FMO DATABASE

FMODB ID: 6N6GZ

Calculation Name: 2Z5H-T-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2Z5H

Chain ID: T

ChEMBL ID:

UniProt ID: P03069

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	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	34
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-125177.767493
FMO2-HF: Nuclear repulsion	111145.684009
FMO2-HF: Total energy	-14032.083484
FMO2-MP2: Total energy	-14074.084189

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(T:66:ILE)

Summations of interaction energy for fragment #1(T:66:ILE)

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.
-14.886	-13.606	8.015	-2.874	-6.422	0.016

Interaction energy analysis for fragmet #1(T:66:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : 0.002

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	T	68	LYS	1	1.036	1.011	3.855	-3.444	-1.616	0.008	-0.842	-0.994	0.001
4	T	69	LYN	0	0.019	-0.002	2.185	-5.955	-6.886	7.970	-2.583	-4.457	0.015
5	T	70	ARG	1	0.935	0.989	3.648	-3.969	-3.759	0.038	0.563	-0.811	0.000
6	T	71	GLN	0	0.078	0.025	4.745	-0.681	-0.508	-0.001	-0.012	-0.160	0.000
7	T	72	ASN	0	-0.052	-0.023	6.025	-0.317	-0.317	0.000	0.000	0.000	0.000
8	T	73	LYS	1	0.774	0.889	7.342	-0.838	-0.838	0.000	0.000	0.000	0.000
9	T	74	ASP	-1	-0.825	-0.914	9.110	0.642	0.642	0.000	0.000	0.000	0.000
10	T	75	LEU	0	-0.004	-0.007	10.675	-0.104	-0.104	0.000	0.000	0.000	0.000
11	T	76	ILE	0	0.013	0.008	11.079	-0.114	-0.114	0.000	0.000	0.000	0.000
12	T	77	GLU	-1	-0.805	-0.895	13.016	0.249	0.249	0.000	0.000	0.000	0.000
13	T	78	LEU	0	-0.039	-0.022	14.794	-0.059	-0.059	0.000	0.000	0.000	0.000
14	T	79	GLN	0	-0.007	-0.006	16.413	-0.050	-0.050	0.000	0.000	0.000	0.000
15	T	80	ALA	0	-0.008	-0.021	16.924	-0.040	-0.040	0.000	0.000	0.000	0.000
16	T	81	LEU	0	0.036	0.019	18.667	-0.038	-0.038	0.000	0.000	0.000	0.000
17	T	82	ILE	0	-0.014	0.018	20.201	-0.017	-0.017	0.000	0.000	0.000	0.000
18	T	83	ASH	0	-0.075	-0.057	21.160	-0.026	-0.026	0.000	0.000	0.000	0.000
19	T	84	SER	0	0.010	-0.003	23.567	-0.019	-0.019	0.000	0.000	0.000	0.000
20	T	85	HIS	1	0.883	0.942	24.847	-0.195	-0.195	0.000	0.000	0.000	0.000
21	T	86	PHE	0	-0.002	0.003	26.634	-0.005	-0.005	0.000	0.000	0.000	0.000
22	T	87	GLU	-1	-0.920	-0.943	28.803	0.082	0.082	0.000	0.000	0.000	0.000
23	T	88	ALA	0	0.075	0.026	29.805	-0.006	-0.006	0.000	0.000	0.000	0.000
24	T	89	ARG	1	0.722	0.842	31.251	-0.116	-0.116	0.000	0.000	0.000	0.000
25	T	90	ARG	1	0.871	0.917	32.961	-0.088	-0.088	0.000	0.000	0.000	0.000
26	T	91	LYS	1	0.811	0.894	34.443	-0.069	-0.069	0.000	0.000	0.000	0.000
27	T	92	GLU	-1	-0.844	-0.912	35.894	0.093	0.093	0.000	0.000	0.000	0.000
28	T	93	GLU	-1	-0.844	-0.914	37.545	0.091	0.091	0.000	0.000	0.000	0.000
29	T	94	GLU	-1	-0.855	-0.906	38.208	0.067	0.067	0.000	0.000	0.000	0.000
30	T	95	GLU	-1	-0.799	-0.901	40.384	0.052	0.052	0.000	0.000	0.000	0.000
31	T	96	LEU	0	-0.059	-0.023	41.392	-0.003	-0.003	0.000	0.000	0.000	0.000
32	T	97	VAL	0	-0.045	-0.015	43.855	-0.002	-0.002	0.000	0.000	0.000	0.000
33	T	98	ALA	0	-0.036	-0.008	44.940	-0.003	-0.003	0.000	0.000	0.000	0.000
34	T	99	LEU	0	-0.090	-0.028	46.066	-0.004	-0.004	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(T:66:ILE)