FMO DATABASE

FMODB ID: 7G71K

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:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
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
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-497198.778527
FMO2-HF: Nuclear repulsion	464535.665623
FMO2-HF: Total energy	-32663.112903
FMO2-MP2: Total energy	-32759.495141

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.
-6.758	-4.273	0.021	-1.346	-1.16	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 : 0.001 / q_NPA : -0.009

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	F	5	ASN	0	0.022	0.006	3.397	-4.421	-1.980	0.022	-1.315	-1.148	0.001
4	F	6	TYR	0	-0.066	-0.070	6.117	0.424	0.424	0.000	0.000	0.000	0.000
5	F	7	LEU	0	0.009	0.001	9.830	0.202	0.202	0.000	0.000	0.000	0.000
6	F	8	ASN	0	0.010	-0.001	12.769	0.079	0.079	0.000	0.000	0.000	0.000
7	F	9	HIS	0	0.019	0.009	16.508	0.063	0.063	0.000	0.000	0.000	0.000
8	F	10	PRO	0	-0.002	-0.013	18.631	0.019	0.019	0.000	0.000	0.000	0.000
9	F	11	THR	0	-0.028	0.002	22.187	0.036	0.036	0.000	0.000	0.000	0.000
10	F	12	PHE	0	-0.029	-0.030	19.739	0.025	0.025	0.000	0.000	0.000	0.000
11	F	13	GLY	0	0.049	0.043	19.506	-0.035	-0.035	0.000	0.000	0.000	0.000
12	F	14	LEU	0	0.003	0.012	13.324	-0.046	-0.046	0.000	0.000	0.000	0.000
13	F	15	LEU	0	-0.039	-0.024	12.746	0.073	0.073	0.000	0.000	0.000	0.000
14	F	16	TYR	0	0.012	-0.005	9.300	-0.044	-0.044	0.000	0.000	0.000	0.000
15	F	17	GLN	0	0.009	0.003	4.100	-1.580	-1.536	-0.001	-0.031	-0.012	0.000
16	F	18	ILE	0	-0.072	-0.024	6.852	-0.308	-0.308	0.000	0.000	0.000	0.000
17	F	19	CYS	0	-0.039	-0.030	6.458	0.203	0.203	0.000	0.000	0.000	0.000
18	F	20	SER	0	0.050	0.017	6.898	-0.201	-0.201	0.000	0.000	0.000	0.000
19	F	21	PHE	0	-0.051	-0.041	8.484	0.251	0.251	0.000	0.000	0.000	0.000
20	F	22	GLY	0	0.006	0.016	11.526	0.082	0.082	0.000	0.000	0.000	0.000
21	F	23	ASP	-1	-0.946	-0.975	11.065	-0.053	-0.053	0.000	0.000	0.000	0.000
22	F	24	SER	0	-0.006	-0.011	12.520	-0.018	-0.018	0.000	0.000	0.000	0.000
23	F	25	LYS	1	0.942	0.996	13.341	0.323	0.323	0.000	0.000	0.000	0.000
24	F	26	GLU	-1	-0.894	-0.945	7.103	-2.078	-2.078	0.000	0.000	0.000	0.000
25	F	27	LEU	0	-0.040	-0.007	9.977	0.115	0.115	0.000	0.000	0.000	0.000
26	F	28	PHE	0	0.031	0.007	8.418	-0.341	-0.341	0.000	0.000	0.000	0.000
27	F	29	ALA	0	-0.006	-0.006	11.675	0.303	0.303	0.000	0.000	0.000	0.000
28	F	30	THR	0	-0.014	-0.020	13.739	-0.115	-0.115	0.000	0.000	0.000	0.000
29	F	31	LEU	0	0.017	0.002	12.764	0.021	0.021	0.000	0.000	0.000	0.000
30	F	32	TYR	0	0.030	0.020	15.960	0.061	0.061	0.000	0.000	0.000	0.000
31	F	33	ALA	0	0.032	0.033	19.519	0.076	0.076	0.000	0.000	0.000	0.000
32	F	34	GLN	0	-0.021	-0.007	19.362	-0.127	-0.127	0.000	0.000	0.000	0.000
33	F	35	ARG	1	0.914	0.944	15.905	0.855	0.855	0.000	0.000	0.000	0.000
34	F	36	LEU	0	-0.071	-0.006	18.878	0.058	0.058	0.000	0.000	0.000	0.000
35	F	37	PHE	0	0.013	-0.003	14.768	-0.075	-0.075	0.000	0.000	0.000	0.000
36	F	38	PHE	0	0.003	-0.011	15.236	0.104	0.104	0.000	0.000	0.000	0.000
37	F	39	LEU	0	0.005	0.004	14.327	-0.138	-0.138	0.000	0.000	0.000	0.000
38	F	40	VAL	0	-0.002	0.004	12.656	0.095	0.095	0.000	0.000	0.000	0.000
39	F	41	ALA	0	0.043	0.004	13.888	0.009	0.009	0.000	0.000	0.000	0.000
40	F	42	PHE	0	-0.029	-0.018	11.623	0.001	0.001	0.000	0.000	0.000	0.000
41	F	43	ASP	-1	-0.746	-0.839	17.325	-0.360	-0.360	0.000	0.000	0.000	0.000
42	F	44	ALA	0	-0.094	-0.028	20.240	0.034	0.034	0.000	0.000	0.000	0.000
43	F	45	ARG	1	0.966	0.980	20.727	0.258	0.258	0.000	0.000	0.000	0.000
44	F	46	GLY	0	0.029	-0.004	21.636	0.025	0.025	0.000	0.000	0.000	0.000
45	F	47	THR	0	0.003	-0.001	16.608	-0.013	-0.013	0.000	0.000	0.000	0.000
46	F	48	ARG	1	0.895	0.939	18.384	0.360	0.360	0.000	0.000	0.000	0.000
47	F	49	PHE	0	0.008	-0.014	15.319	-0.078	-0.078	0.000	0.000	0.000	0.000
48	F	50	GLU	-1	-0.929	-0.959	18.428	-0.345	-0.345	0.000	0.000	0.000	0.000
49	F	51	PRO	0	-0.012	0.011	18.936	-0.052	-0.052	0.000	0.000	0.000	0.000
50	F	52	ILE	0	0.023	0.010	16.798	0.053	0.053	0.000	0.000	0.000	0.000
51	F	53	GLY	0	0.039	0.016	20.222	-0.030	-0.030	0.000	0.000	0.000	0.000
52	F	54	ARG	1	1.005	0.983	19.668	0.396	0.396	0.000	0.000	0.000	0.000
53	F	55	ASN	0	0.004	-0.002	20.017	-0.014	-0.014	0.000	0.000	0.000	0.000
54	F	56	GLU	-1	-0.828	-0.893	19.920	-0.260	-0.260	0.000	0.000	0.000	0.000
55	F	57	ALA	0	0.027	0.005	16.160	0.007	0.007	0.000	0.000	0.000	0.000
56	F	58	ARG	1	0.870	0.923	16.475	0.239	0.239	0.000	0.000	0.000	0.000
57	F	59	MET	0	0.030	0.020	17.951	0.029	0.029	0.000	0.000	0.000	0.000
58	F	60	LEU	0	-0.005	-0.004	15.744	0.036	0.036	0.000	0.000	0.000	0.000
59	F	61	VAL	0	0.010	-0.001	12.133	0.032	0.032	0.000	0.000	0.000	0.000
60	F	62	ASP	-1	-0.844	-0.914	14.373	-0.044	-0.044	0.000	0.000	0.000	0.000
61	F	63	ASN	0	-0.057	-0.039	17.055	0.106	0.106	0.000	0.000	0.000	0.000
62	F	64	ARG	1	0.952	0.997	9.554	-0.220	-0.220	0.000	0.000	0.000	0.000
63	F	65	LEU	0	0.018	-0.028	12.329	0.131	0.131	0.000	0.000	0.000	0.000
64	F	66	ARG	1	0.857	0.928	14.399	0.093	0.093	0.000	0.000	0.000	0.000
65	F	67	GLN	0	0.014	0.012	14.679	0.014	0.014	0.000	0.000	0.000	0.000
66	F	68	LEU	0	-0.053	0.005	9.527	0.049	0.049	0.000	0.000	0.000	0.000
67	F	69	ARG	1	0.908	0.940	13.217	-0.091	-0.091	0.000	0.000	0.000	0.000
68	F	70	ARG	1	0.970	1.011	14.820	-0.610	-0.610	0.000	0.000	0.000	0.000
69	F	79	GLN	0	0.044	0.019	21.990	0.019	0.019	0.000	0.000	0.000	0.000
70	F	80	LEU	0	0.063	0.020	21.158	-0.030	-0.030	0.000	0.000	0.000	0.000
71	F	81	GLN	0	0.046	0.021	22.178	-0.049	-0.049	0.000	0.000	0.000	0.000
72	F	82	GLN	0	0.002	-0.003	24.072	-0.014	-0.014	0.000	0.000	0.000	0.000
73	F	83	VAL	0	0.043	0.014	26.677	-0.020	-0.020	0.000	0.000	0.000	0.000
74	F	84	PHE	0	0.006	-0.004	25.767	-0.019	-0.019	0.000	0.000	0.000	0.000
75	F	85	LYS	1	0.917	0.959	26.023	-0.256	-0.256	0.000	0.000	0.000	0.000
76	F	86	GLN	0	-0.015	-0.002	29.744	-0.001	-0.001	0.000	0.000	0.000	0.000
77	F	87	THR	0	-0.044	-0.021	31.140	-0.011	-0.011	0.000	0.000	0.000	0.000
78	F	88	PHE	0	-0.036	-0.019	29.466	-0.011	-0.011	0.000	0.000	0.000	0.000
79	F	89	LEU	0	-0.028	0.017	29.751	-0.009	-0.009	0.000	0.000	0.000	0.000

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