FMO DATABASE

FMODB ID: VQLN1

Calculation Name: 3NGG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NGG

Chain ID: A

ChEMBL ID:

UniProt ID: P83952

Base Structure: X-ray

Registration Date: 2023-09-23

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	42
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-212930.430608
FMO2-HF: Nuclear repulsion	193061.049395
FMO2-HF: Total energy	-19869.381214
FMO2-MP2: Total energy	-19920.308662

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:5:LYS)

Summations of interaction energy for fragment #1(A:5:LYS)

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.
-44.728	-35.006	6.379	-7.559	-8.54	-0.07

Interaction energy analysis for fragmet #1(A:5:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.929 / q_NPA : 0.971

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	7	PRO	0	-0.029	-0.025	2.058	-38.676	-32.955	4.602	-5.372	-4.951	-0.046
4	A	8	GLY	0	0.041	0.021	3.525	8.252	8.525	0.001	0.013	-0.287	0.000
5	A	9	LEU	0	-0.037	-0.023	3.537	-15.611	-15.092	0.009	-0.240	-0.288	-0.002
6	A	10	CYS	0	-0.040	-0.009	5.902	-1.513	-1.513	0.000	0.000	0.000	0.000
7	A	11	PRO	0	0.040	0.035	7.912	1.278	1.278	0.000	0.000	0.000	0.000
8	A	12	PRO	0	0.042	0.032	11.534	-0.022	-0.022	0.000	0.000	0.000	0.000
9	A	13	ARG	1	0.789	0.869	14.112	18.835	18.835	0.000	0.000	0.000	0.000
10	A	14	PRO	0	0.037	0.025	16.403	0.085	0.085	0.000	0.000	0.000	0.000
11	A	15	GLN	0	0.021	-0.001	16.808	-0.344	-0.344	0.000	0.000	0.000	0.000
12	A	16	LYS	1	0.940	0.992	19.486	11.953	11.953	0.000	0.000	0.000	0.000
13	A	17	PRO	0	0.044	-0.001	21.118	-0.106	-0.106	0.000	0.000	0.000	0.000
14	A	18	CYS	0	-0.108	-0.072	16.378	-0.578	-0.578	0.000	0.000	0.000	0.000
15	A	19	VAL	0	0.020	0.035	17.713	0.253	0.253	0.000	0.000	0.000	0.000
16	A	20	LYS	1	0.923	0.934	13.226	18.311	18.311	0.000	0.000	0.000	0.000
17	A	21	GLU	-1	-0.879	-0.940	14.309	-17.758	-17.758	0.000	0.000	0.000	0.000
18	A	22	CYS	0	-0.059	-0.033	6.182	4.360	4.360	0.000	0.000	0.000	0.000
19	A	23	LYS	1	0.964	0.989	10.195	19.166	19.166	0.000	0.000	0.000	0.000
20	A	24	ASN	0	0.007	-0.030	5.304	0.552	0.552	0.000	0.000	0.000	0.000
21	A	25	ASP	-1	-0.690	-0.841	2.459	-59.889	-57.750	1.667	-1.671	-2.134	-0.022
22	A	26	ASP	-1	-0.892	-0.941	5.193	-31.409	-31.390	-0.001	-0.006	-0.011	0.000
23	A	27	SER	0	-0.072	-0.029	6.753	2.535	2.535	0.000	0.000	0.000	0.000
24	A	28	CYS	0	-0.010	0.020	8.586	-0.580	-0.580	0.000	0.000	0.000	0.000
25	A	29	PRO	0	0.063	0.036	9.592	-1.125	-1.125	0.000	0.000	0.000	0.000
26	A	30	GLY	0	0.032	0.008	11.284	-1.065	-1.065	0.000	0.000	0.000	0.000
27	A	31	GLN	0	0.018	-0.004	9.126	-2.084	-2.084	0.000	0.000	0.000	0.000
28	A	32	GLN	0	-0.042	-0.026	8.323	-3.755	-3.755	0.000	0.000	0.000	0.000
29	A	33	LYS	1	0.815	0.901	2.773	63.764	64.815	0.101	-0.283	-0.869	0.000
30	A	36	ASN	0	0.020	0.001	9.386	2.831	2.831	0.000	0.000	0.000	0.000
31	A	37	TYR	0	-0.031	-0.043	11.511	-1.124	-1.124	0.000	0.000	0.000	0.000
32	A	38	GLY	0	0.027	0.011	14.498	1.568	1.568	0.000	0.000	0.000	0.000
33	A	40	LYS	1	0.833	0.933	15.753	18.327	18.327	0.000	0.000	0.000	0.000
34	A	41	ASP	-1	-0.802	-0.870	12.052	-22.243	-22.243	0.000	0.000	0.000	0.000
35	A	42	GLU	-1	-0.770	-0.869	12.366	-17.540	-17.540	0.000	0.000	0.000	0.000
36	A	44	ARG	1	0.864	0.930	10.469	22.615	22.615	0.000	0.000	0.000	0.000
37	A	45	ASP	-1	-0.819	-0.898	10.285	-24.897	-24.897	0.000	0.000	0.000	0.000
38	A	46	PRO	0	-0.045	-0.013	7.026	0.060	0.060	0.000	0.000	0.000	0.000
39	A	47	ILE	0	0.018	0.005	8.615	3.029	3.029	0.000	0.000	0.000	0.000
40	A	48	PHE	0	-0.020	-0.014	7.147	-4.867	-4.867	0.000	0.000	0.000	0.000
41	A	49	VAL	0	-0.004	-0.008	8.295	2.507	2.507	0.000	0.000	0.000	0.000
42	A	50	GLY	0	0.021	0.025	10.371	0.177	0.177	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:LYS)