FMO DATABASE

FMODB ID: Q1GNY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-217380.611681
FMO2-HF: Nuclear repulsion	193456.754129
FMO2-HF: Total energy	-23923.857552
FMO2-MP2: Total energy	-23994.243146

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.
102.074	104.497	-0.03	-1.36	-1.033	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 : -0.945 / q_NPA : -0.976

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	-0.028	-0.022	3.793	-2.840	-0.417	-0.030	-1.360	-1.033	0.003
4	C	26	LYS	1	0.939	0.977	6.529	-26.248	-26.248	0.000	0.000	0.000	0.000
5	C	27	LYS	1	0.955	0.973	9.459	-16.857	-16.857	0.000	0.000	0.000	0.000
6	C	28	SER	0	0.014	0.002	11.087	0.585	0.585	0.000	0.000	0.000	0.000
7	C	29	LEU	0	-0.051	-0.033	13.262	-0.683	-0.683	0.000	0.000	0.000	0.000
8	C	30	GLU	-1	-0.882	-0.933	16.225	16.397	16.397	0.000	0.000	0.000	0.000
9	C	31	GLU	-1	-0.997	-1.000	18.118	15.119	15.119	0.000	0.000	0.000	0.000
10	C	32	ASP	-1	-0.948	-0.973	20.312	12.028	12.028	0.000	0.000	0.000	0.000
11	C	33	ASP	-1	-0.920	-0.958	22.118	12.051	12.051	0.000	0.000	0.000	0.000
12	C	34	GLU	-1	-1.095	-1.025	24.042	10.440	10.440	0.000	0.000	0.000	0.000
13	C	35	PHE	0	-0.060	-0.038	26.452	-0.184	-0.184	0.000	0.000	0.000	0.000
14	C	36	GLU	-1	-0.916	-0.954	29.617	10.059	10.059	0.000	0.000	0.000	0.000
15	C	37	ASP	-1	-0.920	-0.963	30.983	8.432	8.432	0.000	0.000	0.000	0.000
16	C	38	PHE	0	-0.045	-0.022	34.260	-0.164	-0.164	0.000	0.000	0.000	0.000
17	C	39	PRO	0	-0.030	-0.029	37.535	-0.157	-0.157	0.000	0.000	0.000	0.000
18	C	40	ILE	0	-0.105	-0.044	40.264	-0.160	-0.160	0.000	0.000	0.000	0.000
19	C	41	ASP	-1	-0.941	-0.958	42.894	6.300	6.300	0.000	0.000	0.000	0.000
20	C	53	ALA	0	-0.007	-0.016	49.508	-0.013	-0.013	0.000	0.000	0.000	0.000
21	C	54	VAL	0	0.004	0.004	48.969	-0.033	-0.033	0.000	0.000	0.000	0.000
22	C	55	THR	0	0.028	-0.004	44.404	0.060	0.060	0.000	0.000	0.000	0.000
23	C	56	GLN	0	-0.057	-0.009	45.671	0.071	0.071	0.000	0.000	0.000	0.000
24	C	57	THR	0	-0.003	-0.007	42.708	-0.090	-0.090	0.000	0.000	0.000	0.000
25	C	58	ASN	0	-0.067	-0.036	43.469	0.070	0.070	0.000	0.000	0.000	0.000
26	C	59	ILE	0	0.013	-0.003	37.067	0.011	0.011	0.000	0.000	0.000	0.000
27	C	60	TRP	0	-0.034	-0.014	34.519	0.255	0.255	0.000	0.000	0.000	0.000
28	C	61	GLU	-1	-0.922	-0.960	39.134	7.435	7.435	0.000	0.000	0.000	0.000
29	C	62	GLU	-1	-0.938	-0.966	41.375	6.713	6.713	0.000	0.000	0.000	0.000
30	C	63	ASN	0	-0.042	-0.035	44.296	0.048	0.048	0.000	0.000	0.000	0.000
31	C	64	TRP	0	0.030	0.020	38.301	0.017	0.017	0.000	0.000	0.000	0.000
32	C	65	ASP	-1	-0.988	-0.998	41.540	7.142	7.142	0.000	0.000	0.000	0.000
33	C	66	ASP	-1	-0.961	-0.973	42.892	6.205	6.205	0.000	0.000	0.000	0.000
34	C	67	VAL	0	-0.048	-0.011	43.302	-0.087	-0.087	0.000	0.000	0.000	0.000
35	C	68	GLU	-1	-0.939	-0.953	43.778	6.586	6.586	0.000	0.000	0.000	0.000
36	C	69	VAL	0	-0.082	-0.056	40.479	-0.092	-0.092	0.000	0.000	0.000	0.000
37	C	70	ASP	-1	-0.918	-0.947	42.361	7.145	7.145	0.000	0.000	0.000	0.000
38	C	71	ASP	-1	-0.749	-0.869	36.747	8.405	8.405	0.000	0.000	0.000	0.000
39	C	72	ASP	-1	-0.922	-0.949	36.326	8.033	8.033	0.000	0.000	0.000	0.000
40	C	73	PHE	0	-0.008	-0.004	34.838	-0.088	-0.088	0.000	0.000	0.000	0.000
41	C	74	THR	0	-0.002	-0.033	36.899	-0.184	-0.184	0.000	0.000	0.000	0.000
42	C	75	ASN	0	-0.040	-0.037	40.048	-0.288	-0.288	0.000	0.000	0.000	0.000
43	C	76	GLU	-1	-0.947	-0.963	36.123	8.314	8.314	0.000	0.000	0.000	0.000
44	C	77	LEU	0	-0.026	-0.013	37.411	-0.145	-0.145	0.000	0.000	0.000	0.000
45	C	78	LYS	1	0.896	0.946	40.953	-7.033	-7.033	0.000	0.000	0.000	0.000
46	C	79	ALA	0	-0.002	0.005	42.900	-0.167	-0.167	0.000	0.000	0.000	0.000
47	C	80	GLU	-1	-0.884	-0.924	41.016	7.236	7.236	0.000	0.000	0.000	0.000
48	C	81	LEU	0	-0.023	-0.017	43.548	-0.147	-0.147	0.000	0.000	0.000	0.000
49	C	82	ASP	-1	-0.932	-0.969	46.142	6.063	6.063	0.000	0.000	0.000	0.000
50	C	83	ARG	1	0.783	0.878	41.523	-7.463	-7.463	0.000	0.000	0.000	0.000
51	C	84	TYR	0	0.057	0.035	46.075	-0.143	-0.143	0.000	0.000	0.000	0.000
52	C	85	LYS	1	0.979	0.986	48.002	-5.895	-5.895	0.000	0.000	0.000	0.000
53	C	86	ARG	1	0.882	0.925	50.310	-6.248	-6.248	0.000	0.000	0.000	0.000
54	C	87	GLU	-1	-0.960	-0.970	47.945	6.469	6.469	0.000	0.000	0.000	0.000
55	C	88	ASN	0	-0.116	-0.048	49.599	-0.107	-0.107	0.000	0.000	0.000	0.000
56	C	89	GLN	0	-0.054	-0.016	53.620	-0.099	-0.099	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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