FMO DATABASE

FMODB ID: 14GKZ

Calculation Name: 5DOL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5DOL

Chain ID: A

ChEMBL ID:

UniProt ID: P37542

Base Structure: X-ray

Registration Date: 2023-06-20

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	61
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-275224.05323
FMO2-HF: Nuclear repulsion	249632.374794
FMO2-HF: Total energy	-25591.678436
FMO2-MP2: Total energy	-25667.205856

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:2:ASP)

Summations of interaction energy for fragment #1(A:2: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.
30.074	31.751	9.506	-5.089	-6.094	0.015

Interaction energy analysis for fragmet #1(A:2:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.868 / q_NPA : -0.952

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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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	LYS	1	0.796	0.861	2.932	-39.837	-37.323	0.202	-1.066	-1.650	0.004
4	A	5	GLU	-1	-0.906	-0.941	1.615	36.143	34.655	9.299	-3.959	-3.852	0.011
5	A	6	LEU	0	0.071	0.064	3.264	-5.701	-5.151	0.006	-0.056	-0.499	0.000
6	A	7	PHE	0	0.030	-0.022	4.860	-4.040	-3.939	-0.001	-0.008	-0.093	0.000
7	A	8	ASP	-1	-0.752	-0.859	6.989	27.520	27.520	0.000	0.000	0.000	0.000
8	A	9	THR	0	0.009	0.002	6.476	-2.851	-2.851	0.000	0.000	0.000	0.000
9	A	10	VAL	0	-0.030	-0.017	8.941	-2.089	-2.089	0.000	0.000	0.000	0.000
10	A	11	ILE	0	0.014	0.015	11.058	-1.243	-1.243	0.000	0.000	0.000	0.000
11	A	12	ASN	0	-0.021	0.006	11.886	-1.472	-1.472	0.000	0.000	0.000	0.000
12	A	13	LEU	0	-0.019	-0.013	12.690	-1.345	-1.345	0.000	0.000	0.000	0.000
13	A	14	GLU	-1	-0.929	-0.967	15.082	15.372	15.372	0.000	0.000	0.000	0.000
14	A	15	GLU	-1	-0.889	-0.951	15.843	16.250	16.250	0.000	0.000	0.000	0.000
15	A	16	GLN	0	-0.072	-0.044	15.435	-1.526	-1.526	0.000	0.000	0.000	0.000
16	A	17	ILE	0	-0.003	0.005	19.231	-0.886	-0.886	0.000	0.000	0.000	0.000
17	A	18	GLY	0	0.010	0.006	21.040	-0.667	-0.667	0.000	0.000	0.000	0.000
18	A	19	SER	0	-0.050	-0.036	22.258	-0.803	-0.803	0.000	0.000	0.000	0.000
19	A	20	LEU	0	0.002	-0.002	22.624	-0.540	-0.540	0.000	0.000	0.000	0.000
20	A	21	TYR	0	-0.029	-0.004	25.266	-0.584	-0.584	0.000	0.000	0.000	0.000
21	A	22	ARG	1	0.968	0.982	24.526	-11.504	-11.504	0.000	0.000	0.000	0.000
22	A	23	GLN	0	-0.004	0.001	25.470	-0.494	-0.494	0.000	0.000	0.000	0.000
23	A	24	LEU	0	-0.026	0.000	29.506	-0.353	-0.353	0.000	0.000	0.000	0.000
24	A	25	GLY	0	-0.027	-0.017	31.283	-0.330	-0.330	0.000	0.000	0.000	0.000
25	A	26	ASP	-1	-0.851	-0.934	32.142	8.845	8.845	0.000	0.000	0.000	0.000
26	A	27	LEU	0	-0.018	-0.001	33.718	-0.300	-0.300	0.000	0.000	0.000	0.000
27	A	28	LYS	1	0.932	0.963	35.059	-8.582	-8.582	0.000	0.000	0.000	0.000
28	A	29	GLN	0	-0.007	0.003	37.296	-0.105	-0.105	0.000	0.000	0.000	0.000
29	A	30	HIS	0	0.003	-0.006	37.638	-0.250	-0.250	0.000	0.000	0.000	0.000
30	A	31	ILE	0	-0.033	-0.015	37.825	-0.194	-0.194	0.000	0.000	0.000	0.000
31	A	32	GLY	0	-0.010	-0.004	41.306	-0.179	-0.179	0.000	0.000	0.000	0.000
32	A	33	GLU	-1	-0.898	-0.955	43.160	6.927	6.927	0.000	0.000	0.000	0.000
33	A	34	MET	0	0.023	0.012	43.992	-0.151	-0.151	0.000	0.000	0.000	0.000
34	A	35	ILE	0	-0.055	-0.025	43.674	-0.173	-0.173	0.000	0.000	0.000	0.000
35	A	36	GLU	-1	-0.936	-0.976	47.199	6.117	6.117	0.000	0.000	0.000	0.000
36	A	37	GLU	-1	-0.947	-0.967	48.654	6.070	6.070	0.000	0.000	0.000	0.000
37	A	38	ASN	0	-0.020	-0.015	49.795	-0.175	-0.175	0.000	0.000	0.000	0.000
38	A	39	HIS	0	-0.051	-0.025	51.457	-0.133	-0.133	0.000	0.000	0.000	0.000
39	A	40	HIS	0	0.039	0.005	52.128	-0.239	-0.239	0.000	0.000	0.000	0.000
40	A	41	LEU	0	0.061	0.044	52.835	-0.141	-0.141	0.000	0.000	0.000	0.000
41	A	42	GLN	0	-0.067	-0.033	53.920	-0.119	-0.119	0.000	0.000	0.000	0.000
42	A	43	LEU	0	-0.073	-0.037	57.470	-0.137	-0.137	0.000	0.000	0.000	0.000
43	A	44	GLU	-1	-0.885	-0.937	59.228	5.079	5.079	0.000	0.000	0.000	0.000
44	A	45	ASN	0	-0.005	0.001	59.883	-0.136	-0.136	0.000	0.000	0.000	0.000
45	A	46	LYS	1	0.939	0.959	59.001	-5.285	-5.285	0.000	0.000	0.000	0.000
46	A	47	HIS	0	0.007	0.010	63.604	-0.092	-0.092	0.000	0.000	0.000	0.000
47	A	48	LEU	0	0.018	0.008	63.319	-0.101	-0.101	0.000	0.000	0.000	0.000
48	A	49	ARG	1	0.905	0.947	62.200	-4.951	-4.951	0.000	0.000	0.000	0.000
49	A	50	LYS	1	0.878	0.936	67.551	-4.353	-4.353	0.000	0.000	0.000	0.000
50	A	51	ARG	1	0.943	0.978	69.416	-4.316	-4.316	0.000	0.000	0.000	0.000
51	A	52	LEU	0	0.016	-0.004	69.348	-0.075	-0.075	0.000	0.000	0.000	0.000
52	A	53	ASP	-1	-0.872	-0.919	71.771	4.286	4.286	0.000	0.000	0.000	0.000
53	A	54	ASP	-1	-0.887	-0.929	73.635	4.168	4.168	0.000	0.000	0.000	0.000
54	A	55	THR	0	-0.048	-0.035	74.789	-0.072	-0.072	0.000	0.000	0.000	0.000
55	A	56	THR	0	-0.019	-0.022	74.974	-0.059	-0.059	0.000	0.000	0.000	0.000
56	A	57	GLN	0	0.013	0.008	77.601	-0.066	-0.066	0.000	0.000	0.000	0.000
57	A	58	GLN	0	-0.073	-0.046	78.718	-0.028	-0.028	0.000	0.000	0.000	0.000
58	A	59	ILE	0	-0.043	-0.037	78.784	-0.056	-0.056	0.000	0.000	0.000	0.000
59	A	60	GLU	-1	-0.960	-0.970	81.740	3.822	3.822	0.000	0.000	0.000	0.000
60	A	61	LYS	1	0.870	0.957	83.491	-3.740	-3.740	0.000	0.000	0.000	0.000
61	A	62	PHE	0	-0.018	0.007	84.720	-0.052	-0.052	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:ASP)