FMO DATABASE

FMODB ID: YV812

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	OptH
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	-212550.208145
FMO2-HF: Nuclear repulsion	192681.118234
FMO2-HF: Total energy	-19869.08991
FMO2-MP2: Total energy	-19920.017514

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.
-20.769	-10.934	2.102	-5.571	-6.369	-0.04

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 : 0.948 / q_NPA : 0.978

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	-0.011	-0.013	2.664	-27.104	-21.288	0.923	-3.461	-3.279	-0.020
4	A	8	GLY	0	0.041	0.019	4.011	6.990	7.176	-0.001	-0.013	-0.172	0.000
5	A	9	LEU	0	-0.033	-0.021	4.276	-12.255	-12.111	-0.001	-0.030	-0.113	0.000
6	A	10	CYS	0	-0.027	-0.003	6.539	-1.521	-1.521	0.000	0.000	0.000	0.000
7	A	11	PRO	0	0.027	0.030	8.358	1.078	1.078	0.000	0.000	0.000	0.000
8	A	12	PRO	0	0.058	0.032	12.038	-0.094	-0.094	0.000	0.000	0.000	0.000
9	A	13	ARG	1	0.756	0.842	14.636	18.444	18.444	0.000	0.000	0.000	0.000
10	A	14	PRO	0	0.030	0.024	16.698	0.065	0.065	0.000	0.000	0.000	0.000
11	A	15	GLN	0	0.024	0.000	16.823	-0.276	-0.276	0.000	0.000	0.000	0.000
12	A	16	LYS	1	0.957	1.004	19.535	11.916	11.916	0.000	0.000	0.000	0.000
13	A	17	PRO	0	0.033	-0.010	21.089	-0.106	-0.106	0.000	0.000	0.000	0.000
14	A	18	CYS	0	-0.100	-0.064	16.539	-0.585	-0.585	0.000	0.000	0.000	0.000
15	A	19	VAL	0	0.024	0.033	17.697	0.232	0.232	0.000	0.000	0.000	0.000
16	A	20	LYS	1	1.003	0.990	14.333	17.206	17.206	0.000	0.000	0.000	0.000
17	A	21	GLU	-1	-0.889	-0.946	14.321	-17.365	-17.365	0.000	0.000	0.000	0.000
18	A	22	CYS	0	-0.050	-0.031	6.204	4.209	4.209	0.000	0.000	0.000	0.000
19	A	23	LYS	1	0.950	0.987	10.100	19.547	19.547	0.000	0.000	0.000	0.000
20	A	24	ASN	0	0.028	-0.011	5.598	-1.108	-1.108	0.000	0.000	0.000	0.000
21	A	25	ASP	-1	-0.666	-0.845	2.637	-56.535	-53.893	0.864	-1.714	-1.793	-0.020
22	A	26	ASP	-1	-0.908	-0.948	5.171	-30.602	-30.645	-0.001	-0.005	0.048	0.000
23	A	27	SER	0	-0.118	-0.050	6.754	2.621	2.621	0.000	0.000	0.000	0.000
24	A	28	CYS	0	-0.006	0.020	8.571	-0.491	-0.491	0.000	0.000	0.000	0.000
25	A	29	PRO	0	0.062	0.036	9.581	-1.116	-1.116	0.000	0.000	0.000	0.000
26	A	30	GLY	0	0.036	0.010	11.266	-0.940	-0.940	0.000	0.000	0.000	0.000
27	A	31	GLN	0	0.014	0.002	9.103	-1.454	-1.454	0.000	0.000	0.000	0.000
28	A	32	GLN	0	-0.033	-0.017	8.470	-3.311	-3.311	0.000	0.000	0.000	0.000
29	A	33	LYS	1	0.777	0.886	2.736	71.478	72.568	0.318	-0.348	-1.060	0.000
30	A	36	ASN	0	0.021	0.000	9.419	2.701	2.701	0.000	0.000	0.000	0.000
31	A	37	TYR	0	-0.047	-0.046	11.665	-0.995	-0.995	0.000	0.000	0.000	0.000
32	A	38	GLY	0	0.025	0.011	14.509	1.573	1.573	0.000	0.000	0.000	0.000
33	A	40	LYS	1	0.848	0.952	15.710	17.655	17.655	0.000	0.000	0.000	0.000
34	A	41	ASP	-1	-0.847	-0.915	12.141	-22.576	-22.576	0.000	0.000	0.000	0.000
35	A	42	GLU	-1	-0.768	-0.869	12.419	-17.138	-17.138	0.000	0.000	0.000	0.000
36	A	44	ARG	1	0.856	0.927	10.470	21.809	21.809	0.000	0.000	0.000	0.000
37	A	45	ASP	-1	-0.806	-0.898	10.333	-23.563	-23.563	0.000	0.000	0.000	0.000
38	A	46	PRO	0	-0.067	-0.026	7.640	-0.098	-0.098	0.000	0.000	0.000	0.000
39	A	47	ILE	0	0.030	0.010	9.323	2.655	2.655	0.000	0.000	0.000	0.000
40	A	48	PHE	0	-0.030	-0.019	7.727	-4.024	-4.024	0.000	0.000	0.000	0.000
41	A	49	VAL	0	-0.008	-0.008	8.678	2.210	2.210	0.000	0.000	0.000	0.000
42	A	50	GLY	0	0.022	0.026	10.887	0.099	0.099	0.000	0.000	0.000	0.000

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