FMO DATABASE

FMODB ID: LZ8Y9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1331646.599323
FMO2-HF: Nuclear repulsion	1275853.065492
FMO2-HF: Total energy	-55793.533831
FMO2-MP2: Total energy	-55957.171682

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.
-15.538	-13.645	7.877	-3.791	-5.98	-0.003

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 : -0.020 / q_NPA : -0.010

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	0.103	0.077	3.807	-0.850	1.362	-0.030	-1.183	-1.000	0.005
4	A	4	TYR	0	-0.038	-0.048	6.722	0.070	0.070	0.000	0.000	0.000	0.000
5	A	5	ASP	-1	-0.859	-0.925	10.217	0.270	0.270	0.000	0.000	0.000	0.000
6	A	6	ARG	1	0.942	0.947	13.911	-0.184	-0.184	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.863	-0.931	16.565	0.327	0.327	0.000	0.000	0.000	0.000
8	A	8	GLY	0	-0.045	-0.020	14.078	0.000	0.000	0.000	0.000	0.000	0.000
9	A	9	PHE	0	-0.020	-0.022	13.716	0.149	0.149	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.898	0.965	6.430	-1.989	-1.989	0.000	0.000	0.000	0.000
11	A	11	LYN	0	0.011	0.030	9.684	-0.157	-0.157	0.000	0.000	0.000	0.000
12	A	12	ARG	1	0.895	0.951	8.403	-0.349	-0.349	0.000	0.000	0.000	0.000
13	A	13	ALA	0	0.039	0.027	11.282	0.036	0.036	0.000	0.000	0.000	0.000
14	A	14	ALA	0	0.042	0.023	12.665	-0.047	-0.047	0.000	0.000	0.000	0.000
15	A	15	CYS	0	-0.034	-0.027	15.459	0.007	0.007	0.000	0.000	0.000	0.000
16	A	16	LEU	0	0.003	0.013	18.455	0.003	0.003	0.000	0.000	0.000	0.000
17	A	17	CYS	0	-0.019	0.004	20.192	-0.019	-0.019	0.000	0.000	0.000	0.000
18	A	18	PHE	0	0.083	0.037	22.897	0.024	0.024	0.000	0.000	0.000	0.000
19	A	19	ARG	1	0.976	0.997	26.647	0.162	0.162	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.009	-0.025	28.969	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.911	-0.951	30.467	-0.167	-0.167	0.000	0.000	0.000	0.000
22	A	22	GLN	0	-0.092	-0.038	31.663	0.005	0.005	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.899	-0.957	28.729	-0.106	-0.106	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.891	-0.940	30.649	-0.074	-0.074	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.986	-1.008	30.249	-0.100	-0.100	0.000	0.000	0.000	0.000
26	A	26	VAL	0	-0.019	-0.024	23.990	-0.015	-0.015	0.000	0.000	0.000	0.000
27	A	27	LEU	0	-0.010	0.005	21.611	0.012	0.012	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.044	-0.007	21.924	-0.013	-0.013	0.000	0.000	0.000	0.000
29	A	29	VAL	0	0.039	-0.004	17.184	-0.012	-0.012	0.000	0.000	0.000	0.000
30	A	30	SER	0	0.018	0.000	20.387	0.032	0.032	0.000	0.000	0.000	0.000
31	A	31	SER	0	-0.075	-0.035	17.557	-0.008	-0.008	0.000	0.000	0.000	0.000
32	A	32	SER	0	0.032	0.022	13.337	0.016	0.016	0.000	0.000	0.000	0.000
33	A	33	ARG	1	0.868	0.920	10.563	-0.743	-0.743	0.000	0.000	0.000	0.000
34	A	34	TYR	0	0.017	-0.003	16.363	0.033	0.033	0.000	0.000	0.000	0.000
35	A	35	PRO	0	0.074	0.026	19.432	-0.014	-0.014	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.960	-0.969	21.229	0.006	0.006	0.000	0.000	0.000	0.000
37	A	37	GLN	0	-0.013	0.007	22.623	0.000	0.000	0.000	0.000	0.000	0.000
38	A	38	TRP	0	-0.001	0.020	22.097	-0.019	-0.019	0.000	0.000	0.000	0.000
39	A	39	ILE	0	-0.081	-0.046	16.061	0.052	0.052	0.000	0.000	0.000	0.000
40	A	40	VAL	0	0.020	0.016	18.437	-0.032	-0.032	0.000	0.000	0.000	0.000
41	A	41	PRO	0	0.003	0.014	16.045	0.025	0.025	0.000	0.000	0.000	0.000
42	A	42	GLY	0	0.035	-0.007	13.194	0.019	0.019	0.000	0.000	0.000	0.000
43	A	43	GLY	0	0.012	0.024	9.410	0.116	0.116	0.000	0.000	0.000	0.000
44	A	44	GLY	0	-0.134	-0.083	6.798	0.211	0.211	0.000	0.000	0.000	0.000
45	A	45	MET	0	0.026	0.028	6.837	-0.387	-0.387	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.903	-0.962	2.083	-5.903	-6.316	2.397	-0.533	-1.451	-0.010
47	A	47	PRO	0	-0.128	-0.086	2.132	-0.489	-0.584	5.511	-2.029	-3.387	0.002
48	A	48	GLU	-1	-0.968	-0.978	4.879	0.020	0.209	-0.001	-0.046	-0.142	0.000
49	A	49	GLU	-1	-0.760	-0.836	6.821	-2.254	-2.254	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.909	-0.962	9.183	-0.194	-0.194	0.000	0.000	0.000	0.000
51	A	51	PRO	0	0.008	-0.010	12.247	-0.093	-0.093	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.003	-0.014	13.319	-0.049	-0.049	0.000	0.000	0.000	0.000
53	A	53	GLY	0	-0.002	-0.004	12.106	-0.006	-0.006	0.000	0.000	0.000	0.000
54	A	54	ALA	0	0.042	0.023	9.238	-0.074	-0.074	0.000	0.000	0.000	0.000
55	A	55	ALA	0	-0.041	-0.017	10.397	0.015	0.015	0.000	0.000	0.000	0.000
56	A	56	VAL	0	-0.017	-0.020	13.820	0.007	0.007	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.793	0.882	6.946	2.473	2.473	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.822	-0.905	8.148	-1.475	-1.475	0.000	0.000	0.000	0.000
59	A	59	VAL	0	-0.032	-0.012	11.719	0.095	0.095	0.000	0.000	0.000	0.000
60	A	60	TYR	0	-0.056	-0.011	13.826	0.106	0.106	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.837	-0.913	8.848	-1.979	-1.979	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.886	-0.957	11.679	-0.252	-0.252	0.000	0.000	0.000	0.000
63	A	63	ALA	0	-0.026	-0.038	14.532	0.093	0.093	0.000	0.000	0.000	0.000
64	A	64	GLY	0	0.045	0.011	16.915	0.043	0.043	0.000	0.000	0.000	0.000
65	A	65	VAL	0	-0.063	-0.043	18.410	0.060	0.060	0.000	0.000	0.000	0.000
66	A	66	LYS	1	0.984	0.982	18.799	0.464	0.464	0.000	0.000	0.000	0.000
67	A	67	GLY	0	0.043	-0.001	20.853	0.047	0.047	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.932	0.976	21.691	0.186	0.186	0.000	0.000	0.000	0.000
69	A	69	LEU	0	0.009	0.011	17.897	0.022	0.022	0.000	0.000	0.000	0.000
70	A	70	GLY	0	-0.006	0.001	21.609	0.019	0.019	0.000	0.000	0.000	0.000
71	A	71	ARG	1	0.890	0.937	22.592	0.097	0.097	0.000	0.000	0.000	0.000
72	A	72	LEU	0	-0.014	0.014	18.697	-0.014	-0.014	0.000	0.000	0.000	0.000
73	A	73	LEU	0	-0.029	-0.026	21.860	0.022	0.022	0.000	0.000	0.000	0.000
74	A	74	GLY	0	0.005	-0.017	21.682	0.022	0.022	0.000	0.000	0.000	0.000
75	A	75	ILE	0	-0.022	-0.008	17.716	-0.020	-0.020	0.000	0.000	0.000	0.000
76	A	76	PHE	0	0.031	0.014	19.055	0.012	0.012	0.000	0.000	0.000	0.000
77	A	77	GLU	-1	-0.891	-0.953	18.390	0.331	0.331	0.000	0.000	0.000	0.000
78	A	78	ASN	0	0.028	-0.012	17.183	0.017	0.017	0.000	0.000	0.000	0.000
79	A	79	GLN	0	0.014	-0.001	18.343	0.098	0.098	0.000	0.000	0.000	0.000
80	A	80	ASP	-1	-0.845	-0.898	19.762	0.338	0.338	0.000	0.000	0.000	0.000
81	A	81	ARG	1	0.817	0.894	12.601	-0.573	-0.573	0.000	0.000	0.000	0.000
82	A	82	LYS	1	0.959	0.993	15.020	-0.661	-0.661	0.000	0.000	0.000	0.000
83	A	83	HIS	0	-0.039	-0.007	11.453	0.205	0.205	0.000	0.000	0.000	0.000
84	A	84	ARG	1	0.874	0.928	13.954	-0.382	-0.382	0.000	0.000	0.000	0.000
85	A	85	THR	0	-0.027	0.001	14.027	-0.008	-0.008	0.000	0.000	0.000	0.000
86	A	86	TYR	0	-0.006	0.009	13.854	0.003	0.003	0.000	0.000	0.000	0.000
87	A	87	VAL	0	0.015	0.021	16.002	-0.063	-0.063	0.000	0.000	0.000	0.000
88	A	88	TYR	0	0.059	0.016	16.136	0.015	0.015	0.000	0.000	0.000	0.000
89	A	89	VAL	0	0.012	0.021	20.179	0.006	0.006	0.000	0.000	0.000	0.000
90	A	90	LEU	0	0.026	0.030	19.159	-0.020	-0.020	0.000	0.000	0.000	0.000
91	A	91	THR	0	0.001	0.021	22.680	0.025	0.025	0.000	0.000	0.000	0.000
92	A	92	VAL	0	-0.037	-0.030	22.556	-0.026	-0.026	0.000	0.000	0.000	0.000
93	A	93	THR	0	-0.048	-0.042	24.540	0.033	0.033	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.938	-0.966	23.740	-0.395	-0.395	0.000	0.000	0.000	0.000
95	A	95	ILE	0	-0.035	-0.006	23.342	-0.025	-0.025	0.000	0.000	0.000	0.000
96	A	96	LEU	0	0.008	0.003	20.473	0.010	0.010	0.000	0.000	0.000	0.000
97	A	97	GLU	-1	-0.973	-0.978	23.096	-0.243	-0.243	0.000	0.000	0.000	0.000
98	A	98	ASP	-1	-0.879	-0.925	21.617	-0.342	-0.342	0.000	0.000	0.000	0.000
99	A	99	TRP	0	-0.055	-0.019	16.441	-0.018	-0.018	0.000	0.000	0.000	0.000
100	A	100	GLU	-1	-0.888	-0.945	10.772	-1.348	-1.348	0.000	0.000	0.000	0.000
101	A	101	ASP	-1	-0.800	-0.875	12.281	-0.667	-0.667	0.000	0.000	0.000	0.000
102	A	102	SER	0	-0.092	-0.063	15.004	0.112	0.112	0.000	0.000	0.000	0.000
103	A	103	VAL	0	-0.026	-0.008	18.330	0.061	0.061	0.000	0.000	0.000	0.000
104	A	104	ASN	0	-0.060	-0.040	13.514	-0.079	-0.079	0.000	0.000	0.000	0.000
105	A	105	ILE	0	-0.026	-0.007	13.671	0.076	0.076	0.000	0.000	0.000	0.000
106	A	106	GLY	0	-0.014	0.015	16.308	0.065	0.065	0.000	0.000	0.000	0.000
107	A	107	ARG	1	0.741	0.867	12.369	0.384	0.384	0.000	0.000	0.000	0.000
108	A	108	LYS	1	0.991	0.985	18.754	0.082	0.082	0.000	0.000	0.000	0.000
109	A	109	ARG	1	0.869	0.921	21.384	0.321	0.321	0.000	0.000	0.000	0.000
110	A	110	GLU	-1	-0.886	-0.977	23.131	-0.131	-0.131	0.000	0.000	0.000	0.000
111	A	111	TRP	0	-0.043	-0.007	25.924	0.001	0.001	0.000	0.000	0.000	0.000
112	A	112	PHE	0	0.013	0.019	26.395	0.018	0.018	0.000	0.000	0.000	0.000
113	A	113	LYS	1	0.999	1.006	29.623	0.048	0.048	0.000	0.000	0.000	0.000
114	A	114	VAL	0	0.027	0.004	29.137	0.011	0.011	0.000	0.000	0.000	0.000
115	A	115	GLU	-1	-0.959	-0.978	30.268	0.003	0.003	0.000	0.000	0.000	0.000
116	A	116	ASP	-1	-0.890	-0.957	31.974	-0.020	-0.020	0.000	0.000	0.000	0.000
117	A	117	ALA	0	-0.037	-0.013	26.853	0.006	0.006	0.000	0.000	0.000	0.000
118	A	118	ILE	0	0.027	0.009	27.482	0.011	0.011	0.000	0.000	0.000	0.000
119	A	119	LYS	1	0.921	0.971	28.667	-0.012	-0.012	0.000	0.000	0.000	0.000
120	A	120	VAL	0	-0.035	-0.012	26.236	0.015	0.015	0.000	0.000	0.000	0.000
121	A	121	LEU	0	0.001	-0.001	22.649	0.008	0.008	0.000	0.000	0.000	0.000
122	A	122	GLN	0	-0.047	-0.039	25.025	0.022	0.022	0.000	0.000	0.000	0.000
123	A	123	CYS	0	-0.046	0.001	27.179	0.014	0.014	0.000	0.000	0.000	0.000
124	A	124	HIS	0	0.020	0.008	20.707	0.007	0.007	0.000	0.000	0.000	0.000
125	A	125	LYS	1	0.840	0.911	16.587	-0.225	-0.225	0.000	0.000	0.000	0.000
126	A	126	PRO	0	0.099	0.058	22.080	-0.024	-0.024	0.000	0.000	0.000	0.000
127	A	127	VAL	0	0.030	0.014	20.049	-0.013	-0.013	0.000	0.000	0.000	0.000
128	A	128	HIS	0	0.009	-0.013	16.823	-0.037	-0.037	0.000	0.000	0.000	0.000
129	A	129	ALA	0	0.016	0.016	21.650	-0.027	-0.027	0.000	0.000	0.000	0.000
130	A	130	GLU	-1	-0.864	-0.934	24.056	0.117	0.117	0.000	0.000	0.000	0.000
131	A	131	TYR	0	-0.056	-0.026	17.470	0.002	0.002	0.000	0.000	0.000	0.000
132	A	132	LEU	0	0.030	0.014	24.327	-0.013	-0.013	0.000	0.000	0.000	0.000
133	A	133	GLU	-1	-0.969	-0.992	27.069	0.036	0.036	0.000	0.000	0.000	0.000
134	A	134	LYS	1	0.919	0.968	25.759	0.009	0.009	0.000	0.000	0.000	0.000
135	A	135	LEU	0	-0.086	-0.034	27.413	-0.005	-0.005	0.000	0.000	0.000	0.000
136	A	136	LYS	1	0.966	0.982	30.170	0.009	0.009	0.000	0.000	0.000	0.000
137	A	137	LEU	0	-0.059	-0.003	30.370	0.005	0.005	0.000	0.000	0.000	0.000
138	A	138	GLY	0	-0.009	-0.004	32.318	0.006	0.006	0.000	0.000	0.000	0.000

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