FMO DATABASE

FMODB ID: 82MVY

Calculation Name: 2WKC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2WKC

Chain ID: A

ChEMBL ID:

UniProt ID: Q6JM09

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	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	90
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-549687.21427
FMO2-HF: Nuclear repulsion	516165.309817
FMO2-HF: Total energy	-33521.904453
FMO2-MP2: Total energy	-33622.171451

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(A:0:GLY)

Summations of interaction energy for fragment #1(A:0: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.
-1.242	0.878	-0.017	-1.125	-0.977	0.003

Interaction energy analysis for fragmet #1(A:0:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.041 / q_NPA : 0.023

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	A	2	ILE	0	-0.024	-0.010	3.795	-0.024	2.096	-0.017	-1.125	-0.977	0.003
4	A	3	ILE	0	0.011	0.006	6.848	-0.014	-0.014	0.000	0.000	0.000	0.000
5	A	4	THR	0	0.036	0.006	10.328	0.194	0.194	0.000	0.000	0.000	0.000
6	A	5	VAL	0	0.015	0.013	13.504	0.007	0.007	0.000	0.000	0.000	0.000
7	A	6	THR	0	0.017	0.022	16.780	0.050	0.050	0.000	0.000	0.000	0.000
8	A	7	ALA	0	-0.017	-0.009	20.244	0.005	0.005	0.000	0.000	0.000	0.000
9	A	8	GLN	0	-0.023	-0.007	23.099	0.006	0.006	0.000	0.000	0.000	0.000
10	A	9	ALA	0	0.007	0.025	26.521	-0.001	-0.001	0.000	0.000	0.000	0.000
11	A	10	ASN	0	0.008	-0.017	27.504	0.016	0.016	0.000	0.000	0.000	0.000
12	A	11	GLU	-1	-0.850	-0.950	29.797	-0.086	-0.086	0.000	0.000	0.000	0.000
13	A	12	LYS	1	0.890	0.957	29.951	0.145	0.145	0.000	0.000	0.000	0.000
14	A	13	ASN	0	-0.029	0.001	24.909	0.014	0.014	0.000	0.000	0.000	0.000
15	A	14	THR	0	0.013	-0.005	25.316	-0.010	-0.010	0.000	0.000	0.000	0.000
16	A	15	ARG	1	0.957	0.987	24.574	0.081	0.081	0.000	0.000	0.000	0.000
17	A	16	THR	0	0.035	0.012	28.154	-0.006	-0.006	0.000	0.000	0.000	0.000
18	A	17	VAL	0	-0.043	-0.009	26.983	0.004	0.004	0.000	0.000	0.000	0.000
19	A	18	SER	0	0.076	0.035	30.244	0.001	0.001	0.000	0.000	0.000	0.000
20	A	19	THR	0	-0.080	-0.056	28.102	0.008	0.008	0.000	0.000	0.000	0.000
21	A	20	ALA	0	0.028	-0.002	31.531	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	21	LYS	1	0.911	0.945	27.234	-0.055	-0.055	0.000	0.000	0.000	0.000
23	A	22	GLY	0	0.067	0.059	31.542	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	23	ASP	-1	-0.903	-0.939	31.278	-0.024	-0.024	0.000	0.000	0.000	0.000
25	A	24	LYS	1	0.915	0.964	24.758	-0.010	-0.010	0.000	0.000	0.000	0.000
26	A	25	LYS	1	0.936	0.974	26.503	0.070	0.070	0.000	0.000	0.000	0.000
27	A	26	ILE	0	-0.047	-0.011	22.085	-0.003	-0.003	0.000	0.000	0.000	0.000
28	A	27	ILE	0	0.036	0.023	20.585	0.001	0.001	0.000	0.000	0.000	0.000
29	A	28	SER	0	-0.011	-0.013	20.772	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	29	VAL	0	-0.004	-0.005	17.410	0.008	0.008	0.000	0.000	0.000	0.000
31	A	30	PRO	0	-0.016	-0.002	18.414	-0.006	-0.006	0.000	0.000	0.000	0.000
32	A	31	LEU	0	-0.002	-0.011	12.655	-0.033	-0.033	0.000	0.000	0.000	0.000
33	A	32	PHE	0	0.014	0.009	14.315	-0.098	-0.098	0.000	0.000	0.000	0.000
34	A	33	GLU	-1	-0.931	-0.957	16.795	-0.403	-0.403	0.000	0.000	0.000	0.000
35	A	34	LYS	1	0.887	0.945	20.295	0.208	0.208	0.000	0.000	0.000	0.000
36	A	35	GLU	-1	-0.892	-0.938	23.037	-0.231	-0.231	0.000	0.000	0.000	0.000
37	A	36	LYS	1	0.926	0.941	26.331	0.208	0.208	0.000	0.000	0.000	0.000
38	A	37	GLY	0	0.020	0.017	29.527	0.006	0.006	0.000	0.000	0.000	0.000
39	A	38	SER	0	0.040	0.036	25.487	0.007	0.007	0.000	0.000	0.000	0.000
40	A	39	ASN	0	0.016	-0.019	27.747	0.005	0.005	0.000	0.000	0.000	0.000
41	A	40	VAL	0	-0.001	0.013	22.092	0.011	0.011	0.000	0.000	0.000	0.000
42	A	41	LYS	1	0.923	0.953	22.967	0.134	0.134	0.000	0.000	0.000	0.000
43	A	42	VAL	0	-0.009	0.004	19.032	-0.006	-0.006	0.000	0.000	0.000	0.000
44	A	43	ALA	0	0.038	0.032	16.139	0.032	0.032	0.000	0.000	0.000	0.000
45	A	44	TYR	0	-0.012	-0.016	17.907	-0.043	-0.043	0.000	0.000	0.000	0.000
46	A	45	GLY	0	0.016	0.011	15.879	0.027	0.027	0.000	0.000	0.000	0.000
47	A	46	SER	0	-0.049	-0.034	16.845	0.003	0.003	0.000	0.000	0.000	0.000
48	A	47	ALA	0	0.023	0.004	16.851	0.000	0.000	0.000	0.000	0.000	0.000
49	A	48	PHE	0	-0.028	-0.015	18.623	0.006	0.006	0.000	0.000	0.000	0.000
50	A	49	LEU	0	0.007	-0.001	20.680	-0.017	-0.017	0.000	0.000	0.000	0.000
51	A	50	PRO	0	0.007	-0.002	22.242	0.017	0.017	0.000	0.000	0.000	0.000
52	A	51	ASP	-1	-0.849	-0.927	25.086	-0.045	-0.045	0.000	0.000	0.000	0.000
53	A	52	PHE	0	-0.046	-0.028	25.676	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	53	ILE	0	-0.029	0.003	24.635	-0.004	-0.004	0.000	0.000	0.000	0.000
55	A	54	GLN	0	-0.011	-0.017	28.752	0.010	0.010	0.000	0.000	0.000	0.000
56	A	55	LEU	0	0.004	-0.007	30.245	-0.012	-0.012	0.000	0.000	0.000	0.000
57	A	56	GLY	0	-0.007	0.004	30.785	0.006	0.006	0.000	0.000	0.000	0.000
58	A	57	ASP	-1	-0.796	-0.886	27.842	-0.128	-0.128	0.000	0.000	0.000	0.000
59	A	58	THR	0	-0.018	-0.017	24.655	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	59	VAL	0	-0.021	-0.007	21.658	0.006	0.006	0.000	0.000	0.000	0.000
61	A	60	THR	0	0.036	0.004	16.987	-0.012	-0.012	0.000	0.000	0.000	0.000
62	A	61	VAL	0	-0.023	-0.011	15.029	0.033	0.033	0.000	0.000	0.000	0.000
63	A	62	SER	0	-0.006	-0.011	12.333	-0.090	-0.090	0.000	0.000	0.000	0.000
64	A	63	GLY	0	0.055	0.034	9.418	0.138	0.138	0.000	0.000	0.000	0.000
65	A	64	ARG	1	0.983	0.994	5.445	-1.267	-1.267	0.000	0.000	0.000	0.000
66	A	65	VAL	0	0.009	0.007	7.923	0.176	0.176	0.000	0.000	0.000	0.000
67	A	66	GLN	0	-0.055	-0.023	8.915	-0.018	-0.018	0.000	0.000	0.000	0.000
68	A	67	ALA	0	0.024	0.009	11.102	-0.058	-0.058	0.000	0.000	0.000	0.000
69	A	68	LYS	1	0.886	0.945	13.521	-0.067	-0.067	0.000	0.000	0.000	0.000
70	A	69	GLU	-1	-0.834	-0.922	16.627	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	70	SER	0	-0.054	-0.037	19.869	0.025	0.025	0.000	0.000	0.000	0.000
72	A	71	GLY	0	-0.016	-0.002	23.202	-0.015	-0.015	0.000	0.000	0.000	0.000
73	A	72	GLU	-1	-0.908	-0.953	25.178	-0.021	-0.021	0.000	0.000	0.000	0.000
74	A	73	TYR	0	-0.065	-0.026	23.850	-0.018	-0.018	0.000	0.000	0.000	0.000
75	A	74	VAL	0	0.060	0.039	17.334	0.013	0.013	0.000	0.000	0.000	0.000
76	A	75	ASN	0	-0.082	-0.043	18.648	-0.006	-0.006	0.000	0.000	0.000	0.000
77	A	76	TYR	0	0.053	0.024	13.464	0.006	0.006	0.000	0.000	0.000	0.000
78	A	77	ASN	0	-0.021	-0.012	14.408	-0.034	-0.034	0.000	0.000	0.000	0.000
79	A	78	PHE	0	0.054	0.020	12.236	0.009	0.009	0.000	0.000	0.000	0.000
80	A	79	VAL	0	-0.088	-0.045	10.581	0.077	0.077	0.000	0.000	0.000	0.000
81	A	80	PHE	0	-0.045	-0.032	11.757	0.005	0.005	0.000	0.000	0.000	0.000
82	A	81	PRO	0	-0.020	0.016	12.836	-0.006	-0.006	0.000	0.000	0.000	0.000
83	A	82	THR	0	0.038	0.009	13.743	0.059	0.059	0.000	0.000	0.000	0.000
84	A	83	VAL	0	-0.037	-0.025	15.718	-0.046	-0.046	0.000	0.000	0.000	0.000
85	A	84	GLU	-1	-0.928	-0.949	18.934	-0.273	-0.273	0.000	0.000	0.000	0.000
86	A	85	LYS	1	0.879	0.928	21.431	0.112	0.112	0.000	0.000	0.000	0.000
87	A	86	VAL	0	0.016	0.010	23.399	0.000	0.000	0.000	0.000	0.000	0.000
88	A	87	PHE	0	-0.036	-0.024	25.803	0.015	0.015	0.000	0.000	0.000	0.000
89	A	88	ILE	0	0.000	0.001	28.058	-0.009	-0.009	0.000	0.000	0.000	0.000
90	A	89	THR	0	0.005	0.010	31.630	0.009	0.009	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:GLY)