FMO DATABASE

FMODB ID: 3Q32L

Calculation Name: 3ZDM-B-Xray321

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ZDM

Chain ID: B

ChEMBL ID:

UniProt ID: Q12285

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	52
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-225932.273407
FMO2-HF: Nuclear repulsion	206445.006003
FMO2-HF: Total energy	-19487.267404
FMO2-MP2: Total energy	-19543.183958

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(B:1:ACE )

Summations of interaction energy for fragment #1(B:1:ACE )

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.
-0.499	1.176	-0.007	-0.809	-0.858	-0.003

Interaction energy analysis for fragmet #1(B:1:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.007 / 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	B	3	ALA	0	0.021	0.045	3.800	-0.210	1.465	-0.007	-0.809	-0.858	-0.003
4	B	4	SER	0	0.003	-0.003	5.954	-0.018	-0.018	0.000	0.000	0.000	0.000
5	B	5	LYS	1	0.976	0.959	8.797	0.304	0.304	0.000	0.000	0.000	0.000
6	B	6	GLU	-1	-0.861	-0.915	10.628	-0.125	-0.125	0.000	0.000	0.000	0.000
7	B	7	GLU	-1	-0.859	-0.928	9.200	-0.553	-0.553	0.000	0.000	0.000	0.000
8	B	8	ILE	0	-0.058	-0.028	6.234	0.109	0.109	0.000	0.000	0.000	0.000
9	B	9	ALA	0	0.001	0.004	10.195	0.060	0.060	0.000	0.000	0.000	0.000
10	B	10	ALA	0	0.077	0.024	13.813	0.028	0.028	0.000	0.000	0.000	0.000
11	B	11	LEU	0	-0.027	-0.022	9.716	0.034	0.034	0.000	0.000	0.000	0.000
12	B	12	ILE	0	-0.050	-0.007	12.643	0.029	0.029	0.000	0.000	0.000	0.000
13	B	13	VAL	0	0.030	0.014	15.306	0.006	0.006	0.000	0.000	0.000	0.000
14	B	14	ASN	0	-0.011	-0.003	16.698	0.020	0.020	0.000	0.000	0.000	0.000
15	B	15	TYR	0	0.017	0.017	16.450	0.009	0.009	0.000	0.000	0.000	0.000
16	B	16	PHE	0	0.029	0.011	18.418	0.002	0.002	0.000	0.000	0.000	0.000
17	B	17	SER	0	0.023	0.004	21.192	-0.007	-0.007	0.000	0.000	0.000	0.000
18	B	18	SER	0	-0.079	-0.044	21.191	0.001	0.001	0.000	0.000	0.000	0.000
19	B	19	ILE	0	0.003	-0.001	22.081	-0.002	-0.002	0.000	0.000	0.000	0.000
20	B	20	VAL	0	-0.001	-0.003	24.575	-0.004	-0.004	0.000	0.000	0.000	0.000
21	B	21	GLU	-1	-0.970	-0.984	26.243	0.024	0.024	0.000	0.000	0.000	0.000
22	B	22	LYS	1	0.851	0.934	24.146	-0.074	-0.074	0.000	0.000	0.000	0.000
23	B	23	LYS	1	0.895	0.948	28.895	-0.031	-0.031	0.000	0.000	0.000	0.000
24	B	24	GLU	-1	-0.913	-0.956	25.352	0.090	0.090	0.000	0.000	0.000	0.000
25	B	25	ILE	0	-0.055	-0.016	26.519	0.004	0.004	0.000	0.000	0.000	0.000
26	B	26	SER	0	-0.022	-0.014	29.793	-0.003	-0.003	0.000	0.000	0.000	0.000
27	B	27	GLU	-1	-0.886	-0.955	31.743	0.027	0.027	0.000	0.000	0.000	0.000
28	B	28	ASP	-1	-0.866	-0.912	33.034	0.028	0.028	0.000	0.000	0.000	0.000
29	B	29	GLY	0	-0.040	-0.035	30.020	0.000	0.000	0.000	0.000	0.000	0.000
30	B	30	ALA	0	0.012	-0.019	28.423	0.002	0.002	0.000	0.000	0.000	0.000
31	B	31	ASP	-1	-0.887	-0.932	28.813	0.020	0.020	0.000	0.000	0.000	0.000
32	B	32	SER	0	-0.071	-0.041	28.252	-0.003	-0.003	0.000	0.000	0.000	0.000
33	B	33	LEU	0	-0.017	-0.014	23.027	0.000	0.000	0.000	0.000	0.000	0.000
34	B	34	ASN	0	0.019	0.011	24.637	-0.003	-0.003	0.000	0.000	0.000	0.000
35	B	35	VAL	0	0.032	0.025	26.252	-0.005	-0.005	0.000	0.000	0.000	0.000
36	B	36	ALA	0	-0.026	-0.009	22.331	-0.005	-0.005	0.000	0.000	0.000	0.000
37	B	37	MET	0	-0.022	-0.008	21.161	-0.004	-0.004	0.000	0.000	0.000	0.000
38	B	38	ASP	-1	-0.807	-0.883	21.962	-0.018	-0.018	0.000	0.000	0.000	0.000
39	B	39	CYS	0	-0.064	-0.031	23.377	-0.007	-0.007	0.000	0.000	0.000	0.000
40	B	40	ILE	0	-0.068	-0.033	17.092	-0.005	-0.005	0.000	0.000	0.000	0.000
41	B	41	SER	0	0.003	-0.018	18.916	-0.015	-0.015	0.000	0.000	0.000	0.000
42	B	42	GLU	-1	-0.921	-0.940	20.510	-0.052	-0.052	0.000	0.000	0.000	0.000
43	B	43	ALA	0	-0.080	-0.038	19.087	-0.010	-0.010	0.000	0.000	0.000	0.000
44	B	44	PHE	0	-0.127	-0.085	14.079	-0.015	-0.015	0.000	0.000	0.000	0.000
45	B	45	GLY	0	-0.019	0.011	17.448	-0.026	-0.026	0.000	0.000	0.000	0.000
46	B	46	PHE	0	-0.038	-0.016	16.470	-0.009	-0.009	0.000	0.000	0.000	0.000
47	B	47	GLU	-1	-0.897	-0.956	20.644	-0.043	-0.043	0.000	0.000	0.000	0.000
48	B	48	ARG	1	0.877	0.917	21.836	-0.005	-0.005	0.000	0.000	0.000	0.000
49	B	49	GLU	-1	-0.946	-0.988	22.563	-0.029	-0.029	0.000	0.000	0.000	0.000
50	B	50	ALA	0	-0.070	-0.032	21.031	0.000	0.000	0.000	0.000	0.000	0.000
51	B	51	VAL	0	-0.050	-0.011	17.517	-0.006	-0.006	0.000	0.000	0.000	0.000
52	B	52	NME	0	-0.019	0.004	18.494	-0.009	-0.009	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:1:ACE )