FMO DATABASE

FMODB ID: N21QQ

Calculation Name: 3RFI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3RFI

Chain ID: A

ChEMBL ID:

UniProt ID: Q6B9W9

Base Structure: X-ray

Registration Date: 2023-09-26

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	77
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-459946.572486
FMO2-HF: Nuclear repulsion	426388.679233
FMO2-HF: Total energy	-33557.893253
FMO2-MP2: Total energy	-33647.982661

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:0:ALA)

Summations of interaction energy for fragment #1(A:0:ALA)

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.
-6.022	-1.623	0.468	-1.841	-3.024	-0.004

Interaction energy analysis for fragmet #1(A:0:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : 0.001

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	2	VAL	0	0.053	0.019	3.858	-2.316	-0.765	-0.007	-0.722	-0.821	0.001
4	A	3	SER	0	-0.011	0.004	3.319	-0.857	-0.281	0.028	-0.156	-0.448	-0.001
5	A	4	MET	0	-0.005	-0.007	2.771	-0.027	0.810	0.198	-0.253	-0.783	-0.001
6	A	5	GLU	-1	-0.880	-0.932	5.957	0.216	0.216	0.000	0.000	0.000	0.000
7	A	6	CYS	0	-0.067	-0.018	7.875	0.159	0.159	0.000	0.000	0.000	0.000
8	A	7	LYS	1	0.904	0.926	7.105	1.198	1.198	0.000	0.000	0.000	0.000
9	A	8	THR	0	-0.007	0.017	9.801	0.132	0.132	0.000	0.000	0.000	0.000
10	A	9	ILE	0	-0.005	0.004	11.993	0.081	0.081	0.000	0.000	0.000	0.000
11	A	10	VAL	0	0.005	-0.007	13.370	0.047	0.047	0.000	0.000	0.000	0.000
12	A	11	SER	0	-0.080	-0.060	13.213	0.050	0.050	0.000	0.000	0.000	0.000
13	A	12	GLN	0	-0.031	-0.023	15.164	0.009	0.009	0.000	0.000	0.000	0.000
14	A	13	TYR	0	-0.015	-0.011	15.980	0.047	0.047	0.000	0.000	0.000	0.000
15	A	14	GLY	0	0.036	0.040	18.090	0.024	0.024	0.000	0.000	0.000	0.000
16	A	15	GLU	-1	-0.843	-0.928	19.029	-0.122	-0.122	0.000	0.000	0.000	0.000
17	A	16	MET	0	0.030	0.025	22.217	0.014	0.014	0.000	0.000	0.000	0.000
18	A	17	ILE	0	-0.021	-0.022	18.174	0.017	0.017	0.000	0.000	0.000	0.000
19	A	18	TRP	0	0.001	-0.011	22.082	0.013	0.013	0.000	0.000	0.000	0.000
20	A	19	ASP	-1	-0.850	-0.933	23.540	-0.079	-0.079	0.000	0.000	0.000	0.000
21	A	20	LEU	0	-0.053	-0.019	24.390	0.012	0.012	0.000	0.000	0.000	0.000
22	A	21	LEU	0	-0.053	-0.004	22.717	0.010	0.010	0.000	0.000	0.000	0.000
23	A	22	VAL	0	0.011	-0.003	25.986	0.009	0.009	0.000	0.000	0.000	0.000
24	A	23	SER	0	-0.072	-0.056	28.881	0.007	0.007	0.000	0.000	0.000	0.000
25	A	24	GLY	0	-0.027	0.003	29.426	0.005	0.005	0.000	0.000	0.000	0.000
26	A	25	VAL	0	-0.077	-0.032	29.995	0.006	0.006	0.000	0.000	0.000	0.000
27	A	26	ARG	1	0.953	0.981	32.120	0.005	0.005	0.000	0.000	0.000	0.000
28	A	27	PRO	0	0.042	0.014	35.672	0.002	0.002	0.000	0.000	0.000	0.000
29	A	28	ASP	-1	-0.757	-0.880	38.136	-0.008	-0.008	0.000	0.000	0.000	0.000
30	A	29	GLN	0	-0.070	-0.020	35.734	0.005	0.005	0.000	0.000	0.000	0.000
31	A	30	VAL	0	0.000	0.004	33.878	0.002	0.002	0.000	0.000	0.000	0.000
32	A	31	CYS	0	-0.018	-0.012	36.563	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	32	SER	0	-0.031	-0.020	40.009	0.001	0.001	0.000	0.000	0.000	0.000
34	A	33	GLN	0	-0.072	-0.034	33.212	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	34	ALA	0	-0.043	-0.012	38.522	0.001	0.001	0.000	0.000	0.000	0.000
36	A	35	GLY	0	-0.014	0.005	40.104	0.000	0.000	0.000	0.000	0.000	0.000
37	A	36	LEU	0	-0.062	-0.041	42.780	0.000	0.000	0.000	0.000	0.000	0.000
38	A	37	CYS	0	-0.061	0.015	43.085	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	38	PHE	0	0.039	0.017	44.380	0.001	0.001	0.000	0.000	0.000	0.000
40	A	39	VAL	0	-0.009	-0.001	41.575	0.000	0.000	0.000	0.000	0.000	0.000
41	A	64	GLU	-1	-0.901	-0.966	49.109	-0.005	-0.005	0.000	0.000	0.000	0.000
42	A	65	ALA	0	-0.020	-0.002	49.763	0.000	0.000	0.000	0.000	0.000	0.000
43	A	66	PRO	0	0.050	0.007	49.838	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	67	LEU	0	0.001	-0.010	47.086	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	69	THR	0	0.066	0.023	44.997	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	70	ALA	0	-0.001	-0.004	45.599	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	72	GLU	-1	-0.844	-0.953	40.996	-0.016	-0.016	0.000	0.000	0.000	0.000
48	A	73	MET	0	-0.071	-0.027	40.824	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	74	ALA	0	-0.001	0.000	40.382	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	75	VAL	0	0.026	0.008	35.360	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	76	VAL	0	0.035	0.023	36.349	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	77	TRP	0	-0.031	-0.031	37.252	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	78	MET	0	-0.042	-0.013	33.860	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	79	GLN	0	-0.015	-0.021	32.502	-0.004	-0.004	0.000	0.000	0.000	0.000
55	A	80	ASN	0	0.015	0.005	32.686	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	81	GLN	0	-0.008	0.001	31.478	-0.006	-0.006	0.000	0.000	0.000	0.000
57	A	82	LEU	0	0.010	-0.001	28.110	-0.006	-0.006	0.000	0.000	0.000	0.000
58	A	83	LYS	1	0.919	0.966	28.701	0.044	0.044	0.000	0.000	0.000	0.000
59	A	84	GLN	0	-0.104	-0.037	30.589	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	85	GLU	-1	-0.795	-0.887	27.878	-0.116	-0.116	0.000	0.000	0.000	0.000
61	A	86	GLY	0	0.063	0.035	27.288	-0.009	-0.009	0.000	0.000	0.000	0.000
62	A	87	THR	0	-0.074	-0.046	26.730	-0.009	-0.009	0.000	0.000	0.000	0.000
63	A	88	LYS	1	0.855	0.918	23.950	0.113	0.113	0.000	0.000	0.000	0.000
64	A	89	GLU	-1	-0.887	-0.946	22.961	-0.157	-0.157	0.000	0.000	0.000	0.000
65	A	90	LYS	1	0.918	0.959	21.874	0.108	0.108	0.000	0.000	0.000	0.000
66	A	91	VAL	0	-0.066	-0.023	20.752	-0.015	-0.015	0.000	0.000	0.000	0.000
67	A	92	LEU	0	0.018	0.000	18.548	-0.016	-0.016	0.000	0.000	0.000	0.000
68	A	93	GLU	-1	-0.790	-0.882	17.069	-0.378	-0.378	0.000	0.000	0.000	0.000
69	A	94	TYR	0	-0.056	-0.029	16.699	-0.034	-0.034	0.000	0.000	0.000	0.000
70	A	95	VAL	0	0.009	-0.008	13.951	-0.020	-0.020	0.000	0.000	0.000	0.000
71	A	96	ASN	0	-0.002	0.000	12.624	-0.124	-0.124	0.000	0.000	0.000	0.000
72	A	97	GLN	0	-0.013	-0.018	11.843	-0.118	-0.118	0.000	0.000	0.000	0.000
73	A	98	LEU	0	-0.012	0.001	11.940	-0.050	-0.050	0.000	0.000	0.000	0.000
74	A	100	GLU	-1	-0.884	-0.928	7.072	-1.070	-1.070	0.000	0.000	0.000	0.000
75	A	101	LYS	1	0.788	0.886	8.036	0.391	0.391	0.000	0.000	0.000	0.000
76	A	102	ILE	0	-0.050	-0.006	4.185	0.184	0.247	-0.001	-0.007	-0.054	0.000
77	A	103	PRO	0	-0.018	-0.004	2.925	-3.334	-1.962	0.250	-0.703	-0.918	-0.003

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:ALA)