FMO DATABASE

FMODB ID: 53Z4Z

Calculation Name: 1MN3-A-Xray319

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1MN3

Chain ID: A

ChEMBL ID:

UniProt ID: P54787

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	54
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-252640.578287
FMO2-HF: Nuclear repulsion	230417.578916
FMO2-HF: Total energy	-22222.999371
FMO2-MP2: Total energy	-22285.089237

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:398:SER )

Summations of interaction energy for fragment #1(A:398:SER )

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.
-22.524	-16.264	0.802	-2.897	-4.165	0.008

Interaction energy analysis for fragmet #1(A:398:SER )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.085 / q_NPA : 0.037

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	A	400	LEU	0	0.029	0.013	3.179	-3.836	-1.624	0.025	-1.078	-1.159	0.004
4	A	401	ILE	0	0.077	0.040	2.622	-1.749	-0.170	0.616	-0.674	-1.521	-0.004
5	A	402	LYS	1	0.998	1.004	3.007	-7.341	-5.103	0.161	-1.072	-1.326	0.008
6	A	403	LYS	1	0.924	0.989	5.703	-0.013	-0.013	0.000	0.000	0.000	0.000
7	A	404	ILE	0	-0.015	-0.018	6.949	0.066	0.066	0.000	0.000	0.000	0.000
8	A	405	GLU	-1	-0.865	-0.949	6.971	-1.376	-1.376	0.000	0.000	0.000	0.000
9	A	406	GLU	-1	-0.976	-0.990	9.451	0.552	0.552	0.000	0.000	0.000	0.000
10	A	407	ASN	0	-0.042	-0.038	11.479	0.130	0.130	0.000	0.000	0.000	0.000
11	A	408	GLU	-1	-0.859	-0.927	12.344	-0.532	-0.532	0.000	0.000	0.000	0.000
12	A	409	ARG	1	0.914	0.963	13.875	0.011	0.011	0.000	0.000	0.000	0.000
13	A	410	LYS	1	0.917	0.955	15.364	-0.053	-0.053	0.000	0.000	0.000	0.000
14	A	411	ASP	-1	-0.961	-0.986	17.234	-0.068	-0.068	0.000	0.000	0.000	0.000
15	A	412	THR	0	0.040	0.021	18.444	0.002	0.002	0.000	0.000	0.000	0.000
16	A	413	LEU	0	-0.011	-0.015	19.082	0.014	0.014	0.000	0.000	0.000	0.000
17	A	414	ASN	0	-0.053	-0.010	21.392	0.020	0.020	0.000	0.000	0.000	0.000
18	A	415	THR	0	0.011	0.014	23.420	0.010	0.010	0.000	0.000	0.000	0.000
19	A	416	LEU	0	0.000	-0.017	23.392	0.004	0.004	0.000	0.000	0.000	0.000
20	A	417	GLN	0	0.046	0.001	23.700	-0.009	-0.009	0.000	0.000	0.000	0.000
21	A	418	ASN	0	-0.075	-0.037	27.196	0.011	0.011	0.000	0.000	0.000	0.000
22	A	419	MET	0	-0.067	-0.022	28.218	0.000	0.000	0.000	0.000	0.000	0.000
23	A	420	PHE	0	-0.080	-0.030	29.529	-0.004	-0.004	0.000	0.000	0.000	0.000
24	A	421	PRO	0	0.026	0.008	30.647	0.004	0.004	0.000	0.000	0.000	0.000
25	A	422	ASP	-1	-0.924	-0.952	32.124	0.018	0.018	0.000	0.000	0.000	0.000
26	A	423	MET	0	-0.097	-0.040	29.781	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	424	ASP	-1	-0.845	-0.912	26.754	0.042	0.042	0.000	0.000	0.000	0.000
28	A	425	PRO	0	0.012	-0.030	24.174	-0.009	-0.009	0.000	0.000	0.000	0.000
29	A	426	SER	0	0.010	0.004	22.675	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	427	LEU	0	-0.002	0.020	23.386	-0.016	-0.016	0.000	0.000	0.000	0.000
31	A	428	ILE	0	-0.013	-0.012	23.716	-0.019	-0.019	0.000	0.000	0.000	0.000
32	A	429	GLU	-1	-0.851	-0.929	17.229	-0.008	-0.008	0.000	0.000	0.000	0.000
33	A	430	ASP	-1	-0.945	-0.968	20.953	-0.062	-0.062	0.000	0.000	0.000	0.000
34	A	431	VAL	0	-0.094	-0.050	22.345	-0.023	-0.023	0.000	0.000	0.000	0.000
35	A	432	CYS	0	-0.083	-0.034	22.895	-0.014	-0.014	0.000	0.000	0.000	0.000
36	A	433	ILE	0	-0.010	0.008	16.446	-0.033	-0.033	0.000	0.000	0.000	0.000
37	A	434	ALA	0	-0.057	-0.025	16.366	0.009	0.009	0.000	0.000	0.000	0.000
38	A	435	LYS	1	0.973	0.980	15.741	0.311	0.311	0.000	0.000	0.000	0.000
39	A	436	LYS	1	0.949	0.963	11.673	0.434	0.434	0.000	0.000	0.000	0.000
40	A	437	SER	0	0.035	0.037	10.291	-0.026	-0.026	0.000	0.000	0.000	0.000
41	A	438	ARG	1	0.969	0.976	11.560	0.499	0.499	0.000	0.000	0.000	0.000
42	A	439	ILE	0	0.015	0.008	7.857	-0.090	-0.090	0.000	0.000	0.000	0.000
43	A	440	GLU	-1	-0.892	-0.943	3.998	-6.443	-6.212	0.000	-0.073	-0.159	0.000
44	A	441	PRO	0	0.008	0.008	7.309	0.067	0.067	0.000	0.000	0.000	0.000
45	A	442	CYS	0	-0.064	-0.029	10.471	0.153	0.153	0.000	0.000	0.000	0.000
46	A	443	VAL	0	0.005	-0.001	6.699	0.167	0.167	0.000	0.000	0.000	0.000
47	A	444	ASP	-1	-0.897	-0.944	7.229	-3.143	-3.143	0.000	0.000	0.000	0.000
48	A	445	ALA	0	-0.054	-0.035	9.635	0.257	0.257	0.000	0.000	0.000	0.000
49	A	446	LEU	0	-0.030	-0.031	12.156	0.146	0.146	0.000	0.000	0.000	0.000
50	A	447	LEU	0	-0.028	-0.008	6.910	0.095	0.095	0.000	0.000	0.000	0.000
51	A	448	SER	0	0.001	0.003	11.602	0.136	0.136	0.000	0.000	0.000	0.000
52	A	449	LEU	0	-0.097	-0.048	14.300	0.111	0.111	0.000	0.000	0.000	0.000
53	A	450	SER	0	-0.155	-0.079	14.027	0.076	0.076	0.000	0.000	0.000	0.000
54	A	451	GLU	-2	-1.896	-1.917	14.636	-0.995	-0.995	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:398:SER )