FMO DATABASE

FMODB ID: 2JKMR

Calculation Name: 5WXL-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5WXL

Chain ID: B

ChEMBL ID:

UniProt ID: P36160

Base Structure: X-ray

Registration Date: 2023-06-21

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	78
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-412100.549148
FMO2-HF: Nuclear repulsion	381527.674892
FMO2-HF: Total energy	-30572.874255
FMO2-MP2: Total energy	-30661.935604

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(B:16:GLY)

Summations of interaction energy for fragment #1(B:16:GLY)

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.
-5.032	-4.268	5.606	-3.534	-2.836	-0.022

Interaction energy analysis for fragmet #1(B:16:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.033 / q_NPA : -0.024

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	B	18	GLU	-1	-0.906	-0.957	3.803	-2.041	-0.977	-0.008	-0.446	-0.611	0.001
4	B	19	ALA	0	-0.035	-0.005	6.532	0.158	0.158	0.000	0.000	0.000	0.000
5	B	20	VAL	0	0.003	0.004	8.836	0.182	0.182	0.000	0.000	0.000	0.000
6	B	21	TYR	0	0.021	-0.008	11.810	0.048	0.048	0.000	0.000	0.000	0.000
7	B	22	ASP	-1	-0.743	-0.837	15.364	-0.231	-0.231	0.000	0.000	0.000	0.000
8	B	23	LEU	0	0.034	-0.003	17.963	0.020	0.020	0.000	0.000	0.000	0.000
9	B	24	GLY	0	0.032	0.031	20.751	0.016	0.016	0.000	0.000	0.000	0.000
10	B	25	ASN	0	-0.061	-0.034	21.696	0.032	0.032	0.000	0.000	0.000	0.000
11	B	26	LEU	0	-0.092	-0.047	21.223	-0.004	-0.004	0.000	0.000	0.000	0.000
12	B	27	ALA	0	0.005	0.015	17.986	-0.007	-0.007	0.000	0.000	0.000	0.000
13	B	28	ALA	0	0.013	-0.007	13.064	-0.007	-0.007	0.000	0.000	0.000	0.000
14	B	29	PHE	0	-0.034	-0.016	12.185	0.038	0.038	0.000	0.000	0.000	0.000
15	B	30	ASP	-1	-0.787	-0.891	6.511	-1.717	-1.717	0.000	0.000	0.000	0.000
16	B	31	SER	0	-0.019	-0.012	6.818	-0.029	-0.029	0.000	0.000	0.000	0.000
17	B	32	ASN	0	-0.022	-0.020	2.149	-2.087	-2.423	5.615	-3.077	-2.202	-0.023
18	B	33	VAL	0	-0.014	-0.005	4.669	0.453	0.489	-0.001	-0.011	-0.023	0.000
19	B	34	LEU	0	-0.003	0.001	6.797	0.071	0.071	0.000	0.000	0.000	0.000
20	B	35	ASP	-1	-0.851	-0.920	10.028	-0.051	-0.051	0.000	0.000	0.000	0.000
21	B	36	LYS	1	0.961	0.968	12.780	0.095	0.095	0.000	0.000	0.000	0.000
22	B	37	ASN	0	-0.016	-0.018	16.252	0.004	0.004	0.000	0.000	0.000	0.000
23	B	38	ASP	-1	-0.889	-0.934	13.245	-0.130	-0.130	0.000	0.000	0.000	0.000
24	B	39	LEU	0	-0.030	-0.029	13.578	-0.003	-0.003	0.000	0.000	0.000	0.000
25	B	40	ASP	-1	-0.850	-0.914	17.715	-0.085	-0.085	0.000	0.000	0.000	0.000
26	B	41	SER	0	-0.051	-0.035	20.901	0.000	0.000	0.000	0.000	0.000	0.000
27	B	42	SER	0	0.005	0.003	23.986	0.005	0.005	0.000	0.000	0.000	0.000
28	B	43	ASN	0	-0.077	-0.029	19.150	0.014	0.014	0.000	0.000	0.000	0.000
29	B	44	ALA	0	0.021	-0.003	22.824	-0.008	-0.008	0.000	0.000	0.000	0.000
30	B	45	ARG	1	0.948	0.978	20.357	0.070	0.070	0.000	0.000	0.000	0.000
31	B	46	ARG	1	0.889	0.964	18.825	0.128	0.128	0.000	0.000	0.000	0.000
32	B	47	GLU	-1	-0.871	-0.948	18.619	-0.181	-0.181	0.000	0.000	0.000	0.000
33	B	48	GLU	-1	-0.948	-0.980	19.661	-0.115	-0.115	0.000	0.000	0.000	0.000
34	B	49	LYS	1	0.952	0.984	10.511	0.250	0.250	0.000	0.000	0.000	0.000
35	B	50	ILE	0	0.049	0.022	14.738	-0.043	-0.043	0.000	0.000	0.000	0.000
36	B	51	LYS	1	0.961	0.986	15.839	0.115	0.115	0.000	0.000	0.000	0.000
37	B	52	SER	0	-0.038	-0.015	14.216	-0.008	-0.008	0.000	0.000	0.000	0.000
38	B	53	LEU	0	0.034	0.015	9.377	-0.006	-0.006	0.000	0.000	0.000	0.000
39	B	54	THR	0	-0.008	-0.008	12.378	-0.058	-0.058	0.000	0.000	0.000	0.000
40	B	55	ARG	1	0.793	0.884	14.542	0.249	0.249	0.000	0.000	0.000	0.000
41	B	56	ASP	-1	-0.846	-0.913	11.044	-0.317	-0.317	0.000	0.000	0.000	0.000
42	B	57	ASN	0	-0.001	-0.013	9.864	-0.092	-0.092	0.000	0.000	0.000	0.000
43	B	58	VAL	0	-0.013	-0.005	12.538	0.020	0.020	0.000	0.000	0.000	0.000
44	B	59	GLN	0	-0.046	-0.012	14.896	0.041	0.041	0.000	0.000	0.000	0.000
45	B	60	LEU	0	0.005	0.008	9.744	0.046	0.046	0.000	0.000	0.000	0.000
46	B	61	LEU	0	0.044	0.024	14.261	0.024	0.024	0.000	0.000	0.000	0.000
47	B	62	ILE	0	-0.026	-0.014	16.454	0.038	0.038	0.000	0.000	0.000	0.000
48	B	63	ASN	0	-0.002	-0.014	15.651	0.047	0.047	0.000	0.000	0.000	0.000
49	B	64	GLN	0	-0.007	0.010	14.804	0.050	0.050	0.000	0.000	0.000	0.000
50	B	65	LEU	0	-0.008	-0.009	18.477	0.031	0.031	0.000	0.000	0.000	0.000
51	B	66	LEU	0	-0.044	-0.035	21.647	0.024	0.024	0.000	0.000	0.000	0.000
52	B	67	SER	0	-0.080	-0.022	20.736	0.017	0.017	0.000	0.000	0.000	0.000
53	B	68	LEU	0	-0.017	0.004	22.680	0.007	0.007	0.000	0.000	0.000	0.000
54	B	69	PRO	0	-0.004	-0.006	24.987	0.011	0.011	0.000	0.000	0.000	0.000
55	B	70	MET	0	0.008	0.004	28.310	-0.006	-0.006	0.000	0.000	0.000	0.000
56	B	71	LYS	1	0.893	0.957	30.905	0.092	0.092	0.000	0.000	0.000	0.000
57	B	72	THR	0	0.005	-0.037	34.225	-0.003	-0.003	0.000	0.000	0.000	0.000
58	B	73	THR	0	-0.004	0.047	36.911	0.003	0.003	0.000	0.000	0.000	0.000
59	B	87	MET	0	-0.005	-0.007	35.298	0.001	0.001	0.000	0.000	0.000	0.000
60	B	88	THR	0	-0.002	-0.013	31.545	0.003	0.003	0.000	0.000	0.000	0.000
61	B	89	LEU	0	-0.036	-0.013	31.568	-0.005	-0.005	0.000	0.000	0.000	0.000
62	B	90	LEU	0	0.070	0.036	25.688	0.004	0.004	0.000	0.000	0.000	0.000
63	B	91	GLN	0	-0.055	-0.041	28.678	0.010	0.010	0.000	0.000	0.000	0.000
64	B	92	LEU	0	0.006	0.010	24.423	-0.005	-0.005	0.000	0.000	0.000	0.000
65	B	93	PRO	0	-0.017	-0.002	22.754	0.012	0.012	0.000	0.000	0.000	0.000
66	B	94	ASP	-1	-0.879	-0.944	25.836	-0.131	-0.131	0.000	0.000	0.000	0.000
67	B	95	PRO	0	-0.084	-0.049	23.652	-0.013	-0.013	0.000	0.000	0.000	0.000
68	B	96	THR	0	-0.040	-0.025	20.299	0.001	0.001	0.000	0.000	0.000	0.000
69	B	97	THR	0	-0.053	-0.048	20.029	-0.008	-0.008	0.000	0.000	0.000	0.000
70	B	98	ASP	-1	-0.933	-0.959	21.827	-0.157	-0.157	0.000	0.000	0.000	0.000
71	B	99	LEU	0	-0.035	-0.016	23.536	-0.002	-0.002	0.000	0.000	0.000	0.000
72	B	100	PRO	0	-0.050	-0.012	26.698	0.011	0.011	0.000	0.000	0.000	0.000
73	B	101	ARG	1	0.904	0.935	30.159	0.088	0.088	0.000	0.000	0.000	0.000
74	B	102	GLU	-1	-0.875	-0.940	33.273	-0.088	-0.088	0.000	0.000	0.000	0.000
75	B	103	LYS	1	0.920	0.960	35.678	0.078	0.078	0.000	0.000	0.000	0.000
76	B	104	PRO	0	0.029	0.018	37.844	-0.004	-0.004	0.000	0.000	0.000	0.000
77	B	105	LEU	0	0.016	-0.001	36.946	0.000	0.000	0.000	0.000	0.000	0.000
78	B	106	PRO	0	-0.013	0.010	39.887	0.003	0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:16:GLY)