FMO DATABASE

FMODB ID: QV8NY

Calculation Name: 3HDE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3HDE

Chain ID: A

ChEMBL ID:

UniProt ID: P27359

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	163
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1591521.411786
FMO2-HF: Nuclear repulsion	1527788.009485
FMO2-HF: Total energy	-63733.402301
FMO2-MP2: Total energy	-63917.124575

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:MET)

Summations of interaction energy for fragment #1(A:1: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.
-25.334	-28.432	33.749	-8.417	-22.232	-0.103

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.046 / q_NPA : -0.004

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	PRO	0	0.048	0.015	2.545	-2.517	-0.241	1.049	-1.478	-1.847	-0.009
4	A	4	SER	0	-0.007	-0.015	4.565	0.568	0.772	-0.001	-0.013	-0.189	0.000
5	A	5	LEU	0	0.084	0.037	2.543	-1.532	-0.085	0.656	-0.410	-1.692	0.000
6	A	6	ARG	1	0.987	0.991	1.904	2.046	0.742	10.707	-3.804	-5.600	0.007
7	A	7	LYS	1	0.954	0.964	2.651	4.100	-1.242	-0.058	5.961	-0.561	-0.004
8	A	8	ALA	0	0.021	0.020	6.095	-0.188	-0.188	0.000	0.000	0.000	0.000
9	A	9	VAL	0	0.024	0.005	4.032	-0.744	-0.418	0.004	-0.053	-0.277	0.000
10	A	10	ALA	0	-0.007	-0.010	5.230	-0.516	-0.516	0.000	0.000	0.000	0.000
11	A	11	ALA	0	-0.029	-0.009	6.641	-0.205	-0.205	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.004	-0.005	9.090	-0.114	-0.114	0.000	0.000	0.000	0.000
13	A	13	ILE	0	0.014	0.016	7.393	-0.094	-0.094	0.000	0.000	0.000	0.000
14	A	14	GLY	0	-0.016	0.001	10.836	-0.060	-0.060	0.000	0.000	0.000	0.000
15	A	15	GLY	0	-0.023	-0.011	13.576	-0.032	-0.032	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.009	0.011	14.098	-0.016	-0.016	0.000	0.000	0.000	0.000
17	A	17	ALA	0	-0.004	-0.023	13.234	0.079	0.079	0.000	0.000	0.000	0.000
18	A	18	ILE	0	-0.025	-0.010	13.762	0.072	0.072	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.039	0.021	13.664	0.046	0.046	0.000	0.000	0.000	0.000
20	A	20	ILE	0	0.010	0.016	8.376	0.118	0.118	0.000	0.000	0.000	0.000
21	A	21	ALA	0	0.010	-0.001	10.015	0.191	0.191	0.000	0.000	0.000	0.000
22	A	22	SER	0	-0.011	-0.011	12.132	0.003	0.003	0.000	0.000	0.000	0.000
23	A	23	VAL	0	-0.040	-0.001	7.706	-0.010	-0.010	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.045	-0.008	6.078	0.119	0.119	0.000	0.000	0.000	0.000
25	A	25	ILE	0	0.017	0.005	9.141	-0.083	-0.083	0.000	0.000	0.000	0.000
26	A	26	THR	0	-0.056	-0.031	12.316	-0.062	-0.062	0.000	0.000	0.000	0.000
27	A	27	GLY	0	0.082	0.039	9.349	-0.063	-0.063	0.000	0.000	0.000	0.000
28	A	28	PRO	0	-0.064	-0.039	7.823	-0.063	-0.063	0.000	0.000	0.000	0.000
29	A	29	SER	0	-0.002	0.005	10.610	-0.072	-0.072	0.000	0.000	0.000	0.000
30	A	30	GLY	0	-0.046	-0.013	13.391	-0.070	-0.070	0.000	0.000	0.000	0.000
31	A	31	ASN	0	-0.068	-0.057	14.754	-0.058	-0.058	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.911	-0.950	12.462	0.333	0.333	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.038	0.018	9.846	0.101	0.101	0.000	0.000	0.000	0.000
34	A	34	LEU	0	-0.090	-0.039	7.247	-0.079	-0.079	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.915	-0.955	10.636	0.178	0.178	0.000	0.000	0.000	0.000
36	A	36	GLY	0	0.018	0.017	14.350	0.015	0.015	0.000	0.000	0.000	0.000
37	A	37	VAL	0	-0.004	-0.015	16.923	0.004	0.004	0.000	0.000	0.000	0.000
38	A	38	SER	0	-0.011	0.004	19.401	-0.009	-0.009	0.000	0.000	0.000	0.000
39	A	39	TYR	0	0.014	-0.008	20.642	0.003	0.003	0.000	0.000	0.000	0.000
40	A	40	ILE	0	0.033	0.032	25.806	-0.007	-0.007	0.000	0.000	0.000	0.000
41	A	41	PRO	0	-0.021	-0.010	27.515	0.006	0.006	0.000	0.000	0.000	0.000
42	A	42	TYR	0	-0.011	-0.014	22.329	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.968	0.983	28.068	-0.065	-0.065	0.000	0.000	0.000	0.000
44	A	44	ASP	-1	-0.811	-0.897	24.731	0.098	0.098	0.000	0.000	0.000	0.000
45	A	45	ILE	0	-0.012	-0.019	24.743	-0.007	-0.007	0.000	0.000	0.000	0.000
46	A	46	VAL	0	-0.047	-0.020	26.629	-0.008	-0.008	0.000	0.000	0.000	0.000
47	A	47	GLY	0	-0.033	-0.017	29.061	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	48	VAL	0	-0.016	-0.005	27.791	-0.004	-0.004	0.000	0.000	0.000	0.000
49	A	49	TRP	0	-0.040	-0.018	28.286	0.006	0.006	0.000	0.000	0.000	0.000
50	A	50	THR	0	0.017	0.020	23.201	0.003	0.003	0.000	0.000	0.000	0.000
51	A	51	VAL	0	-0.001	-0.007	25.073	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	52	CYS	0	-0.033	0.001	21.750	0.005	0.005	0.000	0.000	0.000	0.000
53	A	53	HIS	0	0.032	0.020	17.348	0.010	0.010	0.000	0.000	0.000	0.000
54	A	54	GLY	0	0.081	0.058	19.087	0.011	0.011	0.000	0.000	0.000	0.000
55	A	55	HIS	1	0.738	0.848	20.988	-0.148	-0.148	0.000	0.000	0.000	0.000
56	A	56	THR	0	0.058	0.015	23.692	-0.012	-0.012	0.000	0.000	0.000	0.000
57	A	57	GLY	0	0.003	-0.009	26.688	0.001	0.001	0.000	0.000	0.000	0.000
58	A	58	LYS	1	0.914	0.947	30.005	-0.061	-0.061	0.000	0.000	0.000	0.000
59	A	59	ASP	-1	-0.835	-0.890	30.400	0.103	0.103	0.000	0.000	0.000	0.000
60	A	60	ILE	0	-0.027	0.006	27.941	0.005	0.005	0.000	0.000	0.000	0.000
61	A	61	MET	0	0.009	-0.007	31.775	-0.007	-0.007	0.000	0.000	0.000	0.000
62	A	62	LEU	0	0.034	-0.006	33.164	0.004	0.004	0.000	0.000	0.000	0.000
63	A	63	GLY	0	0.006	0.017	33.998	0.002	0.002	0.000	0.000	0.000	0.000
64	A	64	LYS	1	0.821	0.928	31.203	-0.105	-0.105	0.000	0.000	0.000	0.000
65	A	65	THR	0	0.030	0.010	29.484	0.004	0.004	0.000	0.000	0.000	0.000
66	A	66	TYR	0	-0.015	-0.018	27.016	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	67	THR	0	0.032	0.010	27.118	0.009	0.009	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.994	0.971	20.625	-0.204	-0.204	0.000	0.000	0.000	0.000
69	A	69	ALA	0	0.001	0.008	22.962	0.016	0.016	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.782	-0.891	25.059	0.124	0.124	0.000	0.000	0.000	0.000
71	A	72	LYS	1	0.969	0.985	17.121	-0.345	-0.345	0.000	0.000	0.000	0.000
72	A	73	ALA	0	0.025	0.006	21.476	0.007	0.007	0.000	0.000	0.000	0.000
73	A	74	LEU	0	-0.011	-0.009	24.158	-0.006	-0.006	0.000	0.000	0.000	0.000
74	A	75	LEU	0	0.046	0.037	16.372	-0.005	-0.005	0.000	0.000	0.000	0.000
75	A	76	ASN	0	-0.027	-0.005	20.448	0.019	0.019	0.000	0.000	0.000	0.000
76	A	77	LYS	1	0.964	0.971	21.440	-0.124	-0.124	0.000	0.000	0.000	0.000
77	A	78	ASP	-1	-0.785	-0.863	21.847	0.145	0.145	0.000	0.000	0.000	0.000
78	A	79	LEU	0	0.001	-0.006	16.229	-0.010	-0.010	0.000	0.000	0.000	0.000
79	A	80	ALA	0	-0.005	0.002	19.969	-0.013	-0.013	0.000	0.000	0.000	0.000
80	A	81	THR	0	-0.047	-0.028	22.639	-0.024	-0.024	0.000	0.000	0.000	0.000
81	A	82	VAL	0	0.038	0.026	18.681	-0.017	-0.017	0.000	0.000	0.000	0.000
82	A	83	ALA	0	-0.003	-0.002	20.177	-0.018	-0.018	0.000	0.000	0.000	0.000
83	A	84	ARG	1	0.907	0.946	21.454	-0.115	-0.115	0.000	0.000	0.000	0.000
84	A	85	GLN	0	-0.052	-0.017	23.884	-0.008	-0.008	0.000	0.000	0.000	0.000
85	A	86	ILE	0	0.047	0.006	18.593	-0.014	-0.014	0.000	0.000	0.000	0.000
86	A	87	ASN	0	0.042	0.021	20.311	-0.017	-0.017	0.000	0.000	0.000	0.000
87	A	88	PRO	0	0.010	0.019	22.800	-0.012	-0.012	0.000	0.000	0.000	0.000
88	A	89	TYR	0	-0.035	-0.037	24.459	-0.009	-0.009	0.000	0.000	0.000	0.000
89	A	90	ILE	0	-0.057	-0.018	18.702	-0.010	-0.010	0.000	0.000	0.000	0.000
90	A	91	LYS	1	0.896	0.943	22.739	0.013	0.013	0.000	0.000	0.000	0.000
91	A	92	VAL	0	0.013	0.029	19.886	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	93	ASP	-1	-0.882	-0.932	19.557	-0.029	-0.029	0.000	0.000	0.000	0.000
93	A	94	ILE	0	-0.072	-0.049	15.087	-0.024	-0.024	0.000	0.000	0.000	0.000
94	A	95	PRO	0	0.016	0.004	11.454	0.024	0.024	0.000	0.000	0.000	0.000
95	A	96	GLU	-1	-0.784	-0.899	12.542	0.144	0.144	0.000	0.000	0.000	0.000
96	A	97	THR	0	0.017	0.000	7.185	0.070	0.070	0.000	0.000	0.000	0.000
97	A	98	MET	0	0.019	0.019	9.401	0.081	0.081	0.000	0.000	0.000	0.000
98	A	99	ARG	1	0.967	0.979	11.147	-0.025	-0.025	0.000	0.000	0.000	0.000
99	A	100	GLY	0	0.020	0.003	11.603	0.010	0.010	0.000	0.000	0.000	0.000
100	A	101	ALA	0	-0.014	-0.011	9.130	0.069	0.069	0.000	0.000	0.000	0.000
101	A	102	LEU	0	-0.023	-0.016	10.681	-0.035	-0.035	0.000	0.000	0.000	0.000
102	A	103	TYR	0	0.003	0.005	14.348	-0.029	-0.029	0.000	0.000	0.000	0.000
103	A	104	SER	0	0.035	0.007	11.439	0.007	0.007	0.000	0.000	0.000	0.000
104	A	105	PHE	0	0.008	0.011	13.338	-0.039	-0.039	0.000	0.000	0.000	0.000
105	A	106	VAL	0	-0.033	-0.023	14.569	-0.024	-0.024	0.000	0.000	0.000	0.000
106	A	107	TYR	0	-0.106	-0.074	16.161	-0.017	-0.017	0.000	0.000	0.000	0.000
107	A	108	ASN	0	0.019	0.035	15.334	-0.029	-0.029	0.000	0.000	0.000	0.000
108	A	109	VAL	0	-0.024	-0.019	17.216	-0.018	-0.018	0.000	0.000	0.000	0.000
109	A	110	GLY	0	0.071	0.044	19.827	-0.017	-0.017	0.000	0.000	0.000	0.000
110	A	111	ALA	0	0.030	-0.012	22.236	-0.012	-0.012	0.000	0.000	0.000	0.000
111	A	112	GLY	0	-0.030	-0.013	23.805	-0.011	-0.011	0.000	0.000	0.000	0.000
112	A	113	ASN	0	0.028	-0.001	22.242	-0.017	-0.017	0.000	0.000	0.000	0.000
113	A	114	PHE	0	0.023	0.018	18.371	-0.010	-0.010	0.000	0.000	0.000	0.000
114	A	115	ARG	1	0.868	0.940	22.152	-0.055	-0.055	0.000	0.000	0.000	0.000
115	A	116	THR	0	-0.001	0.017	25.453	-0.009	-0.009	0.000	0.000	0.000	0.000
116	A	117	SER	0	-0.027	0.002	21.296	-0.014	-0.014	0.000	0.000	0.000	0.000
117	A	118	THR	0	-0.019	-0.032	22.281	-0.003	-0.003	0.000	0.000	0.000	0.000
118	A	119	LEU	0	-0.010	-0.003	15.610	-0.011	-0.011	0.000	0.000	0.000	0.000
119	A	120	LEU	0	0.016	0.011	19.995	-0.012	-0.012	0.000	0.000	0.000	0.000
120	A	121	ARG	1	0.922	0.963	21.946	0.045	0.045	0.000	0.000	0.000	0.000
121	A	122	LYS	1	0.920	0.954	20.197	0.144	0.144	0.000	0.000	0.000	0.000
122	A	123	ILE	0	0.039	0.029	17.449	-0.009	-0.009	0.000	0.000	0.000	0.000
123	A	124	ASN	0	0.007	0.005	20.350	-0.004	-0.004	0.000	0.000	0.000	0.000
124	A	125	GLN	0	-0.050	-0.008	23.543	-0.005	-0.005	0.000	0.000	0.000	0.000
125	A	126	GLY	0	0.044	0.020	21.476	-0.003	-0.003	0.000	0.000	0.000	0.000
126	A	127	ASP	-1	-0.852	-0.918	19.701	-0.238	-0.238	0.000	0.000	0.000	0.000
127	A	128	ILE	0	0.008	-0.012	14.337	-0.014	-0.014	0.000	0.000	0.000	0.000
128	A	129	LYS	1	0.894	0.947	11.413	0.708	0.708	0.000	0.000	0.000	0.000
129	A	130	GLY	0	0.069	0.048	15.326	-0.032	-0.032	0.000	0.000	0.000	0.000
130	A	131	ALA	0	-0.047	-0.039	16.272	0.014	0.014	0.000	0.000	0.000	0.000
131	A	132	CYS	0	-0.068	-0.036	5.634	-0.151	-0.151	0.000	0.000	0.000	0.000
132	A	133	ASP	-1	-0.792	-0.886	12.749	-0.510	-0.510	0.000	0.000	0.000	0.000
133	A	134	GLN	0	-0.030	-0.020	14.370	0.058	0.058	0.000	0.000	0.000	0.000
134	A	135	LEU	0	0.021	0.027	10.750	0.042	0.042	0.000	0.000	0.000	0.000
135	A	136	ARG	1	0.848	0.910	9.441	0.609	0.609	0.000	0.000	0.000	0.000
136	A	137	ARG	1	0.859	0.935	14.129	0.118	0.118	0.000	0.000	0.000	0.000
137	A	138	TRP	0	-0.039	-0.004	15.944	0.032	0.032	0.000	0.000	0.000	0.000
138	A	139	THR	0	0.003	-0.008	14.391	0.025	0.025	0.000	0.000	0.000	0.000
139	A	140	TYR	0	0.029	0.007	17.061	0.018	0.018	0.000	0.000	0.000	0.000
140	A	141	ALA	0	0.040	0.016	20.760	0.003	0.003	0.000	0.000	0.000	0.000
141	A	142	GLY	0	0.024	0.024	23.080	0.003	0.003	0.000	0.000	0.000	0.000
142	A	143	GLY	0	0.015	0.012	25.949	0.000	0.000	0.000	0.000	0.000	0.000
143	A	144	LYS	1	0.941	0.990	21.613	-0.055	-0.055	0.000	0.000	0.000	0.000
144	A	145	GLN	0	0.042	0.013	17.373	-0.015	-0.015	0.000	0.000	0.000	0.000
145	A	146	TRP	0	0.019	-0.010	17.505	0.015	0.015	0.000	0.000	0.000	0.000
146	A	147	LYS	1	0.951	0.952	12.780	-0.064	-0.064	0.000	0.000	0.000	0.000
147	A	148	GLY	0	0.074	0.029	12.493	0.001	0.001	0.000	0.000	0.000	0.000
148	A	149	LEU	0	0.037	0.028	12.053	0.020	0.020	0.000	0.000	0.000	0.000
149	A	150	MET	0	-0.038	0.001	12.193	-0.010	-0.010	0.000	0.000	0.000	0.000
150	A	151	THR	0	-0.023	-0.010	7.916	-0.053	-0.053	0.000	0.000	0.000	0.000
151	A	152	ARG	1	0.839	0.932	7.491	-0.389	-0.389	0.000	0.000	0.000	0.000
152	A	153	ARG	1	0.774	0.859	8.393	-0.067	-0.067	0.000	0.000	0.000	0.000
153	A	154	GLU	-1	-0.809	-0.890	6.468	-0.777	-0.777	0.000	0.000	0.000	0.000
154	A	155	ILE	0	0.026	0.024	2.819	-1.455	-0.559	0.218	-0.209	-0.905	-0.001
155	A	156	GLU	-1	-0.755	-0.881	4.865	0.602	0.712	-0.001	-0.006	-0.102	0.000
156	A	157	ARG	1	0.852	0.910	7.804	0.963	0.963	0.000	0.000	0.000	0.000
157	A	158	GLU	-1	-0.871	-0.932	1.880	-25.540	-24.774	13.139	-7.267	-6.639	-0.084
158	A	159	ILE	0	-0.039	-0.019	3.246	-0.578	-0.111	0.953	-0.255	-1.165	0.000
159	A	161	LEU	0	0.000	-0.003	7.630	0.064	0.064	0.000	0.000	0.000	0.000
160	A	162	TRP	0	-0.008	-0.001	2.068	0.467	-2.477	7.083	-0.883	-3.255	-0.012
161	A	163	GLY	0	-0.039	-0.023	6.078	0.021	0.021	0.000	0.000	0.000	0.000
162	A	164	GLN	0	0.036	0.002	9.586	-0.037	-0.037	0.000	0.000	0.000	0.000
163	A	165	GLN	0	0.024	0.028	7.103	0.146	0.146	0.000	0.000	0.000	0.000

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