FMO DATABASE

FMODB ID: R9548

Calculation Name: 3FBN-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3FBN

Chain ID: C

ChEMBL ID:

UniProt ID: P38633

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	48
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-206615.125736
FMO2-HF: Nuclear repulsion	187146.620205
FMO2-HF: Total energy	-19468.505531
FMO2-MP2: Total energy	-19524.917056

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:16:THR)

Summations of interaction energy for fragment #1(C:16:THR)

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.
-0.066	2.409	-0.015	-1.412	-1.048	0.006

Interaction energy analysis for fragmet #1(C:16:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.049 / q_NPA : 0.026

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	18	PRO	0	0.005	-0.004	3.891	0.588	3.063	-0.015	-1.412	-1.048	0.006
4	C	19	SER	0	0.039	0.016	6.949	0.295	0.295	0.000	0.000	0.000	0.000
5	C	20	TYR	0	0.013	-0.010	7.824	-0.082	-0.082	0.000	0.000	0.000	0.000
6	C	21	VAL	0	0.054	0.031	7.669	-0.087	-0.087	0.000	0.000	0.000	0.000
7	C	22	LYS	1	0.951	0.990	10.402	-0.638	-0.638	0.000	0.000	0.000	0.000
8	C	23	PHE	0	-0.001	-0.006	12.135	-0.051	-0.051	0.000	0.000	0.000	0.000
9	C	24	PHE	0	0.002	0.012	13.349	-0.056	-0.056	0.000	0.000	0.000	0.000
10	C	25	THR	0	0.002	0.004	15.543	-0.024	-0.024	0.000	0.000	0.000	0.000
11	C	26	GLN	0	0.075	0.027	17.620	-0.031	-0.031	0.000	0.000	0.000	0.000
12	C	27	SER	0	0.123	0.074	20.674	-0.011	-0.011	0.000	0.000	0.000	0.000
13	C	28	ASN	0	-0.093	-0.046	18.452	-0.023	-0.023	0.000	0.000	0.000	0.000
14	C	29	LEU	0	0.027	0.009	18.246	-0.016	-0.016	0.000	0.000	0.000	0.000
15	C	30	GLU	-1	-0.900	-0.960	22.086	0.064	0.064	0.000	0.000	0.000	0.000
16	C	31	LYS	1	0.811	0.887	23.144	-0.119	-0.119	0.000	0.000	0.000	0.000
17	C	32	LEU	0	-0.040	-0.002	21.481	-0.007	-0.007	0.000	0.000	0.000	0.000
18	C	33	PRO	0	0.005	-0.001	25.203	-0.007	-0.007	0.000	0.000	0.000	0.000
19	C	34	LYS	1	1.025	1.013	28.382	-0.032	-0.032	0.000	0.000	0.000	0.000
20	C	35	TYR	0	-0.090	-0.071	24.397	-0.001	-0.001	0.000	0.000	0.000	0.000
21	C	36	LYS	1	0.884	0.937	22.550	0.015	0.015	0.000	0.000	0.000	0.000
22	C	37	GLU	-1	-0.882	-0.935	28.656	0.003	0.003	0.000	0.000	0.000	0.000
23	C	38	LYS	1	0.935	0.969	31.455	-0.036	-0.036	0.000	0.000	0.000	0.000
24	C	39	LYS	1	0.838	0.913	25.400	-0.007	-0.007	0.000	0.000	0.000	0.000
25	C	40	ALA	0	-0.026	0.009	31.335	-0.004	-0.004	0.000	0.000	0.000	0.000
26	C	41	ALA	0	-0.023	-0.008	34.167	-0.001	-0.001	0.000	0.000	0.000	0.000
27	C	60	THR	0	-0.031	-0.027	22.271	0.000	0.000	0.000	0.000	0.000	0.000
28	C	61	CYS	0	-0.067	-0.021	21.905	0.012	0.012	0.000	0.000	0.000	0.000
29	C	62	ALA	0	0.045	0.005	18.530	-0.003	-0.003	0.000	0.000	0.000	0.000
30	C	63	LEU	0	0.028	0.004	18.730	0.004	0.004	0.000	0.000	0.000	0.000
31	C	64	ASP	-1	-0.695	-0.822	20.765	0.015	0.015	0.000	0.000	0.000	0.000
32	C	65	TYR	0	-0.031	-0.012	14.714	-0.011	-0.011	0.000	0.000	0.000	0.000
33	C	66	LEU	0	-0.024	0.006	16.600	-0.013	-0.013	0.000	0.000	0.000	0.000
34	C	67	ILE	0	-0.018	-0.025	18.943	-0.011	-0.011	0.000	0.000	0.000	0.000
35	C	68	PRO	0	0.007	0.011	19.310	-0.004	-0.004	0.000	0.000	0.000	0.000
36	C	69	PRO	0	0.019	0.021	17.115	0.017	0.017	0.000	0.000	0.000	0.000
37	C	70	PRO	0	0.003	0.002	20.268	-0.010	-0.010	0.000	0.000	0.000	0.000
38	C	71	MET	0	0.016	-0.003	22.062	-0.020	-0.020	0.000	0.000	0.000	0.000
39	C	72	PRO	0	-0.007	-0.004	20.611	0.016	0.016	0.000	0.000	0.000	0.000
40	C	73	LYS	1	0.975	0.983	23.439	0.070	0.070	0.000	0.000	0.000	0.000
41	C	74	ASN	0	-0.001	0.010	23.578	0.015	0.015	0.000	0.000	0.000	0.000
42	C	75	GLN	0	0.057	0.030	24.125	-0.021	-0.021	0.000	0.000	0.000	0.000
43	C	76	GLN	0	0.007	0.001	20.816	0.018	0.018	0.000	0.000	0.000	0.000
44	C	77	TYR	0	0.038	0.009	18.097	-0.019	-0.019	0.000	0.000	0.000	0.000
45	C	78	ARG	1	0.867	0.935	22.040	0.122	0.122	0.000	0.000	0.000	0.000
46	C	79	ALA	0	0.023	0.016	22.496	0.013	0.013	0.000	0.000	0.000	0.000
47	C	80	PHE	0	0.016	0.008	22.675	0.008	0.008	0.000	0.000	0.000	0.000
48	C	81	GLY	0	-0.004	0.010	26.804	0.004	0.004	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(C:16:THR)