FMO DATABASE

FMODB ID: Z6NJN

Calculation Name: 4N9G-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4N9G

Chain ID: C

ChEMBL ID:

UniProt ID:

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:

Apendix: None

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	35
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-137044.086671
FMO2-HF: Nuclear repulsion	122775.190694
FMO2-HF: Total energy	-14268.895977
FMO2-MP2: Total energy	-14309.460044

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(C:63:ARG)

Summations of interaction energy for fragment #1(C:63:ARG)

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.
-124.747	-115.433	13.535	-11.737	-11.112	-0.143

Interaction energy analysis for fragmet #1(C:63:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.879 / q_NPA : 0.920

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	C	65	SER	0	0.043	0.014	3.335	1.699	3.777	0.054	-0.702	-1.429	0.002
4	C	66	GLU	-1	-0.855	-0.906	2.690	-26.339	-25.021	0.269	-0.502	-1.085	-0.003
5	C	67	LEU	0	0.060	0.037	4.262	3.291	3.680	0.000	-0.089	-0.300	0.000
6	C	68	LEU	0	-0.014	-0.014	5.956	3.418	3.418	0.000	0.000	0.000	0.000
7	C	69	SER	0	-0.050	-0.049	6.861	2.990	2.990	0.000	0.000	0.000	0.000
8	C	70	LYS	1	0.913	0.952	7.152	25.706	25.706	0.000	0.000	0.000	0.000
9	C	71	ILE	0	-0.003	-0.004	9.169	1.655	1.655	0.000	0.000	0.000	0.000
10	C	72	ASN	0	-0.029	-0.025	11.958	1.975	1.975	0.000	0.000	0.000	0.000
11	C	73	ASP	-1	-0.917	-0.947	13.067	-17.079	-17.079	0.000	0.000	0.000	0.000
12	C	74	MET	0	0.000	0.017	13.167	1.067	1.067	0.000	0.000	0.000	0.000
13	C	75	PRO	0	-0.015	0.004	16.484	0.352	0.352	0.000	0.000	0.000	0.000
14	C	76	ILE	0	-0.016	-0.007	16.265	0.494	0.494	0.000	0.000	0.000	0.000
15	C	77	THR	0	0.041	0.007	20.648	-0.222	-0.222	0.000	0.000	0.000	0.000
16	C	78	ASN	0	0.074	0.021	19.896	-0.727	-0.727	0.000	0.000	0.000	0.000
17	C	79	ASP	-1	-0.848	-0.916	19.224	-14.481	-14.481	0.000	0.000	0.000	0.000
18	C	80	GLN	0	0.033	0.002	18.544	-0.987	-0.987	0.000	0.000	0.000	0.000
19	C	81	LYS	1	0.852	0.946	15.538	14.805	14.805	0.000	0.000	0.000	0.000
20	C	82	LYS	1	0.843	0.922	14.475	13.525	13.525	0.000	0.000	0.000	0.000
21	C	83	LEU	0	-0.013	0.015	14.963	-1.041	-1.041	0.000	0.000	0.000	0.000
22	C	84	MET	0	0.053	0.022	12.261	-0.753	-0.753	0.000	0.000	0.000	0.000
23	C	85	SER	0	-0.014	-0.023	10.562	-2.394	-2.394	0.000	0.000	0.000	0.000
24	C	86	ASN	0	-0.033	-0.036	10.412	-2.811	-2.811	0.000	0.000	0.000	0.000
25	C	87	ASP	-1	-0.828	-0.915	11.410	-22.821	-22.821	0.000	0.000	0.000	0.000
26	C	88	VAL	0	-0.009	0.003	5.366	-2.316	-2.316	0.000	0.000	0.000	0.000
27	C	89	LEU	0	-0.015	-0.018	6.499	-5.254	-5.254	0.000	0.000	0.000	0.000
28	C	90	LYS	1	0.843	0.925	7.233	21.124	21.124	0.000	0.000	0.000	0.000
29	C	91	PHE	0	0.011	0.003	5.399	0.355	0.355	0.000	0.000	0.000	0.000
30	C	92	ALA	0	-0.045	-0.022	2.581	-4.383	-3.446	0.415	-0.422	-0.930	0.001
31	C	93	ALA	0	0.043	0.028	3.485	-2.205	-2.004	0.005	0.036	-0.242	0.000
32	C	94	GLU	-1	-0.893	-0.931	6.551	-22.974	-22.974	0.000	0.000	0.000	0.000
33	C	95	ALA	0	-0.042	-0.020	3.405	2.774	2.967	0.003	-0.048	-0.148	0.000
34	C	96	GLU	-1	-0.861	-0.921	1.757	-124.887	-120.689	12.789	-10.010	-6.978	-0.143
35	C	97	LYS	1	0.777	0.895	6.193	31.697	31.697	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(C:63:ARG)