FMO DATABASE

FMODB ID: 72YMK

Calculation Name: 5GNJ-G-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5GNJ

Chain ID: G

ChEMBL ID:

UniProt ID: Q39204

Base Structure: X-ray

Registration Date: 2023-06-22

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	73
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-356028.862701
FMO2-HF: Nuclear repulsion	327068.600113
FMO2-HF: Total energy	-28960.262588
FMO2-MP2: Total energy	-29045.954884

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(G:452:ASN)

Summations of interaction energy for fragment #1(G:452:ASN)

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.
-7.115	-29.166	24.796	5.348	-8.096	0.016

Interaction energy analysis for fragmet #1(G:452:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.019 / q_NPA : 0.019

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	G	454	VAL	0	0.021	-0.005	2.641	10.213	-0.302	0.086	11.531	-1.103	-0.004
4	G	455	GLU	-1	-0.915	-0.971	2.062	-4.389	-3.379	1.725	-1.052	-1.684	-0.002
5	G	456	ALA	0	0.035	0.000	1.765	-5.454	-16.371	22.696	-6.929	-4.851	0.019
6	G	457	GLU	-1	-0.772	-0.858	2.906	0.629	-1.000	0.289	1.798	-0.458	0.003
7	G	458	ARG	1	0.908	0.954	6.039	-2.380	-2.380	0.000	0.000	0.000	0.000
8	G	459	GLN	0	0.025	0.022	5.539	-0.498	-0.498	0.000	0.000	0.000	0.000
9	G	460	ARG	1	0.888	0.936	7.494	-2.070	-2.070	0.000	0.000	0.000	0.000
10	G	461	ARG	1	0.840	0.900	9.479	-2.014	-2.014	0.000	0.000	0.000	0.000
11	G	462	GLU	-1	-0.834	-0.914	10.977	0.088	0.088	0.000	0.000	0.000	0.000
12	G	463	LYS	1	0.976	1.000	11.956	-0.222	-0.222	0.000	0.000	0.000	0.000
13	G	464	LEU	0	0.006	0.004	13.731	-0.084	-0.084	0.000	0.000	0.000	0.000
14	G	465	ASN	0	0.040	0.003	15.534	-0.060	-0.060	0.000	0.000	0.000	0.000
15	G	466	GLN	0	-0.021	0.001	14.732	-0.051	-0.051	0.000	0.000	0.000	0.000
16	G	467	ARG	1	0.883	0.918	16.565	-0.138	-0.138	0.000	0.000	0.000	0.000
17	G	468	PHE	0	0.027	0.011	19.347	-0.004	-0.004	0.000	0.000	0.000	0.000
18	G	469	TYR	0	0.008	0.007	21.716	-0.013	-0.013	0.000	0.000	0.000	0.000
19	G	470	ALA	0	0.021	0.006	22.998	-0.019	-0.019	0.000	0.000	0.000	0.000
20	G	471	LEU	0	0.009	0.010	24.530	-0.012	-0.012	0.000	0.000	0.000	0.000
21	G	472	ARG	1	0.846	0.904	26.042	-0.214	-0.214	0.000	0.000	0.000	0.000
22	G	473	ALA	0	-0.042	-0.006	27.961	-0.009	-0.009	0.000	0.000	0.000	0.000
23	G	474	VAL	0	-0.025	-0.005	28.792	-0.014	-0.014	0.000	0.000	0.000	0.000
24	G	475	VAL	0	-0.023	0.001	30.624	-0.004	-0.004	0.000	0.000	0.000	0.000
25	G	476	PRO	0	0.026	0.015	32.995	0.002	0.002	0.000	0.000	0.000	0.000
26	G	477	ASN	0	-0.019	-0.011	36.103	0.003	0.003	0.000	0.000	0.000	0.000
27	G	478	VAL	0	0.053	0.038	31.218	0.010	0.010	0.000	0.000	0.000	0.000
28	G	479	SER	0	-0.001	-0.008	31.022	0.012	0.012	0.000	0.000	0.000	0.000
29	G	480	LYS	1	0.945	0.958	30.493	-0.116	-0.116	0.000	0.000	0.000	0.000
30	G	481	MET	0	-0.006	0.018	30.914	0.007	0.007	0.000	0.000	0.000	0.000
31	G	482	ASP	-1	-0.722	-0.842	27.758	0.319	0.319	0.000	0.000	0.000	0.000
32	G	483	LYS	1	0.871	0.941	19.092	-0.500	-0.500	0.000	0.000	0.000	0.000
33	G	484	ALA	0	-0.004	-0.009	25.760	-0.006	-0.006	0.000	0.000	0.000	0.000
34	G	485	SER	0	0.002	-0.031	27.755	-0.018	-0.018	0.000	0.000	0.000	0.000
35	G	486	LEU	0	-0.054	-0.001	25.787	-0.013	-0.013	0.000	0.000	0.000	0.000
36	G	487	LEU	0	0.002	-0.009	24.019	-0.012	-0.012	0.000	0.000	0.000	0.000
37	G	488	GLY	0	0.004	0.008	28.418	-0.013	-0.013	0.000	0.000	0.000	0.000
38	G	489	ASP	-1	-0.831	-0.929	31.908	0.150	0.150	0.000	0.000	0.000	0.000
39	G	490	ALA	0	-0.041	-0.012	29.695	-0.016	-0.016	0.000	0.000	0.000	0.000
40	G	491	ILE	0	-0.024	-0.015	29.845	-0.014	-0.014	0.000	0.000	0.000	0.000
41	G	492	ALA	0	0.001	0.002	33.071	-0.012	-0.012	0.000	0.000	0.000	0.000
42	G	493	TYR	0	0.019	0.006	33.872	-0.013	-0.013	0.000	0.000	0.000	0.000
43	G	494	ILE	0	0.005	-0.005	30.913	-0.012	-0.012	0.000	0.000	0.000	0.000
44	G	495	ASN	0	-0.028	-0.034	35.522	-0.014	-0.014	0.000	0.000	0.000	0.000
45	G	496	GLU	-1	-0.902	-0.943	38.532	0.072	0.072	0.000	0.000	0.000	0.000
46	G	497	LEU	0	-0.007	-0.001	36.259	-0.008	-0.008	0.000	0.000	0.000	0.000
47	G	498	LYS	1	0.877	0.934	36.523	-0.117	-0.117	0.000	0.000	0.000	0.000
48	G	499	SER	0	0.009	0.014	40.741	-0.007	-0.007	0.000	0.000	0.000	0.000
49	G	500	LYS	1	0.973	0.988	43.398	-0.048	-0.048	0.000	0.000	0.000	0.000
50	G	501	VAL	0	-0.008	0.009	41.440	-0.006	-0.006	0.000	0.000	0.000	0.000
51	G	502	VAL	0	0.028	0.012	44.504	-0.005	-0.005	0.000	0.000	0.000	0.000
52	G	503	LYS	1	0.921	0.976	46.886	-0.049	-0.049	0.000	0.000	0.000	0.000
53	G	504	THR	0	-0.023	-0.029	47.538	-0.003	-0.003	0.000	0.000	0.000	0.000
54	G	505	GLU	-1	-0.851	-0.914	46.967	0.020	0.020	0.000	0.000	0.000	0.000
55	G	506	SER	0	-0.017	-0.004	50.090	-0.002	-0.002	0.000	0.000	0.000	0.000
56	G	507	GLU	-1	-0.890	-0.964	52.416	0.036	0.036	0.000	0.000	0.000	0.000
57	G	508	LYS	1	0.858	0.919	49.464	-0.018	-0.018	0.000	0.000	0.000	0.000
58	G	509	LEU	0	-0.005	0.003	54.408	-0.003	-0.003	0.000	0.000	0.000	0.000
59	G	510	GLN	0	-0.018	-0.002	56.109	0.000	0.000	0.000	0.000	0.000	0.000
60	G	511	ILE	0	0.025	0.004	56.761	-0.002	-0.002	0.000	0.000	0.000	0.000
61	G	512	LYS	1	0.864	0.933	57.288	-0.012	-0.012	0.000	0.000	0.000	0.000
62	G	513	ASN	0	-0.012	-0.030	59.369	-0.003	-0.003	0.000	0.000	0.000	0.000
63	G	514	GLN	0	0.005	0.008	62.046	0.001	0.001	0.000	0.000	0.000	0.000
64	G	515	LEU	0	-0.014	0.003	60.865	-0.001	-0.001	0.000	0.000	0.000	0.000
65	G	516	GLU	-1	-0.875	-0.923	62.862	0.003	0.003	0.000	0.000	0.000	0.000
66	G	517	GLU	-1	-0.865	-0.933	65.100	0.010	0.010	0.000	0.000	0.000	0.000
67	G	518	VAL	0	0.023	0.016	66.990	-0.001	-0.001	0.000	0.000	0.000	0.000
68	G	519	LYS	1	0.817	0.902	64.433	-0.002	-0.002	0.000	0.000	0.000	0.000
69	G	520	LEU	0	-0.039	-0.027	68.721	-0.001	-0.001	0.000	0.000	0.000	0.000
70	G	521	GLU	-1	-0.920	-0.954	71.228	0.008	0.008	0.000	0.000	0.000	0.000
71	G	522	LEU	0	-0.063	-0.027	70.688	-0.001	-0.001	0.000	0.000	0.000	0.000
72	G	523	ALA	0	-0.076	-0.030	72.485	-0.001	-0.001	0.000	0.000	0.000	0.000
73	G	524	GLY	0	-0.011	0.005	74.473	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(G:452:ASN)