FMO DATABASE

FMODB ID: K3463

Calculation Name: 4DCZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4DCZ

Chain ID: A

ChEMBL ID:

UniProt ID: P47442

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	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	55
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-298663.254688
FMO2-HF: Nuclear repulsion	276191.996991
FMO2-HF: Total energy	-22471.257696
FMO2-MP2: Total energy	-22538.376924

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:149:GLN)

Summations of interaction energy for fragment #1(A:149:GLN)

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.
2.118	5.199	0.069	-1.623	-1.527	0.004

Interaction energy analysis for fragmet #1(A:149:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / q_NPA : 0.004

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	A	151	LYS	1	0.965	0.974	3.539	1.956	4.912	0.070	-1.618	-1.408	0.004
4	A	152	ASP	-1	-0.921	-0.939	6.179	1.737	1.737	0.000	0.000	0.000	0.000
5	A	153	PRO	0	0.014	-0.004	7.558	-0.468	-0.468	0.000	0.000	0.000	0.000
6	A	154	ASP	-1	-0.897	-0.924	11.233	0.128	0.128	0.000	0.000	0.000	0.000
7	A	155	GLU	-1	-1.013	-1.019	10.348	-0.426	-0.426	0.000	0.000	0.000	0.000
8	A	156	LEU	0	-0.109	-0.019	9.624	-0.227	-0.227	0.000	0.000	0.000	0.000
9	A	157	ARG	1	0.963	0.945	11.992	0.470	0.470	0.000	0.000	0.000	0.000
10	A	158	SER	0	-0.007	0.021	13.386	-0.154	-0.154	0.000	0.000	0.000	0.000
11	A	159	LYS	1	0.904	0.959	12.828	0.956	0.956	0.000	0.000	0.000	0.000
12	A	160	VAL	0	-0.030	-0.021	14.614	-0.025	-0.025	0.000	0.000	0.000	0.000
13	A	161	PRO	0	-0.014	-0.010	18.437	0.035	0.035	0.000	0.000	0.000	0.000
14	A	162	GLY	0	0.001	-0.003	20.527	0.012	0.012	0.000	0.000	0.000	0.000
15	A	163	GLU	-1	-0.971	-0.972	20.149	-0.331	-0.331	0.000	0.000	0.000	0.000
16	A	164	VAL	0	0.000	0.003	17.061	-0.049	-0.049	0.000	0.000	0.000	0.000
17	A	165	THR	0	-0.037	-0.013	16.338	0.029	0.029	0.000	0.000	0.000	0.000
18	A	166	ALA	0	0.049	0.002	16.569	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	167	SER	0	-0.008	-0.014	12.108	0.035	0.035	0.000	0.000	0.000	0.000
20	A	168	ASP	-1	-0.811	-0.901	11.673	-0.781	-0.781	0.000	0.000	0.000	0.000
21	A	169	TRP	0	0.039	0.004	11.728	0.013	0.013	0.000	0.000	0.000	0.000
22	A	170	GLU	-1	-0.933	-0.980	11.820	0.052	0.052	0.000	0.000	0.000	0.000
23	A	171	ALA	0	-0.054	-0.006	7.215	0.081	0.081	0.000	0.000	0.000	0.000
24	A	172	LEU	0	-0.012	-0.005	6.915	0.067	0.067	0.000	0.000	0.000	0.000
25	A	173	VAL	0	0.010	0.014	8.883	0.306	0.306	0.000	0.000	0.000	0.000
26	A	174	GLY	0	-0.005	0.002	9.074	0.033	0.033	0.000	0.000	0.000	0.000
27	A	175	ASP	-1	-0.789	-0.828	5.916	2.909	2.909	0.000	0.000	0.000	0.000
28	A	176	THR	0	0.012	-0.013	8.288	-0.076	-0.076	0.000	0.000	0.000	0.000
29	A	177	ARG	1	0.760	0.828	4.663	-3.854	-3.729	-0.001	-0.005	-0.119	0.000
30	A	178	TYR	0	-0.031	-0.052	7.133	-0.285	-0.285	0.000	0.000	0.000	0.000
31	A	179	GLY	0	0.035	0.001	12.072	-0.193	-0.193	0.000	0.000	0.000	0.000
32	A	180	TYR	0	-0.071	-0.034	13.911	0.177	0.177	0.000	0.000	0.000	0.000
33	A	181	PHE	0	0.029	0.009	13.167	-0.043	-0.043	0.000	0.000	0.000	0.000
34	A	182	ASP	-1	-0.862	-0.918	17.635	0.340	0.340	0.000	0.000	0.000	0.000
35	A	183	GLU	-1	-0.958	-0.989	21.327	0.327	0.327	0.000	0.000	0.000	0.000
36	A	184	THR	0	-0.076	-0.042	23.872	-0.009	-0.009	0.000	0.000	0.000	0.000
37	A	185	GLY	0	-0.052	-0.012	20.481	-0.005	-0.005	0.000	0.000	0.000	0.000
38	A	186	ASP	-1	-0.913	-0.950	20.060	0.251	0.251	0.000	0.000	0.000	0.000
39	A	187	TRP	0	-0.049	-0.015	11.813	0.078	0.078	0.000	0.000	0.000	0.000
40	A	188	SER	0	-0.004	0.000	17.357	-0.071	-0.071	0.000	0.000	0.000	0.000
41	A	189	TRP	0	0.003	-0.001	12.441	0.092	0.092	0.000	0.000	0.000	0.000
42	A	190	LYS	1	0.880	0.932	14.154	-0.928	-0.928	0.000	0.000	0.000	0.000
43	A	191	GLY	0	0.006	-0.013	17.056	0.001	0.001	0.000	0.000	0.000	0.000
44	A	192	TYR	0	-0.044	-0.033	17.576	-0.022	-0.022	0.000	0.000	0.000	0.000
45	A	193	PHE	0	0.008	0.011	12.910	0.000	0.000	0.000	0.000	0.000	0.000
46	A	194	ASP	-1	-0.810	-0.897	18.556	-0.107	-0.107	0.000	0.000	0.000	0.000
47	A	195	GLU	-1	-0.931	-0.964	21.771	-0.135	-0.135	0.000	0.000	0.000	0.000
48	A	196	GLN	0	-0.076	-0.053	22.183	-0.029	-0.029	0.000	0.000	0.000	0.000
49	A	197	GLY	0	0.047	0.029	19.199	-0.054	-0.054	0.000	0.000	0.000	0.000
50	A	198	LYS	1	0.841	0.918	17.204	-0.014	-0.014	0.000	0.000	0.000	0.000
51	A	199	TRP	0	0.005	0.044	14.239	0.006	0.006	0.000	0.000	0.000	0.000
52	A	200	VAL	0	-0.057	-0.026	16.283	0.023	0.023	0.000	0.000	0.000	0.000
53	A	201	TRP	0	0.034	0.005	12.712	0.037	0.037	0.000	0.000	0.000	0.000
54	A	202	ASN	0	-0.019	-0.011	19.014	-0.071	-0.071	0.000	0.000	0.000	0.000
55	A	203	GLU	-1	-0.993	-0.986	20.006	0.327	0.327	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:149:GLN)