FMO DATABASE

FMODB ID: 2JN4R

Calculation Name: 1FMD-4-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1FMD

Chain ID: 4

ChEMBL ID:

UniProt ID: P15072

Base Structure: X-ray

Registration Date: 2023-06-22

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	46
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-140307.334675
FMO2-HF: Nuclear repulsion	122343.914545
FMO2-HF: Total energy	-17963.42013
FMO2-MP2: Total energy	-18014.567973

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(4:15:SER)

Summations of interaction energy for fragment #1(4:15: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.
-4.362	-1.467	0.009	-1.56	-1.344	0.005

Interaction energy analysis for fragmet #1(4:15:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.029 / q_NPA : 0.017

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	4	17	ASN	0	-0.042	-0.023	3.492	-4.083	-1.687	0.000	-1.451	-0.945	0.005
4	4	18	THR	0	-0.014	-0.016	3.312	0.263	0.704	0.010	-0.101	-0.350	0.000
5	4	19	GLY	0	0.049	0.022	4.575	-1.029	-0.971	-0.001	-0.008	-0.049	0.000
6	4	20	SER	0	-0.044	-0.018	7.278	0.063	0.063	0.000	0.000	0.000	0.000
7	4	21	ILE	0	0.014	0.010	8.340	0.080	0.080	0.000	0.000	0.000	0.000
8	4	22	ILE	0	-0.029	0.001	10.563	0.027	0.027	0.000	0.000	0.000	0.000
9	4	23	ASN	0	-0.022	-0.018	9.687	0.031	0.031	0.000	0.000	0.000	0.000
10	4	24	ASN	0	0.004	-0.013	9.388	-0.229	-0.229	0.000	0.000	0.000	0.000
11	4	25	TYR	0	0.029	0.027	11.297	-0.048	-0.048	0.000	0.000	0.000	0.000
12	4	26	TYR	0	-0.001	0.002	13.712	-0.058	-0.058	0.000	0.000	0.000	0.000
13	4	27	MET	0	0.014	0.000	12.980	0.087	0.087	0.000	0.000	0.000	0.000
14	4	28	GLN	0	0.059	0.016	8.414	-0.125	-0.125	0.000	0.000	0.000	0.000
15	4	29	GLN	0	-0.003	-0.013	11.705	0.028	0.028	0.000	0.000	0.000	0.000
16	4	30	TYR	0	-0.034	-0.018	14.337	-0.070	-0.070	0.000	0.000	0.000	0.000
17	4	31	GLN	0	-0.037	0.001	9.239	-0.114	-0.114	0.000	0.000	0.000	0.000
18	4	32	ASN	0	-0.037	-0.027	7.027	0.135	0.135	0.000	0.000	0.000	0.000
19	4	33	SER	0	0.010	0.008	10.857	-0.114	-0.114	0.000	0.000	0.000	0.000
20	4	34	MET	0	-0.034	-0.010	11.491	0.140	0.140	0.000	0.000	0.000	0.000
21	4	35	ASP	-1	-0.867	-0.918	10.199	0.608	0.608	0.000	0.000	0.000	0.000
22	4	36	THR	0	-0.048	-0.031	13.466	-0.031	-0.031	0.000	0.000	0.000	0.000
23	4	37	GLN	0	-0.015	-0.014	13.997	-0.040	-0.040	0.000	0.000	0.000	0.000
24	4	38	LEU	0	0.008	0.005	17.810	-0.004	-0.004	0.000	0.000	0.000	0.000
25	4	39	GLY	0	-0.001	0.011	20.806	-0.011	-0.011	0.000	0.000	0.000	0.000
26	4	65	ASN	0	0.045	0.023	11.918	0.022	0.022	0.000	0.000	0.000	0.000
27	4	66	ASP	-1	-0.826	-0.933	12.759	-0.079	-0.079	0.000	0.000	0.000	0.000
28	4	67	TRP	0	0.017	0.000	15.004	-0.060	-0.060	0.000	0.000	0.000	0.000
29	4	68	PHE	0	0.054	0.024	16.018	0.001	0.001	0.000	0.000	0.000	0.000
30	4	69	SER	0	-0.018	0.015	13.717	0.001	0.001	0.000	0.000	0.000	0.000
31	4	70	LYS	1	0.874	0.931	15.861	0.176	0.176	0.000	0.000	0.000	0.000
32	4	71	LEU	0	0.009	0.011	18.881	0.013	0.013	0.000	0.000	0.000	0.000
33	4	72	ALA	0	0.002	0.013	18.479	0.016	0.016	0.000	0.000	0.000	0.000
34	4	73	SER	0	-0.029	-0.028	18.486	0.003	0.003	0.000	0.000	0.000	0.000
35	4	74	SER	0	-0.093	-0.052	21.096	0.022	0.022	0.000	0.000	0.000	0.000
36	4	75	ALA	0	0.011	0.011	24.100	0.017	0.017	0.000	0.000	0.000	0.000
37	4	76	PHE	0	0.002	0.002	26.005	0.001	0.001	0.000	0.000	0.000	0.000
38	4	77	SER	0	-0.012	-0.012	27.475	-0.007	-0.007	0.000	0.000	0.000	0.000
39	4	78	GLY	0	-0.002	0.008	30.072	0.001	0.001	0.000	0.000	0.000	0.000
40	4	79	LEU	0	0.031	-0.009	33.687	0.000	0.000	0.000	0.000	0.000	0.000
41	4	80	PHE	0	-0.032	0.000	36.583	0.003	0.003	0.000	0.000	0.000	0.000
42	4	81	GLY	0	-0.007	0.009	38.564	0.005	0.005	0.000	0.000	0.000	0.000
43	4	82	ALA	0	-0.023	-0.017	42.020	0.000	0.000	0.000	0.000	0.000	0.000
44	4	83	LEU	0	-0.005	-0.002	40.238	-0.001	-0.001	0.000	0.000	0.000	0.000
45	4	84	LEU	0	0.031	0.020	43.922	0.003	0.003	0.000	0.000	0.000	0.000
46	4	85	ALA	0	-0.031	-0.013	44.253	-0.005	-0.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(4:15:SER)