FMO DATABASE

FMODB ID: MVG4Z

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	OptAll
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	-1333603.786935
FMO2-HF: Nuclear repulsion	1277807.850872
FMO2-HF: Total energy	-55795.936063
FMO2-MP2: Total energy	-55959.447709

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.
-19.056	-13.845	7.511	-5.258	-7.465	-0.027

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 : -0.011 / q_NPA : -0.011

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	0.064	0.065	3.860	-0.532	1.132	-0.010	-0.786	-0.868	0.002
4	A	4	TYR	0	-0.038	-0.043	6.122	0.776	0.776	0.000	0.000	0.000	0.000
5	A	5	ASP	-1	-0.774	-0.866	9.877	-0.328	-0.328	0.000	0.000	0.000	0.000
6	A	6	ARG	1	0.862	0.893	13.321	0.378	0.378	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.812	-0.874	15.953	0.028	0.028	0.000	0.000	0.000	0.000
8	A	8	GLY	0	-0.012	-0.007	14.184	0.044	0.044	0.000	0.000	0.000	0.000
9	A	9	PHE	0	0.014	0.005	14.408	0.095	0.095	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.852	0.934	7.340	-1.012	-1.012	0.000	0.000	0.000	0.000
11	A	11	LYN	0	0.049	0.045	9.557	0.077	0.077	0.000	0.000	0.000	0.000
12	A	12	ARG	1	0.864	0.939	9.248	0.094	0.094	0.000	0.000	0.000	0.000
13	A	13	ALA	0	0.032	0.029	11.103	0.058	0.058	0.000	0.000	0.000	0.000
14	A	14	ALA	0	0.011	0.006	12.586	-0.013	-0.013	0.000	0.000	0.000	0.000
15	A	15	CYS	0	-0.013	0.001	15.360	0.008	0.008	0.000	0.000	0.000	0.000
16	A	16	LEU	0	0.004	0.016	18.382	0.016	0.016	0.000	0.000	0.000	0.000
17	A	17	CYS	0	-0.006	0.013	19.894	-0.013	-0.013	0.000	0.000	0.000	0.000
18	A	18	PHE	0	0.064	0.017	22.699	0.025	0.025	0.000	0.000	0.000	0.000
19	A	19	ARG	1	0.928	0.969	26.499	0.200	0.200	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.016	-0.037	29.087	0.001	0.001	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.798	-0.866	29.452	-0.249	-0.249	0.000	0.000	0.000	0.000
22	A	22	GLN	0	-0.065	-0.025	31.284	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.757	-0.835	27.867	-0.207	-0.207	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.853	-0.907	30.575	-0.135	-0.135	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.968	-0.994	30.603	-0.141	-0.141	0.000	0.000	0.000	0.000
26	A	26	VAL	0	-0.035	-0.025	24.316	-0.017	-0.017	0.000	0.000	0.000	0.000
27	A	27	LEU	0	-0.010	0.006	21.991	0.017	0.017	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.048	-0.016	21.950	-0.019	-0.019	0.000	0.000	0.000	0.000
29	A	29	VAL	0	0.046	0.009	17.054	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	30	SER	0	0.000	-0.007	20.394	0.027	0.027	0.000	0.000	0.000	0.000
31	A	31	SER	0	-0.032	-0.015	17.486	-0.010	-0.010	0.000	0.000	0.000	0.000
32	A	32	SER	0	0.044	0.021	13.220	0.052	0.052	0.000	0.000	0.000	0.000
33	A	33	ARG	1	0.884	0.933	11.093	-0.468	-0.468	0.000	0.000	0.000	0.000
34	A	34	TYR	0	0.011	-0.005	16.935	0.035	0.035	0.000	0.000	0.000	0.000
35	A	35	PRO	0	0.079	0.042	19.748	-0.020	-0.020	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.939	-0.958	21.366	-0.037	-0.037	0.000	0.000	0.000	0.000
37	A	37	GLN	0	-0.011	-0.005	23.058	-0.009	-0.009	0.000	0.000	0.000	0.000
38	A	38	TRP	0	-0.001	-0.003	21.989	-0.013	-0.013	0.000	0.000	0.000	0.000
39	A	39	ILE	0	-0.059	-0.032	16.095	0.038	0.038	0.000	0.000	0.000	0.000
40	A	40	VAL	0	0.036	0.017	18.651	-0.014	-0.014	0.000	0.000	0.000	0.000
41	A	41	PRO	0	0.000	0.013	16.328	0.008	0.008	0.000	0.000	0.000	0.000
42	A	42	GLY	0	0.036	-0.013	13.458	-0.024	-0.024	0.000	0.000	0.000	0.000
43	A	43	GLY	0	0.003	0.010	9.372	0.188	0.188	0.000	0.000	0.000	0.000
44	A	44	GLY	0	-0.117	-0.066	6.845	0.392	0.392	0.000	0.000	0.000	0.000
45	A	45	MET	0	-0.019	0.015	6.157	-0.432	-0.432	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.864	-0.952	2.461	-14.127	-10.903	2.184	-2.361	-3.048	-0.027
47	A	47	PRO	0	-0.091	-0.064	1.998	0.962	0.948	5.337	-1.975	-3.348	-0.001
48	A	48	GLU	-1	-0.937	-0.970	4.282	-0.161	0.176	0.000	-0.136	-0.201	-0.001
49	A	49	GLU	-1	-0.756	-0.831	6.529	-2.794	-2.794	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.905	-0.953	9.085	-0.462	-0.462	0.000	0.000	0.000	0.000
51	A	51	PRO	0	-0.026	-0.033	11.914	-0.125	-0.125	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.024	0.009	13.147	-0.008	-0.008	0.000	0.000	0.000	0.000
53	A	53	GLY	0	0.012	0.003	12.666	0.037	0.037	0.000	0.000	0.000	0.000
54	A	54	ALA	0	0.054	0.032	9.335	-0.022	-0.022	0.000	0.000	0.000	0.000
55	A	55	ALA	0	-0.050	-0.025	10.510	0.032	0.032	0.000	0.000	0.000	0.000
56	A	56	VAL	0	-0.013	-0.016	13.772	0.063	0.063	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.737	0.840	6.732	2.798	2.798	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.793	-0.901	8.165	-1.730	-1.730	0.000	0.000	0.000	0.000
59	A	59	VAL	0	-0.051	-0.022	11.750	0.139	0.139	0.000	0.000	0.000	0.000
60	A	60	TYR	0	-0.031	-0.003	14.073	0.132	0.132	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.823	-0.915	8.994	-1.990	-1.990	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.794	-0.896	12.474	-0.326	-0.326	0.000	0.000	0.000	0.000
63	A	63	ALA	0	-0.015	-0.018	14.693	0.100	0.100	0.000	0.000	0.000	0.000
64	A	64	GLY	0	0.041	0.039	17.279	0.059	0.059	0.000	0.000	0.000	0.000
65	A	65	VAL	0	-0.034	-0.028	18.875	0.060	0.060	0.000	0.000	0.000	0.000
66	A	66	LYS	1	0.848	0.898	18.992	0.397	0.397	0.000	0.000	0.000	0.000
67	A	67	GLY	0	0.041	0.000	20.854	0.051	0.051	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.823	0.913	21.894	0.237	0.237	0.000	0.000	0.000	0.000
69	A	69	LEU	0	0.027	0.014	18.032	0.021	0.021	0.000	0.000	0.000	0.000
70	A	70	GLY	0	0.001	0.000	21.754	0.031	0.031	0.000	0.000	0.000	0.000
71	A	71	ARG	1	0.752	0.830	22.413	0.197	0.197	0.000	0.000	0.000	0.000
72	A	72	LEU	0	0.004	0.014	18.847	-0.015	-0.015	0.000	0.000	0.000	0.000
73	A	73	LEU	0	-0.014	0.001	21.735	0.031	0.031	0.000	0.000	0.000	0.000
74	A	74	GLY	0	-0.001	-0.017	21.768	0.041	0.041	0.000	0.000	0.000	0.000
75	A	75	ILE	0	-0.004	0.010	17.941	-0.044	-0.044	0.000	0.000	0.000	0.000
76	A	76	PHE	0	0.009	0.005	18.984	0.036	0.036	0.000	0.000	0.000	0.000
77	A	77	GLU	-1	-0.841	-0.909	18.366	-0.034	-0.034	0.000	0.000	0.000	0.000
78	A	78	ASN	0	-0.045	-0.039	17.501	0.040	0.040	0.000	0.000	0.000	0.000
79	A	79	GLN	0	0.030	-0.004	18.583	0.037	0.037	0.000	0.000	0.000	0.000
80	A	80	ASP	-1	-0.837	-0.891	20.205	0.143	0.143	0.000	0.000	0.000	0.000
81	A	81	ARG	1	0.858	0.921	13.273	-0.241	-0.241	0.000	0.000	0.000	0.000
82	A	82	LYS	1	0.858	0.943	15.579	-0.251	-0.251	0.000	0.000	0.000	0.000
83	A	83	HIS	0	-0.042	-0.021	11.214	0.055	0.055	0.000	0.000	0.000	0.000
84	A	84	ARG	1	0.763	0.840	14.016	0.083	0.083	0.000	0.000	0.000	0.000
85	A	85	THR	0	-0.035	-0.012	14.167	-0.097	-0.097	0.000	0.000	0.000	0.000
86	A	86	TYR	0	0.018	0.013	14.141	0.057	0.057	0.000	0.000	0.000	0.000
87	A	87	VAL	0	0.002	0.003	15.769	-0.070	-0.070	0.000	0.000	0.000	0.000
88	A	88	TYR	0	0.033	0.007	15.851	0.024	0.024	0.000	0.000	0.000	0.000
89	A	89	VAL	0	0.009	0.006	19.943	0.018	0.018	0.000	0.000	0.000	0.000
90	A	90	LEU	0	-0.001	-0.017	19.150	-0.024	-0.024	0.000	0.000	0.000	0.000
91	A	91	THR	0	-0.049	-0.026	22.750	0.011	0.011	0.000	0.000	0.000	0.000
92	A	92	VAL	0	-0.018	-0.010	22.941	-0.019	-0.019	0.000	0.000	0.000	0.000
93	A	93	THR	0	-0.052	-0.037	24.864	0.034	0.034	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.844	-0.891	23.608	-0.396	-0.396	0.000	0.000	0.000	0.000
95	A	95	ILE	0	-0.015	-0.010	23.760	-0.024	-0.024	0.000	0.000	0.000	0.000
96	A	96	LEU	0	0.009	0.014	20.355	0.018	0.018	0.000	0.000	0.000	0.000
97	A	97	GLU	-1	-0.889	-0.940	22.502	-0.250	-0.250	0.000	0.000	0.000	0.000
98	A	98	ASP	-1	-0.927	-0.945	21.631	-0.283	-0.283	0.000	0.000	0.000	0.000
99	A	99	TRP	0	-0.037	-0.030	16.483	-0.016	-0.016	0.000	0.000	0.000	0.000
100	A	100	GLU	-1	-0.900	-0.939	11.324	-1.063	-1.063	0.000	0.000	0.000	0.000
101	A	101	ASP	-1	-0.772	-0.881	13.320	-0.394	-0.394	0.000	0.000	0.000	0.000
102	A	102	SER	0	-0.052	-0.044	15.186	0.096	0.096	0.000	0.000	0.000	0.000
103	A	103	VAL	0	-0.038	-0.023	18.075	0.058	0.058	0.000	0.000	0.000	0.000
104	A	104	ASN	0	-0.064	-0.021	12.914	0.066	0.066	0.000	0.000	0.000	0.000
105	A	105	ILE	0	-0.040	-0.017	13.997	0.079	0.079	0.000	0.000	0.000	0.000
106	A	106	GLY	0	-0.007	0.018	16.544	0.047	0.047	0.000	0.000	0.000	0.000
107	A	107	ARG	1	0.649	0.800	12.776	0.434	0.434	0.000	0.000	0.000	0.000
108	A	108	LYS	1	0.902	0.951	18.927	0.097	0.097	0.000	0.000	0.000	0.000
109	A	109	ARG	1	0.809	0.877	21.092	0.314	0.314	0.000	0.000	0.000	0.000
110	A	110	GLU	-1	-0.841	-0.925	23.056	-0.158	-0.158	0.000	0.000	0.000	0.000
111	A	111	TRP	0	-0.036	-0.017	25.842	-0.015	-0.015	0.000	0.000	0.000	0.000
112	A	112	PHE	0	-0.016	-0.004	26.537	0.022	0.022	0.000	0.000	0.000	0.000
113	A	113	LYS	1	0.877	0.929	29.596	0.090	0.090	0.000	0.000	0.000	0.000
114	A	114	VAL	0	0.056	0.025	29.041	0.006	0.006	0.000	0.000	0.000	0.000
115	A	115	GLU	-1	-0.835	-0.900	30.181	-0.088	-0.088	0.000	0.000	0.000	0.000
116	A	116	ASP	-1	-0.816	-0.895	31.988	-0.087	-0.087	0.000	0.000	0.000	0.000
117	A	117	ALA	0	0.003	0.007	26.711	0.006	0.006	0.000	0.000	0.000	0.000
118	A	118	ILE	0	0.003	0.000	27.292	0.005	0.005	0.000	0.000	0.000	0.000
119	A	119	LYS	1	0.862	0.925	28.545	0.062	0.062	0.000	0.000	0.000	0.000
120	A	120	VAL	0	0.005	0.009	26.247	0.013	0.013	0.000	0.000	0.000	0.000
121	A	121	LEU	0	0.005	0.016	22.746	0.008	0.008	0.000	0.000	0.000	0.000
122	A	122	GLN	0	0.024	0.001	25.030	0.022	0.022	0.000	0.000	0.000	0.000
123	A	123	CYS	0	-0.071	-0.016	27.245	0.014	0.014	0.000	0.000	0.000	0.000
124	A	124	HIS	0	-0.014	0.001	21.675	0.017	0.017	0.000	0.000	0.000	0.000
125	A	125	LYS	1	0.803	0.899	18.421	-0.031	-0.031	0.000	0.000	0.000	0.000
126	A	126	PRO	0	0.083	0.048	22.380	-0.025	-0.025	0.000	0.000	0.000	0.000
127	A	127	VAL	0	0.067	0.031	19.637	-0.015	-0.015	0.000	0.000	0.000	0.000
128	A	128	HIS	0	-0.020	-0.012	16.754	-0.012	-0.012	0.000	0.000	0.000	0.000
129	A	129	ALA	0	-0.005	0.015	21.814	-0.019	-0.019	0.000	0.000	0.000	0.000
130	A	130	GLU	-1	-0.845	-0.941	24.150	-0.070	-0.070	0.000	0.000	0.000	0.000
131	A	131	TYR	0	-0.020	-0.020	17.826	-0.025	-0.025	0.000	0.000	0.000	0.000
132	A	132	LEU	0	0.024	0.010	24.023	-0.008	-0.008	0.000	0.000	0.000	0.000
133	A	133	GLU	-1	-0.922	-0.981	26.963	-0.072	-0.072	0.000	0.000	0.000	0.000
134	A	134	LYS	1	0.869	0.928	25.527	0.180	0.180	0.000	0.000	0.000	0.000
135	A	135	LEU	0	-0.041	-0.009	26.979	-0.006	-0.006	0.000	0.000	0.000	0.000
136	A	136	LYS	1	0.844	0.914	29.948	0.098	0.098	0.000	0.000	0.000	0.000
137	A	137	LEU	0	-0.051	-0.010	30.577	0.008	0.008	0.000	0.000	0.000	0.000
138	A	138	GLY	0	-0.024	-0.012	31.720	-0.003	-0.003	0.000	0.000	0.000	0.000

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