FMO DATABASE

FMODB ID: Q162Y

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

Total energy (hartree)

FMO2-HF: Electronic energy	-578740.024571
FMO2-HF: Nuclear repulsion	542900.62444
FMO2-HF: Total energy	-35839.400131
FMO2-MP2: Total energy	-35945.082685

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.
-1.91	0.917	0.611	-1.452	-1.986	-0.004

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 : 0.016 / q_NPA : 0.008

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	-0.003	-0.003	2.645	-4.177	-1.350	0.611	-1.452	-1.986	-0.004
4	D	6	TYR	0	-0.061	-0.063	5.544	0.571	0.571	0.000	0.000	0.000	0.000
5	D	7	LEU	0	-0.007	0.004	9.373	0.186	0.186	0.000	0.000	0.000	0.000
6	D	8	ASN	0	0.009	-0.002	12.422	0.004	0.004	0.000	0.000	0.000	0.000
7	D	9	HIS	0	0.065	0.044	16.238	0.049	0.049	0.000	0.000	0.000	0.000
8	D	10	PRO	0	-0.018	-0.025	18.649	0.015	0.015	0.000	0.000	0.000	0.000
9	D	11	THR	0	-0.041	-0.012	21.968	0.039	0.039	0.000	0.000	0.000	0.000
10	D	12	PHE	0	-0.006	-0.023	19.593	0.019	0.019	0.000	0.000	0.000	0.000
11	D	13	GLY	0	0.021	0.031	19.591	-0.029	-0.029	0.000	0.000	0.000	0.000
12	D	14	LEU	0	0.015	0.021	13.202	-0.041	-0.041	0.000	0.000	0.000	0.000
13	D	15	LEU	0	-0.033	-0.021	12.831	0.067	0.067	0.000	0.000	0.000	0.000
14	D	16	TYR	0	0.030	0.013	8.911	0.050	0.050	0.000	0.000	0.000	0.000
15	D	17	GLN	0	-0.038	-0.027	5.314	-0.300	-0.300	0.000	0.000	0.000	0.000
16	D	18	ILE	0	-0.062	-0.028	6.930	-0.328	-0.328	0.000	0.000	0.000	0.000
17	D	19	CYS	0	-0.039	-0.032	6.495	0.157	0.157	0.000	0.000	0.000	0.000
18	D	20	SER	0	0.012	0.011	6.969	-0.097	-0.097	0.000	0.000	0.000	0.000
19	D	21	PHE	0	-0.084	-0.052	8.470	0.135	0.135	0.000	0.000	0.000	0.000
20	D	22	GLY	0	0.046	0.011	11.298	-0.043	-0.043	0.000	0.000	0.000	0.000
21	D	23	ASP	-1	-0.839	-0.876	11.976	0.290	0.290	0.000	0.000	0.000	0.000
22	D	24	SER	0	-0.001	-0.035	13.263	-0.013	-0.013	0.000	0.000	0.000	0.000
23	D	25	LYS	1	0.825	0.910	13.573	0.221	0.221	0.000	0.000	0.000	0.000
24	D	26	GLU	-1	-0.801	-0.874	8.251	-0.564	-0.564	0.000	0.000	0.000	0.000
25	D	27	LEU	0	-0.027	-0.017	9.598	0.110	0.110	0.000	0.000	0.000	0.000
26	D	28	PHE	0	0.057	0.014	8.538	-0.390	-0.390	0.000	0.000	0.000	0.000
27	D	29	ALA	0	-0.013	-0.008	11.323	0.280	0.280	0.000	0.000	0.000	0.000
28	D	30	THR	0	-0.007	-0.002	13.380	-0.132	-0.132	0.000	0.000	0.000	0.000
29	D	31	LEU	0	-0.008	-0.009	12.714	0.036	0.036	0.000	0.000	0.000	0.000
30	D	32	TYR	0	0.059	0.024	15.451	0.067	0.067	0.000	0.000	0.000	0.000
31	D	33	ALA	0	0.038	0.037	18.848	0.083	0.083	0.000	0.000	0.000	0.000
32	D	34	GLN	0	-0.010	0.001	19.005	-0.129	-0.129	0.000	0.000	0.000	0.000
33	D	35	ARG	1	0.829	0.890	14.737	0.968	0.968	0.000	0.000	0.000	0.000
34	D	36	LEU	0	-0.024	0.010	18.717	0.059	0.059	0.000	0.000	0.000	0.000
35	D	37	PHE	0	0.008	-0.012	14.628	-0.094	-0.094	0.000	0.000	0.000	0.000
36	D	38	PHE	0	0.029	0.005	15.027	0.102	0.102	0.000	0.000	0.000	0.000
37	D	39	LEU	0	0.019	0.029	14.026	-0.114	-0.114	0.000	0.000	0.000	0.000
38	D	40	VAL	0	-0.007	0.000	12.460	0.030	0.030	0.000	0.000	0.000	0.000
39	D	41	ALA	0	0.026	0.007	13.936	0.030	0.030	0.000	0.000	0.000	0.000
40	D	42	PHE	0	0.011	-0.004	11.295	0.006	0.006	0.000	0.000	0.000	0.000
41	D	43	ASP	-1	-0.807	-0.891	16.973	-0.250	-0.250	0.000	0.000	0.000	0.000
42	D	44	ALA	0	-0.016	-0.006	18.890	0.026	0.026	0.000	0.000	0.000	0.000
43	D	45	ARG	1	0.877	0.936	20.633	0.247	0.247	0.000	0.000	0.000	0.000
44	D	46	GLY	0	0.005	-0.022	20.807	0.012	0.012	0.000	0.000	0.000	0.000
45	D	47	THR	0	-0.058	-0.013	16.254	-0.046	-0.046	0.000	0.000	0.000	0.000
46	D	48	ARG	1	0.862	0.914	17.997	0.285	0.285	0.000	0.000	0.000	0.000
47	D	49	PHE	0	0.046	0.009	15.443	-0.071	-0.071	0.000	0.000	0.000	0.000
48	D	50	GLU	-1	-0.803	-0.865	18.215	-0.278	-0.278	0.000	0.000	0.000	0.000
49	D	51	PRO	0	-0.021	-0.009	18.789	-0.036	-0.036	0.000	0.000	0.000	0.000
50	D	52	ILE	0	0.006	0.016	16.328	0.041	0.041	0.000	0.000	0.000	0.000
51	D	53	GLY	0	0.033	0.020	20.370	-0.029	-0.029	0.000	0.000	0.000	0.000
52	D	54	ARG	1	0.966	0.973	19.370	0.394	0.394	0.000	0.000	0.000	0.000
53	D	55	ASN	0	-0.005	-0.014	19.613	-0.031	-0.031	0.000	0.000	0.000	0.000
54	D	56	GLU	-1	-0.813	-0.905	20.083	-0.268	-0.268	0.000	0.000	0.000	0.000
55	D	57	ALA	0	0.038	0.015	15.891	0.013	0.013	0.000	0.000	0.000	0.000
56	D	58	ARG	1	0.838	0.899	16.018	0.219	0.219	0.000	0.000	0.000	0.000
57	D	59	MET	0	0.012	0.003	17.398	0.040	0.040	0.000	0.000	0.000	0.000
58	D	60	LEU	0	-0.004	0.016	15.381	0.049	0.049	0.000	0.000	0.000	0.000
59	D	61	VAL	0	0.035	0.016	11.966	0.057	0.057	0.000	0.000	0.000	0.000
60	D	62	ASP	-1	-0.782	-0.853	14.034	-0.051	-0.051	0.000	0.000	0.000	0.000
61	D	63	ASN	0	-0.039	-0.033	16.948	0.095	0.095	0.000	0.000	0.000	0.000
62	D	64	ARG	1	0.858	0.931	9.512	-0.284	-0.284	0.000	0.000	0.000	0.000
63	D	65	LEU	0	0.026	0.006	12.724	0.129	0.129	0.000	0.000	0.000	0.000
64	D	66	ARG	1	0.824	0.888	14.207	0.075	0.075	0.000	0.000	0.000	0.000
65	D	67	GLN	0	-0.016	-0.008	14.511	0.010	0.010	0.000	0.000	0.000	0.000
66	D	68	LEU	0	0.051	0.024	9.512	0.040	0.040	0.000	0.000	0.000	0.000
67	D	69	ARG	1	0.836	0.926	13.409	-0.422	-0.422	0.000	0.000	0.000	0.000
68	D	70	ARG	1	0.864	0.932	15.925	-0.304	-0.304	0.000	0.000	0.000	0.000
69	D	71	ASP	-1	-0.787	-0.894	12.658	1.051	1.051	0.000	0.000	0.000	0.000
70	D	72	ALA	0	-0.029	-0.007	15.239	-0.010	-0.010	0.000	0.000	0.000	0.000
71	D	73	SER	0	0.078	0.016	12.511	-0.040	-0.040	0.000	0.000	0.000	0.000
72	D	74	LEU	0	-0.042	-0.018	10.398	0.061	0.061	0.000	0.000	0.000	0.000
73	D	75	GLN	0	-0.020	-0.005	12.825	-0.090	-0.090	0.000	0.000	0.000	0.000
74	D	76	GLU	-1	-0.877	-0.914	15.587	0.906	0.906	0.000	0.000	0.000	0.000
75	D	77	TYR	0	-0.015	-0.014	11.826	0.034	0.034	0.000	0.000	0.000	0.000
76	D	78	ASN	0	-0.015	-0.019	13.491	0.009	0.009	0.000	0.000	0.000	0.000
77	D	79	GLN	0	0.001	0.004	15.654	-0.053	-0.053	0.000	0.000	0.000	0.000
78	D	80	LEU	0	0.028	0.016	16.198	-0.062	-0.062	0.000	0.000	0.000	0.000
79	D	81	GLN	0	0.011	0.008	13.806	0.043	0.043	0.000	0.000	0.000	0.000
80	D	82	GLN	0	-0.058	-0.033	17.366	-0.055	-0.055	0.000	0.000	0.000	0.000
81	D	83	VAL	0	0.012	0.016	20.555	-0.052	-0.052	0.000	0.000	0.000	0.000
82	D	84	PHE	0	0.032	0.028	19.708	-0.035	-0.035	0.000	0.000	0.000	0.000
83	D	85	LYS	1	0.996	0.992	21.659	-0.292	-0.292	0.000	0.000	0.000	0.000
84	D	86	GLN	0	-0.061	-0.029	23.349	-0.044	-0.044	0.000	0.000	0.000	0.000
85	D	87	THR	0	-0.023	-0.004	24.834	-0.024	-0.024	0.000	0.000	0.000	0.000
86	D	88	PHE	0	-0.027	-0.015	22.934	-0.007	-0.007	0.000	0.000	0.000	0.000
87	D	89	LEU	0	-0.085	-0.039	22.113	-0.035	-0.035	0.000	0.000	0.000	0.000

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