FMO DATABASE

FMODB ID: Q1RJY

Calculation Name: 1MN3-A-Xray372

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: 2023-06-20

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	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	54
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-252712.921549
FMO2-HF: Nuclear repulsion	230489.117882
FMO2-HF: Total energy	-22223.803667
FMO2-MP2: Total energy	-22285.885027

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.
-21.724	-15.411	0.795	-2.909	-4.2	0.009

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 : 0.083 / q_NPA : 0.036

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	0.028	0.012	3.177	-3.779	-1.534	0.020	-1.087	-1.178	0.005
4	A	401	ILE	0	0.071	0.036	2.622	-1.677	-0.097	0.617	-0.668	-1.529	-0.004
5	A	402	LYS	1	1.001	1.006	3.007	-7.255	-4.997	0.159	-1.083	-1.334	0.008
6	A	403	LYS	1	0.925	0.989	5.703	0.014	0.014	0.000	0.000	0.000	0.000
7	A	404	ILE	0	-0.019	-0.020	6.948	0.080	0.080	0.000	0.000	0.000	0.000
8	A	405	GLU	-1	-0.864	-0.949	6.969	-1.400	-1.400	0.000	0.000	0.000	0.000
9	A	406	GLU	-1	-0.976	-0.990	9.451	0.518	0.518	0.000	0.000	0.000	0.000
10	A	407	ASN	0	-0.042	-0.039	11.479	0.132	0.132	0.000	0.000	0.000	0.000
11	A	408	GLU	-1	-0.857	-0.927	12.344	-0.536	-0.536	0.000	0.000	0.000	0.000
12	A	409	ARG	1	0.912	0.962	13.876	0.022	0.022	0.000	0.000	0.000	0.000
13	A	410	LYS	1	0.918	0.956	15.364	-0.044	-0.044	0.000	0.000	0.000	0.000
14	A	411	ASP	-1	-0.962	-0.987	17.234	-0.073	-0.073	0.000	0.000	0.000	0.000
15	A	412	THR	0	0.041	0.021	18.443	0.004	0.004	0.000	0.000	0.000	0.000
16	A	413	LEU	0	-0.011	-0.015	19.080	0.014	0.014	0.000	0.000	0.000	0.000
17	A	414	ASN	0	-0.052	-0.010	21.392	0.020	0.020	0.000	0.000	0.000	0.000
18	A	415	THR	0	0.010	0.014	23.420	0.011	0.011	0.000	0.000	0.000	0.000
19	A	416	LEU	0	0.002	-0.016	23.392	0.004	0.004	0.000	0.000	0.000	0.000
20	A	417	GLN	0	0.043	0.001	23.696	-0.009	-0.009	0.000	0.000	0.000	0.000
21	A	418	ASN	0	-0.072	-0.036	27.197	0.011	0.011	0.000	0.000	0.000	0.000
22	A	419	MET	0	-0.067	-0.022	28.214	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	0.027	0.008	30.644	0.004	0.004	0.000	0.000	0.000	0.000
25	A	422	ASP	-1	-0.923	-0.951	32.121	0.015	0.015	0.000	0.000	0.000	0.000
26	A	423	MET	0	-0.100	-0.040	29.802	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	424	ASP	-1	-0.841	-0.910	26.751	0.037	0.037	0.000	0.000	0.000	0.000
28	A	425	PRO	0	0.010	-0.031	24.171	-0.009	-0.009	0.000	0.000	0.000	0.000
29	A	426	SER	0	0.010	0.004	22.672	-0.005	-0.005	0.000	0.000	0.000	0.000
30	A	427	LEU	0	0.000	0.021	23.383	-0.015	-0.015	0.000	0.000	0.000	0.000
31	A	428	ILE	0	-0.013	-0.012	23.713	-0.018	-0.018	0.000	0.000	0.000	0.000
32	A	429	GLU	-1	-0.854	-0.931	17.226	-0.017	-0.017	0.000	0.000	0.000	0.000
33	A	430	ASP	-1	-0.942	-0.968	20.950	-0.066	-0.066	0.000	0.000	0.000	0.000
34	A	431	VAL	0	-0.093	-0.049	22.342	-0.022	-0.022	0.000	0.000	0.000	0.000
35	A	432	CYS	0	-0.081	-0.033	22.892	-0.013	-0.013	0.000	0.000	0.000	0.000
36	A	433	ILE	0	-0.013	0.008	16.444	-0.032	-0.032	0.000	0.000	0.000	0.000
37	A	434	ALA	0	-0.057	-0.025	16.364	0.010	0.010	0.000	0.000	0.000	0.000
38	A	435	LYS	1	0.976	0.981	15.738	0.312	0.312	0.000	0.000	0.000	0.000
39	A	436	LYS	1	0.950	0.963	11.671	0.437	0.437	0.000	0.000	0.000	0.000
40	A	437	SER	0	0.038	0.039	10.290	-0.022	-0.022	0.000	0.000	0.000	0.000
41	A	438	ARG	1	0.968	0.977	11.559	0.500	0.500	0.000	0.000	0.000	0.000
42	A	439	ILE	0	0.015	0.008	7.857	-0.085	-0.085	0.000	0.000	0.000	0.000
43	A	440	GLU	-1	-0.889	-0.941	3.998	-6.397	-6.167	-0.001	-0.071	-0.159	0.000
44	A	441	PRO	0	0.011	0.010	7.309	0.059	0.059	0.000	0.000	0.000	0.000
45	A	442	CYS	0	-0.062	-0.028	10.471	0.149	0.149	0.000	0.000	0.000	0.000
46	A	443	VAL	0	0.005	-0.001	6.699	0.178	0.178	0.000	0.000	0.000	0.000
47	A	444	ASP	-1	-0.894	-0.943	7.229	-3.087	-3.087	0.000	0.000	0.000	0.000
48	A	445	ALA	0	-0.051	-0.033	9.635	0.249	0.249	0.000	0.000	0.000	0.000
49	A	446	LEU	0	-0.015	-0.024	12.156	0.146	0.146	0.000	0.000	0.000	0.000
50	A	447	LEU	0	-0.025	-0.004	6.911	0.123	0.123	0.000	0.000	0.000	0.000
51	A	448	SER	0	-0.001	0.000	11.603	0.142	0.142	0.000	0.000	0.000	0.000
52	A	449	LEU	0	-0.075	-0.034	14.301	0.109	0.109	0.000	0.000	0.000	0.000
53	A	450	SER	0	-0.114	-0.052	13.991	0.080	0.080	0.000	0.000	0.000	0.000
54	A	451	GLU	-1	-0.993	-0.977	14.639	-0.536	-0.536	0.000	0.000	0.000	0.000

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