FMO DATABASE

FMODB ID: K3YM3

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

Total energy (hartree)

FMO2-HF: Electronic energy	-252685.502456
FMO2-HF: Nuclear repulsion	230461.325807
FMO2-HF: Total energy	-22224.176649
FMO2-MP2: Total energy	-22286.220314

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.
-40.6	-35.975	8.125	-6.001	-6.75	0.043

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 : 0.121 / q_NPA : 0.056

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	0.022	0.011	3.017	-3.469	-1.297	0.023	-1.025	-1.171	0.004
4	A	401	ILE	0	0.073	0.037	2.705	-1.245	0.324	0.522	-0.622	-1.469	-0.003
5	A	402	LYS	1	0.963	0.975	1.875	-23.033	-23.156	7.574	-3.808	-3.644	0.046
6	A	403	LYS	1	0.799	0.907	5.701	0.134	0.134	0.000	0.000	0.000	0.000
7	A	404	ILE	0	-0.002	-0.012	6.940	0.133	0.133	0.000	0.000	0.000	0.000
8	A	405	GLU	-1	-0.847	-0.938	7.007	-1.600	-1.600	0.000	0.000	0.000	0.000
9	A	406	GLU	-1	-0.894	-0.938	9.443	0.462	0.462	0.000	0.000	0.000	0.000
10	A	407	ASN	0	-0.017	-0.022	11.460	0.163	0.163	0.000	0.000	0.000	0.000
11	A	408	GLU	-1	-0.825	-0.885	12.330	-0.634	-0.634	0.000	0.000	0.000	0.000
12	A	409	ARG	1	0.832	0.886	13.868	-0.014	-0.014	0.000	0.000	0.000	0.000
13	A	410	LYS	1	0.941	0.970	15.353	-0.016	-0.016	0.000	0.000	0.000	0.000
14	A	411	ASP	-1	-0.946	-0.973	17.217	-0.097	-0.097	0.000	0.000	0.000	0.000
15	A	412	THR	0	0.010	0.001	18.268	0.005	0.005	0.000	0.000	0.000	0.000
16	A	413	LEU	0	0.005	-0.004	18.791	0.016	0.016	0.000	0.000	0.000	0.000
17	A	414	ASN	0	-0.059	-0.026	20.934	0.025	0.025	0.000	0.000	0.000	0.000
18	A	415	THR	0	0.030	0.030	23.408	0.013	0.013	0.000	0.000	0.000	0.000
19	A	416	LEU	0	0.004	-0.011	23.161	0.005	0.005	0.000	0.000	0.000	0.000
20	A	417	GLN	0	0.032	-0.004	22.976	-0.005	-0.005	0.000	0.000	0.000	0.000
21	A	418	ASN	0	-0.105	-0.062	26.897	0.011	0.011	0.000	0.000	0.000	0.000
22	A	419	MET	0	-0.058	-0.016	28.004	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	420	PHE	0	-0.072	-0.029	29.084	-0.004	-0.004	0.000	0.000	0.000	0.000
24	A	421	PRO	0	0.035	0.013	30.456	0.006	0.006	0.000	0.000	0.000	0.000
25	A	422	ASP	-1	-0.934	-0.958	31.937	0.022	0.022	0.000	0.000	0.000	0.000
26	A	423	MET	0	-0.095	-0.036	29.667	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	424	ASP	-1	-0.827	-0.897	26.705	0.068	0.068	0.000	0.000	0.000	0.000
28	A	425	PRO	0	0.031	-0.014	24.008	-0.011	-0.011	0.000	0.000	0.000	0.000
29	A	426	SER	0	-0.021	-0.025	22.502	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	427	LEU	0	-0.006	0.013	23.212	-0.016	-0.016	0.000	0.000	0.000	0.000
31	A	428	ILE	0	-0.013	-0.008	23.784	-0.021	-0.021	0.000	0.000	0.000	0.000
32	A	429	GLU	-1	-0.799	-0.869	16.866	0.024	0.024	0.000	0.000	0.000	0.000
33	A	430	ASP	-1	-0.943	-0.963	20.772	-0.039	-0.039	0.000	0.000	0.000	0.000
34	A	431	VAL	0	-0.096	-0.053	22.173	-0.025	-0.025	0.000	0.000	0.000	0.000
35	A	432	CYS	0	-0.073	-0.026	22.749	-0.018	-0.018	0.000	0.000	0.000	0.000
36	A	433	ILE	0	-0.028	-0.001	16.308	-0.040	-0.040	0.000	0.000	0.000	0.000
37	A	434	ALA	0	-0.050	-0.016	16.176	0.016	0.016	0.000	0.000	0.000	0.000
38	A	435	LYS	1	0.995	0.988	15.571	0.311	0.311	0.000	0.000	0.000	0.000
39	A	436	LYS	1	0.937	0.959	11.547	0.425	0.425	0.000	0.000	0.000	0.000
40	A	437	SER	0	0.025	0.007	10.234	-0.041	-0.041	0.000	0.000	0.000	0.000
41	A	438	ARG	1	0.954	0.970	11.421	0.563	0.563	0.000	0.000	0.000	0.000
42	A	439	ILE	0	0.021	-0.002	7.719	-0.101	-0.101	0.000	0.000	0.000	0.000
43	A	440	GLU	-1	-0.877	-0.929	3.433	-9.710	-8.703	0.006	-0.546	-0.466	-0.004
44	A	441	PRO	0	0.007	0.005	7.303	0.048	0.048	0.000	0.000	0.000	0.000
45	A	442	CYS	0	-0.099	-0.036	10.470	0.141	0.141	0.000	0.000	0.000	0.000
46	A	443	VAL	0	0.028	0.008	6.671	0.179	0.179	0.000	0.000	0.000	0.000
47	A	444	ASP	-1	-0.896	-0.940	7.259	-3.482	-3.482	0.000	0.000	0.000	0.000
48	A	445	ALA	0	-0.059	-0.035	9.614	0.285	0.285	0.000	0.000	0.000	0.000
49	A	446	LEU	0	-0.020	-0.022	12.251	0.166	0.166	0.000	0.000	0.000	0.000
50	A	447	LEU	0	-0.022	0.007	7.085	0.139	0.139	0.000	0.000	0.000	0.000
51	A	448	SER	0	-0.013	-0.019	11.723	0.119	0.119	0.000	0.000	0.000	0.000
52	A	449	LEU	0	-0.090	-0.036	14.259	0.132	0.132	0.000	0.000	0.000	0.000
53	A	450	SER	0	-0.081	-0.040	14.167	0.087	0.087	0.000	0.000	0.000	0.000
54	A	451	GLU	-1	-0.990	-0.977	14.471	-0.671	-0.671	0.000	0.000	0.000	0.000

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