FMO DATABASE

FMODB ID: K3L23

Calculation Name: 3T5V-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3T5V

Chain ID: C

ChEMBL ID:

UniProt ID: P46674

Base Structure: X-ray

Registration Date: 2023-06-19

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	56
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-217346.264351
FMO2-HF: Nuclear repulsion	193422.043555
FMO2-HF: Total energy	-23924.220795
FMO2-MP2: Total energy	-23994.636143

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:23:GLU)

Summations of interaction energy for fragment #1(C:23:GLU)

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.
102.844	104.58	-0.015	-0.913	-0.808	0.003

Interaction energy analysis for fragmet #1(C:23:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.931 / q_NPA : -0.968

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	25	ASN	0	-0.020	-0.021	3.878	-0.975	0.761	-0.015	-0.913	-0.808	0.003
4	C	26	LYS	1	0.945	0.977	6.369	-25.712	-25.712	0.000	0.000	0.000	0.000
5	C	27	LYS	1	0.947	0.966	9.529	-16.548	-16.548	0.000	0.000	0.000	0.000
6	C	28	SER	0	0.024	0.009	11.255	0.264	0.264	0.000	0.000	0.000	0.000
7	C	29	LEU	0	-0.081	-0.041	13.121	-0.716	-0.716	0.000	0.000	0.000	0.000
8	C	30	GLU	-1	-0.840	-0.896	15.706	16.281	16.281	0.000	0.000	0.000	0.000
9	C	31	GLU	-1	-1.006	-1.015	18.263	14.774	14.774	0.000	0.000	0.000	0.000
10	C	32	ASP	-1	-0.949	-0.979	20.460	11.898	11.898	0.000	0.000	0.000	0.000
11	C	33	ASP	-1	-0.934	-0.966	22.222	11.965	11.965	0.000	0.000	0.000	0.000
12	C	34	GLU	-1	-1.072	-1.025	24.230	10.381	10.381	0.000	0.000	0.000	0.000
13	C	35	PHE	0	-0.075	-0.045	26.419	-0.179	-0.179	0.000	0.000	0.000	0.000
14	C	36	GLU	-1	-0.928	-0.960	29.819	9.784	9.784	0.000	0.000	0.000	0.000
15	C	37	ASP	-1	-0.923	-0.955	30.913	8.260	8.260	0.000	0.000	0.000	0.000
16	C	38	PHE	0	-0.017	-0.013	34.150	-0.152	-0.152	0.000	0.000	0.000	0.000
17	C	39	PRO	0	-0.047	-0.035	37.171	-0.213	-0.213	0.000	0.000	0.000	0.000
18	C	40	ILE	0	-0.104	-0.039	39.958	-0.165	-0.165	0.000	0.000	0.000	0.000
19	C	41	ASP	-1	-0.954	-0.971	42.784	6.365	6.365	0.000	0.000	0.000	0.000
20	C	53	ALA	0	0.011	-0.009	49.695	-0.001	-0.001	0.000	0.000	0.000	0.000
21	C	54	VAL	0	-0.009	-0.001	49.156	-0.030	-0.030	0.000	0.000	0.000	0.000
22	C	55	THR	0	0.025	-0.001	44.354	0.039	0.039	0.000	0.000	0.000	0.000
23	C	56	GLN	0	-0.046	-0.006	45.725	0.102	0.102	0.000	0.000	0.000	0.000
24	C	57	THR	0	-0.015	-0.013	42.999	-0.093	-0.093	0.000	0.000	0.000	0.000
25	C	58	ASN	0	-0.071	-0.034	43.662	0.066	0.066	0.000	0.000	0.000	0.000
26	C	59	ILE	0	-0.001	-0.013	37.274	0.017	0.017	0.000	0.000	0.000	0.000
27	C	60	TRP	0	-0.013	-0.006	34.780	0.278	0.278	0.000	0.000	0.000	0.000
28	C	61	GLU	-1	-0.911	-0.956	39.558	7.460	7.460	0.000	0.000	0.000	0.000
29	C	62	GLU	-1	-0.932	-0.968	41.527	6.758	6.758	0.000	0.000	0.000	0.000
30	C	63	ASN	0	-0.045	-0.027	44.262	-0.013	-0.013	0.000	0.000	0.000	0.000
31	C	64	TRP	0	0.030	0.018	38.625	0.004	0.004	0.000	0.000	0.000	0.000
32	C	65	ASP	-1	-0.961	-0.976	41.596	7.233	7.233	0.000	0.000	0.000	0.000
33	C	66	ASP	-1	-0.958	-0.972	43.196	6.172	6.172	0.000	0.000	0.000	0.000
34	C	67	VAL	0	-0.062	-0.023	43.261	-0.120	-0.120	0.000	0.000	0.000	0.000
35	C	68	GLU	-1	-0.971	-0.975	43.489	6.621	6.621	0.000	0.000	0.000	0.000
36	C	69	VAL	0	-0.055	-0.038	40.606	-0.065	-0.065	0.000	0.000	0.000	0.000
37	C	70	ASP	-1	-0.931	-0.951	42.785	7.110	7.110	0.000	0.000	0.000	0.000
38	C	71	ASP	-1	-0.756	-0.868	36.877	8.441	8.441	0.000	0.000	0.000	0.000
39	C	72	ASP	-1	-0.922	-0.948	36.682	7.997	7.997	0.000	0.000	0.000	0.000
40	C	73	PHE	0	-0.017	-0.005	35.001	-0.070	-0.070	0.000	0.000	0.000	0.000
41	C	74	THR	0	0.007	-0.033	37.119	-0.178	-0.178	0.000	0.000	0.000	0.000
42	C	75	ASN	0	-0.041	-0.038	40.184	-0.328	-0.328	0.000	0.000	0.000	0.000
43	C	76	GLU	-1	-0.972	-0.981	36.463	8.268	8.268	0.000	0.000	0.000	0.000
44	C	77	LEU	0	-0.004	-0.001	37.884	-0.142	-0.142	0.000	0.000	0.000	0.000
45	C	78	LYS	1	0.882	0.937	41.271	-7.074	-7.074	0.000	0.000	0.000	0.000
46	C	79	ALA	0	-0.024	-0.010	43.331	-0.173	-0.173	0.000	0.000	0.000	0.000
47	C	80	GLU	-1	-0.894	-0.932	41.066	7.280	7.280	0.000	0.000	0.000	0.000
48	C	81	LEU	0	0.008	0.005	43.769	-0.139	-0.139	0.000	0.000	0.000	0.000
49	C	82	ASP	-1	-0.827	-0.915	46.283	5.934	5.934	0.000	0.000	0.000	0.000
50	C	83	ARG	1	0.833	0.906	41.147	-7.516	-7.516	0.000	0.000	0.000	0.000
51	C	84	TYR	0	0.058	0.037	46.223	-0.137	-0.137	0.000	0.000	0.000	0.000
52	C	85	LYS	1	0.854	0.916	48.185	-6.077	-6.077	0.000	0.000	0.000	0.000
53	C	86	ARG	1	0.867	0.927	50.576	-6.261	-6.261	0.000	0.000	0.000	0.000
54	C	87	GLU	-1	-0.916	-0.943	48.316	6.463	6.463	0.000	0.000	0.000	0.000
55	C	88	ASN	0	-0.123	-0.064	49.756	-0.144	-0.144	0.000	0.000	0.000	0.000
56	C	89	GLN	0	-0.097	-0.036	53.640	-0.150	-0.150	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(C:23:GLU)