FMO DATABASE

FMODB ID: R53V8

Calculation Name: 2DWK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2DWK

Chain ID: A

ChEMBL ID:

UniProt ID: Q9D394

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:

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	162
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1603897.406738
FMO2-HF: Nuclear repulsion	1538922.270716
FMO2-HF: Total energy	-64975.136023
FMO2-MP2: Total energy	-65158.379899

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:83:MET)

Summations of interaction energy for fragment #1(A:83:MET)

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.
-12.613	-3.252	12.485	-7.135	-14.709	-0.048

Interaction energy analysis for fragmet #1(A:83:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : 0.006

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

Sort

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	85	ASN	0	0.013	0.001	3.085	-1.873	0.298	0.008	-0.926	-1.253	0.001
4	A	86	GLU	-1	-0.840	-0.917	2.348	-9.167	-7.056	2.737	-1.783	-3.065	-0.025
5	A	87	ARG	1	0.765	0.877	2.763	0.663	2.051	0.172	-0.367	-1.192	0.000
6	A	88	MET	0	0.045	0.022	5.435	0.573	0.573	0.000	0.000	0.000	0.000
7	A	89	ASN	0	-0.042	-0.027	7.826	0.434	0.434	0.000	0.000	0.000	0.000
8	A	90	LEU	0	0.017	0.011	6.206	0.266	0.266	0.000	0.000	0.000	0.000
9	A	91	MET	0	0.035	0.034	9.517	0.229	0.229	0.000	0.000	0.000	0.000
10	A	92	ASN	0	-0.009	-0.006	11.423	0.165	0.165	0.000	0.000	0.000	0.000
11	A	93	MET	0	0.013	0.012	11.776	0.077	0.077	0.000	0.000	0.000	0.000
12	A	94	ALA	0	0.020	-0.003	13.622	0.066	0.066	0.000	0.000	0.000	0.000
13	A	95	LYS	1	0.875	0.934	14.706	0.309	0.309	0.000	0.000	0.000	0.000
14	A	96	LEU	0	-0.024	-0.009	17.461	0.039	0.039	0.000	0.000	0.000	0.000
15	A	97	SER	0	0.020	-0.007	18.399	0.012	0.012	0.000	0.000	0.000	0.000
16	A	98	ILE	0	-0.030	-0.013	17.823	0.024	0.024	0.000	0.000	0.000	0.000
17	A	99	LYS	1	0.819	0.897	21.172	0.166	0.166	0.000	0.000	0.000	0.000
18	A	100	GLY	0	0.041	0.027	22.978	0.015	0.015	0.000	0.000	0.000	0.000
19	A	101	LEU	0	-0.017	0.001	23.625	0.013	0.013	0.000	0.000	0.000	0.000
20	A	102	ILE	0	0.011	0.000	24.458	0.013	0.013	0.000	0.000	0.000	0.000
21	A	103	GLU	-1	-0.805	-0.888	27.289	-0.122	-0.122	0.000	0.000	0.000	0.000
22	A	104	SER	0	-0.045	-0.027	28.004	0.008	0.008	0.000	0.000	0.000	0.000
23	A	105	ALA	0	0.008	0.000	29.622	0.007	0.007	0.000	0.000	0.000	0.000
24	A	106	LEU	0	-0.037	-0.013	31.028	0.008	0.008	0.000	0.000	0.000	0.000
25	A	107	ASN	0	-0.084	-0.045	32.608	0.010	0.010	0.000	0.000	0.000	0.000
26	A	108	LEU	0	-0.092	-0.035	33.575	0.003	0.003	0.000	0.000	0.000	0.000
27	A	109	GLY	0	0.018	0.005	35.437	0.004	0.004	0.000	0.000	0.000	0.000
28	A	110	ARG	1	0.860	0.939	35.395	0.094	0.094	0.000	0.000	0.000	0.000
29	A	111	THR	0	0.020	-0.011	35.169	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	112	LEU	0	-0.075	-0.034	29.476	-0.005	-0.005	0.000	0.000	0.000	0.000
31	A	113	ASP	-1	-0.731	-0.871	31.774	-0.095	-0.095	0.000	0.000	0.000	0.000
32	A	114	SER	0	-0.039	-0.035	28.807	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	115	ASP	-1	-0.884	-0.922	28.789	-0.127	-0.127	0.000	0.000	0.000	0.000
34	A	116	TYR	0	0.001	-0.004	28.481	-0.008	-0.008	0.000	0.000	0.000	0.000
35	A	117	ALA	0	0.076	0.032	26.617	-0.010	-0.010	0.000	0.000	0.000	0.000
36	A	118	PRO	0	-0.009	-0.003	24.828	-0.019	-0.019	0.000	0.000	0.000	0.000
37	A	119	LEU	0	0.029	0.017	23.718	-0.015	-0.015	0.000	0.000	0.000	0.000
38	A	120	GLN	0	-0.060	-0.044	23.163	-0.022	-0.022	0.000	0.000	0.000	0.000
39	A	121	GLN	0	0.000	0.015	19.416	-0.027	-0.027	0.000	0.000	0.000	0.000
40	A	122	PHE	0	0.051	0.024	18.595	-0.036	-0.036	0.000	0.000	0.000	0.000
41	A	123	PHE	0	-0.007	-0.009	18.407	-0.020	-0.020	0.000	0.000	0.000	0.000
42	A	124	VAL	0	-0.017	0.002	16.209	-0.014	-0.014	0.000	0.000	0.000	0.000
43	A	125	VAL	0	0.027	0.019	13.849	-0.056	-0.056	0.000	0.000	0.000	0.000
44	A	126	MET	0	0.015	0.016	13.476	-0.051	-0.051	0.000	0.000	0.000	0.000
45	A	127	GLU	-1	-0.749	-0.829	14.130	-0.301	-0.301	0.000	0.000	0.000	0.000
46	A	128	HIS	0	-0.011	-0.018	10.449	-0.031	-0.031	0.000	0.000	0.000	0.000
47	A	129	CYS	0	-0.064	-0.029	9.320	-0.123	-0.123	0.000	0.000	0.000	0.000
48	A	130	LEU	0	-0.005	-0.004	9.703	0.085	0.085	0.000	0.000	0.000	0.000
49	A	131	LYS	1	0.864	0.927	9.438	0.518	0.518	0.000	0.000	0.000	0.000
50	A	132	HIS	0	-0.026	-0.007	1.993	1.412	1.085	4.818	-1.349	-3.142	0.002
51	A	133	GLY	0	0.047	0.010	4.151	0.570	0.866	0.027	-0.072	-0.250	0.000
52	A	134	LEU	0	-0.046	-0.005	4.912	-0.129	-0.076	0.002	-0.009	-0.046	0.000
53	A	135	LYS	1	0.864	0.944	7.748	-0.551	-0.551	0.000	0.000	0.000	0.000
54	A	136	ALA	0	-0.040	-0.013	9.496	-0.119	-0.119	0.000	0.000	0.000	0.000
55	A	144	ASN	0	0.044	0.011	13.606	0.023	0.023	0.000	0.000	0.000	0.000
56	A	145	LYS	1	0.833	0.879	17.554	-0.020	-0.020	0.000	0.000	0.000	0.000
57	A	146	SER	0	0.044	0.025	13.049	-0.022	-0.022	0.000	0.000	0.000	0.000
58	A	147	PHE	0	0.063	0.014	13.001	0.029	0.029	0.000	0.000	0.000	0.000
59	A	148	TRP	0	-0.044	-0.037	14.370	0.012	0.012	0.000	0.000	0.000	0.000
60	A	149	GLY	0	-0.027	-0.009	16.677	0.011	0.011	0.000	0.000	0.000	0.000
61	A	150	PRO	0	0.039	0.011	13.584	0.006	0.006	0.000	0.000	0.000	0.000
62	A	151	LEU	0	-0.027	-0.009	16.562	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	152	GLU	-1	-0.769	-0.849	19.290	-0.007	-0.007	0.000	0.000	0.000	0.000
64	A	153	LEU	0	-0.022	-0.019	17.721	0.001	0.001	0.000	0.000	0.000	0.000
65	A	154	VAL	0	0.017	0.012	20.488	0.004	0.004	0.000	0.000	0.000	0.000
66	A	155	GLU	-1	-0.829	-0.916	22.683	-0.008	-0.008	0.000	0.000	0.000	0.000
67	A	156	LYS	1	0.886	0.952	22.827	-0.041	-0.041	0.000	0.000	0.000	0.000
68	A	157	LEU	0	-0.097	-0.041	20.655	0.007	0.007	0.000	0.000	0.000	0.000
69	A	158	VAL	0	0.007	-0.005	24.675	0.001	0.001	0.000	0.000	0.000	0.000
70	A	159	PRO	0	0.039	0.015	27.193	-0.006	-0.006	0.000	0.000	0.000	0.000
71	A	160	GLU	-1	-0.808	-0.888	29.999	-0.027	-0.027	0.000	0.000	0.000	0.000
72	A	161	ALA	0	0.007	0.016	26.185	-0.005	-0.005	0.000	0.000	0.000	0.000
73	A	162	ALA	0	-0.006	0.008	28.167	-0.004	-0.004	0.000	0.000	0.000	0.000
74	A	163	GLU	-1	-0.857	-0.911	30.409	-0.039	-0.039	0.000	0.000	0.000	0.000
75	A	164	ILE	0	0.012	0.018	26.208	-0.004	-0.004	0.000	0.000	0.000	0.000
76	A	165	THR	0	-0.031	-0.037	25.310	-0.008	-0.008	0.000	0.000	0.000	0.000
77	A	166	ALA	0	-0.032	-0.019	27.753	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	167	SER	0	0.048	0.007	30.568	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	168	VAL	0	-0.071	-0.035	25.195	-0.005	-0.005	0.000	0.000	0.000	0.000
80	A	169	LYS	1	0.750	0.883	26.760	0.017	0.017	0.000	0.000	0.000	0.000
81	A	170	ASP	-1	-0.884	-0.926	29.310	-0.037	-0.037	0.000	0.000	0.000	0.000
82	A	171	LEU	0	-0.025	-0.008	28.722	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	172	PRO	0	0.027	-0.008	31.552	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	173	GLY	0	-0.018	-0.002	31.927	-0.005	-0.005	0.000	0.000	0.000	0.000
85	A	174	LEU	0	-0.016	0.017	25.468	-0.010	-0.010	0.000	0.000	0.000	0.000
86	A	175	LYS	1	0.952	0.961	27.155	0.083	0.083	0.000	0.000	0.000	0.000
87	A	176	THR	0	0.006	0.009	21.690	0.003	0.003	0.000	0.000	0.000	0.000
88	A	177	PRO	0	0.039	0.025	18.896	0.001	0.001	0.000	0.000	0.000	0.000
89	A	178	VAL	0	0.042	0.026	16.393	0.001	0.001	0.000	0.000	0.000	0.000
90	A	179	GLY	0	0.001	0.008	18.973	-0.007	-0.007	0.000	0.000	0.000	0.000
91	A	180	ARG	1	0.969	0.974	22.475	0.076	0.076	0.000	0.000	0.000	0.000
92	A	181	GLY	0	0.026	0.017	19.109	0.008	0.008	0.000	0.000	0.000	0.000
93	A	182	ARG	1	0.783	0.844	17.423	0.258	0.258	0.000	0.000	0.000	0.000
94	A	183	ALA	0	0.014	0.010	21.326	0.001	0.001	0.000	0.000	0.000	0.000
95	A	184	TRP	0	0.059	0.024	21.193	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	185	LEU	0	-0.003	-0.009	17.717	0.003	0.003	0.000	0.000	0.000	0.000
97	A	186	ARG	1	0.874	0.941	21.444	0.174	0.174	0.000	0.000	0.000	0.000
98	A	187	LEU	0	0.070	0.027	25.518	0.004	0.004	0.000	0.000	0.000	0.000
99	A	188	ALA	0	0.030	0.023	23.959	0.006	0.006	0.000	0.000	0.000	0.000
100	A	189	LEU	0	-0.061	-0.036	24.222	0.003	0.003	0.000	0.000	0.000	0.000
101	A	190	MET	0	-0.021	0.012	26.186	0.002	0.002	0.000	0.000	0.000	0.000
102	A	191	GLN	0	0.017	0.025	28.732	0.002	0.002	0.000	0.000	0.000	0.000
103	A	192	LYS	1	0.814	0.913	27.885	0.073	0.073	0.000	0.000	0.000	0.000
104	A	193	LYS	1	0.850	0.894	26.593	0.032	0.032	0.000	0.000	0.000	0.000
105	A	194	LEU	0	-0.007	-0.001	19.957	0.004	0.004	0.000	0.000	0.000	0.000
106	A	195	SER	0	0.030	0.011	20.940	0.007	0.007	0.000	0.000	0.000	0.000
107	A	196	GLU	-1	-0.863	-0.912	21.419	-0.014	-0.014	0.000	0.000	0.000	0.000
108	A	197	TYR	0	-0.001	-0.038	22.047	0.014	0.014	0.000	0.000	0.000	0.000
109	A	198	MET	0	-0.009	-0.004	17.061	0.008	0.008	0.000	0.000	0.000	0.000
110	A	199	LYS	1	0.985	0.988	17.633	0.016	0.016	0.000	0.000	0.000	0.000
111	A	200	ALA	0	0.007	0.008	19.484	0.019	0.019	0.000	0.000	0.000	0.000
112	A	201	LEU	0	0.003	0.001	16.486	0.016	0.016	0.000	0.000	0.000	0.000
113	A	202	ILE	0	0.014	0.021	13.538	0.028	0.028	0.000	0.000	0.000	0.000
114	A	203	ASN	0	-0.134	-0.069	15.367	0.033	0.033	0.000	0.000	0.000	0.000
115	A	204	LYS	1	0.940	0.968	17.090	-0.068	-0.068	0.000	0.000	0.000	0.000
116	A	205	LYS	1	0.934	0.949	10.960	-0.162	-0.162	0.000	0.000	0.000	0.000
117	A	206	GLU	-1	-0.920	-0.940	14.308	0.207	0.207	0.000	0.000	0.000	0.000
118	A	207	LEU	0	0.013	0.009	16.833	0.009	0.009	0.000	0.000	0.000	0.000
119	A	208	LEU	0	0.011	-0.007	12.419	0.002	0.002	0.000	0.000	0.000	0.000
120	A	209	SER	0	-0.036	-0.008	12.069	0.038	0.038	0.000	0.000	0.000	0.000
121	A	210	GLU	-1	-0.947	-0.962	12.850	0.171	0.171	0.000	0.000	0.000	0.000
122	A	211	PHE	0	-0.027	-0.035	12.869	-0.016	-0.016	0.000	0.000	0.000	0.000
123	A	212	TYR	0	-0.086	-0.061	7.986	-0.044	-0.044	0.000	0.000	0.000	0.000
124	A	213	GLU	-1	-0.848	-0.932	4.960	0.841	0.901	-0.001	-0.017	-0.043	0.000
125	A	214	VAL	0	0.002	-0.017	6.522	-0.100	-0.100	0.000	0.000	0.000	0.000
126	A	215	ASN	0	-0.010	-0.002	2.423	-2.255	-0.355	3.002	-1.257	-3.645	-0.008
127	A	216	ALA	0	0.052	0.029	2.502	-3.406	-1.756	1.721	-1.350	-2.020	-0.018
128	A	217	LEU	0	0.016	0.004	4.979	-0.752	-0.693	-0.001	-0.005	-0.053	0.000
129	A	218	MET	0	-0.041	-0.021	6.550	-0.053	-0.053	0.000	0.000	0.000	0.000
130	A	219	MET	0	-0.035	-0.002	7.351	-0.063	-0.063	0.000	0.000	0.000	0.000
131	A	220	GLU	-1	-0.854	-0.901	5.151	0.153	0.153	0.000	0.000	0.000	0.000
132	A	221	GLU	-1	-0.947	-0.971	8.465	0.029	0.029	0.000	0.000	0.000	0.000
133	A	222	GLU	-1	-0.796	-0.917	7.114	-0.600	-0.600	0.000	0.000	0.000	0.000
134	A	223	GLY	0	0.040	0.022	9.855	0.004	0.004	0.000	0.000	0.000	0.000
135	A	224	ALA	0	-0.019	-0.022	11.444	0.013	0.013	0.000	0.000	0.000	0.000
136	A	225	ILE	0	-0.015	0.003	13.719	0.003	0.003	0.000	0.000	0.000	0.000
137	A	226	ILE	0	0.003	-0.005	11.397	-0.002	-0.002	0.000	0.000	0.000	0.000
138	A	227	ALA	0	-0.003	-0.005	15.295	0.010	0.010	0.000	0.000	0.000	0.000
139	A	228	GLY	0	-0.002	0.002	17.587	0.010	0.010	0.000	0.000	0.000	0.000
140	A	229	LEU	0	-0.015	-0.022	16.535	0.002	0.002	0.000	0.000	0.000	0.000
141	A	230	LEU	0	-0.009	-0.006	17.607	0.000	0.000	0.000	0.000	0.000	0.000
142	A	231	VAL	0	-0.028	-0.004	21.010	0.006	0.006	0.000	0.000	0.000	0.000
143	A	232	GLY	0	0.009	0.015	23.803	0.006	0.006	0.000	0.000	0.000	0.000
144	A	233	LEU	0	-0.001	-0.016	21.543	-0.001	-0.001	0.000	0.000	0.000	0.000
145	A	234	ASN	0	0.012	0.011	25.607	-0.004	-0.004	0.000	0.000	0.000	0.000
146	A	235	VAL	0	-0.005	0.005	28.243	0.006	0.006	0.000	0.000	0.000	0.000
147	A	236	ILE	0	-0.047	-0.028	26.828	0.000	0.000	0.000	0.000	0.000	0.000
148	A	237	ASP	-1	-0.849	-0.875	30.072	-0.064	-0.064	0.000	0.000	0.000	0.000
149	A	238	ALA	0	0.014	0.001	29.838	-0.005	-0.005	0.000	0.000	0.000	0.000
150	A	239	ASN	0	0.043	0.006	31.785	0.004	0.004	0.000	0.000	0.000	0.000
151	A	240	PHE	0	-0.052	-0.053	27.342	-0.006	-0.006	0.000	0.000	0.000	0.000
152	A	241	CYS	0	-0.052	-0.023	32.257	-0.001	-0.001	0.000	0.000	0.000	0.000
153	A	242	MET	0	0.015	0.008	35.463	-0.001	-0.001	0.000	0.000	0.000	0.000
154	A	243	LYS	1	0.919	0.963	36.397	0.080	0.080	0.000	0.000	0.000	0.000
155	A	244	GLY	0	0.018	0.010	40.214	0.001	0.001	0.000	0.000	0.000	0.000
156	A	245	GLU	-1	-0.892	-0.960	40.445	-0.061	-0.061	0.000	0.000	0.000	0.000
157	A	246	ASP	-1	-0.952	-0.975	41.058	-0.065	-0.065	0.000	0.000	0.000	0.000
158	A	247	LEU	0	-0.105	-0.056	44.151	0.001	0.001	0.000	0.000	0.000	0.000
159	A	248	ASP	-1	-0.930	-0.944	47.103	-0.039	-0.039	0.000	0.000	0.000	0.000
160	A	249	SER	0	-0.032	-0.030	49.391	-0.001	-0.001	0.000	0.000	0.000	0.000
161	A	250	GLN	0	-0.050	-0.012	52.642	0.002	0.002	0.000	0.000	0.000	0.000
162	A	251	VAL	0	-0.003	0.003	55.730	0.000	0.000	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:83:MET)