FMO DATABASE

FMODB ID: 72QLK

Calculation Name: 3RCZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3RCZ

Chain ID: A

ChEMBL ID:

UniProt ID: Q9USX3

Base Structure: X-ray

Registration Date: 2023-09-19

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	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422
Remarks

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. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-500222.709115
FMO2-HF: Nuclear repulsion	469956.753732
FMO2-HF: Total energy	-30265.955383
FMO2-MP2: Total energy	-30355.561323

3D Structure Molmil

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:330:HIS)

Summations of interaction energy for fragment #1(A:330:HIS)

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.
-6.926	-3.839	-0.015	-1.389	-1.684	0.002

Interaction energy analysis for fragmet #1(A:330:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.006 / q_NPA : -0.017

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	333	LEU	0	-0.051	-0.014	3.219	-2.938	-0.033	-0.014	-1.361	-1.531	0.002
4	A	334	ILE	0	0.070	0.061	4.300	-0.899	-0.717	-0.001	-0.028	-0.153	0.000
5	A	335	THR	0	-0.028	-0.025	7.078	0.506	0.506	0.000	0.000	0.000	0.000
6	A	336	LEU	0	0.034	0.039	9.977	-0.138	-0.138	0.000	0.000	0.000	0.000
7	A	337	LEU	0	-0.050	-0.028	13.405	0.113	0.113	0.000	0.000	0.000	0.000
8	A	338	LEU	0	-0.007	0.002	16.060	-0.020	-0.020	0.000	0.000	0.000	0.000
9	A	339	ARG	1	0.855	0.915	19.392	0.149	0.149	0.000	0.000	0.000	0.000
10	A	340	SER	0	0.019	0.010	22.854	0.000	0.000	0.000	0.000	0.000	0.000
11	A	341	SER	0	-0.043	-0.027	26.091	0.000	0.000	0.000	0.000	0.000	0.000
12	A	342	LYS	1	0.911	0.925	29.477	-0.021	-0.021	0.000	0.000	0.000	0.000
13	A	343	SER	0	-0.012	0.015	26.054	0.011	0.011	0.000	0.000	0.000	0.000
14	A	344	GLU	-1	-0.906	-0.945	25.582	0.054	0.054	0.000	0.000	0.000	0.000
15	A	345	ASP	-1	-0.823	-0.892	21.320	-0.059	-0.059	0.000	0.000	0.000	0.000
16	A	346	LEU	0	-0.018	-0.003	18.134	0.028	0.028	0.000	0.000	0.000	0.000
17	A	347	ARG	1	0.911	0.963	14.820	0.112	0.112	0.000	0.000	0.000	0.000
18	A	348	LEU	0	-0.021	-0.008	13.825	0.089	0.089	0.000	0.000	0.000	0.000
19	A	349	SER	0	0.041	0.027	8.515	-0.082	-0.082	0.000	0.000	0.000	0.000
20	A	350	ILE	0	-0.060	-0.030	9.717	0.291	0.291	0.000	0.000	0.000	0.000
21	A	351	PRO	0	0.008	-0.014	7.542	-0.130	-0.130	0.000	0.000	0.000	0.000
22	A	352	VAL	0	0.054	0.027	6.337	0.005	0.005	0.000	0.000	0.000	0.000
23	A	353	ASP	-1	-0.945	-0.970	8.887	0.908	0.908	0.000	0.000	0.000	0.000
24	A	354	PHE	0	-0.040	-0.018	10.881	0.129	0.129	0.000	0.000	0.000	0.000
25	A	355	THR	0	-0.004	0.005	13.492	-0.120	-0.120	0.000	0.000	0.000	0.000
26	A	356	VAL	0	0.076	0.049	16.525	0.032	0.032	0.000	0.000	0.000	0.000
27	A	357	LYS	1	0.942	0.966	18.144	-0.131	-0.131	0.000	0.000	0.000	0.000
28	A	358	ASP	-1	-0.895	-0.940	16.453	0.348	0.348	0.000	0.000	0.000	0.000
29	A	359	LEU	0	0.003	0.009	14.466	0.048	0.048	0.000	0.000	0.000	0.000
30	A	360	ILE	0	0.014	0.005	16.919	0.016	0.016	0.000	0.000	0.000	0.000
31	A	361	LYS	1	0.874	0.936	20.356	-0.229	-0.229	0.000	0.000	0.000	0.000
32	A	362	ARG	1	0.966	0.980	13.877	-0.622	-0.622	0.000	0.000	0.000	0.000
33	A	363	TYR	0	0.100	0.045	18.891	0.010	0.010	0.000	0.000	0.000	0.000
34	A	364	CYS	0	-0.061	-0.027	20.107	-0.009	-0.009	0.000	0.000	0.000	0.000
35	A	365	THR	0	-0.022	-0.018	20.977	0.001	0.001	0.000	0.000	0.000	0.000
36	A	366	GLU	-1	-0.987	-0.982	18.674	0.417	0.417	0.000	0.000	0.000	0.000
37	A	367	VAL	0	-0.004	-0.001	21.554	-0.006	-0.006	0.000	0.000	0.000	0.000
38	A	368	LYS	1	0.838	0.934	24.432	-0.260	-0.260	0.000	0.000	0.000	0.000
39	A	369	ILE	0	0.021	0.020	25.988	-0.019	-0.019	0.000	0.000	0.000	0.000
40	A	370	SER	0	-0.045	-0.029	27.217	0.018	0.018	0.000	0.000	0.000	0.000
41	A	371	PHE	0	0.056	0.012	24.225	-0.007	-0.007	0.000	0.000	0.000	0.000
42	A	372	HIS	0	-0.020	-0.025	27.443	-0.004	-0.004	0.000	0.000	0.000	0.000
43	A	373	GLU	-1	-0.892	-0.964	27.836	0.098	0.098	0.000	0.000	0.000	0.000
44	A	374	ARG	1	0.914	0.974	28.798	-0.062	-0.062	0.000	0.000	0.000	0.000
45	A	375	ILE	0	-0.066	-0.019	24.976	-0.013	-0.013	0.000	0.000	0.000	0.000
46	A	376	ARG	1	0.946	0.979	25.019	0.043	0.043	0.000	0.000	0.000	0.000
47	A	377	LEU	0	0.017	0.009	18.907	0.012	0.012	0.000	0.000	0.000	0.000
48	A	378	GLU	-1	-0.917	-0.962	22.758	-0.186	-0.186	0.000	0.000	0.000	0.000
49	A	379	PHE	0	0.058	0.017	17.610	0.031	0.031	0.000	0.000	0.000	0.000
50	A	380	GLU	-1	-0.888	-0.935	20.834	-0.438	-0.438	0.000	0.000	0.000	0.000
51	A	381	GLY	0	-0.063	-0.026	23.586	0.007	0.007	0.000	0.000	0.000	0.000
52	A	382	GLU	-1	-0.956	-0.969	23.831	-0.226	-0.226	0.000	0.000	0.000	0.000
53	A	383	TRP	0	-0.107	-0.077	24.109	0.009	0.009	0.000	0.000	0.000	0.000
54	A	384	LEU	0	0.059	0.029	18.057	0.001	0.001	0.000	0.000	0.000	0.000
55	A	385	ASP	-1	-0.833	-0.914	21.547	-0.014	-0.014	0.000	0.000	0.000	0.000
56	A	386	PRO	0	-0.061	-0.045	20.847	0.005	0.005	0.000	0.000	0.000	0.000
57	A	387	ASN	0	-0.054	-0.056	20.854	0.057	0.057	0.000	0.000	0.000	0.000
58	A	388	ASP	-1	-0.845	-0.890	17.782	-0.128	-0.128	0.000	0.000	0.000	0.000
59	A	389	GLN	0	-0.038	-0.028	13.132	-0.030	-0.030	0.000	0.000	0.000	0.000
60	A	390	VAL	0	0.068	0.028	10.832	-0.066	-0.066	0.000	0.000	0.000	0.000
61	A	391	GLN	0	-0.067	-0.041	8.956	-0.286	-0.286	0.000	0.000	0.000	0.000
62	A	392	SER	0	-0.092	-0.044	11.045	-0.046	-0.046	0.000	0.000	0.000	0.000
63	A	393	THR	0	-0.069	-0.034	13.863	0.037	0.037	0.000	0.000	0.000	0.000
64	A	394	GLU	-1	-0.895	-0.949	14.088	-0.690	-0.690	0.000	0.000	0.000	0.000
65	A	395	LEU	0	-0.101	-0.039	13.264	-0.016	-0.016	0.000	0.000	0.000	0.000
66	A	396	GLU	-1	-0.941	-0.968	10.905	-1.296	-1.296	0.000	0.000	0.000	0.000
67	A	397	ASP	-1	-0.924	-0.987	8.104	-0.633	-0.633	0.000	0.000	0.000	0.000
68	A	398	GLU	-1	-0.957	-0.999	10.196	-0.239	-0.239	0.000	0.000	0.000	0.000
69	A	399	ASP	-1	-0.811	-0.871	13.138	-0.577	-0.577	0.000	0.000	0.000	0.000
70	A	400	GLN	0	-0.081	-0.053	15.411	0.083	0.083	0.000	0.000	0.000	0.000
71	A	401	VAL	0	0.013	0.012	16.710	-0.011	-0.011	0.000	0.000	0.000	0.000
72	A	402	SER	0	-0.024	-0.016	19.456	0.039	0.039	0.000	0.000	0.000	0.000
73	A	403	VAL	0	-0.022	-0.013	21.658	0.006	0.006	0.000	0.000	0.000	0.000
74	A	404	VAL	0	-0.068	-0.039	24.108	0.012	0.012	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:330:HIS)