FMO DATABASE

FMODB ID: 9G192

Calculation Name: 3W6K-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3W6K

Chain ID: B

ChEMBL ID:

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:

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	82
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-480242.886921
FMO2-HF: Nuclear repulsion	449743.559863
FMO2-HF: Total energy	-30499.327059
FMO2-MP2: Total energy	-30589.967196

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.
-2.703	0.413	0.981	-1.757	-2.342	-0.004

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 : 0.009 / q_NPA : -0.022

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	0.109	0.064	3.776	-0.809	1.611	-0.019	-1.157	-1.244	-0.005
4	B	15	LYS	1	0.904	0.969	2.555	-1.851	-1.253	1.001	-0.590	-1.010	0.001
5	B	16	PRO	0	0.038	0.026	5.277	0.218	0.316	-0.001	-0.010	-0.088	0.000
6	B	17	ALA	0	0.078	0.034	7.923	0.113	0.113	0.000	0.000	0.000	0.000
7	B	18	LYS	1	0.907	0.939	7.633	0.205	0.205	0.000	0.000	0.000	0.000
8	B	19	ALA	0	-0.023	-0.010	9.416	0.086	0.086	0.000	0.000	0.000	0.000
9	B	20	ILE	0	-0.006	0.003	11.250	0.042	0.042	0.000	0.000	0.000	0.000
10	B	21	VAL	0	0.035	0.012	13.205	0.028	0.028	0.000	0.000	0.000	0.000
11	B	22	GLU	-1	-0.911	-0.954	13.956	0.094	0.094	0.000	0.000	0.000	0.000
12	B	23	ALA	0	-0.024	-0.017	15.383	0.013	0.013	0.000	0.000	0.000	0.000
13	B	24	LEU	0	-0.002	-0.007	17.340	0.008	0.008	0.000	0.000	0.000	0.000
14	B	25	LEU	0	-0.012	-0.013	18.225	0.007	0.007	0.000	0.000	0.000	0.000
15	B	26	PHE	0	-0.067	-0.037	19.801	0.010	0.010	0.000	0.000	0.000	0.000
16	B	27	ALA	0	-0.038	-0.025	21.525	0.005	0.005	0.000	0.000	0.000	0.000
17	B	28	ALA	0	-0.031	0.003	23.348	0.001	0.001	0.000	0.000	0.000	0.000
18	B	29	GLY	0	-0.006	0.012	25.077	0.001	0.001	0.000	0.000	0.000	0.000
19	B	30	ASP	-1	-0.954	-0.988	26.401	-0.015	-0.015	0.000	0.000	0.000	0.000
20	B	31	GLU	-1	-0.936	-0.979	28.897	-0.025	-0.025	0.000	0.000	0.000	0.000
21	B	32	GLY	0	-0.072	-0.014	25.162	-0.005	-0.005	0.000	0.000	0.000	0.000
22	B	33	LEU	0	0.006	-0.005	21.503	-0.002	-0.002	0.000	0.000	0.000	0.000
23	B	34	SER	0	0.035	0.024	23.945	-0.008	-0.008	0.000	0.000	0.000	0.000
24	B	35	LEU	0	0.019	-0.006	19.657	-0.005	-0.005	0.000	0.000	0.000	0.000
25	B	36	SER	0	-0.003	-0.016	21.700	-0.011	-0.011	0.000	0.000	0.000	0.000
26	B	37	GLN	0	0.013	0.021	23.242	-0.006	-0.006	0.000	0.000	0.000	0.000
27	B	38	ILE	0	0.012	0.017	17.603	-0.005	-0.005	0.000	0.000	0.000	0.000
28	B	39	ALA	0	-0.002	-0.010	18.468	-0.016	-0.016	0.000	0.000	0.000	0.000
29	B	40	ALA	0	-0.020	-0.008	19.407	-0.013	-0.013	0.000	0.000	0.000	0.000
30	B	41	VAL	0	-0.043	-0.023	18.634	0.000	0.000	0.000	0.000	0.000	0.000
31	B	42	LEU	0	-0.082	-0.049	14.191	-0.001	-0.001	0.000	0.000	0.000	0.000
32	B	43	GLU	-1	-0.974	-0.963	16.183	-0.184	-0.184	0.000	0.000	0.000	0.000
33	B	44	VAL	0	-0.061	-0.019	13.854	-0.038	-0.038	0.000	0.000	0.000	0.000
34	B	45	SER	0	-0.029	-0.041	17.116	0.045	0.045	0.000	0.000	0.000	0.000
35	B	46	GLU	-1	-0.808	-0.920	18.043	-0.155	-0.155	0.000	0.000	0.000	0.000
36	B	47	LEU	0	-0.021	-0.010	17.429	-0.002	-0.002	0.000	0.000	0.000	0.000
37	B	48	GLU	-1	-0.846	-0.907	13.932	-0.453	-0.453	0.000	0.000	0.000	0.000
38	B	49	ALA	0	0.044	0.024	14.084	-0.033	-0.033	0.000	0.000	0.000	0.000
39	B	50	LYS	1	0.912	0.969	15.662	0.152	0.152	0.000	0.000	0.000	0.000
40	B	51	ALA	0	0.016	0.011	12.747	0.016	0.016	0.000	0.000	0.000	0.000
41	B	52	VAL	0	-0.024	-0.008	10.434	-0.009	-0.009	0.000	0.000	0.000	0.000
42	B	53	ILE	0	-0.010	-0.012	12.478	0.044	0.044	0.000	0.000	0.000	0.000
43	B	54	GLU	-1	-0.905	-0.970	15.616	-0.127	-0.127	0.000	0.000	0.000	0.000
44	B	55	GLU	-1	-0.964	-0.966	9.294	-0.120	-0.120	0.000	0.000	0.000	0.000
45	B	56	LEU	0	-0.010	-0.008	12.762	0.055	0.055	0.000	0.000	0.000	0.000
46	B	57	GLN	0	-0.033	-0.012	13.492	0.036	0.036	0.000	0.000	0.000	0.000
47	B	58	GLN	0	0.032	0.027	14.234	0.016	0.016	0.000	0.000	0.000	0.000
48	B	59	ASP	-1	-0.853	-0.932	10.853	0.040	0.040	0.000	0.000	0.000	0.000
49	B	60	CYS	0	-0.051	-0.020	14.281	0.030	0.030	0.000	0.000	0.000	0.000
50	B	61	ARG	1	0.860	0.924	17.452	0.054	0.054	0.000	0.000	0.000	0.000
51	B	62	ARG	1	0.943	0.984	14.032	-0.088	-0.088	0.000	0.000	0.000	0.000
52	B	63	GLU	-1	-0.928	-0.976	18.834	0.050	0.050	0.000	0.000	0.000	0.000
53	B	64	GLU	-1	-0.942	-0.959	16.440	0.138	0.138	0.000	0.000	0.000	0.000
54	B	65	ARG	1	0.844	0.939	14.748	-0.083	-0.083	0.000	0.000	0.000	0.000
55	B	66	GLY	0	0.045	0.010	19.903	-0.010	-0.010	0.000	0.000	0.000	0.000
56	B	67	ILE	0	-0.057	-0.036	18.873	-0.006	-0.006	0.000	0.000	0.000	0.000
57	B	68	GLN	0	-0.034	-0.028	20.583	0.000	0.000	0.000	0.000	0.000	0.000
58	B	69	LEU	0	0.035	0.022	17.503	0.002	0.002	0.000	0.000	0.000	0.000
59	B	70	VAL	0	-0.042	-0.029	21.007	-0.002	-0.002	0.000	0.000	0.000	0.000
60	B	71	GLU	-1	-0.908	-0.961	23.967	-0.094	-0.094	0.000	0.000	0.000	0.000
61	B	72	LEU	0	-0.033	-0.021	25.542	0.005	0.005	0.000	0.000	0.000	0.000
62	B	73	GLY	0	-0.001	0.000	29.191	-0.001	-0.001	0.000	0.000	0.000	0.000
63	B	74	GLY	0	-0.004	0.005	28.145	0.000	0.000	0.000	0.000	0.000	0.000
64	B	75	VAL	0	-0.010	0.002	26.019	-0.006	-0.006	0.000	0.000	0.000	0.000
65	B	76	PHE	0	-0.023	-0.029	21.517	-0.001	-0.001	0.000	0.000	0.000	0.000
66	B	77	LEU	0	0.049	0.026	23.479	0.003	0.003	0.000	0.000	0.000	0.000
67	B	78	LEU	0	0.006	0.008	18.680	0.000	0.000	0.000	0.000	0.000	0.000
68	B	79	ALA	0	0.023	0.011	22.768	0.003	0.003	0.000	0.000	0.000	0.000
69	B	80	THR	0	0.036	0.015	24.470	0.001	0.001	0.000	0.000	0.000	0.000
70	B	81	LYS	1	0.873	0.960	20.919	-0.043	-0.043	0.000	0.000	0.000	0.000
71	B	82	LYS	1	0.896	0.937	26.850	-0.002	-0.002	0.000	0.000	0.000	0.000
72	B	83	GLU	-1	-0.876	-0.937	26.631	0.028	0.028	0.000	0.000	0.000	0.000
73	B	84	HIS	0	0.029	0.016	25.173	0.000	0.000	0.000	0.000	0.000	0.000
74	B	85	ALA	0	0.017	0.003	30.639	0.001	0.001	0.000	0.000	0.000	0.000
75	B	86	PRO	0	-0.055	-0.043	33.502	0.000	0.000	0.000	0.000	0.000	0.000
76	B	87	TYR	0	0.022	0.005	32.225	0.001	0.001	0.000	0.000	0.000	0.000
77	B	88	LEU	0	0.007	0.007	29.934	0.001	0.001	0.000	0.000	0.000	0.000
78	B	89	LYS	1	0.976	0.988	34.003	-0.017	-0.017	0.000	0.000	0.000	0.000
79	B	90	LYS	1	0.927	0.978	36.836	-0.033	-0.033	0.000	0.000	0.000	0.000
80	B	91	LEU	0	-0.038	-0.009	32.624	0.002	0.002	0.000	0.000	0.000	0.000
81	B	92	VAL	0	-0.020	-0.011	36.763	0.000	0.000	0.000	0.000	0.000	0.000
82	B	93	GLU	-1	-0.989	-0.980	39.248	0.022	0.022	0.000	0.000	0.000	0.000

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