FMO DATABASE

FMODB ID: V5531

Calculation Name: 5GNA-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5GNA

Chain ID: B

ChEMBL ID:

UniProt ID: P16328

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	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	56
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-222134.290043
FMO2-HF: Nuclear repulsion	199388.56051
FMO2-HF: Total energy	-22745.729533
FMO2-MP2: Total energy	-22810.254256

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(B:412:ASN)

Summations of interaction energy for fragment #1(B:412: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.
-4.331	-3.266	0.001	-0.52	-0.545	0.003

Interaction energy analysis for fragmet #1(B:412:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / q_NPA : -0.009

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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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	B	414	THR	0	0.034	0.003	3.836	-2.429	-1.364	0.001	-0.520	-0.545	0.003
4	B	415	LEU	0	0.123	0.056	6.347	0.604	0.604	0.000	0.000	0.000	0.000
5	B	416	LYS	1	0.955	0.983	8.242	-0.321	-0.321	0.000	0.000	0.000	0.000
6	B	417	SER	0	0.012	0.002	8.353	-0.094	-0.094	0.000	0.000	0.000	0.000
7	B	418	LEU	0	0.054	0.029	5.358	-0.114	-0.114	0.000	0.000	0.000	0.000
8	B	419	THR	0	-0.006	-0.016	9.693	-0.229	-0.229	0.000	0.000	0.000	0.000
9	B	420	LYS	1	0.927	0.958	12.827	-0.897	-0.897	0.000	0.000	0.000	0.000
10	B	421	GLN	0	-0.010	0.001	8.951	-0.087	-0.087	0.000	0.000	0.000	0.000
11	B	422	TYR	0	0.025	0.016	13.554	-0.114	-0.114	0.000	0.000	0.000	0.000
12	B	423	LEU	0	0.016	0.002	15.164	-0.109	-0.109	0.000	0.000	0.000	0.000
13	B	424	SER	0	0.009	0.017	17.446	-0.084	-0.084	0.000	0.000	0.000	0.000
14	B	425	VAL	0	-0.010	-0.014	16.254	-0.071	-0.071	0.000	0.000	0.000	0.000
15	B	426	SER	0	0.019	0.002	19.014	-0.075	-0.075	0.000	0.000	0.000	0.000
16	B	427	ASN	0	0.006	0.004	20.985	-0.061	-0.061	0.000	0.000	0.000	0.000
17	B	428	SER	0	0.021	0.018	22.173	-0.035	-0.035	0.000	0.000	0.000	0.000
18	B	429	ILE	0	-0.025	0.000	21.000	-0.048	-0.048	0.000	0.000	0.000	0.000
19	B	430	ASP	-1	-0.877	-0.935	24.754	0.399	0.399	0.000	0.000	0.000	0.000
20	B	431	GLU	-1	-0.958	-0.982	26.589	0.425	0.425	0.000	0.000	0.000	0.000
21	B	432	THR	0	-0.074	-0.058	26.718	-0.034	-0.034	0.000	0.000	0.000	0.000
22	B	433	VAL	0	0.000	-0.004	28.354	-0.031	-0.031	0.000	0.000	0.000	0.000
23	B	434	ALA	0	-0.023	-0.010	30.779	-0.028	-0.028	0.000	0.000	0.000	0.000
24	B	435	ARG	1	0.928	0.975	28.698	-0.401	-0.401	0.000	0.000	0.000	0.000
25	B	436	TYR	0	0.019	0.003	29.891	-0.019	-0.019	0.000	0.000	0.000	0.000
26	B	437	LYS	1	0.978	0.997	33.167	-0.290	-0.290	0.000	0.000	0.000	0.000
27	B	438	ALA	0	0.010	0.025	36.907	-0.016	-0.016	0.000	0.000	0.000	0.000
28	B	439	GLN	0	0.013	-0.004	37.961	-0.010	-0.010	0.000	0.000	0.000	0.000
29	B	440	PHE	0	0.007	0.003	39.008	-0.010	-0.010	0.000	0.000	0.000	0.000
30	B	441	THR	0	0.020	-0.002	40.782	-0.013	-0.013	0.000	0.000	0.000	0.000
31	B	442	GLN	0	-0.038	-0.011	41.809	-0.004	-0.004	0.000	0.000	0.000	0.000
32	B	443	LEU	0	0.002	-0.001	41.665	-0.009	-0.009	0.000	0.000	0.000	0.000
33	B	444	ASP	-1	-0.908	-0.938	44.919	0.142	0.142	0.000	0.000	0.000	0.000
34	B	445	THR	0	-0.013	-0.026	46.778	-0.010	-0.010	0.000	0.000	0.000	0.000
35	B	446	MET	0	-0.066	-0.034	48.189	-0.006	-0.006	0.000	0.000	0.000	0.000
36	B	447	MET	0	0.022	0.002	47.535	-0.008	-0.008	0.000	0.000	0.000	0.000
37	B	448	SER	0	0.031	0.018	50.858	-0.008	-0.008	0.000	0.000	0.000	0.000
38	B	449	LYS	1	0.898	0.946	52.763	-0.122	-0.122	0.000	0.000	0.000	0.000
39	B	450	LEU	0	0.035	0.014	52.077	-0.005	-0.005	0.000	0.000	0.000	0.000
40	B	451	ASN	0	0.012	0.035	55.546	-0.006	-0.006	0.000	0.000	0.000	0.000
41	B	452	ASN	0	-0.017	-0.014	57.652	-0.005	-0.005	0.000	0.000	0.000	0.000
42	B	453	THR	0	0.027	0.008	57.810	-0.003	-0.003	0.000	0.000	0.000	0.000
43	B	454	SER	0	0.007	-0.004	58.450	-0.003	-0.003	0.000	0.000	0.000	0.000
44	B	455	SER	0	-0.002	0.021	61.098	-0.005	-0.005	0.000	0.000	0.000	0.000
45	B	456	TYR	0	0.008	-0.002	63.321	-0.003	-0.003	0.000	0.000	0.000	0.000
46	B	457	LEU	0	0.022	-0.011	60.852	-0.003	-0.003	0.000	0.000	0.000	0.000
47	B	458	THR	0	-0.022	-0.012	64.577	-0.002	-0.002	0.000	0.000	0.000	0.000
48	B	459	GLN	0	-0.020	-0.016	66.878	-0.004	-0.004	0.000	0.000	0.000	0.000
49	B	460	GLN	0	-0.021	-0.001	67.499	-0.003	-0.003	0.000	0.000	0.000	0.000
50	B	461	PHE	0	0.025	0.029	68.035	-0.002	-0.002	0.000	0.000	0.000	0.000
51	B	462	THR	0	-0.017	-0.008	69.973	-0.002	-0.002	0.000	0.000	0.000	0.000
52	B	463	ALA	0	0.007	-0.006	72.754	-0.002	-0.002	0.000	0.000	0.000	0.000
53	B	464	MET	0	-0.033	-0.017	70.990	-0.002	-0.002	0.000	0.000	0.000	0.000
54	B	465	ASN	0	-0.028	-0.022	72.165	-0.001	-0.001	0.000	0.000	0.000	0.000
55	B	466	LYS	1	0.836	0.947	75.775	-0.063	-0.063	0.000	0.000	0.000	0.000
56	B	467	SER	0	0.012	0.006	78.795	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:412:ASN)