FMO DATABASE

FMODB ID: ZV9QN

Calculation Name: 1B34-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1B34

Chain ID: B

ChEMBL ID:

UniProt ID: P62314

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	74
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-467286.275627
FMO2-HF: Nuclear repulsion	437203.476305
FMO2-HF: Total energy	-30082.799322
FMO2-MP2: Total energy	-30167.976703

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:26:THR)

Summations of interaction energy for fragment #1(B:26:THR)

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.
-6.51	-0.815	2.559	-2.945	-5.308	0.014

Interaction energy analysis for fragmet #1(B:26:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.032 / q_NPA : -0.002

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	B	28	PRO	0	0.043	0.023	3.872	0.125	1.306	-0.006	-0.585	-0.590	0.001
4	B	29	LEU	0	0.028	-0.004	2.387	-1.202	0.275	1.062	-0.695	-1.844	0.000
5	B	30	SER	0	-0.034	-0.013	2.522	-0.646	1.816	1.460	-1.462	-2.461	0.011
6	B	31	VAL	0	0.028	0.009	3.808	-1.951	-1.458	0.044	-0.197	-0.339	0.002
7	B	32	LEU	0	0.020	0.027	6.804	-0.257	-0.257	0.000	0.000	0.000	0.000
8	B	33	THR	0	0.001	-0.003	5.543	-0.514	-0.514	0.000	0.000	0.000	0.000
9	B	34	GLN	0	0.006	0.014	7.675	-0.367	-0.367	0.000	0.000	0.000	0.000
10	B	35	SER	0	-0.026	-0.034	9.613	-0.194	-0.194	0.000	0.000	0.000	0.000
11	B	36	VAL	0	-0.025	-0.006	11.293	-0.085	-0.085	0.000	0.000	0.000	0.000
12	B	37	LYS	1	0.934	0.975	11.924	-0.142	-0.142	0.000	0.000	0.000	0.000
13	B	38	ASN	0	-0.018	-0.017	13.505	-0.054	-0.054	0.000	0.000	0.000	0.000
14	B	39	ASN	0	0.027	0.019	15.522	-0.022	-0.022	0.000	0.000	0.000	0.000
15	B	40	THR	0	0.007	0.018	14.380	-0.030	-0.030	0.000	0.000	0.000	0.000
16	B	41	GLN	0	-0.055	-0.020	16.195	0.015	0.015	0.000	0.000	0.000	0.000
17	B	42	VAL	0	0.000	-0.002	12.181	-0.007	-0.007	0.000	0.000	0.000	0.000
18	B	43	LEU	0	0.029	0.009	15.248	-0.007	-0.007	0.000	0.000	0.000	0.000
19	B	44	ILE	0	-0.005	-0.006	13.112	-0.006	-0.006	0.000	0.000	0.000	0.000
20	B	45	ASN	0	0.012	0.014	14.379	-0.022	-0.022	0.000	0.000	0.000	0.000
21	B	46	CYS	0	0.016	-0.017	14.984	0.007	0.007	0.000	0.000	0.000	0.000
22	B	47	ARG	1	0.929	0.947	15.013	-0.029	-0.029	0.000	0.000	0.000	0.000
23	B	48	ASN	0	0.007	0.018	19.184	-0.001	-0.001	0.000	0.000	0.000	0.000
24	B	49	ASN	0	0.044	0.027	21.262	-0.001	-0.001	0.000	0.000	0.000	0.000
25	B	50	LYS	1	0.937	0.962	21.053	-0.048	-0.048	0.000	0.000	0.000	0.000
26	B	51	LYS	1	0.888	0.950	19.172	-0.021	-0.021	0.000	0.000	0.000	0.000
27	B	52	LEU	0	0.025	0.019	17.880	0.001	0.001	0.000	0.000	0.000	0.000
28	B	53	LEU	0	-0.001	0.008	17.886	0.014	0.014	0.000	0.000	0.000	0.000
29	B	54	GLY	0	0.059	0.024	18.256	-0.011	-0.011	0.000	0.000	0.000	0.000
30	B	55	ARG	1	0.847	0.932	17.336	-0.124	-0.124	0.000	0.000	0.000	0.000
31	B	56	VAL	0	0.030	0.007	11.736	-0.013	-0.013	0.000	0.000	0.000	0.000
32	B	57	LYS	1	0.918	0.974	15.018	-0.183	-0.183	0.000	0.000	0.000	0.000
33	B	58	ALA	0	0.019	0.002	14.195	0.002	0.002	0.000	0.000	0.000	0.000
34	B	59	PHE	0	-0.024	-0.013	6.804	-0.005	-0.005	0.000	0.000	0.000	0.000
35	B	60	ASP	-1	-0.717	-0.840	10.357	0.398	0.398	0.000	0.000	0.000	0.000
36	B	61	ARG	1	0.943	0.950	4.329	-0.942	-0.860	-0.001	-0.006	-0.074	0.000
37	B	62	HIS	0	0.012	0.018	7.602	-0.030	-0.030	0.000	0.000	0.000	0.000
38	B	63	CYS	0	-0.049	-0.022	7.527	-0.025	-0.025	0.000	0.000	0.000	0.000
39	B	64	ASN	0	-0.002	-0.005	9.888	-0.099	-0.099	0.000	0.000	0.000	0.000
40	B	65	MET	0	-0.062	-0.036	10.708	0.099	0.099	0.000	0.000	0.000	0.000
41	B	66	VAL	0	0.017	0.031	14.631	-0.055	-0.055	0.000	0.000	0.000	0.000
42	B	67	LEU	0	-0.016	-0.019	14.951	0.036	0.036	0.000	0.000	0.000	0.000
43	B	68	GLU	-1	-0.826	-0.919	18.657	0.120	0.120	0.000	0.000	0.000	0.000
44	B	69	ASN	0	-0.036	-0.023	21.170	-0.003	-0.003	0.000	0.000	0.000	0.000
45	B	70	VAL	0	0.003	0.002	20.284	0.000	0.000	0.000	0.000	0.000	0.000
46	B	71	LYS	1	0.924	0.974	22.521	-0.089	-0.089	0.000	0.000	0.000	0.000
47	B	72	GLU	-1	-0.847	-0.911	22.628	0.077	0.077	0.000	0.000	0.000	0.000
48	B	73	MET	0	-0.001	-0.002	22.366	-0.008	-0.008	0.000	0.000	0.000	0.000
49	B	93	ASP	-1	-0.888	-0.947	28.556	0.045	0.045	0.000	0.000	0.000	0.000
50	B	94	ARG	1	0.842	0.894	26.573	-0.066	-0.066	0.000	0.000	0.000	0.000
51	B	95	TYR	0	0.009	0.003	26.812	0.007	0.007	0.000	0.000	0.000	0.000
52	B	96	ILE	0	-0.019	-0.017	24.430	-0.002	-0.002	0.000	0.000	0.000	0.000
53	B	97	SER	0	-0.003	0.005	24.815	0.011	0.011	0.000	0.000	0.000	0.000
54	B	98	LYS	1	0.895	0.929	23.562	-0.100	-0.100	0.000	0.000	0.000	0.000
55	B	99	MET	0	0.016	0.021	20.050	-0.007	-0.007	0.000	0.000	0.000	0.000
56	B	100	PHE	0	0.022	0.015	17.758	0.021	0.021	0.000	0.000	0.000	0.000
57	B	101	LEU	0	-0.008	-0.007	14.895	-0.023	-0.023	0.000	0.000	0.000	0.000
58	B	102	ARG	1	0.905	0.925	16.263	-0.074	-0.074	0.000	0.000	0.000	0.000
59	B	103	GLY	0	0.066	0.021	12.729	-0.014	-0.014	0.000	0.000	0.000	0.000
60	B	104	ASP	-1	-0.817	-0.879	13.070	0.077	0.077	0.000	0.000	0.000	0.000
61	B	105	SER	0	-0.028	-0.014	15.181	-0.031	-0.031	0.000	0.000	0.000	0.000
62	B	106	VAL	0	-0.039	-0.020	10.752	-0.016	-0.016	0.000	0.000	0.000	0.000
63	B	107	ILE	0	-0.032	0.003	12.897	-0.021	-0.021	0.000	0.000	0.000	0.000
64	B	108	VAL	0	0.011	-0.003	10.761	-0.052	-0.052	0.000	0.000	0.000	0.000
65	B	109	VAL	0	-0.006	-0.004	9.033	0.049	0.049	0.000	0.000	0.000	0.000
66	B	110	LEU	0	0.023	0.016	10.406	-0.052	-0.052	0.000	0.000	0.000	0.000
67	B	111	ARG	1	0.933	0.959	10.765	0.056	0.056	0.000	0.000	0.000	0.000
68	B	112	ASN	0	-0.019	-0.011	14.080	-0.039	-0.039	0.000	0.000	0.000	0.000
69	B	113	PRO	0	-0.010	-0.005	16.389	0.012	0.012	0.000	0.000	0.000	0.000
70	B	114	LEU	0	0.010	0.007	18.792	-0.007	-0.007	0.000	0.000	0.000	0.000
71	B	115	ILE	0	-0.002	-0.010	19.135	0.000	0.000	0.000	0.000	0.000	0.000
72	B	116	ALA	0	0.022	0.022	23.205	0.002	0.002	0.000	0.000	0.000	0.000
73	B	117	GLY	0	0.023	0.013	26.126	-0.004	-0.004	0.000	0.000	0.000	0.000
74	B	118	LYS	1	0.985	0.995	25.301	0.017	0.017	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(B:26:THR)