FMO DATABASE

FMODB ID: 6NZYZ

Calculation Name: 5DDJ-4-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5DDJ

Chain ID: 4

ChEMBL ID:

UniProt ID: Q6PMW3

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
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-140339.016058
FMO2-HF: Nuclear repulsion	122375.67366
FMO2-HF: Total energy	-17963.342399
FMO2-MP2: Total energy	-18014.449538

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.
-4.601	-1.027	1.317	-2.085	-2.806	-0.014

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 : -0.004 / q_NPA : -0.018

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	0.002	-0.010	3.863	0.045	1.855	-0.015	-0.902	-0.893	-0.001
4	4	18	THR	0	0.002	0.007	2.386	-5.393	-3.789	1.334	-1.163	-1.775	-0.013
5	4	19	GLY	0	0.007	0.011	4.187	0.458	0.572	-0.001	-0.020	-0.094	0.000
6	4	20	SER	0	-0.041	-0.023	7.165	0.106	0.106	0.000	0.000	0.000	0.000
7	4	21	ILE	0	0.019	0.002	9.211	0.105	0.105	0.000	0.000	0.000	0.000
8	4	22	ILE	0	0.006	0.007	11.498	0.067	0.067	0.000	0.000	0.000	0.000
9	4	23	ASN	0	0.013	0.005	10.815	-0.128	-0.128	0.000	0.000	0.000	0.000
10	4	24	ASN	0	-0.018	-0.022	7.121	0.123	0.123	0.000	0.000	0.000	0.000
11	4	25	TYR	0	-0.016	0.017	11.362	0.014	0.014	0.000	0.000	0.000	0.000
12	4	26	TYR	0	0.012	0.000	12.917	0.068	0.068	0.000	0.000	0.000	0.000
13	4	27	MET	0	0.034	0.006	12.237	-0.044	-0.044	0.000	0.000	0.000	0.000
14	4	28	GLN	0	0.047	0.011	9.840	-0.017	-0.017	0.000	0.000	0.000	0.000
15	4	29	GLN	0	-0.004	-0.010	10.682	0.031	0.031	0.000	0.000	0.000	0.000
16	4	30	TYR	0	-0.046	-0.021	12.616	0.015	0.015	0.000	0.000	0.000	0.000
17	4	31	GLN	0	-0.069	-0.012	7.526	-0.171	-0.171	0.000	0.000	0.000	0.000
18	4	32	ASN	0	0.036	0.013	4.902	-0.664	-0.618	-0.001	0.000	-0.044	0.000
19	4	33	SER	0	-0.027	-0.013	9.268	-0.022	-0.022	0.000	0.000	0.000	0.000
20	4	34	MET	0	-0.015	-0.008	10.455	0.094	0.094	0.000	0.000	0.000	0.000
21	4	35	ASP	-1	-0.887	-0.939	8.960	0.946	0.946	0.000	0.000	0.000	0.000
22	4	36	THR	0	-0.061	-0.024	12.096	-0.016	-0.016	0.000	0.000	0.000	0.000
23	4	37	GLN	0	-0.007	-0.004	15.406	-0.024	-0.024	0.000	0.000	0.000	0.000
24	4	38	LEU	0	0.013	0.005	17.199	-0.039	-0.039	0.000	0.000	0.000	0.000
25	4	39	GLY	0	-0.019	0.003	20.685	0.010	0.010	0.000	0.000	0.000	0.000
26	4	65	ASN	0	0.025	0.011	11.282	-0.046	-0.046	0.000	0.000	0.000	0.000
27	4	66	ASP	-1	-0.834	-0.929	13.079	0.309	0.309	0.000	0.000	0.000	0.000
28	4	67	TRP	0	0.054	0.034	15.397	-0.018	-0.018	0.000	0.000	0.000	0.000
29	4	68	PHE	0	0.057	0.005	16.369	-0.010	-0.010	0.000	0.000	0.000	0.000
30	4	69	SER	0	0.031	0.019	15.569	-0.007	-0.007	0.000	0.000	0.000	0.000
31	4	70	LYS	1	0.812	0.917	17.640	-0.332	-0.332	0.000	0.000	0.000	0.000
32	4	71	LEU	0	0.010	0.008	20.852	-0.016	-0.016	0.000	0.000	0.000	0.000
33	4	72	ALA	0	0.001	0.027	19.506	-0.015	-0.015	0.000	0.000	0.000	0.000
34	4	73	SER	0	-0.078	-0.058	19.856	-0.003	-0.003	0.000	0.000	0.000	0.000
35	4	74	SER	0	-0.039	-0.043	22.383	-0.005	-0.005	0.000	0.000	0.000	0.000
36	4	75	ALA	0	-0.016	0.014	25.609	-0.013	-0.013	0.000	0.000	0.000	0.000
37	4	76	PHE	0	-0.010	-0.001	27.504	0.003	0.003	0.000	0.000	0.000	0.000
38	4	77	SER	0	0.011	-0.007	30.644	-0.005	-0.005	0.000	0.000	0.000	0.000
39	4	78	GLY	0	-0.011	0.005	32.502	-0.002	-0.002	0.000	0.000	0.000	0.000
40	4	79	LEU	0	0.007	-0.006	36.037	-0.002	-0.002	0.000	0.000	0.000	0.000
41	4	80	PHE	0	-0.026	-0.010	36.919	0.000	0.000	0.000	0.000	0.000	0.000
42	4	81	GLY	0	0.027	-0.001	41.646	-0.004	-0.004	0.000	0.000	0.000	0.000
43	4	82	ALA	0	-0.028	-0.004	44.409	0.002	0.002	0.000	0.000	0.000	0.000
44	4	83	LEU	0	0.003	0.013	41.207	-0.001	-0.001	0.000	0.000	0.000	0.000
45	4	84	LEU	0	0.000	-0.003	44.427	-0.001	-0.001	0.000	0.000	0.000	0.000
46	4	85	ALA	0	0.006	0.010	46.414	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)