FMO DATABASE

FMODB ID: VRYL1

Calculation Name: 3QOQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3QOQ

Chain ID: A

ChEMBL ID:

UniProt ID: G3XCY4

Base Structure: X-ray

Registration Date: 2023-03-14

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	50
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-220601.398739
FMO2-HF: Nuclear repulsion	200377.539484
FMO2-HF: Total energy	-20223.859255
FMO2-MP2: Total energy	-20282.029152

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(A:10:THR)

Summations of interaction energy for fragment #1(A:10: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.
-5.622	-2.842	-0.029	-1.408	-1.343	0

Interaction energy analysis for fragmet #1(A:10:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.002 / 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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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].
3	A	12	SER	0	0.010	0.013	3.828	-2.177	0.470	-0.028	-1.373	-1.246
4	A	13	SER	0	0.071	0.016	6.017	-0.747	-0.747	0.000	0.000	0.000
5	A	14	ARG	1	0.956	0.970	7.773	-1.843	-1.843	0.000	0.000	0.000
6	A	15	THR	0	-0.011	0.001	4.408	0.316	0.449	-0.001	-0.035	-0.097
7	A	16	ALA	0	0.011	0.024	7.522	-0.336	-0.336	0.000	0.000	0.000
8	A	17	ASP	-1	-0.835	-0.880	9.630	-0.159	-0.159	0.000	0.000	0.000
9	A	18	LYS	1	0.800	0.893	11.143	-0.397	-0.397	0.000	0.000	0.000
10	A	19	PHE	0	0.040	0.011	15.666	-0.055	-0.055	0.000	0.000	0.000
11	A	20	VAL	0	-0.056	-0.019	19.134	0.023	0.023	0.000	0.000	0.000
12	A	21	VAL	0	0.049	0.026	22.498	-0.021	-0.021	0.000	0.000	0.000
13	A	22	ARG	1	0.921	0.949	24.924	-0.063	-0.063	0.000	0.000	0.000
14	A	23	LEU	0	-0.001	0.003	26.844	-0.006	-0.006	0.000	0.000	0.000
15	A	24	PRO	0	0.052	0.023	30.218	-0.002	-0.002	0.000	0.000	0.000
16	A	25	GLU	-1	-0.891	-0.949	33.705	0.076	0.076	0.000	0.000	0.000
17	A	26	GLY	0	-0.015	-0.007	35.619	-0.001	-0.001	0.000	0.000	0.000
18	A	27	MET	0	0.038	0.026	30.491	0.002	0.002	0.000	0.000	0.000
19	A	28	ARG	1	0.958	0.971	25.830	-0.185	-0.185	0.000	0.000	0.000
20	A	29	GLU	-1	-0.809	-0.891	30.499	0.165	0.165	0.000	0.000	0.000
21	A	30	GLN	0	0.056	0.039	33.054	0.004	0.004	0.000	0.000	0.000
22	A	31	ILE	0	-0.004	-0.008	26.227	0.006	0.006	0.000	0.000	0.000
23	A	32	ALA	0	-0.034	-0.016	28.546	0.014	0.014	0.000	0.000	0.000
24	A	33	GLU	-1	-0.922	-0.964	29.589	0.135	0.135	0.000	0.000	0.000
25	A	34	VAL	0	0.005	0.008	28.678	0.002	0.002	0.000	0.000	0.000
26	A	35	ALA	0	-0.019	-0.010	25.551	0.007	0.007	0.000	0.000	0.000
27	A	36	ARG	1	0.803	0.876	27.000	-0.157	-0.157	0.000	0.000	0.000
28	A	37	SER	0	-0.026	0.001	29.137	0.003	0.003	0.000	0.000	0.000
29	A	38	HIS	0	-0.055	-0.037	26.643	-0.011	-0.011	0.000	0.000	0.000
30	A	39	HIS	0	-0.039	-0.006	26.132	0.027	0.027	0.000	0.000	0.000
31	A	40	ARG	1	0.885	0.936	21.575	-0.215	-0.215	0.000	0.000	0.000
32	A	41	SER	0	0.005	0.002	19.135	-0.021	-0.021	0.000	0.000	0.000
33	A	42	MET	0	0.058	0.007	21.846	-0.012	-0.012	0.000	0.000	0.000
34	A	43	ASN	0	-0.046	-0.017	16.223	-0.008	-0.008	0.000	0.000	0.000
35	A	44	SER	0	0.085	0.025	17.468	-0.017	-0.017	0.000	0.000	0.000
36	A	45	GLU	-1	-0.807	-0.860	19.316	0.194	0.194	0.000	0.000	0.000
37	A	46	ILE	0	-0.002	-0.004	21.242	-0.023	-0.023	0.000	0.000	0.000
38	A	47	ILE	0	-0.001	-0.003	16.414	-0.027	-0.027	0.000	0.000	0.000
39	A	48	ALA	0	0.031	0.020	19.628	-0.029	-0.029	0.000	0.000	0.000
40	A	49	ARG	1	0.885	0.929	21.580	-0.181	-0.181	0.000	0.000	0.000
41	A	50	LEU	0	-0.010	-0.003	20.754	-0.022	-0.022	0.000	0.000	0.000
42	A	51	GLU	-1	-0.934	-0.965	17.735	0.208	0.208	0.000	0.000	0.000
43	A	52	GLN	0	-0.048	-0.027	20.882	-0.012	-0.012	0.000	0.000	0.000
44	A	53	SER	0	-0.009	-0.017	24.280	-0.017	-0.017	0.000	0.000	0.000
45	A	54	LEU	0	-0.020	-0.020	20.994	-0.014	-0.014	0.000	0.000	0.000
46	A	55	LEU	0	-0.008	-0.006	20.656	-0.019	-0.019	0.000	0.000	0.000
47	A	56	GLN	0	-0.052	-0.016	24.193	0.002	0.002	0.000	0.000	0.000
48	A	57	GLU	-1	-0.962	-0.973	26.879	-0.008	-0.008	0.000	0.000	0.000
49	A	58	GLY	0	-0.042	-0.006	25.067	-0.011	-0.011	0.000	0.000	0.000
50	A	59	ALA	0	-0.059	-0.017	26.138	-0.010	-0.010	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:10:THR)