FMO DATABASE

FMODB ID: R5278

Calculation Name: 2XG8-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2XG8

Chain ID: D

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:

Apendix: None

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	87
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-577545.975624
FMO2-HF: Nuclear repulsion	541706.976656
FMO2-HF: Total energy	-35838.998969
FMO2-MP2: Total energy	-35944.69566

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(D:3:SER)

Summations of interaction energy for fragment #1(D: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.
-1.789	0.696	0.016	-1.19	-1.31	0.003

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / q_NPA : 0.005

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

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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	D	5	ASN	0	0.002	-0.005	3.354	-3.043	-0.593	0.017	-1.182	-1.285	0.003
4	D	6	TYR	0	-0.069	-0.070	6.096	0.458	0.458	0.000	0.000	0.000	0.000
5	D	7	LEU	0	0.004	0.000	9.793	0.181	0.181	0.000	0.000	0.000	0.000
6	D	8	ASN	0	0.005	0.003	12.736	0.027	0.027	0.000	0.000	0.000	0.000
7	D	9	HIS	0	0.036	0.025	16.478	0.059	0.059	0.000	0.000	0.000	0.000
8	D	10	PRO	0	-0.010	-0.017	18.572	0.016	0.016	0.000	0.000	0.000	0.000
9	D	11	THR	0	-0.034	-0.009	22.125	0.031	0.031	0.000	0.000	0.000	0.000
10	D	12	PHE	0	-0.017	-0.029	19.731	0.021	0.021	0.000	0.000	0.000	0.000
11	D	13	GLY	0	0.039	0.033	19.462	-0.036	-0.036	0.000	0.000	0.000	0.000
12	D	14	LEU	0	-0.001	0.020	13.341	-0.046	-0.046	0.000	0.000	0.000	0.000
13	D	15	LEU	0	-0.037	-0.023	12.679	0.065	0.065	0.000	0.000	0.000	0.000
14	D	16	TYR	0	0.025	0.005	9.224	-0.024	-0.024	0.000	0.000	0.000	0.000
15	D	17	GLN	0	0.017	0.008	4.607	-0.840	-0.805	-0.001	-0.008	-0.025	0.000
16	D	18	ILE	0	-0.058	-0.019	6.810	-0.320	-0.320	0.000	0.000	0.000	0.000
17	D	19	CYS	0	-0.022	-0.023	6.508	0.088	0.088	0.000	0.000	0.000	0.000
18	D	20	SER	0	-0.009	-0.035	7.194	-0.030	-0.030	0.000	0.000	0.000	0.000
19	D	21	PHE	0	-0.086	-0.042	8.837	0.139	0.139	0.000	0.000	0.000	0.000
20	D	22	GLY	0	0.045	0.011	11.479	-0.032	-0.032	0.000	0.000	0.000	0.000
21	D	23	ASP	-1	-0.873	-0.914	12.069	0.213	0.213	0.000	0.000	0.000	0.000
22	D	24	SER	0	-0.012	-0.022	13.074	0.000	0.000	0.000	0.000	0.000	0.000
23	D	25	LYS	1	0.870	0.927	12.941	0.269	0.269	0.000	0.000	0.000	0.000
24	D	26	GLU	-1	-0.830	-0.882	8.364	-0.711	-0.711	0.000	0.000	0.000	0.000
25	D	27	LEU	0	-0.053	-0.007	9.997	0.093	0.093	0.000	0.000	0.000	0.000
26	D	28	PHE	0	0.036	-0.003	8.710	-0.347	-0.347	0.000	0.000	0.000	0.000
27	D	29	ALA	0	-0.009	-0.004	11.646	0.277	0.277	0.000	0.000	0.000	0.000
28	D	30	THR	0	-0.010	-0.010	13.688	-0.121	-0.121	0.000	0.000	0.000	0.000
29	D	31	LEU	0	-0.001	-0.001	12.706	0.023	0.023	0.000	0.000	0.000	0.000
30	D	32	TYR	0	0.050	0.020	16.022	0.058	0.058	0.000	0.000	0.000	0.000
31	D	33	ALA	0	0.039	0.037	19.465	0.076	0.076	0.000	0.000	0.000	0.000
32	D	34	GLN	0	-0.014	0.008	19.359	-0.127	-0.127	0.000	0.000	0.000	0.000
33	D	35	ARG	1	0.893	0.920	15.122	0.887	0.887	0.000	0.000	0.000	0.000
34	D	36	LEU	0	-0.062	-0.008	18.810	0.058	0.058	0.000	0.000	0.000	0.000
35	D	37	PHE	0	0.010	-0.008	14.796	-0.083	-0.083	0.000	0.000	0.000	0.000
36	D	38	PHE	0	0.017	-0.002	15.218	0.098	0.098	0.000	0.000	0.000	0.000
37	D	39	LEU	0	0.001	0.005	14.306	-0.118	-0.118	0.000	0.000	0.000	0.000
38	D	40	VAL	0	-0.002	0.003	12.619	0.074	0.074	0.000	0.000	0.000	0.000
39	D	41	ALA	0	0.032	0.010	13.854	0.018	0.018	0.000	0.000	0.000	0.000
40	D	42	PHE	0	0.022	-0.002	11.284	0.004	0.004	0.000	0.000	0.000	0.000
41	D	43	ASP	-1	-0.816	-0.896	17.086	-0.295	-0.295	0.000	0.000	0.000	0.000
42	D	44	ALA	0	-0.002	-0.002	19.062	0.027	0.027	0.000	0.000	0.000	0.000
43	D	45	ARG	1	0.876	0.940	21.104	0.289	0.289	0.000	0.000	0.000	0.000
44	D	46	GLY	0	0.001	-0.030	21.787	0.014	0.014	0.000	0.000	0.000	0.000
45	D	47	THR	0	-0.086	-0.030	16.741	-0.046	-0.046	0.000	0.000	0.000	0.000
46	D	48	ARG	1	0.882	0.942	18.670	0.315	0.315	0.000	0.000	0.000	0.000
47	D	49	PHE	0	0.049	0.002	15.515	-0.072	-0.072	0.000	0.000	0.000	0.000
48	D	50	GLU	-1	-0.818	-0.869	18.466	-0.308	-0.308	0.000	0.000	0.000	0.000
49	D	51	PRO	0	-0.004	0.013	18.936	-0.043	-0.043	0.000	0.000	0.000	0.000
50	D	52	ILE	0	0.030	0.025	16.751	0.040	0.040	0.000	0.000	0.000	0.000
51	D	53	GLY	0	0.033	0.018	20.200	-0.034	-0.034	0.000	0.000	0.000	0.000
52	D	54	ARG	1	0.992	0.978	19.667	0.362	0.362	0.000	0.000	0.000	0.000
53	D	55	ASN	0	0.009	-0.002	20.015	-0.020	-0.020	0.000	0.000	0.000	0.000
54	D	56	GLU	-1	-0.843	-0.915	20.202	-0.257	-0.257	0.000	0.000	0.000	0.000
55	D	57	ALA	0	0.038	0.020	16.117	0.013	0.013	0.000	0.000	0.000	0.000
56	D	58	ARG	1	0.820	0.887	16.459	0.179	0.179	0.000	0.000	0.000	0.000
57	D	59	MET	0	0.005	-0.001	17.983	0.045	0.045	0.000	0.000	0.000	0.000
58	D	60	LEU	0	-0.012	-0.001	15.760	0.048	0.048	0.000	0.000	0.000	0.000
59	D	61	VAL	0	0.033	0.009	12.361	0.043	0.043	0.000	0.000	0.000	0.000
60	D	62	ASP	-1	-0.773	-0.847	14.390	-0.006	-0.006	0.000	0.000	0.000	0.000
61	D	63	ASN	0	-0.038	-0.031	17.121	0.095	0.095	0.000	0.000	0.000	0.000
62	D	64	ARG	1	0.900	0.964	9.781	-0.284	-0.284	0.000	0.000	0.000	0.000
63	D	65	LEU	0	0.020	-0.003	12.492	0.128	0.128	0.000	0.000	0.000	0.000
64	D	66	ARG	1	0.834	0.894	14.399	0.044	0.044	0.000	0.000	0.000	0.000
65	D	67	GLN	0	-0.037	-0.028	14.783	0.019	0.019	0.000	0.000	0.000	0.000
66	D	68	LEU	0	0.041	0.027	9.734	0.038	0.038	0.000	0.000	0.000	0.000
67	D	69	ARG	1	0.887	0.951	13.542	-0.483	-0.483	0.000	0.000	0.000	0.000
68	D	70	ARG	1	0.873	0.940	15.770	-0.268	-0.268	0.000	0.000	0.000	0.000
69	D	71	ASP	-1	-0.817	-0.907	13.059	0.978	0.978	0.000	0.000	0.000	0.000
70	D	72	ALA	0	-0.021	-0.013	15.504	0.040	0.040	0.000	0.000	0.000	0.000
71	D	73	SER	0	0.113	0.055	12.001	-0.021	-0.021	0.000	0.000	0.000	0.000
72	D	74	LEU	0	-0.034	0.008	10.694	0.088	0.088	0.000	0.000	0.000	0.000
73	D	75	GLN	0	-0.041	-0.029	12.874	-0.065	-0.065	0.000	0.000	0.000	0.000
74	D	76	GLU	-1	-0.912	-0.949	15.664	0.844	0.844	0.000	0.000	0.000	0.000
75	D	77	TYR	0	-0.021	-0.003	11.928	0.056	0.056	0.000	0.000	0.000	0.000
76	D	78	ASN	0	-0.003	-0.034	13.326	0.021	0.021	0.000	0.000	0.000	0.000
77	D	79	GLN	0	-0.023	-0.002	15.574	-0.063	-0.063	0.000	0.000	0.000	0.000
78	D	80	LEU	0	0.045	0.023	16.415	-0.061	-0.061	0.000	0.000	0.000	0.000
79	D	81	GLN	0	0.002	0.001	13.982	0.073	0.073	0.000	0.000	0.000	0.000
80	D	82	GLN	0	-0.070	-0.040	17.594	-0.065	-0.065	0.000	0.000	0.000	0.000
81	D	83	VAL	0	-0.009	0.003	20.605	-0.050	-0.050	0.000	0.000	0.000	0.000
82	D	84	PHE	0	0.045	0.027	19.872	-0.040	-0.040	0.000	0.000	0.000	0.000
83	D	85	LYS	1	0.986	0.980	21.816	-0.336	-0.336	0.000	0.000	0.000	0.000
84	D	86	GLN	0	-0.039	-0.011	23.661	-0.040	-0.040	0.000	0.000	0.000	0.000
85	D	87	THR	0	-0.025	0.005	24.904	-0.023	-0.023	0.000	0.000	0.000	0.000
86	D	88	PHE	0	-0.040	-0.011	23.052	-0.014	-0.014	0.000	0.000	0.000	0.000
87	D	89	LEU	0	-0.051	-0.029	22.251	-0.049	-0.049	0.000	0.000	0.000	0.000

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