0.019	0.003	10.126	0.095	0.095	0.000	0.000	0.000	0.000
55	A	48	HIS	0	0.027	0.029	4.652	-3.563	-3.468	-0.001	-0.007	-0.086	0.000
56	A	49	ILE	0	-0.033	-0.003	8.429	-1.046	-1.046	0.000	0.000	0.000	0.000
57	A	50	GLY	0	0.015	0.004	7.919	3.452	3.452	0.000	0.000	0.000	0.000
58	A	51	PHE	0	-0.051	-0.022	9.057	-2.798	-2.798	0.000	0.000	0.000	0.000
59	A	52	VAL	0	0.052	0.029	10.523	2.257	2.257	0.000	0.000	0.000	0.000
60	A	53	MET	0	-0.024	-0.018	11.693	-1.367	-1.367	0.000	0.000	0.000	0.000
61	A	54	ASN	0	0.032	0.022	15.428	0.127	0.127	0.000	0.000	0.000	0.000
62	A	55	LYS	1	0.873	0.931	18.816	-13.126	-13.126	0.000	0.000	0.000	0.000
63	A	56	ILE	0	0.070	0.042	21.547	-0.591	-0.591	0.000	0.000	0.000	0.000
64	A	57	ASP	-1	-0.828	-0.916	24.457	11.039	11.039	0.000	0.000	0.000	0.000
65	A	58	ARG	1	0.961	0.982	27.480	-11.126	-11.126	0.000	0.000	0.000	0.000
66	A	59	ASN	0	-0.016	-0.022	28.680	-0.263	-0.263	0.000	0.000	0.000	0.000
67	A	60	ASP	-1	-0.863	-0.919	29.137	10.240	10.240	0.000	0.000	0.000	0.000
68	A	61	ALA	0	-0.017	0.001	26.400	0.003	0.003	0.000	0.000	0.000	0.000
69	A	62	LEU	0	-0.045	-0.029	28.203	-0.056	-0.056	0.000	0.000	0.000	0.000
70	A	63	GLN	0	-0.010	-0.018	30.907	-0.397	-0.397	0.000	0.000	0.000	0.000
71	A	64	SER	0	-0.028	-0.018	29.149	-0.023	-0.023	0.000	0.000	0.000	0.000
72	A	65	LEU	0	-0.027	-0.023	25.677	0.074	0.074	0.000	0.000	0.000	0.000
73	A	66	GLU	-1	-0.929	-0.955	29.590	9.008	9.008	0.000	0.000	0.000	0.000
74	A	67	LEU	0	0.046	0.024	32.247	-0.046	-0.046	0.000	0.000	0.000	0.000
75	A	68	TYR	0	-0.021	-0.020	26.627	0.103	0.103	0.000	0.000	0.000	0.000
76	A	69	GLN	0	0.025	0.015	29.300	0.172	0.172	0.000	0.000	0.000	0.000
77	A	70	GLU	-1	-0.949	-0.958	31.137	8.526	8.526	0.000	0.000	0.000	0.000
78	A	71	ILE	0	-0.048	-0.030	29.610	-0.120	-0.120	0.000	0.000	0.000	0.000
79	A	72	VAL	0	0.010	0.000	27.461	-0.024	-0.024	0.000	0.000	0.000	0.000
80	A	73	SER	0	-0.027	-0.026	30.307	-0.148	-0.148	0.000	0.000	0.000	0.000
81	A	74	LYS	1	0.850	0.935	33.788	-8.727	-8.727	0.000	0.000	0.000	0.000
82	A	75	LEU	0	-0.074	-0.043	30.287	-0.195	-0.195	0.000	0.000	0.000	0.000
83	A	76	GLU	-1	-0.983	-0.963	29.203	10.708	10.708	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:-6:GLU)