FMO DATABASE

FMODB ID: GNKG1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-275004.422431
FMO2-HF: Nuclear repulsion	249412.385625
FMO2-HF: Total energy	-25592.036805
FMO2-MP2: Total energy	-25667.489111

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.
-15.688	-10.901	14.294	-9.051	-10.032	0.031

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 : -0.870 / q_NPA : -0.943

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	LYS	1	0.768	0.848	1.900	-69.337	-67.115	7.476	-4.833	-4.866	0.063
4	A	5	GLU	-1	-0.842	-0.929	2.054	18.683	20.415	6.807	-4.018	-4.522	-0.032
5	A	6	LEU	0	0.055	0.047	3.118	-7.738	-7.041	0.012	-0.190	-0.519	0.000
6	A	7	PHE	0	0.032	-0.017	4.758	-4.969	-4.833	-0.001	-0.010	-0.125	0.000
7	A	8	ASP	-1	-0.767	-0.856	6.927	32.031	32.031	0.000	0.000	0.000	0.000
8	A	9	THR	0	-0.016	-0.019	6.549	-3.830	-3.830	0.000	0.000	0.000	0.000
9	A	10	VAL	0	-0.044	-0.023	8.963	-2.276	-2.276	0.000	0.000	0.000	0.000
10	A	11	ILE	0	0.030	0.015	10.988	-1.589	-1.589	0.000	0.000	0.000	0.000
11	A	12	ASN	0	-0.023	-0.010	12.275	-1.844	-1.844	0.000	0.000	0.000	0.000
12	A	13	LEU	0	-0.010	-0.002	12.359	-1.473	-1.473	0.000	0.000	0.000	0.000
13	A	14	GLU	-1	-0.927	-0.962	15.227	16.490	16.490	0.000	0.000	0.000	0.000
14	A	15	GLU	-1	-0.901	-0.941	15.686	17.189	17.189	0.000	0.000	0.000	0.000
15	A	16	GLN	0	-0.065	-0.036	15.340	-1.679	-1.679	0.000	0.000	0.000	0.000
16	A	17	ILE	0	0.006	0.005	19.289	-0.934	-0.934	0.000	0.000	0.000	0.000
17	A	18	GLY	0	0.024	0.010	21.183	-0.710	-0.710	0.000	0.000	0.000	0.000
18	A	19	SER	0	-0.023	-0.016	22.363	-0.857	-0.857	0.000	0.000	0.000	0.000
19	A	20	LEU	0	-0.006	0.003	22.597	-0.565	-0.565	0.000	0.000	0.000	0.000
20	A	21	TYR	0	-0.025	-0.004	25.282	-0.624	-0.624	0.000	0.000	0.000	0.000
21	A	22	ARG	1	0.916	0.957	25.209	-11.693	-11.693	0.000	0.000	0.000	0.000
22	A	23	GLN	0	-0.001	-0.003	25.533	-0.507	-0.507	0.000	0.000	0.000	0.000
23	A	24	LEU	0	-0.022	-0.004	29.475	-0.364	-0.364	0.000	0.000	0.000	0.000
24	A	25	GLY	0	-0.041	-0.027	31.323	-0.352	-0.352	0.000	0.000	0.000	0.000
25	A	26	ASP	-1	-0.833	-0.934	31.791	9.234	9.234	0.000	0.000	0.000	0.000
26	A	27	LEU	0	-0.025	-0.002	33.687	-0.306	-0.306	0.000	0.000	0.000	0.000
27	A	28	LYS	1	0.933	0.961	34.685	-8.904	-8.904	0.000	0.000	0.000	0.000
28	A	29	GLN	0	-0.060	-0.025	37.203	-0.029	-0.029	0.000	0.000	0.000	0.000
29	A	30	HIS	0	0.003	-0.007	37.803	-0.283	-0.283	0.000	0.000	0.000	0.000
30	A	31	ILE	0	-0.032	-0.014	37.543	-0.195	-0.195	0.000	0.000	0.000	0.000
31	A	32	GLY	0	-0.010	-0.003	41.235	-0.182	-0.182	0.000	0.000	0.000	0.000
32	A	33	GLU	-1	-0.845	-0.919	43.217	7.068	7.068	0.000	0.000	0.000	0.000
33	A	34	MET	0	0.026	0.016	44.313	-0.151	-0.151	0.000	0.000	0.000	0.000
34	A	35	ILE	0	-0.059	-0.031	43.575	-0.169	-0.169	0.000	0.000	0.000	0.000
35	A	36	GLU	-1	-0.880	-0.938	47.117	6.161	6.161	0.000	0.000	0.000	0.000
36	A	37	GLU	-1	-0.949	-0.967	48.440	6.178	6.178	0.000	0.000	0.000	0.000
37	A	38	ASN	0	0.022	-0.001	49.787	-0.229	-0.229	0.000	0.000	0.000	0.000
38	A	39	HIS	0	-0.061	-0.015	51.325	-0.126	-0.126	0.000	0.000	0.000	0.000
39	A	40	HIS	0	-0.009	-0.029	52.051	-0.255	-0.255	0.000	0.000	0.000	0.000
40	A	41	LEU	0	0.052	0.035	52.902	-0.146	-0.146	0.000	0.000	0.000	0.000
41	A	42	GLN	0	-0.070	-0.045	52.936	-0.183	-0.183	0.000	0.000	0.000	0.000
42	A	43	LEU	0	-0.070	-0.017	57.224	-0.130	-0.130	0.000	0.000	0.000	0.000
43	A	44	GLU	-1	-0.871	-0.937	59.236	5.127	5.127	0.000	0.000	0.000	0.000
44	A	45	ASN	0	0.011	0.001	59.724	-0.136	-0.136	0.000	0.000	0.000	0.000
45	A	46	LYS	1	0.887	0.938	58.584	-5.345	-5.345	0.000	0.000	0.000	0.000
46	A	47	HIS	0	0.020	0.017	63.673	-0.094	-0.094	0.000	0.000	0.000	0.000
47	A	48	LEU	0	0.005	-0.002	63.135	-0.101	-0.101	0.000	0.000	0.000	0.000
48	A	49	ARG	1	0.894	0.945	61.859	-5.002	-5.002	0.000	0.000	0.000	0.000
49	A	50	LYS	1	0.866	0.927	67.606	-4.395	-4.395	0.000	0.000	0.000	0.000
50	A	51	ARG	1	0.925	0.953	69.517	-4.336	-4.336	0.000	0.000	0.000	0.000
51	A	52	LEU	0	0.012	0.006	69.191	-0.074	-0.074	0.000	0.000	0.000	0.000
52	A	53	ASP	-1	-0.871	-0.924	71.521	4.346	4.346	0.000	0.000	0.000	0.000
53	A	54	ASP	-1	-0.868	-0.916	73.522	4.187	4.187	0.000	0.000	0.000	0.000
54	A	55	THR	0	-0.029	-0.028	75.052	-0.069	-0.069	0.000	0.000	0.000	0.000
55	A	56	THR	0	-0.025	-0.020	74.940	-0.057	-0.057	0.000	0.000	0.000	0.000
56	A	57	GLN	0	0.024	0.014	76.983	-0.080	-0.080	0.000	0.000	0.000	0.000
57	A	58	GLN	0	-0.061	-0.029	78.477	-0.020	-0.020	0.000	0.000	0.000	0.000
58	A	59	ILE	0	-0.007	0.001	78.418	-0.056	-0.056	0.000	0.000	0.000	0.000
59	A	60	GLU	-1	-0.953	-0.959	81.376	3.838	3.838	0.000	0.000	0.000	0.000
60	A	61	LYS	1	0.887	0.965	83.327	-3.773	-3.773	0.000	0.000	0.000	0.000
61	A	62	PHE	0	-0.074	-0.058	84.698	-0.053	-0.053	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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