FMO DATABASE

FMODB ID: R52J8

Calculation Name: 2ZXX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2ZXX

Chain ID: A

ChEMBL ID:

UniProt ID: Q8R4E9

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	OptHSide
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	70
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-327501.479885
FMO2-HF: Nuclear repulsion	298278.394233
FMO2-HF: Total energy	-29223.085652
FMO2-MP2: Total energy	-29309.347662

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:88:LYS)

Summations of interaction energy for fragment #1(A:88:LYS)

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.
27.014	34.836	5.687	-4.953	-8.558	-0.004

Interaction energy analysis for fragmet #1(A:88:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.981 / q_NPA : 0.973

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

Sort

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	90	ASN	0	-0.025	-0.002	2.258	7.005	11.083	1.748	-2.588	-3.239	0.005
4	A	91	PRO	0	0.038	0.016	3.694	-0.757	-0.471	0.000	0.031	-0.318	0.000
5	A	92	SER	0	-0.033	-0.021	5.847	0.589	0.589	0.000	0.000	0.000	0.000
6	A	93	SER	0	-0.011	-0.010	2.345	-5.768	-4.589	3.046	-1.438	-2.787	-0.011
7	A	94	GLN	0	0.045	0.022	4.282	5.675	5.789	-0.001	-0.029	-0.084	0.000
8	A	95	TYR	0	0.045	0.025	2.993	-1.309	0.461	0.890	-0.870	-1.790	0.002
9	A	96	TRP	0	0.009	-0.031	3.663	3.658	4.053	0.004	-0.059	-0.340	0.000
10	A	97	LYS	1	0.889	0.952	6.995	22.325	22.325	0.000	0.000	0.000	0.000
11	A	98	GLU	-1	-0.933	-0.964	8.086	-27.574	-27.574	0.000	0.000	0.000	0.000
12	A	99	VAL	0	0.014	0.009	7.165	1.946	1.946	0.000	0.000	0.000	0.000
13	A	100	ALA	0	-0.010	-0.006	9.979	1.507	1.507	0.000	0.000	0.000	0.000
14	A	101	GLU	-1	-0.764	-0.847	12.407	-13.462	-13.462	0.000	0.000	0.000	0.000
15	A	102	GLN	0	-0.029	-0.008	11.205	0.183	0.183	0.000	0.000	0.000	0.000
16	A	103	ARG	1	0.989	0.982	10.792	18.872	18.872	0.000	0.000	0.000	0.000
17	A	104	ARG	1	0.916	0.967	15.704	14.121	14.121	0.000	0.000	0.000	0.000
18	A	105	LYS	1	0.864	0.914	17.835	15.426	15.426	0.000	0.000	0.000	0.000
19	A	106	ALA	0	0.010	0.003	18.569	0.564	0.564	0.000	0.000	0.000	0.000
20	A	107	LEU	0	0.003	-0.006	19.752	0.500	0.500	0.000	0.000	0.000	0.000
21	A	108	TYR	0	-0.010	-0.012	21.664	0.547	0.547	0.000	0.000	0.000	0.000
22	A	109	GLU	-1	-0.852	-0.913	23.421	-10.170	-10.170	0.000	0.000	0.000	0.000
23	A	110	ALA	0	0.017	0.002	24.152	0.393	0.393	0.000	0.000	0.000	0.000
24	A	111	LEU	0	-0.038	-0.015	25.120	0.346	0.346	0.000	0.000	0.000	0.000
25	A	112	LYS	1	0.853	0.911	27.214	10.523	10.523	0.000	0.000	0.000	0.000
26	A	113	GLU	-1	-0.830	-0.919	28.940	-8.415	-8.415	0.000	0.000	0.000	0.000
27	A	114	ASN	0	-0.004	0.003	29.527	0.384	0.384	0.000	0.000	0.000	0.000
28	A	115	GLU	-1	-0.868	-0.921	31.399	-7.965	-7.965	0.000	0.000	0.000	0.000
29	A	116	LYS	1	0.852	0.919	33.653	8.387	8.387	0.000	0.000	0.000	0.000
30	A	117	LEU	0	-0.039	-0.023	32.466	0.254	0.254	0.000	0.000	0.000	0.000
31	A	118	HIS	0	-0.033	-0.017	33.479	0.302	0.302	0.000	0.000	0.000	0.000
32	A	119	LYS	1	0.917	0.953	37.270	7.818	7.818	0.000	0.000	0.000	0.000
33	A	120	GLU	-1	-0.926	-0.955	38.293	-7.248	-7.248	0.000	0.000	0.000	0.000
34	A	121	ILE	0	-0.016	-0.028	38.156	0.171	0.171	0.000	0.000	0.000	0.000
35	A	122	GLU	-1	-0.921	-0.942	41.681	-6.736	-6.736	0.000	0.000	0.000	0.000
36	A	123	GLN	0	-0.013	-0.016	43.618	0.126	0.126	0.000	0.000	0.000	0.000
37	A	124	LYS	1	0.898	0.942	41.792	7.043	7.043	0.000	0.000	0.000	0.000
38	A	125	ASP	-1	-0.862	-0.915	45.007	-6.339	-6.339	0.000	0.000	0.000	0.000
39	A	126	SER	0	-0.097	-0.041	47.336	0.163	0.163	0.000	0.000	0.000	0.000
40	A	127	GLU	-1	-0.833	-0.921	49.476	-5.494	-5.494	0.000	0.000	0.000	0.000
41	A	128	ILE	0	-0.017	-0.013	47.894	0.134	0.134	0.000	0.000	0.000	0.000
42	A	129	ALA	0	-0.025	-0.018	51.524	0.117	0.117	0.000	0.000	0.000	0.000
43	A	130	ARG	1	0.785	0.878	53.460	5.476	5.476	0.000	0.000	0.000	0.000
44	A	131	LEU	0	0.036	0.016	53.358	0.101	0.101	0.000	0.000	0.000	0.000
45	A	132	ARG	1	0.937	0.974	50.679	5.735	5.735	0.000	0.000	0.000	0.000
46	A	133	LYS	1	0.766	0.876	57.038	4.875	4.875	0.000	0.000	0.000	0.000
47	A	134	GLU	-1	-0.838	-0.918	59.391	-5.009	-5.009	0.000	0.000	0.000	0.000
48	A	135	ASN	0	-0.032	-0.013	59.338	0.061	0.061	0.000	0.000	0.000	0.000
49	A	136	LYS	1	0.948	0.971	60.299	4.987	4.987	0.000	0.000	0.000	0.000
50	A	137	ASP	-1	-0.827	-0.895	62.753	-4.654	-4.654	0.000	0.000	0.000	0.000
51	A	138	LEU	0	-0.012	-0.004	63.727	0.077	0.077	0.000	0.000	0.000	0.000
52	A	139	ALA	0	-0.017	-0.010	65.052	0.027	0.027	0.000	0.000	0.000	0.000
53	A	140	GLU	-1	-0.866	-0.929	66.473	-4.210	-4.210	0.000	0.000	0.000	0.000
54	A	141	VAL	0	-0.024	-0.015	67.964	0.039	0.039	0.000	0.000	0.000	0.000
55	A	142	ALA	0	-0.002	-0.010	65.798	0.013	0.013	0.000	0.000	0.000	0.000
56	A	143	GLU	-1	-0.925	-0.962	67.764	-4.342	-4.342	0.000	0.000	0.000	0.000
57	A	144	HIS	0	-0.022	-0.012	70.378	0.038	0.038	0.000	0.000	0.000	0.000
58	A	145	VAL	0	-0.017	-0.014	67.357	0.029	0.029	0.000	0.000	0.000	0.000
59	A	146	GLN	0	-0.007	0.001	67.574	0.003	0.003	0.000	0.000	0.000	0.000
60	A	147	TYR	0	0.005	0.020	70.455	0.046	0.046	0.000	0.000	0.000	0.000
61	A	148	MET	0	-0.007	-0.013	73.024	0.058	0.058	0.000	0.000	0.000	0.000
62	A	149	ALA	0	-0.010	0.005	70.036	0.016	0.016	0.000	0.000	0.000	0.000
63	A	150	GLU	-1	-0.809	-0.895	72.016	-3.968	-3.968	0.000	0.000	0.000	0.000
64	A	151	VAL	0	-0.042	-0.027	74.194	0.037	0.037	0.000	0.000	0.000	0.000
65	A	152	ILE	0	-0.041	-0.021	73.363	0.045	0.045	0.000	0.000	0.000	0.000
66	A	153	GLU	-1	-0.930	-0.969	71.852	-4.251	-4.251	0.000	0.000	0.000	0.000
67	A	154	ARG	1	0.794	0.885	75.018	3.931	3.931	0.000	0.000	0.000	0.000
68	A	155	LEU	0	-0.113	-0.047	78.263	0.055	0.055	0.000	0.000	0.000	0.000
69	A	156	SER	0	-0.066	-0.034	76.360	0.005	0.005	0.000	0.000	0.000	0.000
70	A	157	ASN	0	0.004	0.020	77.533	-0.048	-0.048	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:88:LYS)