FMO DATABASE

FMODB ID: 6N34Z

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	OptHSide
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	-412217.444913
FMO2-HF: Nuclear repulsion	381644.114271
FMO2-HF: Total energy	-30573.330642
FMO2-MP2: Total energy	-30662.399239

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.
-4.83	-2.628	3.255	-2.802	-2.655	-0.02

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 : -0.026 / 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	B	18	GLU	-1	-0.817	-0.919	3.803	-2.713	-1.672	-0.008	-0.451	-0.582	0.002
4	B	19	ALA	0	-0.039	-0.005	6.532	0.472	0.472	0.000	0.000	0.000	0.000
5	B	20	VAL	0	-0.021	-0.008	8.819	0.056	0.056	0.000	0.000	0.000	0.000
6	B	21	TYR	0	-0.025	-0.035	11.304	0.099	0.099	0.000	0.000	0.000	0.000
7	B	22	ASP	-1	-0.738	-0.820	15.346	-0.070	-0.070	0.000	0.000	0.000	0.000
8	B	23	LEU	0	0.031	-0.004	17.909	0.016	0.016	0.000	0.000	0.000	0.000
9	B	24	GLY	0	0.030	0.031	20.733	0.009	0.009	0.000	0.000	0.000	0.000
10	B	25	ASN	0	-0.082	-0.056	21.621	0.018	0.018	0.000	0.000	0.000	0.000
11	B	26	LEU	0	-0.094	-0.047	21.188	0.004	0.004	0.000	0.000	0.000	0.000
12	B	27	ALA	0	0.002	0.012	18.068	0.002	0.002	0.000	0.000	0.000	0.000
13	B	28	ALA	0	0.011	-0.006	13.110	-0.028	-0.028	0.000	0.000	0.000	0.000
14	B	29	PHE	0	-0.035	-0.015	12.165	0.060	0.060	0.000	0.000	0.000	0.000
15	B	30	ASP	-1	-0.767	-0.862	6.474	-0.634	-0.634	0.000	0.000	0.000	0.000
16	B	31	SER	0	-0.011	-0.009	6.112	-0.006	-0.006	0.000	0.000	0.000	0.000
17	B	32	ASN	0	-0.071	-0.050	2.282	-1.509	-0.380	3.264	-2.341	-2.052	-0.022
18	B	33	VAL	0	-0.007	-0.003	4.661	-0.213	-0.181	-0.001	-0.010	-0.021	0.000
19	B	34	LEU	0	0.008	0.008	6.789	-0.303	-0.303	0.000	0.000	0.000	0.000
20	B	35	ASP	-1	-0.805	-0.903	10.018	0.383	0.383	0.000	0.000	0.000	0.000
21	B	36	LYS	1	0.972	0.979	12.775	-0.321	-0.321	0.000	0.000	0.000	0.000
22	B	37	ASN	0	-0.061	-0.047	16.067	-0.060	-0.060	0.000	0.000	0.000	0.000
23	B	38	ASP	-1	-0.837	-0.896	13.341	0.151	0.151	0.000	0.000	0.000	0.000
24	B	39	LEU	0	-0.025	-0.022	13.549	-0.032	-0.032	0.000	0.000	0.000	0.000
25	B	40	ASP	-1	-0.802	-0.877	17.705	0.115	0.115	0.000	0.000	0.000	0.000
26	B	41	SER	0	-0.025	-0.010	20.892	-0.012	-0.012	0.000	0.000	0.000	0.000
27	B	42	SER	0	-0.063	-0.046	23.976	-0.015	-0.015	0.000	0.000	0.000	0.000
28	B	43	ASN	0	-0.080	-0.035	19.235	-0.024	-0.024	0.000	0.000	0.000	0.000
29	B	44	ALA	0	0.031	0.001	22.817	-0.005	-0.005	0.000	0.000	0.000	0.000
30	B	45	ARG	1	0.839	0.901	20.210	-0.022	-0.022	0.000	0.000	0.000	0.000
31	B	46	ARG	1	0.844	0.925	18.815	-0.090	-0.090	0.000	0.000	0.000	0.000
32	B	47	GLU	-1	-0.825	-0.915	18.607	0.035	0.035	0.000	0.000	0.000	0.000
33	B	48	GLU	-1	-0.844	-0.910	19.648	-0.002	-0.002	0.000	0.000	0.000	0.000
34	B	49	LYS	1	0.871	0.936	10.991	-0.158	-0.158	0.000	0.000	0.000	0.000
35	B	50	ILE	0	0.045	0.020	14.726	-0.016	-0.016	0.000	0.000	0.000	0.000
36	B	51	LYS	1	0.952	0.985	15.823	0.016	0.016	0.000	0.000	0.000	0.000
37	B	52	SER	0	-0.008	-0.002	14.080	-0.022	-0.022	0.000	0.000	0.000	0.000
38	B	53	LEU	0	0.017	0.011	9.385	-0.032	-0.032	0.000	0.000	0.000	0.000
39	B	54	THR	0	-0.006	-0.011	12.361	-0.054	-0.054	0.000	0.000	0.000	0.000
40	B	55	ARG	1	0.775	0.871	14.486	0.215	0.215	0.000	0.000	0.000	0.000
41	B	56	ASP	-1	-0.823	-0.905	11.153	-0.283	-0.283	0.000	0.000	0.000	0.000
42	B	57	ASN	0	-0.018	-0.030	9.398	-0.139	-0.139	0.000	0.000	0.000	0.000
43	B	58	VAL	0	-0.005	-0.002	12.520	-0.003	-0.003	0.000	0.000	0.000	0.000
44	B	59	GLN	0	-0.051	-0.010	14.831	0.024	0.024	0.000	0.000	0.000	0.000
45	B	60	LEU	0	0.015	0.008	9.710	0.022	0.022	0.000	0.000	0.000	0.000
46	B	61	LEU	0	0.029	0.020	14.247	0.006	0.006	0.000	0.000	0.000	0.000
47	B	62	ILE	0	-0.018	-0.015	16.437	0.023	0.023	0.000	0.000	0.000	0.000
48	B	63	ASN	0	-0.009	-0.011	15.802	0.048	0.048	0.000	0.000	0.000	0.000
49	B	64	GLN	0	0.004	0.018	14.189	0.055	0.055	0.000	0.000	0.000	0.000
50	B	65	LEU	0	-0.009	-0.007	18.472	0.026	0.026	0.000	0.000	0.000	0.000
51	B	66	LEU	0	-0.053	-0.039	21.635	0.020	0.020	0.000	0.000	0.000	0.000
52	B	67	SER	0	-0.078	-0.023	20.709	0.003	0.003	0.000	0.000	0.000	0.000
53	B	68	LEU	0	-0.017	0.007	22.624	0.004	0.004	0.000	0.000	0.000	0.000
54	B	69	PRO	0	-0.009	-0.011	24.984	0.008	0.008	0.000	0.000	0.000	0.000
55	B	70	MET	0	0.019	0.006	27.742	0.004	0.004	0.000	0.000	0.000	0.000
56	B	71	LYS	1	0.881	0.940	30.901	0.083	0.083	0.000	0.000	0.000	0.000
57	B	72	THR	0	0.002	-0.007	34.217	-0.003	-0.003	0.000	0.000	0.000	0.000
58	B	73	THR	0	0.002	0.018	36.907	0.002	0.002	0.000	0.000	0.000	0.000
59	B	87	MET	0	0.015	0.016	35.939	0.002	0.002	0.000	0.000	0.000	0.000
60	B	88	THR	0	-0.016	-0.032	31.385	0.002	0.002	0.000	0.000	0.000	0.000
61	B	89	LEU	0	-0.039	-0.014	31.567	-0.001	-0.001	0.000	0.000	0.000	0.000
62	B	90	LEU	0	0.056	0.035	25.715	-0.001	-0.001	0.000	0.000	0.000	0.000
63	B	91	GLN	0	-0.041	-0.025	28.669	0.013	0.013	0.000	0.000	0.000	0.000
64	B	92	LEU	0	0.011	0.011	24.510	-0.009	-0.009	0.000	0.000	0.000	0.000
65	B	93	PRO	0	-0.017	-0.002	22.679	0.009	0.009	0.000	0.000	0.000	0.000
66	B	94	ASP	-1	-0.889	-0.950	25.820	-0.068	-0.068	0.000	0.000	0.000	0.000
67	B	95	PRO	0	-0.075	-0.039	23.632	-0.010	-0.010	0.000	0.000	0.000	0.000
68	B	96	THR	0	0.013	-0.011	19.944	0.000	0.000	0.000	0.000	0.000	0.000
69	B	97	THR	0	-0.095	-0.062	20.134	0.013	0.013	0.000	0.000	0.000	0.000
70	B	98	ASP	-1	-0.930	-0.957	21.809	-0.002	-0.002	0.000	0.000	0.000	0.000
71	B	99	LEU	0	-0.028	-0.013	23.502	0.011	0.011	0.000	0.000	0.000	0.000
72	B	100	PRO	0	-0.047	-0.013	26.679	-0.003	-0.003	0.000	0.000	0.000	0.000
73	B	101	ARG	1	0.902	0.935	30.140	0.003	0.003	0.000	0.000	0.000	0.000
74	B	102	GLU	-1	-0.800	-0.897	33.254	0.000	0.000	0.000	0.000	0.000	0.000
75	B	103	LYS	1	0.836	0.912	35.658	0.004	0.004	0.000	0.000	0.000	0.000
76	B	104	PRO	0	0.037	0.024	37.825	-0.002	-0.002	0.000	0.000	0.000	0.000
77	B	105	LEU	0	0.010	-0.001	36.422	-0.002	-0.002	0.000	0.000	0.000	0.000
78	B	106	PRO	0	-0.006	0.009	39.869	0.001	0.001	0.000	0.000	0.000	0.000

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