FMO DATABASE

FMODB ID: 7G17K

Calculation Name: 3W6K-B-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3W6K

Chain ID: B

ChEMBL ID:
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UniProt ID: A0A0E0

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	OptAll
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	82
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-482843.041114
FMO2-HF: Nuclear repulsion	452343.100781
FMO2-HF: Total energy	-30499.940333
FMO2-MP2: Total energy	-30590.553656

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:12:GLY)

Summations of interaction energy for fragment #1(B:12: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.
-24.366	-26.613	13.013	-5.606	-5.16	0.045

Interaction energy analysis for fragmet #1(B:12:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.066 / q_NPA : 0.025

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	14	LEU	0	0.092	0.049	3.883	0.108	1.558	-0.001	-0.737	-0.712	0.001
4	B	15	LYS	1	0.890	0.940	1.963	-25.309	-29.006	13.014	-4.869	-4.448	0.044
5	B	16	PRO	0	0.015	0.012	4.906	0.791	0.791	0.000	0.000	0.000	0.000
6	B	17	ALA	0	0.064	0.035	7.712	0.441	0.441	0.000	0.000	0.000	0.000
7	B	18	LYS	1	0.845	0.883	7.306	0.089	0.089	0.000	0.000	0.000	0.000
8	B	19	ALA	0	0.005	0.003	9.503	0.212	0.212	0.000	0.000	0.000	0.000
9	B	20	ILE	0	-0.003	0.003	11.267	0.139	0.139	0.000	0.000	0.000	0.000
10	B	21	VAL	0	0.041	0.016	13.119	0.112	0.112	0.000	0.000	0.000	0.000
11	B	22	GLU	-1	-0.841	-0.913	13.606	0.068	0.068	0.000	0.000	0.000	0.000
12	B	23	ALA	0	-0.023	-0.018	15.364	0.057	0.057	0.000	0.000	0.000	0.000
13	B	24	LEU	0	-0.002	-0.003	17.270	0.040	0.040	0.000	0.000	0.000	0.000
14	B	25	LEU	0	-0.009	-0.014	17.734	0.036	0.036	0.000	0.000	0.000	0.000
15	B	26	PHE	0	-0.067	-0.026	19.694	0.037	0.037	0.000	0.000	0.000	0.000
16	B	27	ALA	0	-0.042	-0.027	21.369	0.018	0.018	0.000	0.000	0.000	0.000
17	B	28	ALA	0	-0.023	0.001	23.092	0.009	0.009	0.000	0.000	0.000	0.000
18	B	29	GLY	0	-0.006	0.013	24.937	0.012	0.012	0.000	0.000	0.000	0.000
19	B	30	ASP	-1	-0.977	-1.005	26.024	-0.072	-0.072	0.000	0.000	0.000	0.000
20	B	31	GLU	-1	-0.938	-0.971	28.513	-0.098	-0.098	0.000	0.000	0.000	0.000
21	B	32	GLY	0	-0.030	0.000	24.884	-0.004	-0.004	0.000	0.000	0.000	0.000
22	B	33	LEU	0	-0.012	-0.017	21.259	-0.016	-0.016	0.000	0.000	0.000	0.000
23	B	34	SER	0	0.034	0.011	23.613	-0.004	-0.004	0.000	0.000	0.000	0.000
24	B	35	LEU	0	-0.004	-0.003	19.150	-0.023	-0.023	0.000	0.000	0.000	0.000
25	B	36	SER	0	-0.001	-0.032	21.113	-0.032	-0.032	0.000	0.000	0.000	0.000
26	B	37	GLN	0	-0.013	0.008	22.931	-0.016	-0.016	0.000	0.000	0.000	0.000
27	B	38	ILE	0	0.008	0.010	17.044	-0.030	-0.030	0.000	0.000	0.000	0.000
28	B	39	ALA	0	-0.012	-0.014	18.038	-0.061	-0.061	0.000	0.000	0.000	0.000
29	B	40	ALA	0	-0.004	0.004	18.983	-0.046	-0.046	0.000	0.000	0.000	0.000
30	B	41	VAL	0	-0.033	-0.018	18.791	-0.017	-0.017	0.000	0.000	0.000	0.000
31	B	42	LEU	0	-0.072	-0.039	13.083	-0.050	-0.050	0.000	0.000	0.000	0.000
32	B	43	GLU	-1	-0.984	-0.973	15.862	-0.609	-0.609	0.000	0.000	0.000	0.000
33	B	44	VAL	0	-0.059	-0.013	13.650	-0.053	-0.053	0.000	0.000	0.000	0.000
34	B	45	SER	0	-0.036	-0.067	17.111	0.103	0.103	0.000	0.000	0.000	0.000
35	B	46	GLU	-1	-0.785	-0.908	17.702	-0.292	-0.292	0.000	0.000	0.000	0.000
36	B	47	LEU	0	-0.029	-0.002	17.140	0.014	0.014	0.000	0.000	0.000	0.000
37	B	48	GLU	-1	-0.834	-0.882	13.594	-0.735	-0.735	0.000	0.000	0.000	0.000
38	B	49	ALA	0	0.028	0.016	13.607	-0.050	-0.050	0.000	0.000	0.000	0.000
39	B	50	LYS	1	0.835	0.921	15.200	0.170	0.170	0.000	0.000	0.000	0.000
40	B	51	ALA	0	0.014	0.013	12.572	0.040	0.040	0.000	0.000	0.000	0.000
41	B	52	VAL	0	-0.025	-0.015	9.731	0.016	0.016	0.000	0.000	0.000	0.000
42	B	53	ILE	0	0.003	0.004	11.803	0.069	0.069	0.000	0.000	0.000	0.000
43	B	54	GLU	-1	-0.912	-0.965	15.002	-0.067	-0.067	0.000	0.000	0.000	0.000
44	B	55	GLU	-1	-0.881	-0.922	8.170	0.393	0.393	0.000	0.000	0.000	0.000
45	B	56	LEU	0	-0.009	-0.003	11.886	0.118	0.118	0.000	0.000	0.000	0.000
46	B	57	GLN	0	-0.006	-0.005	12.903	0.090	0.090	0.000	0.000	0.000	0.000
47	B	58	GLN	0	0.004	0.013	13.108	-0.005	-0.005	0.000	0.000	0.000	0.000
48	B	59	ASP	-1	-0.777	-0.866	10.355	0.602	0.602	0.000	0.000	0.000	0.000
49	B	60	CYS	0	-0.093	-0.046	13.762	0.017	0.017	0.000	0.000	0.000	0.000
50	B	61	ARG	1	0.842	0.898	17.172	-0.078	-0.078	0.000	0.000	0.000	0.000
51	B	62	ARG	1	0.802	0.914	11.302	-0.624	-0.624	0.000	0.000	0.000	0.000
52	B	63	GLU	-1	-0.952	-0.980	18.143	0.198	0.198	0.000	0.000	0.000	0.000
53	B	64	GLU	-1	-0.874	-0.950	16.374	0.389	0.389	0.000	0.000	0.000	0.000
54	B	65	ARG	1	0.789	0.900	14.589	-0.174	-0.174	0.000	0.000	0.000	0.000
55	B	66	GLY	0	0.042	0.014	19.538	-0.018	-0.018	0.000	0.000	0.000	0.000
56	B	67	ILE	0	-0.056	-0.040	18.661	-0.021	-0.021	0.000	0.000	0.000	0.000
57	B	68	GLN	0	-0.019	-0.020	20.487	0.027	0.027	0.000	0.000	0.000	0.000
58	B	69	LEU	0	0.038	0.028	16.727	-0.013	-0.013	0.000	0.000	0.000	0.000
59	B	70	VAL	0	-0.022	-0.011	20.402	0.016	0.016	0.000	0.000	0.000	0.000
60	B	71	GLU	-1	-0.788	-0.899	22.767	-0.150	-0.150	0.000	0.000	0.000	0.000
61	B	72	LEU	0	-0.027	-0.020	24.605	0.017	0.017	0.000	0.000	0.000	0.000
62	B	73	GLY	0	0.005	0.002	28.337	-0.009	-0.009	0.000	0.000	0.000	0.000
63	B	74	GLY	0	-0.008	0.006	27.631	-0.003	-0.003	0.000	0.000	0.000	0.000
64	B	75	VAL	0	-0.020	-0.007	25.345	-0.020	-0.020	0.000	0.000	0.000	0.000
65	B	76	PHE	0	-0.020	-0.017	20.781	0.014	0.014	0.000	0.000	0.000	0.000
66	B	77	LEU	0	0.039	0.029	23.020	-0.010	-0.010	0.000	0.000	0.000	0.000
67	B	78	LEU	0	0.005	0.000	18.103	0.017	0.017	0.000	0.000	0.000	0.000
68	B	79	ALA	0	0.017	0.009	22.230	0.001	0.001	0.000	0.000	0.000	0.000
69	B	80	THR	0	0.031	0.012	24.021	0.011	0.011	0.000	0.000	0.000	0.000
70	B	81	LYS	1	0.880	0.975	20.605	-0.171	-0.171	0.000	0.000	0.000	0.000
71	B	82	LYS	1	0.879	0.921	26.404	-0.013	-0.013	0.000	0.000	0.000	0.000
72	B	83	GLU	-1	-0.848	-0.918	26.037	0.120	0.120	0.000	0.000	0.000	0.000
73	B	84	HIS	0	0.001	-0.007	25.079	-0.010	-0.010	0.000	0.000	0.000	0.000
74	B	85	ALA	0	0.013	0.005	30.551	-0.004	-0.004	0.000	0.000	0.000	0.000
75	B	86	PRO	0	-0.044	-0.031	33.481	-0.006	-0.006	0.000	0.000	0.000	0.000
76	B	87	TYR	0	0.038	0.014	31.676	-0.004	-0.004	0.000	0.000	0.000	0.000
77	B	88	LEU	0	-0.005	0.002	29.784	-0.005	-0.005	0.000	0.000	0.000	0.000
78	B	89	LYS	1	0.938	0.968	33.865	-0.040	-0.040	0.000	0.000	0.000	0.000
79	B	90	LYS	1	0.885	0.912	37.288	-0.047	-0.047	0.000	0.000	0.000	0.000
80	B	91	LEU	0	-0.025	0.014	32.386	0.001	0.001	0.000	0.000	0.000	0.000
81	B	92	VAL	0	-0.008	0.007	36.438	-0.005	-0.005	0.000	0.000	0.000	0.000
82	B	93	GLU	-1	-0.934	-0.945	39.163	0.036	0.036	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:12:GLY)