FMO DATABASE

FMODB ID: M3QYZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-480995.863087
FMO2-HF: Nuclear repulsion	450496.052306
FMO2-HF: Total energy	-30499.810781
FMO2-MP2: Total energy	-30590.455409

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.
-3.908	-0.236	0.909	-2.157	-2.424	0

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 : 0.037 / q_NPA : 0.011

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	0.106	0.059	3.776	-1.314	1.488	-0.028	-1.458	-1.316	-0.001
4	B	15	LYS	1	0.924	0.978	2.542	-2.995	-2.217	0.938	-0.689	-1.027	0.001
5	B	16	PRO	0	0.035	0.020	5.271	0.491	0.583	-0.001	-0.010	-0.081	0.000
6	B	17	ALA	0	0.070	0.035	7.916	0.338	0.338	0.000	0.000	0.000	0.000
7	B	18	LYS	1	0.866	0.896	7.661	0.380	0.380	0.000	0.000	0.000	0.000
8	B	19	ALA	0	-0.021	-0.010	9.404	0.181	0.181	0.000	0.000	0.000	0.000
9	B	20	ILE	0	-0.004	0.001	11.243	0.125	0.125	0.000	0.000	0.000	0.000
10	B	21	VAL	0	0.029	0.012	13.200	0.099	0.099	0.000	0.000	0.000	0.000
11	B	22	GLU	-1	-0.852	-0.915	13.647	-0.086	-0.086	0.000	0.000	0.000	0.000
12	B	23	ALA	0	-0.026	-0.018	15.377	0.052	0.052	0.000	0.000	0.000	0.000
13	B	24	LEU	0	0.007	0.000	17.333	0.040	0.040	0.000	0.000	0.000	0.000
14	B	25	LEU	0	-0.019	-0.017	18.147	0.035	0.035	0.000	0.000	0.000	0.000
15	B	26	PHE	0	-0.072	-0.036	19.796	0.032	0.032	0.000	0.000	0.000	0.000
16	B	27	ALA	0	-0.033	-0.020	21.519	0.019	0.019	0.000	0.000	0.000	0.000
17	B	28	ALA	0	-0.028	0.002	23.344	0.011	0.011	0.000	0.000	0.000	0.000
18	B	29	GLY	0	0.001	0.018	25.077	0.013	0.013	0.000	0.000	0.000	0.000
19	B	30	ASP	-1	-0.974	-0.999	26.396	-0.091	-0.091	0.000	0.000	0.000	0.000
20	B	31	GLU	-1	-0.935	-0.975	28.893	-0.101	-0.101	0.000	0.000	0.000	0.000
21	B	32	GLY	0	-0.058	-0.013	25.158	-0.004	-0.004	0.000	0.000	0.000	0.000
22	B	33	LEU	0	0.002	-0.005	21.550	-0.010	-0.010	0.000	0.000	0.000	0.000
23	B	34	SER	0	0.034	0.019	23.941	-0.007	-0.007	0.000	0.000	0.000	0.000
24	B	35	LEU	0	0.014	-0.005	19.603	-0.020	-0.020	0.000	0.000	0.000	0.000
25	B	36	SER	0	0.010	-0.020	21.700	-0.025	-0.025	0.000	0.000	0.000	0.000
26	B	37	GLN	0	-0.003	0.014	23.242	-0.015	-0.015	0.000	0.000	0.000	0.000
27	B	38	ILE	0	0.004	0.013	17.606	-0.025	-0.025	0.000	0.000	0.000	0.000
28	B	39	ALA	0	-0.006	-0.011	18.467	-0.047	-0.047	0.000	0.000	0.000	0.000
29	B	40	ALA	0	-0.017	-0.007	19.407	-0.033	-0.033	0.000	0.000	0.000	0.000
30	B	41	VAL	0	-0.041	-0.026	18.793	-0.014	-0.014	0.000	0.000	0.000	0.000
31	B	42	LEU	0	-0.073	-0.042	13.638	-0.035	-0.035	0.000	0.000	0.000	0.000
32	B	43	GLU	-1	-0.980	-0.968	16.183	-0.509	-0.509	0.000	0.000	0.000	0.000
33	B	44	VAL	0	-0.063	-0.017	13.699	-0.061	-0.061	0.000	0.000	0.000	0.000
34	B	45	SER	0	-0.034	-0.065	17.116	0.087	0.087	0.000	0.000	0.000	0.000
35	B	46	GLU	-1	-0.789	-0.905	18.053	-0.269	-0.269	0.000	0.000	0.000	0.000
36	B	47	LEU	0	-0.030	-0.011	17.409	0.000	0.000	0.000	0.000	0.000	0.000
37	B	48	GLU	-1	-0.834	-0.883	13.716	-0.675	-0.675	0.000	0.000	0.000	0.000
38	B	49	ALA	0	0.033	0.020	14.092	-0.044	-0.044	0.000	0.000	0.000	0.000
39	B	50	LYS	1	0.878	0.955	15.668	0.183	0.183	0.000	0.000	0.000	0.000
40	B	51	ALA	0	0.002	0.010	12.810	0.030	0.030	0.000	0.000	0.000	0.000
41	B	52	VAL	0	-0.028	-0.012	10.316	0.007	0.007	0.000	0.000	0.000	0.000
42	B	53	ILE	0	-0.003	-0.013	12.483	0.052	0.052	0.000	0.000	0.000	0.000
43	B	54	GLU	-1	-0.903	-0.965	15.627	-0.109	-0.109	0.000	0.000	0.000	0.000
44	B	55	GLU	-1	-0.894	-0.924	9.184	0.123	0.123	0.000	0.000	0.000	0.000
45	B	56	LEU	0	-0.010	-0.009	12.700	0.080	0.080	0.000	0.000	0.000	0.000
46	B	57	GLN	0	-0.004	0.004	13.492	0.066	0.066	0.000	0.000	0.000	0.000
47	B	58	GLN	0	0.015	0.012	14.246	0.006	0.006	0.000	0.000	0.000	0.000
48	B	59	ASP	-1	-0.794	-0.885	10.688	0.231	0.231	0.000	0.000	0.000	0.000
49	B	60	CYS	0	-0.092	-0.039	14.283	0.027	0.027	0.000	0.000	0.000	0.000
50	B	61	ARG	1	0.837	0.900	17.453	0.014	0.014	0.000	0.000	0.000	0.000
51	B	62	ARG	1	0.836	0.933	12.339	-0.304	-0.304	0.000	0.000	0.000	0.000
52	B	63	GLU	-1	-0.945	-0.978	18.838	0.103	0.103	0.000	0.000	0.000	0.000
53	B	64	GLU	-1	-0.888	-0.947	16.604	0.210	0.210	0.000	0.000	0.000	0.000
54	B	65	ARG	1	0.789	0.902	14.732	-0.005	-0.005	0.000	0.000	0.000	0.000
55	B	66	GLY	0	0.063	0.023	19.904	-0.004	-0.004	0.000	0.000	0.000	0.000
56	B	67	ILE	0	-0.069	-0.042	19.005	-0.008	-0.008	0.000	0.000	0.000	0.000
57	B	68	GLN	0	-0.021	-0.014	20.583	0.015	0.015	0.000	0.000	0.000	0.000
58	B	69	LEU	0	0.039	0.024	17.420	-0.009	-0.009	0.000	0.000	0.000	0.000
59	B	70	VAL	0	-0.029	-0.019	21.006	0.014	0.014	0.000	0.000	0.000	0.000
60	B	71	GLU	-1	-0.844	-0.938	23.745	-0.161	-0.161	0.000	0.000	0.000	0.000
61	B	72	LEU	0	-0.026	-0.016	25.541	0.016	0.016	0.000	0.000	0.000	0.000
62	B	73	GLY	0	0.009	0.004	29.189	-0.006	-0.006	0.000	0.000	0.000	0.000
63	B	74	GLY	0	-0.016	-0.003	28.151	-0.003	-0.003	0.000	0.000	0.000	0.000
64	B	75	VAL	0	-0.003	0.006	26.009	-0.014	-0.014	0.000	0.000	0.000	0.000
65	B	76	PHE	0	-0.035	-0.031	21.479	0.010	0.010	0.000	0.000	0.000	0.000
66	B	77	LEU	0	0.044	0.025	23.481	-0.006	-0.006	0.000	0.000	0.000	0.000
67	B	78	LEU	0	0.009	0.003	18.617	0.011	0.011	0.000	0.000	0.000	0.000
68	B	79	ALA	0	0.016	0.010	22.765	0.006	0.006	0.000	0.000	0.000	0.000
69	B	80	THR	0	0.034	0.013	24.469	0.005	0.005	0.000	0.000	0.000	0.000
70	B	81	LYS	1	0.892	0.980	21.062	-0.063	-0.063	0.000	0.000	0.000	0.000
71	B	82	LYS	1	0.867	0.915	26.850	0.032	0.032	0.000	0.000	0.000	0.000
72	B	83	GLU	-1	-0.848	-0.922	26.396	0.050	0.050	0.000	0.000	0.000	0.000
73	B	84	HIS	0	0.003	-0.004	25.213	-0.005	-0.005	0.000	0.000	0.000	0.000
74	B	85	ALA	0	0.023	0.006	30.640	-0.002	-0.002	0.000	0.000	0.000	0.000
75	B	86	PRO	0	-0.052	-0.036	33.502	-0.003	-0.003	0.000	0.000	0.000	0.000
76	B	87	TYR	0	0.029	0.009	32.194	0.000	0.000	0.000	0.000	0.000	0.000
77	B	88	LEU	0	-0.003	0.004	29.897	-0.003	-0.003	0.000	0.000	0.000	0.000
78	B	89	LYS	1	0.970	0.983	34.001	-0.009	-0.009	0.000	0.000	0.000	0.000
79	B	90	LYS	1	0.839	0.922	37.117	-0.016	-0.016	0.000	0.000	0.000	0.000
80	B	91	LEU	0	-0.018	-0.002	32.639	0.002	0.002	0.000	0.000	0.000	0.000
81	B	92	VAL	0	-0.031	-0.011	36.761	-0.002	-0.002	0.000	0.000	0.000	0.000
82	B	93	GLU	-1	-0.901	-0.928	39.245	0.008	0.008	0.000	0.000	0.000	0.000

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