FMO DATABASE

FMODB ID: 4NMMN

Calculation Name: 2XG8-F-Xray316

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2XG8

Chain ID: F

ChEMBL ID:

UniProt ID: P0A3F4

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
Remarks	Structural optimization was performed under the unconstrained condition of hydrogen and heavy atoms fixed using MOE with Auto-FMO protocol as OptH.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	82
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-503876.550695
FMO2-HF: Nuclear repulsion	470891.251686
FMO2-HF: Total energy	-32985.299009
FMO2-MP2: Total energy	-33082.662397

3D Structure Molmil

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:2:ACE )

Summations of interaction energy for fragment #1(F:2:ACE )

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.
-0.504	0.465	-0.005	-0.394	-0.57	-0.001

Interaction energy analysis for fragmet #1(F:2:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.014 / q_NPA : -0.020

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	4	GLU	-1	-0.883	-0.886	3.840	0.180	1.149	-0.005	-0.394	-0.570	-0.001
4	F	5	ASN	0	0.023	0.008	6.618	-0.166	-0.166	0.000	0.000	0.000	0.000
5	F	6	TYR	0	-0.064	-0.069	9.316	0.164	0.164	0.000	0.000	0.000	0.000
6	F	7	LEU	0	0.008	-0.002	13.212	-0.007	-0.007	0.000	0.000	0.000	0.000
7	F	8	ASN	0	0.010	-0.001	16.749	0.037	0.037	0.000	0.000	0.000	0.000
8	F	9	HIS	0	-0.010	-0.003	20.223	0.006	0.006	0.000	0.000	0.000	0.000
9	F	10	PRO	0	-0.003	-0.012	22.489	0.003	0.003	0.000	0.000	0.000	0.000
10	F	11	THR	0	-0.029	0.002	25.906	0.005	0.005	0.000	0.000	0.000	0.000
11	F	12	PHE	0	-0.027	-0.029	22.908	0.006	0.006	0.000	0.000	0.000	0.000
12	F	13	GLY	0	0.047	0.042	22.243	0.002	0.002	0.000	0.000	0.000	0.000
13	F	14	LEU	0	0.005	0.014	15.523	-0.007	-0.007	0.000	0.000	0.000	0.000
14	F	15	LEU	0	-0.039	-0.023	16.222	0.026	0.026	0.000	0.000	0.000	0.000
15	F	16	TYR	0	0.011	-0.007	10.827	-0.040	-0.040	0.000	0.000	0.000	0.000
16	F	17	GLN	0	0.010	0.003	8.573	-0.066	-0.066	0.000	0.000	0.000	0.000
17	F	18	ILE	0	-0.074	-0.025	9.137	0.050	0.050	0.000	0.000	0.000	0.000
18	F	19	CYS	0	-0.038	-0.030	8.862	0.088	0.088	0.000	0.000	0.000	0.000
19	F	20	SER	0	0.049	0.016	9.924	-0.053	-0.053	0.000	0.000	0.000	0.000
20	F	21	PHE	0	-0.050	-0.042	11.693	0.049	0.049	0.000	0.000	0.000	0.000
21	F	22	GLY	0	0.007	0.016	14.920	0.022	0.022	0.000	0.000	0.000	0.000
22	F	23	ASP	-1	-0.943	-0.973	14.100	-0.127	-0.127	0.000	0.000	0.000	0.000
23	F	24	SER	0	-0.003	-0.009	16.315	-0.001	-0.001	0.000	0.000	0.000	0.000
24	F	25	LYS	1	0.937	0.992	17.384	0.074	0.074	0.000	0.000	0.000	0.000
25	F	26	GLU	-1	-0.895	-0.945	11.664	-0.448	-0.448	0.000	0.000	0.000	0.000
26	F	27	LEU	0	-0.037	-0.007	13.455	0.024	0.024	0.000	0.000	0.000	0.000
27	F	28	PHE	0	0.028	0.006	12.611	-0.007	-0.007	0.000	0.000	0.000	0.000
28	F	29	ALA	0	-0.007	-0.006	14.850	0.033	0.033	0.000	0.000	0.000	0.000
29	F	30	THR	0	-0.014	-0.020	16.408	-0.018	-0.018	0.000	0.000	0.000	0.000
30	F	31	LEU	0	0.019	0.003	14.353	0.020	0.020	0.000	0.000	0.000	0.000
31	F	32	TYR	0	0.029	0.021	17.564	0.011	0.011	0.000	0.000	0.000	0.000
32	F	33	ALA	0	0.032	0.032	21.184	0.008	0.008	0.000	0.000	0.000	0.000
33	F	34	GLN	0	-0.019	-0.005	20.405	0.003	0.003	0.000	0.000	0.000	0.000
34	F	35	ARG	1	0.912	0.941	16.848	-0.037	-0.037	0.000	0.000	0.000	0.000
35	F	36	LEU	0	-0.069	-0.003	21.025	0.004	0.004	0.000	0.000	0.000	0.000
36	F	37	PHE	0	0.004	-0.006	16.532	0.000	0.000	0.000	0.000	0.000	0.000
37	F	38	PHE	0	0.012	-0.008	18.376	0.001	0.001	0.000	0.000	0.000	0.000
38	F	39	LEU	0	0.007	0.006	17.829	-0.009	-0.009	0.000	0.000	0.000	0.000
39	F	40	VAL	0	0.000	0.002	17.031	0.007	0.007	0.000	0.000	0.000	0.000
40	F	41	ALA	0	0.035	0.001	18.218	-0.006	-0.006	0.000	0.000	0.000	0.000
41	F	42	PHE	0	-0.031	-0.015	16.706	0.010	0.010	0.000	0.000	0.000	0.000
42	F	43	ASP	-1	-0.757	-0.844	22.040	-0.102	-0.102	0.000	0.000	0.000	0.000
43	F	44	ALA	0	-0.084	-0.024	24.950	0.007	0.007	0.000	0.000	0.000	0.000
44	F	45	ARG	1	0.971	0.983	25.699	0.069	0.069	0.000	0.000	0.000	0.000
45	F	46	GLY	0	0.030	-0.003	26.668	0.010	0.010	0.000	0.000	0.000	0.000
46	F	47	THR	0	-0.034	-0.016	20.797	0.003	0.003	0.000	0.000	0.000	0.000
47	F	48	ARG	1	0.927	0.948	23.059	0.099	0.099	0.000	0.000	0.000	0.000
48	F	49	PHE	0	0.024	-0.005	21.632	-0.009	-0.009	0.000	0.000	0.000	0.000
49	F	50	GLU	-1	-0.918	-0.954	22.485	-0.052	-0.052	0.000	0.000	0.000	0.000
50	F	51	PRO	0	-0.008	0.011	22.619	-0.002	-0.002	0.000	0.000	0.000	0.000
51	F	52	ILE	0	0.020	0.009	19.522	0.006	0.006	0.000	0.000	0.000	0.000
52	F	53	GLY	0	0.038	0.015	22.835	0.003	0.003	0.000	0.000	0.000	0.000
53	F	54	ARG	1	1.003	0.982	20.746	-0.054	-0.054	0.000	0.000	0.000	0.000
54	F	55	ASN	0	0.006	-0.001	21.395	0.016	0.016	0.000	0.000	0.000	0.000
55	F	56	GLU	-1	-0.831	-0.895	22.357	0.018	0.018	0.000	0.000	0.000	0.000
56	F	57	ALA	0	0.031	0.007	18.090	0.005	0.005	0.000	0.000	0.000	0.000
57	F	58	ARG	1	0.872	0.924	17.969	-0.066	-0.066	0.000	0.000	0.000	0.000
58	F	59	MET	0	0.028	0.020	18.631	0.015	0.015	0.000	0.000	0.000	0.000
59	F	60	LEU	0	-0.004	-0.004	17.869	0.009	0.009	0.000	0.000	0.000	0.000
60	F	61	VAL	0	0.009	-0.001	12.788	0.004	0.004	0.000	0.000	0.000	0.000
61	F	62	ASP	-1	-0.840	-0.912	14.832	0.162	0.162	0.000	0.000	0.000	0.000
62	F	63	ASN	0	-0.058	-0.039	17.012	0.019	0.019	0.000	0.000	0.000	0.000
63	F	64	ARG	1	0.954	0.998	11.013	0.008	0.008	0.000	0.000	0.000	0.000
64	F	65	LEU	0	0.015	-0.029	11.663	0.028	0.028	0.000	0.000	0.000	0.000
65	F	66	ARG	1	0.862	0.931	13.961	-0.093	-0.093	0.000	0.000	0.000	0.000
66	F	67	GLN	0	0.027	0.015	15.055	0.013	0.013	0.000	0.000	0.000	0.000
67	F	68	LEU	0	-0.054	0.013	9.181	-0.008	-0.008	0.000	0.000	0.000	0.000
68	F	69	ARG	1	0.917	0.947	12.228	-0.298	-0.298	0.000	0.000	0.000	0.000
69	F	70	ARG	1	0.935	0.976	13.571	-0.171	-0.171	0.000	0.000	0.000	0.000
70	F	71	NME	0	0.006	0.013	15.474	-0.010	-0.010	0.000	0.000	0.000	0.000
71	F	78	ACE	0	0.034	0.009	19.855	-0.003	-0.003	0.000	0.000	0.000	0.000
72	F	79	GLN	0	-0.011	-0.024	20.706	0.012	0.012	0.000	0.000	0.000	0.000
73	F	80	LEU	0	0.068	0.037	21.830	-0.003	-0.003	0.000	0.000	0.000	0.000
74	F	81	GLN	0	0.026	0.016	23.184	0.000	0.000	0.000	0.000	0.000	0.000
75	F	82	GLN	0	0.000	0.002	24.937	0.000	0.000	0.000	0.000	0.000	0.000
76	F	83	VAL	0	0.064	0.018	26.943	0.000	0.000	0.000	0.000	0.000	0.000
77	F	84	PHE	0	-0.019	-0.016	27.032	-0.001	-0.001	0.000	0.000	0.000	0.000
78	F	85	LYS	1	0.893	0.951	28.180	0.041	0.041	0.000	0.000	0.000	0.000
79	F	86	GLN	0	0.012	0.019	30.872	0.000	0.000	0.000	0.000	0.000	0.000
80	F	87	THR	0	-0.061	-0.032	31.946	0.003	0.003	0.000	0.000	0.000	0.000
81	F	88	PHE	0	-0.079	-0.047	30.486	0.001	0.001	0.000	0.000	0.000	0.000
82	F	89	LEU	-1	-0.928	-0.933	31.606	-0.024	-0.024	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(F:2:ACE )