FMO DATABASE

FMODB ID: LZ3N9

Calculation Name: 1XDT-R-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1XDT

Chain ID: R

ChEMBL ID:

UniProt ID: P00588

Base Structure: X-ray

Registration Date: 2023-09-19

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	38
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-181421.120045
FMO2-HF: Nuclear repulsion	163558.156144
FMO2-HF: Total energy	-17862.963901
FMO2-MP2: Total energy	-17910.446368

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(R:107:PRO)

Summations of interaction energy for fragment #1(R:107:PRO)

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.
-23.011	-14.079	5.585	-5.234	-9.283	0.016

Interaction energy analysis for fragmet #1(R:107:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.035 / q_NPA : 0.010

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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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	R	109	LEU	0	0.002	0.017	3.523	-3.062	-0.196	0.012	-1.329	-1.550	0.002
4	R	110	ARG	1	0.931	0.957	2.229	-17.182	-15.106	4.109	-2.546	-3.638	0.023
5	R	111	LYS	1	0.947	0.980	3.391	0.062	0.468	0.011	-0.080	-0.337	0.000
6	R	112	TYR	0	0.022	0.003	2.594	-0.912	0.168	0.405	-0.314	-1.171	0.000
7	R	113	LYS	1	0.903	0.941	6.107	-0.354	-0.354	0.000	0.000	0.000	0.000
8	R	114	ASP	-1	-0.814	-0.881	8.222	0.230	0.230	0.000	0.000	0.000	0.000
9	R	115	PHE	0	0.026	0.014	8.362	-0.075	-0.075	0.000	0.000	0.000	0.000
10	R	116	CYS	0	-0.054	0.004	8.600	-0.072	-0.072	0.000	0.000	0.000	0.000
11	R	117	ILE	0	0.002	0.003	11.989	0.067	0.067	0.000	0.000	0.000	0.000
12	R	118	HIS	1	0.887	0.955	15.646	0.005	0.005	0.000	0.000	0.000	0.000
13	R	119	GLY	0	0.087	0.035	14.398	-0.026	-0.026	0.000	0.000	0.000	0.000
14	R	120	GLU	-1	-0.860	-0.900	10.798	0.284	0.284	0.000	0.000	0.000	0.000
15	R	122	LYS	1	0.850	0.911	6.192	0.056	0.056	0.000	0.000	0.000	0.000
16	R	123	TYR	0	-0.057	-0.026	2.714	-3.062	-0.658	1.049	-0.954	-2.499	-0.009
17	R	124	VAL	0	0.046	0.029	4.659	-0.022	0.078	-0.001	-0.011	-0.088	0.000
18	R	125	LYS	1	0.851	0.896	6.537	0.748	0.748	0.000	0.000	0.000	0.000
19	R	126	GLU	-1	-0.805	-0.898	7.284	-0.691	-0.691	0.000	0.000	0.000	0.000
20	R	127	LEU	0	0.017	0.014	9.943	0.069	0.069	0.000	0.000	0.000	0.000
21	R	128	ARG	1	0.914	0.966	7.305	1.122	1.122	0.000	0.000	0.000	0.000
22	R	129	ALA	0	0.052	0.042	6.944	-0.146	-0.146	0.000	0.000	0.000	0.000
23	R	130	PRO	0	-0.045	-0.029	5.188	-0.231	-0.231	0.000	0.000	0.000	0.000
24	R	131	SER	0	-0.011	-0.008	6.208	0.211	0.211	0.000	0.000	0.000	0.000
25	R	133	ILE	0	0.032	0.013	11.367	0.014	0.014	0.000	0.000	0.000	0.000
26	R	134	CYS	0	-0.096	-0.024	13.695	0.082	0.082	0.000	0.000	0.000	0.000
27	R	135	HIS	0	0.005	-0.010	14.788	-0.015	-0.015	0.000	0.000	0.000	0.000
28	R	136	PRO	0	0.019	-0.013	18.810	-0.015	-0.015	0.000	0.000	0.000	0.000
29	R	137	GLY	0	0.048	0.037	22.483	0.009	0.009	0.000	0.000	0.000	0.000
30	R	138	TYR	0	-0.033	-0.017	19.660	-0.001	-0.001	0.000	0.000	0.000	0.000
31	R	139	HIS	0	-0.020	-0.024	19.619	-0.014	-0.014	0.000	0.000	0.000	0.000
32	R	140	GLY	0	0.035	0.016	18.491	0.012	0.012	0.000	0.000	0.000	0.000
33	R	141	GLU	-1	-0.875	-0.944	14.413	-0.197	-0.197	0.000	0.000	0.000	0.000
34	R	142	ARG	1	0.858	0.899	13.040	0.054	0.054	0.000	0.000	0.000	0.000
35	R	144	HIS	0	0.036	0.014	16.599	0.028	0.028	0.000	0.000	0.000	0.000
36	R	145	GLY	0	0.016	0.017	18.962	0.019	0.019	0.000	0.000	0.000	0.000
37	R	146	LEU	0	-0.007	-0.009	21.757	0.000	0.000	0.000	0.000	0.000	0.000
38	R	147	SER	0	0.013	0.019	24.517	-0.006	-0.006	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(R:107:PRO)