FMO DATABASE

FMODB ID: N1Y1Q

Calculation Name: 3O6Q-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3O6Q

Chain ID: B

ChEMBL ID:

UniProt ID: O34853

Base Structure: X-ray

Registration Date: 2023-06-20

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	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	43
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-142516.166365
FMO2-HF: Nuclear repulsion	125112.630891
FMO2-HF: Total energy	-17403.535475
FMO2-MP2: Total energy	-17454.548727

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(B:9:CYM)

Summations of interaction energy for fragment #1(B:9:CYM)

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.
-98.615	-95.703	-0.032	-1.556	-1.324	0.008

Interaction energy analysis for fragmet #1(B:9:CYM)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.915 / q_NPA : -0.952

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	B	11	PRO	0	-0.008	0.012	3.772	-7.613	-4.701	-0.032	-1.556	-1.324	0.008
4	B	12	ARG	1	0.804	0.884	6.097	-34.049	-34.049	0.000	0.000	0.000	0.000
5	B	13	ALA	0	-0.002	-0.004	9.459	-0.328	-0.328	0.000	0.000	0.000	0.000
6	B	14	ALA	0	0.049	0.023	12.895	-0.421	-0.421	0.000	0.000	0.000	0.000
7	B	15	LYS	1	0.959	0.965	15.740	-13.972	-13.972	0.000	0.000	0.000	0.000
8	B	16	PRO	0	-0.019	0.011	15.480	-0.617	-0.617	0.000	0.000	0.000	0.000
9	B	17	PHE	0	0.021	0.008	17.994	-0.642	-0.642	0.000	0.000	0.000	0.000
10	B	18	LYS	1	0.955	0.966	18.265	-14.580	-14.580	0.000	0.000	0.000	0.000
11	B	19	ILE	0	0.037	0.014	20.995	-0.640	-0.640	0.000	0.000	0.000	0.000
12	B	20	LEU	0	-0.003	0.015	21.814	0.448	0.448	0.000	0.000	0.000	0.000
13	B	21	LYS	1	0.990	0.989	23.158	-11.928	-11.928	0.000	0.000	0.000	0.000
14	B	22	LYS	1	0.978	0.978	24.249	-10.312	-10.312	0.000	0.000	0.000	0.000
15	B	23	ARG	1	0.911	0.958	26.838	-10.138	-10.138	0.000	0.000	0.000	0.000
16	B	24	SER	0	-0.015	-0.018	28.711	-0.070	-0.070	0.000	0.000	0.000	0.000
17	B	25	THR	0	0.034	0.013	32.185	-0.100	-0.100	0.000	0.000	0.000	0.000
18	B	26	THR	0	0.031	0.033	32.651	-0.157	-0.157	0.000	0.000	0.000	0.000
19	B	27	SER	0	-0.024	-0.016	33.525	0.217	0.217	0.000	0.000	0.000	0.000
20	B	28	VAL	0	0.029	0.012	32.788	-0.165	-0.165	0.000	0.000	0.000	0.000
21	B	29	ALA	0	0.033	0.038	35.163	0.046	0.046	0.000	0.000	0.000	0.000
22	B	30	SER	0	0.023	0.005	33.394	0.190	0.190	0.000	0.000	0.000	0.000
23	B	31	TYR	0	-0.012	-0.015	30.810	-0.176	-0.176	0.000	0.000	0.000	0.000
24	B	32	GLN	0	0.016	-0.002	32.962	-0.244	-0.244	0.000	0.000	0.000	0.000
25	B	33	VAL	0	-0.023	0.010	33.375	0.060	0.060	0.000	0.000	0.000	0.000
26	B	34	SER	0	0.015	0.018	35.297	-0.320	-0.320	0.000	0.000	0.000	0.000
27	B	35	PRO	0	0.105	0.011	37.768	0.076	0.076	0.000	0.000	0.000	0.000
28	B	36	HIS	0	-0.005	0.009	37.310	-0.150	-0.150	0.000	0.000	0.000	0.000
29	B	37	THR	0	0.065	0.019	33.679	-0.020	-0.020	0.000	0.000	0.000	0.000
30	B	38	ALA	0	-0.010	0.005	36.113	0.103	0.103	0.000	0.000	0.000	0.000
31	B	39	ARG	1	0.963	0.976	37.674	-7.247	-7.247	0.000	0.000	0.000	0.000
32	B	40	ILE	0	0.016	0.025	35.187	-0.031	-0.031	0.000	0.000	0.000	0.000
33	B	41	PHE	0	-0.035	-0.025	30.706	0.075	0.075	0.000	0.000	0.000	0.000
34	B	42	LYS	1	0.789	0.866	35.756	-8.092	-8.092	0.000	0.000	0.000	0.000
35	B	43	GLU	-1	-0.787	-0.858	39.033	7.151	7.151	0.000	0.000	0.000	0.000
36	B	44	ASN	0	-0.019	-0.018	34.558	-0.103	-0.103	0.000	0.000	0.000	0.000
37	B	45	GLU	-1	-0.817	-0.881	36.072	8.179	8.179	0.000	0.000	0.000	0.000
38	B	46	ARG	1	0.842	0.881	37.366	-7.283	-7.283	0.000	0.000	0.000	0.000
39	B	47	LEU	0	0.036	0.034	39.768	-0.110	-0.110	0.000	0.000	0.000	0.000
40	B	48	ILE	0	-0.077	-0.048	33.958	0.021	0.021	0.000	0.000	0.000	0.000
41	B	49	ASP	-1	-0.968	-0.992	38.147	7.696	7.696	0.000	0.000	0.000	0.000
42	B	50	GLU	-1	-0.980	-0.974	40.424	6.830	6.830	0.000	0.000	0.000	0.000
43	B	51	TYR	0	-0.120	-0.037	40.126	-0.199	-0.199	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(B:9:CYM)