FMO DATABASE

FMODB ID: GNGN1

Calculation Name: 1XAK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1XAK

Chain ID: A

ChEMBL ID:

UniProt ID: P59635

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	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	66
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-391615.266948
FMO2-HF: Nuclear repulsion	364008.093354
FMO2-HF: Total energy	-27607.173593
FMO2-MP2: Total energy	-27684.620116

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(A:-1:CYS)

Summations of interaction energy for fragment #1(A:-1:CYS)

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.
-7.666	-2.908	1.529	-2.511	-3.776	-0.017

Interaction energy analysis for fragmet #1(A:-1:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / q_NPA : 0.003

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	A	2	LEU	0	-0.036	-0.010	3.814	0.454	1.875	-0.013	-0.556	-0.852	0.001
4	A	3	TYR	0	0.022	0.004	6.624	-0.691	-0.691	0.000	0.000	0.000	0.000
5	A	4	HIS	1	0.842	0.918	9.386	-0.356	-0.356	0.000	0.000	0.000	0.000
6	A	5	TYR	0	0.014	-0.001	13.284	-0.056	-0.056	0.000	0.000	0.000	0.000
7	A	6	GLN	0	-0.007	-0.001	16.853	-0.020	-0.020	0.000	0.000	0.000	0.000
8	A	7	GLU	-1	-0.892	-0.947	20.168	0.179	0.179	0.000	0.000	0.000	0.000
9	A	8	CYS	0	-0.074	-0.005	23.727	-0.003	-0.003	0.000	0.000	0.000	0.000
10	A	9	VAL	0	0.018	0.014	26.080	0.004	0.004	0.000	0.000	0.000	0.000
11	A	10	ARG	1	1.013	0.978	28.639	-0.068	-0.068	0.000	0.000	0.000	0.000
12	A	11	GLY	0	-0.029	-0.003	29.985	-0.001	-0.001	0.000	0.000	0.000	0.000
13	A	12	THR	0	-0.039	-0.020	29.397	-0.007	-0.007	0.000	0.000	0.000	0.000
14	A	13	THR	0	0.015	0.003	27.442	-0.005	-0.005	0.000	0.000	0.000	0.000
15	A	14	VAL	0	-0.009	-0.005	22.290	0.009	0.009	0.000	0.000	0.000	0.000
16	A	15	ILE	0	0.006	-0.001	23.409	-0.019	-0.019	0.000	0.000	0.000	0.000
17	A	16	LEU	0	-0.033	-0.011	17.776	0.030	0.030	0.000	0.000	0.000	0.000
18	A	17	LYS	1	0.810	0.878	16.790	0.074	0.074	0.000	0.000	0.000	0.000
19	A	18	GLU	-1	-0.896	-0.964	15.134	-0.267	-0.267	0.000	0.000	0.000	0.000
20	A	19	PRO	0	-0.056	-0.028	10.042	0.048	0.048	0.000	0.000	0.000	0.000
21	A	20	CYS	0	-0.044	-0.020	7.063	0.488	0.488	0.000	0.000	0.000	0.000
22	A	21	PRO	0	-0.006	0.002	12.084	0.029	0.029	0.000	0.000	0.000	0.000
23	A	22	SER	0	0.007	-0.009	13.961	-0.067	-0.067	0.000	0.000	0.000	0.000
24	A	23	GLY	0	0.043	0.045	12.562	-0.081	-0.081	0.000	0.000	0.000	0.000
25	A	24	THR	0	-0.013	-0.013	12.060	0.072	0.072	0.000	0.000	0.000	0.000
26	A	25	TYR	0	-0.038	-0.052	12.526	-0.072	-0.072	0.000	0.000	0.000	0.000
27	A	26	GLU	-1	-0.932	-0.955	14.441	-0.408	-0.408	0.000	0.000	0.000	0.000
28	A	27	GLY	0	0.024	-0.009	15.594	0.028	0.028	0.000	0.000	0.000	0.000
29	A	28	ASN	0	-0.051	-0.028	18.246	-0.017	-0.017	0.000	0.000	0.000	0.000
30	A	29	SER	0	0.001	0.012	21.506	0.019	0.019	0.000	0.000	0.000	0.000
31	A	30	PRO	0	-0.018	0.017	21.939	-0.021	-0.021	0.000	0.000	0.000	0.000
32	A	31	PHE	0	0.004	0.007	18.062	0.013	0.013	0.000	0.000	0.000	0.000
33	A	32	HIS	0	0.010	0.008	22.193	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	33	PRO	0	0.007	0.007	22.184	0.012	0.012	0.000	0.000	0.000	0.000
35	A	34	LEU	0	0.005	-0.007	23.044	0.020	0.020	0.000	0.000	0.000	0.000
36	A	35	ALA	0	0.021	0.015	23.734	-0.018	-0.018	0.000	0.000	0.000	0.000
37	A	36	ASP	-1	-0.884	-0.946	23.593	-0.067	-0.067	0.000	0.000	0.000	0.000
38	A	37	ASN	0	-0.002	0.013	18.246	0.042	0.042	0.000	0.000	0.000	0.000
39	A	38	LYS	1	0.960	0.996	18.786	0.031	0.031	0.000	0.000	0.000	0.000
40	A	39	PHE	0	0.033	0.024	16.649	-0.024	-0.024	0.000	0.000	0.000	0.000
41	A	40	ALA	0	0.000	0.002	21.552	0.027	0.027	0.000	0.000	0.000	0.000
42	A	41	LEU	0	0.036	0.018	20.230	-0.014	-0.014	0.000	0.000	0.000	0.000
43	A	42	THR	0	0.016	0.016	24.410	0.012	0.012	0.000	0.000	0.000	0.000
44	A	44	THR	0	-0.004	-0.027	24.938	0.000	0.000	0.000	0.000	0.000	0.000
45	A	45	SER	0	-0.015	-0.021	23.689	0.006	0.006	0.000	0.000	0.000	0.000
46	A	46	THR	0	0.024	0.043	20.594	-0.013	-0.013	0.000	0.000	0.000	0.000
47	A	47	HIS	0	0.053	0.014	15.100	0.043	0.043	0.000	0.000	0.000	0.000
48	A	48	PHE	0	-0.009	0.002	15.420	-0.020	-0.020	0.000	0.000	0.000	0.000
49	A	49	ALA	0	-0.029	-0.021	10.592	0.080	0.080	0.000	0.000	0.000	0.000
50	A	50	PHE	0	0.033	0.014	10.614	0.039	0.039	0.000	0.000	0.000	0.000
51	A	51	ALA	0	0.021	0.015	7.756	-0.206	-0.206	0.000	0.000	0.000	0.000
52	A	53	ALA	0	0.046	0.016	7.561	-0.416	-0.416	0.000	0.000	0.000	0.000
53	A	54	ASP	-1	-0.880	-0.926	5.769	-1.903	-1.903	0.000	0.000	0.000	0.000
54	A	55	GLY	0	-0.005	0.004	4.447	-0.281	-0.107	-0.001	-0.026	-0.146	0.000
55	A	56	THR	0	-0.081	-0.052	2.494	-7.317	-4.874	1.532	-1.680	-2.295	-0.019
56	A	57	ARG	1	0.916	0.968	3.477	2.072	2.792	0.011	-0.249	-0.483	0.001
57	A	58	HIS	0	0.009	0.003	5.684	1.172	1.172	0.000	0.000	0.000	0.000
58	A	59	THR	0	0.020	0.008	8.239	-0.173	-0.173	0.000	0.000	0.000	0.000
59	A	60	TYR	0	-0.027	-0.035	10.888	0.241	0.241	0.000	0.000	0.000	0.000
60	A	61	GLN	0	0.007	0.015	14.193	0.000	0.000	0.000	0.000	0.000	0.000
61	A	62	LEU	0	-0.001	-0.001	17.175	0.024	0.024	0.000	0.000	0.000	0.000
62	A	63	ARG	1	0.954	0.981	20.542	-0.194	-0.194	0.000	0.000	0.000	0.000
63	A	64	ALA	0	0.009	-0.009	23.390	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	65	ARG	1	0.907	0.963	26.694	-0.119	-0.119	0.000	0.000	0.000	0.000
65	A	66	SER	0	-0.005	-0.002	29.614	-0.007	-0.007	0.000	0.000	0.000	0.000
66	A	67	VAL	0	0.049	0.023	33.007	0.004	0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-1:CYS)