FMO DATABASE

FMODB ID: 1NKYZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-212926.782818
FMO2-HF: Nuclear repulsion	193057.348469
FMO2-HF: Total energy	-19869.434349
FMO2-MP2: Total energy	-19920.389142

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.
-73.345	-66.577	14.34	-10.584	-10.523	-0.11

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 : 0.899 / q_NPA : 0.953

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	7	PRO	0	0.001	-0.006	1.779	-45.759	-45.102	11.825	-7.051	-5.431	-0.070
4	A	8	GLY	0	0.026	0.018	3.532	3.391	3.930	0.021	-0.134	-0.425	-0.002
5	A	9	LEU	0	-0.035	-0.021	2.539	-28.869	-26.739	0.741	-1.411	-1.460	-0.017
6	A	10	CYS	0	-0.053	-0.022	4.980	-2.209	-2.098	-0.002	-0.006	-0.103	0.000
7	A	11	PRO	0	0.049	0.041	7.478	1.462	1.462	0.000	0.000	0.000	0.000
8	A	12	PRO	0	0.022	0.021	11.019	0.063	0.063	0.000	0.000	0.000	0.000
9	A	13	ARG	1	0.811	0.881	13.806	19.012	19.012	0.000	0.000	0.000	0.000
10	A	14	PRO	0	0.042	0.025	16.126	-0.038	-0.038	0.000	0.000	0.000	0.000
11	A	15	GLN	0	-0.002	-0.014	16.802	-0.118	-0.118	0.000	0.000	0.000	0.000
12	A	16	LYS	1	0.938	0.986	19.191	12.329	12.329	0.000	0.000	0.000	0.000
13	A	17	PRO	0	0.066	0.017	20.801	-0.279	-0.279	0.000	0.000	0.000	0.000
14	A	18	CYS	0	-0.119	-0.059	16.577	-0.613	-0.613	0.000	0.000	0.000	0.000
15	A	19	VAL	0	0.030	0.027	17.736	0.413	0.413	0.000	0.000	0.000	0.000
16	A	20	LYS	1	0.879	0.903	12.922	18.458	18.458	0.000	0.000	0.000	0.000
17	A	21	GLU	-1	-0.847	-0.918	14.297	-17.913	-17.913	0.000	0.000	0.000	0.000
18	A	22	CYS	0	-0.036	-0.013	6.160	4.566	4.566	0.000	0.000	0.000	0.000
19	A	23	LYS	1	0.952	0.981	10.359	18.572	18.572	0.000	0.000	0.000	0.000
20	A	24	ASN	0	-0.009	-0.041	5.126	0.828	0.828	0.000	0.000	0.000	0.000
21	A	25	ASP	-1	-0.689	-0.833	2.471	-59.130	-56.936	1.648	-1.671	-2.171	-0.022
22	A	26	ASP	-1	-0.880	-0.932	5.213	-31.026	-31.024	-0.001	-0.004	0.003	0.000
23	A	27	SER	0	-0.056	-0.018	7.109	2.489	2.489	0.000	0.000	0.000	0.000
24	A	28	CYS	0	-0.003	0.014	8.896	-0.684	-0.684	0.000	0.000	0.000	0.000
25	A	29	PRO	0	0.038	0.023	9.987	-1.089	-1.089	0.000	0.000	0.000	0.000
26	A	30	GLY	0	0.036	0.010	11.795	-0.990	-0.990	0.000	0.000	0.000	0.000
27	A	31	GLN	0	0.016	-0.005	9.298	-2.263	-2.263	0.000	0.000	0.000	0.000
28	A	32	GLN	0	-0.041	-0.025	8.262	-4.014	-4.014	0.000	0.000	0.000	0.000
29	A	33	LYS	1	0.835	0.902	2.709	61.000	62.135	0.108	-0.307	-0.936	0.001
30	A	36	ASN	0	0.035	0.012	9.269	2.714	2.714	0.000	0.000	0.000	0.000
31	A	37	TYR	0	-0.034	-0.041	11.378	-1.129	-1.129	0.000	0.000	0.000	0.000
32	A	38	GLY	0	0.042	0.015	14.492	1.448	1.448	0.000	0.000	0.000	0.000
33	A	40	LYS	1	0.809	0.915	15.785	18.122	18.122	0.000	0.000	0.000	0.000
34	A	41	ASP	-1	-0.825	-0.884	11.982	-21.830	-21.830	0.000	0.000	0.000	0.000
35	A	42	GLU	-1	-0.757	-0.861	12.431	-17.613	-17.613	0.000	0.000	0.000	0.000
36	A	44	ARG	1	0.839	0.917	10.288	22.725	22.725	0.000	0.000	0.000	0.000
37	A	45	ASP	-1	-0.800	-0.890	9.811	-25.640	-25.640	0.000	0.000	0.000	0.000
38	A	46	PRO	0	-0.040	-0.006	6.424	0.163	0.163	0.000	0.000	0.000	0.000
39	A	47	ILE	0	0.020	0.006	7.954	3.109	3.109	0.000	0.000	0.000	0.000
40	A	48	PHE	0	-0.018	-0.019	6.934	-6.008	-6.008	0.000	0.000	0.000	0.000
41	A	49	VAL	0	-0.006	0.002	7.729	3.045	3.045	0.000	0.000	0.000	0.000
42	A	50	GLY	0	0.014	0.016	9.691	-0.040	-0.040	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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