FMO DATABASE

FMODB ID: 6621Z

Calculation Name: 2XG8-F-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2XG8

Chain ID: F

ChEMBL ID:

UniProt ID: P0A3F4

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	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	79
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-498317.684773
FMO2-HF: Nuclear repulsion	465653.573447
FMO2-HF: Total energy	-32664.111326
FMO2-MP2: Total energy	-32760.388918

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(F:3:SER)

Summations of interaction energy for fragment #1(F:3:SER)

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.
-2.81	-0.093	0.004	-1.293	-1.427	0.001

Interaction energy analysis for fragmet #1(F:3:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / q_NPA : 0.006

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	F	5	ASN	0	-0.019	0.005	3.514	-0.684	1.867	0.004	-1.215	-1.340	0.001
4	F	6	TYR	0	-0.069	-0.066	5.491	0.624	0.624	0.000	0.000	0.000	0.000
5	F	7	LEU	0	-0.018	0.000	9.310	0.238	0.238	0.000	0.000	0.000	0.000
6	F	8	ASN	0	0.014	-0.004	12.309	0.053	0.053	0.000	0.000	0.000	0.000
7	F	9	HIS	0	0.048	0.034	16.144	0.040	0.040	0.000	0.000	0.000	0.000
8	F	10	PRO	0	-0.017	-0.026	18.514	0.021	0.021	0.000	0.000	0.000	0.000
9	F	11	THR	0	-0.037	-0.009	21.816	0.043	0.043	0.000	0.000	0.000	0.000
10	F	12	PHE	0	-0.011	-0.024	19.451	0.024	0.024	0.000	0.000	0.000	0.000
11	F	13	GLY	0	0.022	0.031	19.489	-0.024	-0.024	0.000	0.000	0.000	0.000
12	F	14	LEU	0	0.027	0.023	13.020	-0.043	-0.043	0.000	0.000	0.000	0.000
13	F	15	LEU	0	-0.041	-0.026	12.646	0.090	0.090	0.000	0.000	0.000	0.000
14	F	16	TYR	0	0.021	0.004	8.671	0.043	0.043	0.000	0.000	0.000	0.000
15	F	17	GLN	0	-0.027	-0.016	3.762	-1.895	-1.729	0.000	-0.078	-0.087	0.000
16	F	18	ILE	0	-0.062	-0.028	6.925	-0.135	-0.135	0.000	0.000	0.000	0.000
17	F	19	CYS	0	-0.038	-0.024	6.127	0.290	0.290	0.000	0.000	0.000	0.000
18	F	20	SER	0	0.077	0.032	6.565	-0.306	-0.306	0.000	0.000	0.000	0.000
19	F	21	PHE	0	-0.028	-0.020	7.928	0.335	0.335	0.000	0.000	0.000	0.000
20	F	22	GLY	0	0.022	0.032	11.494	0.119	0.119	0.000	0.000	0.000	0.000
21	F	23	ASP	-1	-0.934	-0.979	10.757	-0.065	-0.065	0.000	0.000	0.000	0.000
22	F	24	SER	0	-0.010	0.000	13.589	-0.038	-0.038	0.000	0.000	0.000	0.000
23	F	25	LYS	1	0.885	0.936	13.039	0.331	0.331	0.000	0.000	0.000	0.000
24	F	26	GLU	-1	-0.845	-0.913	6.676	-2.485	-2.485	0.000	0.000	0.000	0.000
25	F	27	LEU	0	-0.047	-0.017	9.679	0.109	0.109	0.000	0.000	0.000	0.000
26	F	28	PHE	0	0.057	0.014	8.452	-0.393	-0.393	0.000	0.000	0.000	0.000
27	F	29	ALA	0	-0.018	-0.015	11.119	0.320	0.320	0.000	0.000	0.000	0.000
28	F	30	THR	0	0.009	0.009	13.188	-0.133	-0.133	0.000	0.000	0.000	0.000
29	F	31	LEU	0	0.019	0.012	12.414	0.040	0.040	0.000	0.000	0.000	0.000
30	F	32	TYR	0	0.057	0.022	15.379	0.078	0.078	0.000	0.000	0.000	0.000
31	F	33	ALA	0	0.017	0.022	18.839	0.078	0.078	0.000	0.000	0.000	0.000
32	F	34	GLN	0	0.009	-0.001	18.845	-0.122	-0.122	0.000	0.000	0.000	0.000
33	F	35	ARG	1	0.813	0.890	15.024	0.886	0.886	0.000	0.000	0.000	0.000
34	F	36	LEU	0	-0.046	0.002	18.493	0.060	0.060	0.000	0.000	0.000	0.000
35	F	37	PHE	0	0.017	-0.005	14.390	-0.090	-0.090	0.000	0.000	0.000	0.000
36	F	38	PHE	0	0.020	0.002	14.784	0.110	0.110	0.000	0.000	0.000	0.000
37	F	39	LEU	0	-0.013	0.001	13.717	-0.154	-0.154	0.000	0.000	0.000	0.000
38	F	40	VAL	0	0.000	0.007	12.429	0.111	0.111	0.000	0.000	0.000	0.000
39	F	41	ALA	0	0.058	0.022	13.734	0.003	0.003	0.000	0.000	0.000	0.000
40	F	42	PHE	0	-0.019	-0.023	10.506	0.006	0.006	0.000	0.000	0.000	0.000
41	F	43	ASP	-1	-0.780	-0.858	16.781	-0.330	-0.330	0.000	0.000	0.000	0.000
42	F	44	ALA	0	-0.032	0.000	19.817	0.030	0.030	0.000	0.000	0.000	0.000
43	F	45	ARG	1	0.926	0.949	20.444	0.267	0.267	0.000	0.000	0.000	0.000
44	F	46	GLY	0	0.014	-0.013	21.014	0.021	0.021	0.000	0.000	0.000	0.000
45	F	47	THR	0	-0.017	0.006	16.037	-0.010	-0.010	0.000	0.000	0.000	0.000
46	F	48	ARG	1	0.837	0.903	17.944	0.377	0.377	0.000	0.000	0.000	0.000
47	F	49	PHE	0	0.029	0.002	15.315	-0.062	-0.062	0.000	0.000	0.000	0.000
48	F	50	GLU	-1	-0.787	-0.874	18.104	-0.342	-0.342	0.000	0.000	0.000	0.000
49	F	51	PRO	0	-0.022	-0.004	18.510	-0.051	-0.051	0.000	0.000	0.000	0.000
50	F	52	ILE	0	0.013	0.011	16.323	0.052	0.052	0.000	0.000	0.000	0.000
51	F	53	GLY	0	0.050	0.023	20.011	-0.026	-0.026	0.000	0.000	0.000	0.000
52	F	54	ARG	1	0.989	0.972	19.168	0.397	0.397	0.000	0.000	0.000	0.000
53	F	55	ASN	0	-0.009	-0.006	19.690	-0.011	-0.011	0.000	0.000	0.000	0.000
54	F	56	GLU	-1	-0.821	-0.895	19.568	-0.247	-0.247	0.000	0.000	0.000	0.000
55	F	57	ALA	0	0.014	0.004	15.733	0.002	0.002	0.000	0.000	0.000	0.000
56	F	58	ARG	1	0.889	0.941	15.702	0.248	0.248	0.000	0.000	0.000	0.000
57	F	59	MET	0	0.040	0.023	17.197	0.028	0.028	0.000	0.000	0.000	0.000
58	F	60	LEU	0	0.016	0.012	15.452	0.042	0.042	0.000	0.000	0.000	0.000
59	F	61	VAL	0	0.003	-0.003	11.706	0.046	0.046	0.000	0.000	0.000	0.000
60	F	62	ASP	-1	-0.844	-0.899	13.888	0.013	0.013	0.000	0.000	0.000	0.000
61	F	63	ASN	0	-0.004	-0.012	16.740	0.097	0.097	0.000	0.000	0.000	0.000
62	F	64	ARG	1	0.866	0.931	10.046	-0.085	-0.085	0.000	0.000	0.000	0.000
63	F	65	LEU	0	-0.011	-0.005	12.405	0.142	0.142	0.000	0.000	0.000	0.000
64	F	66	ARG	1	0.783	0.855	13.951	0.099	0.099	0.000	0.000	0.000	0.000
65	F	67	GLN	0	0.034	0.037	14.684	0.051	0.051	0.000	0.000	0.000	0.000
66	F	68	LEU	0	0.006	0.021	8.638	0.044	0.044	0.000	0.000	0.000	0.000
67	F	69	ARG	1	0.903	0.953	13.022	-0.085	-0.085	0.000	0.000	0.000	0.000
68	F	70	ARG	1	0.924	0.959	15.075	-0.604	-0.604	0.000	0.000	0.000	0.000
69	F	79	GLN	0	0.057	0.020	21.996	0.026	0.026	0.000	0.000	0.000	0.000
70	F	80	LEU	0	0.038	0.011	21.331	-0.029	-0.029	0.000	0.000	0.000	0.000
71	F	81	GLN	0	0.045	0.013	22.012	-0.050	-0.050	0.000	0.000	0.000	0.000
72	F	82	GLN	0	0.000	0.004	23.975	-0.014	-0.014	0.000	0.000	0.000	0.000
73	F	83	VAL	0	0.040	0.016	26.823	-0.020	-0.020	0.000	0.000	0.000	0.000
74	F	84	PHE	0	-0.001	0.009	25.989	-0.018	-0.018	0.000	0.000	0.000	0.000
75	F	85	LYS	1	0.933	0.956	26.314	-0.266	-0.266	0.000	0.000	0.000	0.000
76	F	86	GLN	0	-0.013	0.005	29.828	0.000	0.000	0.000	0.000	0.000	0.000
77	F	87	THR	0	-0.055	-0.030	31.263	-0.012	-0.012	0.000	0.000	0.000	0.000
78	F	88	PHE	0	-0.028	-0.019	29.132	-0.010	-0.010	0.000	0.000	0.000	0.000
79	F	89	LEU	0	-0.017	0.015	29.759	-0.005	-0.005	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(F:3:SER)