FMO DATABASE

FMODB ID: 94JZ2

Calculation Name: 2DUK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2DUK

Chain ID: A

ChEMBL ID:

UniProt ID: Q8R2U6

Base Structure: X-ray

Registration Date: 2023-09-20

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	138
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1332976.586932
FMO2-HF: Nuclear repulsion	1277181.611762
FMO2-HF: Total energy	-55794.97517
FMO2-MP2: Total energy	-55958.595249

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:1:THR)

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

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.
-19.537	-14.529	6.76	-5.318	-6.452	-0.015

Interaction energy analysis for fragmet #1(A:1:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.012 / q_NPA : -0.013

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	3	THR	0	0.105	0.070	3.807	-1.228	1.022	-0.030	-1.196	-1.024	0.005
4	A	4	TYR	0	-0.030	-0.038	6.484	0.483	0.483	0.000	0.000	0.000	0.000
5	A	5	ASP	-1	-0.824	-0.918	10.224	-0.171	-0.171	0.000	0.000	0.000	0.000
6	A	6	ARG	1	0.898	0.931	13.591	0.269	0.269	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.803	-0.888	16.200	0.098	0.098	0.000	0.000	0.000	0.000
8	A	8	GLY	0	-0.026	-0.009	14.076	0.035	0.035	0.000	0.000	0.000	0.000
9	A	9	PHE	0	-0.006	-0.012	13.711	0.130	0.130	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.887	0.959	6.915	-1.432	-1.432	0.000	0.000	0.000	0.000
11	A	11	LYN	0	0.010	0.033	9.722	0.032	0.032	0.000	0.000	0.000	0.000
12	A	12	ARG	1	0.900	0.961	9.084	0.044	0.044	0.000	0.000	0.000	0.000
13	A	13	ALA	0	0.030	0.025	11.216	0.105	0.105	0.000	0.000	0.000	0.000
14	A	14	ALA	0	0.035	0.022	12.692	-0.054	-0.054	0.000	0.000	0.000	0.000
15	A	15	CYS	0	-0.020	-0.021	15.481	0.003	0.003	0.000	0.000	0.000	0.000
16	A	16	LEU	0	-0.020	0.012	18.429	0.012	0.012	0.000	0.000	0.000	0.000
17	A	17	CYS	0	-0.018	0.010	20.156	-0.009	-0.009	0.000	0.000	0.000	0.000
18	A	18	PHE	0	0.085	0.025	22.986	0.031	0.031	0.000	0.000	0.000	0.000
19	A	19	ARG	1	0.962	0.994	26.699	0.217	0.217	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.012	-0.034	29.062	0.003	0.003	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.786	-0.873	29.532	-0.267	-0.267	0.000	0.000	0.000	0.000
22	A	22	GLN	0	-0.071	-0.033	31.571	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.807	-0.871	28.024	-0.221	-0.221	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.845	-0.907	30.644	-0.140	-0.140	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.986	-1.005	30.467	-0.158	-0.158	0.000	0.000	0.000	0.000
26	A	26	VAL	0	-0.021	-0.029	24.336	-0.018	-0.018	0.000	0.000	0.000	0.000
27	A	27	LEU	0	-0.019	0.006	22.410	0.016	0.016	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.044	-0.008	21.955	-0.027	-0.027	0.000	0.000	0.000	0.000
29	A	29	VAL	0	0.046	-0.001	17.026	0.001	0.001	0.000	0.000	0.000	0.000
30	A	30	SER	0	0.009	-0.003	20.385	0.029	0.029	0.000	0.000	0.000	0.000
31	A	31	SER	0	-0.078	-0.036	17.554	-0.012	-0.012	0.000	0.000	0.000	0.000
32	A	32	SER	0	0.041	0.036	13.199	0.039	0.039	0.000	0.000	0.000	0.000
33	A	33	ARG	1	0.889	0.924	10.523	-0.506	-0.506	0.000	0.000	0.000	0.000
34	A	34	TYR	0	0.021	0.002	16.363	0.039	0.039	0.000	0.000	0.000	0.000
35	A	35	PRO	0	0.072	0.024	19.373	-0.019	-0.019	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.954	-0.960	21.229	-0.050	-0.050	0.000	0.000	0.000	0.000
37	A	37	GLN	0	-0.038	-0.014	22.599	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	38	TRP	0	0.018	0.016	22.119	-0.018	-0.018	0.000	0.000	0.000	0.000
39	A	39	ILE	0	-0.074	-0.040	15.956	0.039	0.039	0.000	0.000	0.000	0.000
40	A	40	VAL	0	0.018	0.014	18.631	-0.018	-0.018	0.000	0.000	0.000	0.000
41	A	41	PRO	0	-0.002	0.014	16.073	0.003	0.003	0.000	0.000	0.000	0.000
42	A	42	GLY	0	0.031	-0.018	13.390	0.021	0.021	0.000	0.000	0.000	0.000
43	A	43	GLY	0	-0.020	-0.007	9.468	0.168	0.168	0.000	0.000	0.000	0.000
44	A	44	GLY	0	-0.121	-0.060	6.789	0.198	0.198	0.000	0.000	0.000	0.000
45	A	45	MET	0	0.010	0.015	6.773	-0.296	-0.296	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.920	-0.972	2.440	-11.811	-9.557	0.619	-1.222	-1.651	-0.012
47	A	47	PRO	0	-0.123	-0.085	1.868	0.609	0.547	6.171	-2.610	-3.500	-0.007
48	A	48	GLU	-1	-0.972	-0.978	4.259	-0.273	0.293	0.000	-0.290	-0.277	-0.001
49	A	49	GLU	-1	-0.740	-0.817	7.017	-2.933	-2.933	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.905	-0.960	9.543	-0.474	-0.474	0.000	0.000	0.000	0.000
51	A	51	PRO	0	-0.008	-0.018	12.480	-0.112	-0.112	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.018	-0.006	13.441	-0.057	-0.057	0.000	0.000	0.000	0.000
53	A	53	GLY	0	-0.006	-0.005	12.288	0.026	0.026	0.000	0.000	0.000	0.000
54	A	54	ALA	0	0.036	0.024	9.328	-0.044	-0.044	0.000	0.000	0.000	0.000
55	A	55	ALA	0	-0.030	-0.018	10.436	0.040	0.040	0.000	0.000	0.000	0.000
56	A	56	VAL	0	-0.013	-0.019	13.784	0.029	0.029	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.746	0.847	6.937	3.052	3.052	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.795	-0.890	8.250	-1.985	-1.985	0.000	0.000	0.000	0.000
59	A	59	VAL	0	-0.030	-0.014	11.843	0.143	0.143	0.000	0.000	0.000	0.000
60	A	60	TYR	0	-0.047	0.000	13.975	0.139	0.139	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.789	-0.889	9.119	-2.155	-2.155	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.789	-0.887	12.305	-0.449	-0.449	0.000	0.000	0.000	0.000
63	A	63	ALA	0	-0.030	-0.032	14.772	0.110	0.110	0.000	0.000	0.000	0.000
64	A	64	GLY	0	0.034	0.002	17.164	0.060	0.060	0.000	0.000	0.000	0.000
65	A	65	VAL	0	-0.066	-0.045	18.588	0.072	0.072	0.000	0.000	0.000	0.000
66	A	66	LYS	1	0.855	0.896	18.850	0.433	0.433	0.000	0.000	0.000	0.000
67	A	67	GLY	0	0.044	0.002	20.741	0.056	0.056	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.813	0.915	21.638	0.250	0.250	0.000	0.000	0.000	0.000
69	A	69	LEU	0	0.012	0.007	17.922	0.019	0.019	0.000	0.000	0.000	0.000
70	A	70	GLY	0	-0.001	0.004	21.627	0.029	0.029	0.000	0.000	0.000	0.000
71	A	71	ARG	1	0.778	0.845	22.672	0.210	0.210	0.000	0.000	0.000	0.000
72	A	72	LEU	0	-0.014	0.011	19.038	-0.024	-0.024	0.000	0.000	0.000	0.000
73	A	73	LEU	0	-0.015	-0.010	21.966	0.034	0.034	0.000	0.000	0.000	0.000
74	A	74	GLY	0	0.018	-0.004	21.746	0.043	0.043	0.000	0.000	0.000	0.000
75	A	75	ILE	0	-0.015	-0.003	17.958	-0.042	-0.042	0.000	0.000	0.000	0.000
76	A	76	PHE	0	0.017	0.011	19.070	0.038	0.038	0.000	0.000	0.000	0.000
77	A	77	GLU	-1	-0.845	-0.917	18.381	0.027	0.027	0.000	0.000	0.000	0.000
78	A	78	ASN	0	0.031	-0.015	17.192	0.040	0.040	0.000	0.000	0.000	0.000
79	A	79	GLN	0	0.008	-0.003	18.336	0.059	0.059	0.000	0.000	0.000	0.000
80	A	80	ASP	-1	-0.847	-0.901	19.711	0.160	0.160	0.000	0.000	0.000	0.000
81	A	81	ARG	1	0.828	0.908	12.702	-0.261	-0.261	0.000	0.000	0.000	0.000
82	A	82	LYS	1	0.894	0.957	15.085	-0.363	-0.363	0.000	0.000	0.000	0.000
83	A	83	HIS	0	-0.044	-0.012	10.864	0.058	0.058	0.000	0.000	0.000	0.000
84	A	84	ARG	1	0.796	0.873	13.945	0.009	0.009	0.000	0.000	0.000	0.000
85	A	85	THR	0	-0.028	-0.005	14.076	-0.097	-0.097	0.000	0.000	0.000	0.000
86	A	86	TYR	0	0.010	0.008	14.160	0.068	0.068	0.000	0.000	0.000	0.000
87	A	87	VAL	0	0.024	0.022	16.008	-0.077	-0.077	0.000	0.000	0.000	0.000
88	A	88	TYR	0	0.042	0.010	16.096	0.019	0.019	0.000	0.000	0.000	0.000
89	A	89	VAL	0	0.001	0.010	20.174	0.008	0.008	0.000	0.000	0.000	0.000
90	A	90	LEU	0	0.011	0.014	19.091	-0.016	-0.016	0.000	0.000	0.000	0.000
91	A	91	THR	0	-0.036	-0.008	22.587	0.018	0.018	0.000	0.000	0.000	0.000
92	A	92	VAL	0	-0.018	-0.015	22.791	-0.023	-0.023	0.000	0.000	0.000	0.000
93	A	93	THR	0	-0.052	-0.040	24.483	0.039	0.039	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.823	-0.892	23.728	-0.435	-0.435	0.000	0.000	0.000	0.000
95	A	95	ILE	0	-0.029	-0.002	23.438	-0.033	-0.033	0.000	0.000	0.000	0.000
96	A	96	LEU	0	0.023	0.019	20.455	0.017	0.017	0.000	0.000	0.000	0.000
97	A	97	GLU	-1	-0.922	-0.957	23.167	-0.275	-0.275	0.000	0.000	0.000	0.000
98	A	98	ASP	-1	-0.925	-0.945	21.327	-0.334	-0.334	0.000	0.000	0.000	0.000
99	A	99	TRP	0	-0.055	-0.022	16.667	-0.010	-0.010	0.000	0.000	0.000	0.000
100	A	100	GLU	-1	-0.894	-0.949	10.895	-1.269	-1.269	0.000	0.000	0.000	0.000
101	A	101	ASP	-1	-0.800	-0.885	12.793	-0.577	-0.577	0.000	0.000	0.000	0.000
102	A	102	SER	0	-0.058	-0.039	14.936	0.107	0.107	0.000	0.000	0.000	0.000
103	A	103	VAL	0	-0.032	-0.018	18.227	0.062	0.062	0.000	0.000	0.000	0.000
104	A	104	ASN	0	-0.048	-0.031	13.344	0.025	0.025	0.000	0.000	0.000	0.000
105	A	105	ILE	0	-0.027	-0.008	13.704	0.086	0.086	0.000	0.000	0.000	0.000
106	A	106	GLY	0	-0.025	0.013	16.311	0.058	0.058	0.000	0.000	0.000	0.000
107	A	107	ARG	1	0.654	0.814	12.397	0.568	0.568	0.000	0.000	0.000	0.000
108	A	108	LYS	1	0.963	0.976	18.754	0.137	0.137	0.000	0.000	0.000	0.000
109	A	109	ARG	1	0.851	0.908	21.382	0.358	0.358	0.000	0.000	0.000	0.000
110	A	110	GLU	-1	-0.854	-0.952	23.190	-0.185	-0.185	0.000	0.000	0.000	0.000
111	A	111	TRP	0	-0.054	-0.026	25.941	-0.009	-0.009	0.000	0.000	0.000	0.000
112	A	112	PHE	0	0.005	0.012	26.539	0.023	0.023	0.000	0.000	0.000	0.000
113	A	113	LYS	1	0.981	1.006	29.806	0.097	0.097	0.000	0.000	0.000	0.000
114	A	114	VAL	0	0.032	0.008	29.122	0.008	0.008	0.000	0.000	0.000	0.000
115	A	115	GLU	-1	-0.850	-0.908	30.262	-0.091	-0.091	0.000	0.000	0.000	0.000
116	A	116	ASP	-1	-0.883	-0.956	31.968	-0.093	-0.093	0.000	0.000	0.000	0.000
117	A	117	ALA	0	-0.025	-0.008	26.845	0.005	0.005	0.000	0.000	0.000	0.000
118	A	118	ILE	0	0.027	0.010	27.476	0.005	0.005	0.000	0.000	0.000	0.000
119	A	119	LYS	1	0.867	0.935	28.661	0.062	0.062	0.000	0.000	0.000	0.000
120	A	120	VAL	0	-0.030	-0.014	26.514	0.014	0.014	0.000	0.000	0.000	0.000
121	A	121	LEU	0	0.018	0.014	23.075	0.002	0.002	0.000	0.000	0.000	0.000
122	A	122	GLN	0	-0.024	-0.018	25.020	0.021	0.021	0.000	0.000	0.000	0.000
123	A	123	CYS	0	-0.046	0.000	27.138	0.017	0.017	0.000	0.000	0.000	0.000
124	A	124	HIS	0	0.037	0.011	20.851	0.012	0.012	0.000	0.000	0.000	0.000
125	A	125	LYS	1	0.808	0.895	17.726	-0.026	-0.026	0.000	0.000	0.000	0.000
126	A	126	PRO	0	0.098	0.051	22.074	-0.027	-0.027	0.000	0.000	0.000	0.000
127	A	127	VAL	0	0.046	0.026	19.767	-0.013	-0.013	0.000	0.000	0.000	0.000
128	A	128	HIS	0	-0.005	-0.012	16.590	-0.016	-0.016	0.000	0.000	0.000	0.000
129	A	129	ALA	0	0.002	0.013	21.643	-0.023	-0.023	0.000	0.000	0.000	0.000
130	A	130	GLU	-1	-0.841	-0.931	24.188	-0.057	-0.057	0.000	0.000	0.000	0.000
131	A	131	TYR	0	-0.031	-0.021	17.991	-0.027	-0.027	0.000	0.000	0.000	0.000
132	A	132	LEU	0	0.027	0.013	24.319	-0.006	-0.006	0.000	0.000	0.000	0.000
133	A	133	GLU	-1	-0.966	-0.993	27.126	-0.071	-0.071	0.000	0.000	0.000	0.000
134	A	134	LYS	1	0.890	0.941	25.591	0.180	0.180	0.000	0.000	0.000	0.000
135	A	135	LEU	0	-0.080	-0.028	27.028	-0.003	-0.003	0.000	0.000	0.000	0.000
136	A	136	LYS	1	0.868	0.915	30.107	0.100	0.100	0.000	0.000	0.000	0.000
137	A	137	LEU	0	-0.060	-0.009	30.661	0.011	0.011	0.000	0.000	0.000	0.000
138	A	138	GLY	0	-0.005	-0.001	32.338	0.002	0.002	0.000	0.000	0.000	0.000

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