FMO DATABASE

FMODB ID: 39JKL

Calculation Name: 1FOD-4-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1FOD

Chain ID: 4

ChEMBL ID:

UniProt ID: P87677

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

Total energy (hartree)

FMO2-HF: Electronic energy	-140181.103216
FMO2-HF: Nuclear repulsion	122218.628751
FMO2-HF: Total energy	-17962.474465
FMO2-MP2: Total energy	-18013.69602

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.
-0.031	2.057	0.932	-1.166	-1.853	0.004

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 : 0.002 / q_NPA : -0.006

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	-0.011	-0.016	3.776	-1.645	-0.214	-0.017	-0.667	-0.747	0.003
4	4	18	THR	0	-0.005	-0.001	3.128	2.572	3.158	0.950	-0.497	-1.039	0.001
5	4	19	GLY	0	0.023	-0.001	5.400	0.142	0.213	-0.001	-0.002	-0.067	0.000
6	4	20	SER	0	-0.015	0.002	7.308	-0.430	-0.430	0.000	0.000	0.000	0.000
7	4	21	ILE	0	0.039	0.031	8.038	0.073	0.073	0.000	0.000	0.000	0.000
8	4	22	ILE	0	-0.074	-0.027	10.581	-0.165	-0.165	0.000	0.000	0.000	0.000
9	4	23	ASN	0	-0.009	-0.022	9.885	0.216	0.216	0.000	0.000	0.000	0.000
10	4	24	ASN	0	0.019	0.004	8.811	-0.092	-0.092	0.000	0.000	0.000	0.000
11	4	25	TYR	0	0.031	0.030	11.242	-0.111	-0.111	0.000	0.000	0.000	0.000
12	4	26	TYR	0	-0.011	-0.002	13.611	-0.112	-0.112	0.000	0.000	0.000	0.000
13	4	27	MET	0	0.029	0.006	13.010	0.012	0.012	0.000	0.000	0.000	0.000
14	4	28	GLN	0	0.046	0.007	9.377	0.039	0.039	0.000	0.000	0.000	0.000
15	4	29	GLN	0	0.001	-0.019	11.903	0.025	0.025	0.000	0.000	0.000	0.000
16	4	30	TYR	0	-0.046	-0.006	14.285	-0.002	-0.002	0.000	0.000	0.000	0.000
17	4	31	GLN	0	-0.003	0.014	9.019	-0.064	-0.064	0.000	0.000	0.000	0.000
18	4	32	ASN	0	-0.041	-0.023	7.309	0.210	0.210	0.000	0.000	0.000	0.000
19	4	33	SER	0	0.014	0.010	10.579	-0.004	-0.004	0.000	0.000	0.000	0.000
20	4	34	MET	0	-0.046	-0.018	10.509	-0.070	-0.070	0.000	0.000	0.000	0.000
21	4	35	ASP	-1	-0.881	-0.940	9.586	-0.894	-0.894	0.000	0.000	0.000	0.000
22	4	36	THR	0	-0.083	-0.039	12.576	0.026	0.026	0.000	0.000	0.000	0.000
23	4	37	GLN	0	0.009	0.003	13.481	-0.064	-0.064	0.000	0.000	0.000	0.000
24	4	38	LEU	0	0.015	0.006	17.199	0.053	0.053	0.000	0.000	0.000	0.000
25	4	39	GLY	0	-0.008	-0.001	20.242	-0.031	-0.031	0.000	0.000	0.000	0.000
26	4	65	ASN	0	0.060	-0.015	9.697	0.105	0.105	0.000	0.000	0.000	0.000
27	4	66	ASP	-1	-0.834	-0.950	12.788	-0.644	-0.644	0.000	0.000	0.000	0.000
28	4	67	TRP	0	-0.071	-0.031	14.703	0.040	0.040	0.000	0.000	0.000	0.000
29	4	68	PHE	0	0.095	0.025	16.237	0.033	0.033	0.000	0.000	0.000	0.000
30	4	69	SER	0	0.022	0.063	14.225	0.046	0.046	0.000	0.000	0.000	0.000
31	4	70	LYS	1	0.889	0.968	16.348	0.557	0.557	0.000	0.000	0.000	0.000
32	4	71	LEU	0	-0.026	-0.011	19.273	0.035	0.035	0.000	0.000	0.000	0.000
33	4	72	ALA	0	0.005	0.017	18.755	0.030	0.030	0.000	0.000	0.000	0.000
34	4	73	SER	0	-0.008	-0.022	18.975	0.021	0.021	0.000	0.000	0.000	0.000
35	4	74	SER	0	-0.119	-0.061	21.369	0.027	0.027	0.000	0.000	0.000	0.000
36	4	75	ALA	0	0.011	0.026	24.333	0.019	0.019	0.000	0.000	0.000	0.000
37	4	76	PHE	0	-0.010	-0.005	26.284	0.002	0.002	0.000	0.000	0.000	0.000
38	4	77	SER	0	0.030	-0.015	27.293	0.004	0.004	0.000	0.000	0.000	0.000
39	4	78	GLY	0	-0.072	-0.014	29.935	0.007	0.007	0.000	0.000	0.000	0.000
40	4	79	LEU	0	0.045	0.027	33.546	0.004	0.004	0.000	0.000	0.000	0.000
41	4	80	PHE	0	-0.002	-0.004	37.007	-0.004	-0.004	0.000	0.000	0.000	0.000
42	4	81	GLY	0	-0.030	-0.015	39.217	0.003	0.003	0.000	0.000	0.000	0.000
43	4	82	ALA	0	0.036	0.030	42.358	-0.003	-0.003	0.000	0.000	0.000	0.000
44	4	83	LEU	0	-0.033	-0.022	40.385	0.001	0.001	0.000	0.000	0.000	0.000
45	4	84	LEU	0	-0.026	-0.009	43.923	0.001	0.001	0.000	0.000	0.000	0.000
46	4	85	ALA	0	0.036	0.018	43.612	0.001	0.001	0.000	0.000	0.000	0.000

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