FMO DATABASE

FMODB ID: 223LR

Calculation Name: 3T5V-F-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3T5V

Chain ID: F

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:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
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	47
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-176617.099492
FMO2-HF: Nuclear repulsion	156258.747779
FMO2-HF: Total energy	-20358.351713
FMO2-MP2: Total energy	-20418.22602

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(F:30:GLU)

Summations of interaction energy for fragment #1(F:30: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.
179.336	184.235	0.706	-2.201	-3.404	-0.001

Interaction energy analysis for fragmet #1(F:30:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.996 / q_NPA : -1.012

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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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	F	32	ASP	-1	-0.971	-0.992	3.181	22.770	25.947	0.063	-1.426	-1.813	0.004
4	F	33	ASP	-1	-0.913	-0.945	2.494	30.143	31.744	0.644	-0.760	-1.485	-0.005
5	F	34	GLU	-1	-1.096	-1.033	4.415	24.404	24.525	-0.001	-0.015	-0.106	0.000
6	F	35	PHE	0	-0.088	-0.048	6.837	-1.632	-1.632	0.000	0.000	0.000	0.000
7	F	36	GLU	-1	-0.914	-0.953	10.436	19.252	19.252	0.000	0.000	0.000	0.000
8	F	37	ASP	-1	-0.942	-0.963	12.720	15.720	15.720	0.000	0.000	0.000	0.000
9	F	38	PHE	0	-0.050	-0.033	16.089	-0.542	-0.542	0.000	0.000	0.000	0.000
10	F	39	PRO	0	-0.067	-0.030	18.819	-0.579	-0.579	0.000	0.000	0.000	0.000
11	F	53	ALA	0	-0.031	-0.025	30.784	-0.014	-0.014	0.000	0.000	0.000	0.000
12	F	54	VAL	0	0.011	0.001	27.527	-0.119	-0.119	0.000	0.000	0.000	0.000
13	F	55	THR	0	-0.023	-0.008	29.977	-0.024	-0.024	0.000	0.000	0.000	0.000
14	F	56	GLN	0	0.047	0.002	27.741	0.252	0.252	0.000	0.000	0.000	0.000
15	F	57	THR	0	-0.050	-0.037	25.947	0.204	0.204	0.000	0.000	0.000	0.000
16	F	58	ASN	0	0.006	0.019	26.328	0.488	0.488	0.000	0.000	0.000	0.000
17	F	59	ILE	0	0.002	-0.001	20.624	-0.223	-0.223	0.000	0.000	0.000	0.000
18	F	60	TRP	0	-0.042	-0.004	19.196	0.428	0.428	0.000	0.000	0.000	0.000
19	F	61	GLU	-1	-0.924	-0.958	25.409	9.829	9.829	0.000	0.000	0.000	0.000
20	F	62	GLU	-1	-0.974	-1.000	27.907	9.408	9.408	0.000	0.000	0.000	0.000
21	F	63	ASN	0	0.016	-0.005	30.592	-0.127	-0.127	0.000	0.000	0.000	0.000
22	F	64	TRP	0	-0.004	0.002	26.681	0.125	0.125	0.000	0.000	0.000	0.000
23	F	65	ASP	-1	-0.978	-0.998	30.835	8.945	8.945	0.000	0.000	0.000	0.000
24	F	66	ASP	-1	-0.974	-0.962	33.313	7.789	7.789	0.000	0.000	0.000	0.000
25	F	67	VAL	0	-0.118	-0.041	33.660	-0.323	-0.323	0.000	0.000	0.000	0.000
26	F	68	GLU	-1	-0.869	-0.944	34.049	8.952	8.952	0.000	0.000	0.000	0.000
27	F	69	VAL	0	-0.098	-0.047	34.059	-0.274	-0.274	0.000	0.000	0.000	0.000
28	F	70	ASP	-1	-0.977	-0.991	36.010	7.672	7.672	0.000	0.000	0.000	0.000
29	F	71	ASP	-1	-0.831	-0.942	33.218	9.548	9.548	0.000	0.000	0.000	0.000
30	F	72	ASP	-1	-0.910	-0.940	35.081	8.343	8.343	0.000	0.000	0.000	0.000
31	F	73	PHE	0	0.043	0.028	32.037	-0.161	-0.161	0.000	0.000	0.000	0.000
32	F	74	THR	0	0.028	0.001	34.916	-0.202	-0.202	0.000	0.000	0.000	0.000
33	F	75	ASN	0	-0.015	-0.010	36.950	-0.257	-0.257	0.000	0.000	0.000	0.000
34	F	76	GLU	-1	-0.976	-0.985	36.609	8.417	8.417	0.000	0.000	0.000	0.000
35	F	77	LEU	0	-0.022	-0.006	34.961	-0.206	-0.206	0.000	0.000	0.000	0.000
36	F	78	LYS	1	0.941	0.969	39.177	-7.783	-7.783	0.000	0.000	0.000	0.000
37	F	79	ALA	0	0.010	0.010	42.361	-0.202	-0.202	0.000	0.000	0.000	0.000
38	F	80	GLU	-1	-0.930	-0.971	40.918	7.234	7.234	0.000	0.000	0.000	0.000
39	F	81	LEU	0	-0.025	-0.015	41.731	-0.174	-0.174	0.000	0.000	0.000	0.000
40	F	82	ASP	-1	-0.945	-0.973	44.664	6.439	6.439	0.000	0.000	0.000	0.000
41	F	83	ARG	1	0.816	0.911	42.893	-7.426	-7.426	0.000	0.000	0.000	0.000
42	F	84	TYR	0	0.098	0.057	45.815	-0.177	-0.177	0.000	0.000	0.000	0.000
43	F	85	LYS	1	0.953	0.969	47.868	-6.291	-6.291	0.000	0.000	0.000	0.000
44	F	86	ARG	1	0.903	0.941	49.620	-6.401	-6.401	0.000	0.000	0.000	0.000
45	F	87	GLU	-1	-1.006	-0.994	49.002	6.392	6.392	0.000	0.000	0.000	0.000
46	F	88	ASN	0	-0.061	-0.025	49.409	-0.174	-0.174	0.000	0.000	0.000	0.000
47	F	89	GLN	0	-0.091	-0.027	53.101	-0.107	-0.107	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(F:30:GLU)