FMO DATABASE

FMODB ID: 9GR12

Calculation Name: 3U28-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3U28

Chain ID: B

ChEMBL ID:

UniProt ID: P33322

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:

Apendix: None

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	48
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-202713.643603
FMO2-HF: Nuclear repulsion	183245.662485
FMO2-HF: Total energy	-19467.981119
FMO2-MP2: Total energy	-19524.207201

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(B:1:MET)

Summations of interaction energy for fragment #1(B:1:MET)

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.
-7.623	-2.18	3.319	-2.851	-5.91	-0.011

Interaction energy analysis for fragmet #1(B:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / 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].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	B	3	LEU	0	-0.039	0.003	2.922	-3.183	-0.156	0.015	-1.430	-1.611	-0.001
4	B	4	MET	0	0.040	0.046	4.496	-1.114	-1.019	-0.001	-0.024	-0.070	0.000
5	B	5	TYR	0	-0.028	-0.029	7.123	0.263	0.263	0.000	0.000	0.000	0.000
6	B	6	THR	0	0.019	0.021	10.487	-0.098	-0.098	0.000	0.000	0.000	0.000
7	B	7	LEU	0	0.009	0.005	13.965	0.017	0.017	0.000	0.000	0.000	0.000
8	B	8	GLY	0	0.044	0.027	16.933	0.017	0.017	0.000	0.000	0.000	0.000
9	B	9	PRO	0	0.011	-0.006	19.773	-0.019	-0.019	0.000	0.000	0.000	0.000
10	B	10	ASP	-1	-0.834	-0.909	21.287	-0.095	-0.095	0.000	0.000	0.000	0.000
11	B	11	GLY	0	0.003	0.008	20.564	-0.008	-0.008	0.000	0.000	0.000	0.000
12	B	12	LYS	1	0.849	0.917	18.152	0.060	0.060	0.000	0.000	0.000	0.000
13	B	13	ARG	1	0.837	0.914	9.154	0.549	0.549	0.000	0.000	0.000	0.000
14	B	14	ILE	0	0.038	0.032	14.571	0.047	0.047	0.000	0.000	0.000	0.000
15	B	15	TYR	0	0.004	-0.009	8.986	-0.071	-0.071	0.000	0.000	0.000	0.000
16	B	16	THR	0	0.009	0.000	9.817	0.054	0.054	0.000	0.000	0.000	0.000
17	B	17	LEU	0	0.052	0.021	7.809	0.024	0.024	0.000	0.000	0.000	0.000
18	B	18	LYS	1	0.926	0.978	9.412	-0.269	-0.269	0.000	0.000	0.000	0.000
19	B	19	LYS	1	0.928	0.946	5.436	0.525	0.525	0.000	0.000	0.000	0.000
20	B	20	VAL	0	0.023	0.021	10.901	-0.074	-0.074	0.000	0.000	0.000	0.000
21	B	21	THR	0	-0.029	-0.017	14.603	0.072	0.072	0.000	0.000	0.000	0.000
22	B	22	GLU	-1	-0.920	-0.967	16.477	0.097	0.097	0.000	0.000	0.000	0.000
23	B	23	SER	0	-0.012	-0.010	19.890	0.004	0.004	0.000	0.000	0.000	0.000
24	B	24	GLY	0	0.026	0.026	19.587	-0.008	-0.008	0.000	0.000	0.000	0.000
25	B	25	GLU	-1	-0.891	-0.941	16.198	-0.277	-0.277	0.000	0.000	0.000	0.000
26	B	26	ILE	0	0.026	0.009	12.628	0.017	0.017	0.000	0.000	0.000	0.000
27	B	27	THR	0	-0.064	-0.046	10.238	-0.096	-0.096	0.000	0.000	0.000	0.000
28	B	28	LYS	1	0.893	0.941	9.370	0.303	0.303	0.000	0.000	0.000	0.000
29	B	29	SER	0	0.018	0.009	4.416	-0.142	-0.032	-0.001	-0.011	-0.098	0.000
30	B	30	ALA	0	-0.013	-0.013	5.143	0.116	0.116	0.000	0.000	0.000	0.000
31	B	31	HIS	0	0.012	0.008	2.423	-5.201	-2.990	3.306	-1.386	-4.131	-0.010
32	B	32	PRO	0	0.026	0.012	5.403	-0.018	-0.018	0.000	0.000	0.000	0.000
33	B	33	ALA	0	0.010	0.000	6.683	-0.463	-0.463	0.000	0.000	0.000	0.000
34	B	34	ARG	1	0.970	0.984	8.647	1.009	1.009	0.000	0.000	0.000	0.000
35	B	35	PHE	0	0.023	0.011	9.500	0.172	0.172	0.000	0.000	0.000	0.000
36	B	36	SER	0	-0.062	-0.061	12.913	-0.026	-0.026	0.000	0.000	0.000	0.000
37	B	37	PRO	0	0.017	-0.001	15.529	0.015	0.015	0.000	0.000	0.000	0.000
38	B	38	ASP	-1	-0.864	-0.892	18.786	-0.424	-0.424	0.000	0.000	0.000	0.000
39	B	39	ASP	-1	-0.848	-0.884	17.219	-0.550	-0.550	0.000	0.000	0.000	0.000
40	B	40	LYS	1	0.995	0.987	19.667	0.310	0.310	0.000	0.000	0.000	0.000
41	B	41	TYR	0	-0.051	-0.028	18.836	0.054	0.054	0.000	0.000	0.000	0.000
42	B	42	SER	0	0.042	0.010	21.651	-0.024	-0.024	0.000	0.000	0.000	0.000
43	B	43	ARG	1	0.995	1.001	23.039	0.239	0.239	0.000	0.000	0.000	0.000
44	B	44	GLN	0	0.045	0.021	23.015	0.001	0.001	0.000	0.000	0.000	0.000
45	B	45	ARG	1	0.838	0.891	17.234	0.538	0.538	0.000	0.000	0.000	0.000
46	B	46	VAL	0	-0.033	-0.014	21.957	0.002	0.002	0.000	0.000	0.000	0.000
47	B	47	THR	0	-0.057	-0.037	24.747	0.016	0.016	0.000	0.000	0.000	0.000
48	B	48	LEU	0	-0.014	0.020	21.320	0.016	0.016	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:1:MET)