FMO DATABASE

FMODB ID: 6NK9Z

Calculation Name: 3RCZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

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:

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
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-500292.027177
FMO2-HF: Nuclear repulsion	470025.315078
FMO2-HF: Total energy	-30266.712099
FMO2-MP2: Total energy	-30356.346128

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: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.
-5.811	-2.848	-0.014	-1.357	-1.592	0.001

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 : -0.013 / q_NPA : -0.021

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	-0.070	-0.020	3.422	-2.665	0.094	-0.014	-1.305	-1.440	0.001
4	A	334	ILE	0	0.061	0.048	4.113	-1.136	-0.932	0.000	-0.052	-0.152	0.000
5	A	335	THR	0	-0.091	-0.072	6.965	0.516	0.516	0.000	0.000	0.000	0.000
6	A	336	LEU	0	0.043	0.033	9.840	-0.143	-0.143	0.000	0.000	0.000	0.000
7	A	337	LEU	0	-0.045	-0.019	13.256	0.105	0.105	0.000	0.000	0.000	0.000
8	A	338	LEU	0	0.004	0.014	16.456	-0.017	-0.017	0.000	0.000	0.000	0.000
9	A	339	ARG	1	0.821	0.867	19.311	0.136	0.136	0.000	0.000	0.000	0.000
10	A	340	SER	0	0.010	0.002	22.872	-0.004	-0.004	0.000	0.000	0.000	0.000
11	A	341	SER	0	-0.009	-0.020	26.294	-0.006	-0.006	0.000	0.000	0.000	0.000
12	A	342	LYS	1	0.856	0.917	29.300	-0.031	-0.031	0.000	0.000	0.000	0.000
13	A	343	SER	0	-0.006	0.018	26.702	0.011	0.011	0.000	0.000	0.000	0.000
14	A	344	GLU	-1	-0.880	-0.938	25.681	0.053	0.053	0.000	0.000	0.000	0.000
15	A	345	ASP	-1	-0.811	-0.865	21.632	-0.057	-0.057	0.000	0.000	0.000	0.000
16	A	346	LEU	0	-0.030	-0.018	18.486	0.022	0.022	0.000	0.000	0.000	0.000
17	A	347	ARG	1	0.808	0.900	14.827	0.178	0.178	0.000	0.000	0.000	0.000
18	A	348	LEU	0	-0.039	-0.024	14.019	0.085	0.085	0.000	0.000	0.000	0.000
19	A	349	SER	0	0.026	0.021	8.911	-0.067	-0.067	0.000	0.000	0.000	0.000
20	A	350	ILE	0	-0.042	-0.022	9.596	0.206	0.206	0.000	0.000	0.000	0.000
21	A	351	PRO	0	-0.012	-0.017	7.850	-0.082	-0.082	0.000	0.000	0.000	0.000
22	A	352	VAL	0	0.061	0.035	6.190	-0.039	-0.039	0.000	0.000	0.000	0.000
23	A	353	ASP	-1	-0.801	-0.878	8.877	1.193	1.193	0.000	0.000	0.000	0.000
24	A	354	PHE	0	-0.044	-0.023	11.333	0.093	0.093	0.000	0.000	0.000	0.000
25	A	355	THR	0	0.010	-0.014	13.815	-0.109	-0.109	0.000	0.000	0.000	0.000
26	A	356	VAL	0	0.047	0.026	16.792	0.028	0.028	0.000	0.000	0.000	0.000
27	A	357	LYS	1	0.852	0.914	18.284	-0.144	-0.144	0.000	0.000	0.000	0.000
28	A	358	ASP	-1	-0.871	-0.905	16.806	0.357	0.357	0.000	0.000	0.000	0.000
29	A	359	LEU	0	0.021	0.021	14.620	0.045	0.045	0.000	0.000	0.000	0.000
30	A	360	ILE	0	-0.001	0.004	17.178	0.005	0.005	0.000	0.000	0.000	0.000
31	A	361	LYS	1	0.864	0.940	20.871	-0.224	-0.224	0.000	0.000	0.000	0.000
32	A	362	ARG	1	0.913	0.965	16.037	-0.547	-0.547	0.000	0.000	0.000	0.000
33	A	363	TYR	0	0.111	0.048	19.299	0.006	0.006	0.000	0.000	0.000	0.000
34	A	364	CYS	0	-0.077	-0.033	20.642	-0.013	-0.013	0.000	0.000	0.000	0.000
35	A	365	THR	0	-0.047	-0.029	21.385	0.010	0.010	0.000	0.000	0.000	0.000
36	A	366	GLU	-1	-0.865	-0.933	19.015	0.418	0.418	0.000	0.000	0.000	0.000
37	A	367	VAL	0	0.029	0.015	22.089	-0.005	-0.005	0.000	0.000	0.000	0.000
38	A	368	LYS	1	0.734	0.882	23.235	-0.291	-0.291	0.000	0.000	0.000	0.000
39	A	369	ILE	0	0.012	0.013	26.422	-0.017	-0.017	0.000	0.000	0.000	0.000
40	A	370	SER	0	-0.028	-0.023	27.622	0.018	0.018	0.000	0.000	0.000	0.000
41	A	371	PHE	0	0.055	0.014	24.483	-0.008	-0.008	0.000	0.000	0.000	0.000
42	A	372	HIS	0	-0.031	-0.040	27.644	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	373	GLU	-1	-0.791	-0.903	27.873	0.137	0.137	0.000	0.000	0.000	0.000
44	A	374	ARG	1	0.935	0.985	29.212	-0.073	-0.073	0.000	0.000	0.000	0.000
45	A	375	ILE	0	-0.068	-0.018	25.165	-0.014	-0.014	0.000	0.000	0.000	0.000
46	A	376	ARG	1	0.901	0.955	24.849	0.018	0.018	0.000	0.000	0.000	0.000
47	A	377	LEU	0	0.040	0.019	18.798	0.010	0.010	0.000	0.000	0.000	0.000
48	A	378	GLU	-1	-0.885	-0.921	22.738	-0.151	-0.151	0.000	0.000	0.000	0.000
49	A	379	PHE	0	0.038	0.017	17.619	0.022	0.022	0.000	0.000	0.000	0.000
50	A	380	GLU	-1	-0.902	-0.939	20.948	-0.364	-0.364	0.000	0.000	0.000	0.000
51	A	381	GLY	0	-0.046	-0.016	23.563	0.007	0.007	0.000	0.000	0.000	0.000
52	A	382	GLU	-1	-0.975	-0.983	24.139	-0.158	-0.158	0.000	0.000	0.000	0.000
53	A	383	TRP	0	-0.064	-0.060	24.011	0.008	0.008	0.000	0.000	0.000	0.000
54	A	384	LEU	0	0.060	0.034	17.962	0.004	0.004	0.000	0.000	0.000	0.000
55	A	385	ASP	-1	-0.821	-0.902	21.888	0.039	0.039	0.000	0.000	0.000	0.000
56	A	386	PRO	0	-0.023	-0.029	21.242	0.008	0.008	0.000	0.000	0.000	0.000
57	A	387	ASN	0	-0.115	-0.088	21.206	0.054	0.054	0.000	0.000	0.000	0.000
58	A	388	ASP	-1	-0.804	-0.877	18.544	-0.067	-0.067	0.000	0.000	0.000	0.000
59	A	389	GLN	0	-0.059	-0.034	13.797	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	390	VAL	0	0.040	0.016	11.156	-0.055	-0.055	0.000	0.000	0.000	0.000
61	A	391	GLN	0	-0.053	-0.036	9.823	-0.146	-0.146	0.000	0.000	0.000	0.000
62	A	392	SER	0	-0.099	-0.052	11.489	-0.067	-0.067	0.000	0.000	0.000	0.000
63	A	393	THR	0	-0.074	-0.039	14.211	0.017	0.017	0.000	0.000	0.000	0.000
64	A	394	GLU	-1	-0.913	-0.964	14.010	-0.564	-0.564	0.000	0.000	0.000	0.000
65	A	395	LEU	0	-0.080	-0.017	13.122	-0.008	-0.008	0.000	0.000	0.000	0.000
66	A	396	GLU	-1	-0.917	-0.960	10.788	-1.258	-1.258	0.000	0.000	0.000	0.000
67	A	397	ASP	-1	-0.847	-0.924	7.335	-0.590	-0.590	0.000	0.000	0.000	0.000
68	A	398	GLU	-1	-0.893	-0.950	9.988	-0.157	-0.157	0.000	0.000	0.000	0.000
69	A	399	ASP	-1	-0.774	-0.878	12.952	-0.447	-0.447	0.000	0.000	0.000	0.000
70	A	400	GLN	0	-0.082	-0.032	15.285	0.078	0.078	0.000	0.000	0.000	0.000
71	A	401	VAL	0	0.035	0.019	16.350	-0.011	-0.011	0.000	0.000	0.000	0.000
72	A	402	SER	0	-0.033	-0.042	19.202	0.036	0.036	0.000	0.000	0.000	0.000
73	A	403	VAL	0	-0.036	-0.021	21.620	0.009	0.009	0.000	0.000	0.000	0.000
74	A	404	VAL	0	-0.053	-0.028	24.110	0.006	0.006	0.000	0.000	0.000	0.000

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