FMO DATABASE

FMODB ID: YV8Z2

Calculation Name: 3HFO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3HFO

Chain ID: A

ChEMBL ID:

UniProt ID: P74112

Base Structure: X-ray

Registration Date: 2023-09-23

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	65
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-356420.007832
FMO2-HF: Nuclear repulsion	331887.556137
FMO2-HF: Total energy	-24532.451695
FMO2-MP2: Total energy	-24605.949874

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:5:ASP)

Summations of interaction energy for fragment #1(A:5:ASP)

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.
-31.306	-29.123	-0.018	-1.059	-1.106	0.006

Interaction energy analysis for fragmet #1(A:5:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.907 / q_NPA : -0.956

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].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	7	GLY	0	0.048	0.016	3.860	-2.464	-0.281	-0.018	-1.059	-1.106	0.006
4	A	8	LEU	0	-0.006	-0.001	5.823	-3.516	-3.516	0.000	0.000	0.000	0.000
5	A	9	PRO	0	0.039	0.022	7.074	-1.279	-1.279	0.000	0.000	0.000	0.000
6	A	10	SER	0	0.038	0.005	8.355	-0.417	-0.417	0.000	0.000	0.000	0.000
7	A	11	VAL	0	0.061	0.044	11.674	-0.714	-0.714	0.000	0.000	0.000	0.000
8	A	12	ARG	1	0.931	0.967	6.011	-38.056	-38.056	0.000	0.000	0.000	0.000
9	A	13	GLN	0	0.022	0.003	9.351	1.857	1.857	0.000	0.000	0.000	0.000
10	A	14	VAL	0	0.054	0.026	11.662	-1.072	-1.072	0.000	0.000	0.000	0.000
11	A	15	GLN	0	0.029	0.015	12.362	-1.247	-1.247	0.000	0.000	0.000	0.000
12	A	16	LEU	0	-0.055	-0.027	9.842	-0.393	-0.393	0.000	0.000	0.000	0.000
13	A	17	LEU	0	0.004	0.006	13.925	-1.039	-1.039	0.000	0.000	0.000	0.000
14	A	18	ILE	0	-0.023	0.007	17.023	-0.883	-0.883	0.000	0.000	0.000	0.000
15	A	19	LYS	1	0.746	0.857	13.375	-20.287	-20.287	0.000	0.000	0.000	0.000
16	A	20	ASP	-1	-0.829	-0.897	15.776	18.020	18.020	0.000	0.000	0.000	0.000
17	A	21	GLN	0	-0.021	-0.018	18.994	-0.974	-0.974	0.000	0.000	0.000	0.000
18	A	22	THR	0	-0.024	0.001	19.078	-0.275	-0.275	0.000	0.000	0.000	0.000
19	A	23	PRO	0	0.014	0.009	21.297	-0.048	-0.048	0.000	0.000	0.000	0.000
20	A	24	VAL	0	-0.006	-0.011	20.479	0.402	0.402	0.000	0.000	0.000	0.000
21	A	25	GLU	-1	-0.796	-0.862	23.457	10.694	10.694	0.000	0.000	0.000	0.000
22	A	26	ILE	0	-0.009	-0.020	22.795	0.738	0.738	0.000	0.000	0.000	0.000
23	A	27	LYS	1	0.828	0.937	24.830	-11.100	-11.100	0.000	0.000	0.000	0.000
24	A	28	LEU	0	0.045	0.010	25.918	0.419	0.419	0.000	0.000	0.000	0.000
25	A	29	LEU	0	-0.022	-0.026	26.473	-0.143	-0.143	0.000	0.000	0.000	0.000
26	A	30	THR	0	-0.063	-0.061	29.535	-0.084	-0.084	0.000	0.000	0.000	0.000
27	A	31	GLY	0	0.012	0.018	31.360	-0.268	-0.268	0.000	0.000	0.000	0.000
28	A	32	ASP	-1	-0.867	-0.891	32.103	9.049	9.049	0.000	0.000	0.000	0.000
29	A	33	SER	0	-0.055	-0.055	28.942	0.282	0.282	0.000	0.000	0.000	0.000
30	A	34	LEU	0	-0.007	0.015	28.058	-0.342	-0.342	0.000	0.000	0.000	0.000
31	A	35	PHE	0	0.005	-0.020	27.619	0.441	0.441	0.000	0.000	0.000	0.000
32	A	36	GLY	0	0.006	0.006	26.867	-0.377	-0.377	0.000	0.000	0.000	0.000
33	A	37	THR	0	-0.004	0.006	23.068	0.230	0.230	0.000	0.000	0.000	0.000
34	A	38	ILE	0	-0.011	-0.001	19.152	-0.343	-0.343	0.000	0.000	0.000	0.000
35	A	39	ARG	1	0.796	0.842	22.020	-10.644	-10.644	0.000	0.000	0.000	0.000
36	A	40	TRP	0	-0.011	0.003	20.852	0.199	0.199	0.000	0.000	0.000	0.000
37	A	41	GLN	0	-0.005	-0.030	14.455	-0.119	-0.119	0.000	0.000	0.000	0.000
38	A	42	ASP	-1	-0.803	-0.897	19.854	12.809	12.809	0.000	0.000	0.000	0.000
39	A	43	THR	0	-0.016	-0.016	18.986	0.513	0.513	0.000	0.000	0.000	0.000
40	A	44	ASP	-1	-0.863	-0.900	20.653	11.310	11.310	0.000	0.000	0.000	0.000
41	A	45	GLY	0	-0.043	-0.028	23.487	-0.464	-0.464	0.000	0.000	0.000	0.000
42	A	46	LEU	0	-0.032	-0.006	20.624	0.690	0.690	0.000	0.000	0.000	0.000
43	A	47	GLY	0	0.042	0.026	23.213	-0.585	-0.585	0.000	0.000	0.000	0.000
44	A	48	LEU	0	-0.037	-0.016	24.541	0.442	0.442	0.000	0.000	0.000	0.000
45	A	49	VAL	0	0.000	0.001	26.209	-0.422	-0.422	0.000	0.000	0.000	0.000
46	A	50	ASP	-1	-0.732	-0.833	28.210	9.564	9.564	0.000	0.000	0.000	0.000
47	A	51	ASP	-1	-0.931	-0.971	30.797	9.309	9.309	0.000	0.000	0.000	0.000
48	A	52	SER	0	-0.088	-0.058	32.980	-0.313	-0.313	0.000	0.000	0.000	0.000
49	A	53	GLU	-1	-0.785	-0.863	31.384	9.783	9.783	0.000	0.000	0.000	0.000
50	A	54	ARG	1	0.854	0.925	33.674	-8.732	-8.732	0.000	0.000	0.000	0.000
51	A	55	SER	0	-0.029	-0.017	30.611	0.425	0.425	0.000	0.000	0.000	0.000
52	A	56	THR	0	-0.014	-0.012	29.719	-0.408	-0.408	0.000	0.000	0.000	0.000
53	A	57	ILE	0	-0.015	-0.006	27.694	0.419	0.419	0.000	0.000	0.000	0.000
54	A	58	VAL	0	-0.004	0.005	25.388	-0.287	-0.287	0.000	0.000	0.000	0.000
55	A	59	ARG	1	0.835	0.880	25.370	-10.433	-10.433	0.000	0.000	0.000	0.000
56	A	60	LEU	0	0.041	0.018	19.587	-0.012	-0.012	0.000	0.000	0.000	0.000
57	A	61	ALA	0	-0.016	-0.011	23.444	0.137	0.137	0.000	0.000	0.000	0.000
58	A	62	ALA	0	-0.013	-0.001	25.491	-0.301	-0.301	0.000	0.000	0.000	0.000
59	A	63	ILE	0	-0.032	-0.006	21.978	-0.236	-0.236	0.000	0.000	0.000	0.000
60	A	64	ALA	0	-0.027	-0.009	24.181	0.154	0.154	0.000	0.000	0.000	0.000
61	A	65	TYR	0	-0.060	-0.058	21.135	0.557	0.557	0.000	0.000	0.000	0.000
62	A	66	ILE	0	0.008	0.001	18.707	-0.487	-0.487	0.000	0.000	0.000	0.000
63	A	67	THR	0	-0.015	-0.006	19.246	1.044	1.044	0.000	0.000	0.000	0.000
64	A	68	PRO	0	0.010	0.007	18.251	-0.604	-0.604	0.000	0.000	0.000	0.000
65	A	69	ARG	1	0.867	0.949	21.084	-11.425	-11.425	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:ASP)