FMO DATABASE

FMODB ID: 6N58Z

Calculation Name: 3BDB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BDB

Chain ID: A

ChEMBL ID:

UniProt ID: Q8UWK4

Base Structure: X-ray

Registration Date: 2023-06-26

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	125
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1027778.282508
FMO2-HF: Nuclear repulsion	977134.469955
FMO2-HF: Total energy	-50643.812553
FMO2-MP2: Total energy	-50788.8439

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:3:ILE)

Summations of interaction energy for fragment #1(A:3:ILE)

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.
-3.544	-1.28	-0.021	-1.023	-1.22	0.004

Interaction energy analysis for fragmet #1(A:3:ILE)

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 : -0.010

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

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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	5	GLU	-1	-0.913	-0.958	3.802	-4.325	-2.061	-0.021	-1.023	-1.220	0.004
4	A	6	LEU	0	-0.049	-0.012	6.231	0.547	0.547	0.000	0.000	0.000	0.000
5	A	7	HIS	0	0.008	0.005	8.708	0.148	0.148	0.000	0.000	0.000	0.000
6	A	8	VAL	0	0.019	0.001	12.030	0.103	0.103	0.000	0.000	0.000	0.000
7	A	9	LYS	1	0.880	0.949	14.379	0.476	0.476	0.000	0.000	0.000	0.000
8	A	10	THR	0	-0.009	0.001	17.918	0.006	0.006	0.000	0.000	0.000	0.000
9	A	11	VAL	0	-0.038	-0.024	20.867	0.010	0.010	0.000	0.000	0.000	0.000
10	A	12	LYS	1	0.887	0.966	24.280	0.210	0.210	0.000	0.000	0.000	0.000
11	A	13	ARG	1	0.848	0.933	27.307	0.188	0.188	0.000	0.000	0.000	0.000
12	A	14	GLY	0	-0.002	-0.011	29.701	0.007	0.007	0.000	0.000	0.000	0.000
13	A	15	GLU	-1	-0.815	-0.883	26.404	-0.215	-0.215	0.000	0.000	0.000	0.000
14	A	16	ASN	0	0.006	-0.009	27.062	0.019	0.019	0.000	0.000	0.000	0.000
15	A	17	VAL	0	-0.045	-0.009	21.866	-0.011	-0.011	0.000	0.000	0.000	0.000
16	A	18	THR	0	0.034	0.011	21.317	0.016	0.016	0.000	0.000	0.000	0.000
17	A	19	MET	0	-0.040	-0.006	16.415	-0.049	-0.049	0.000	0.000	0.000	0.000
18	A	20	GLU	-1	-0.867	-0.917	16.875	-0.270	-0.270	0.000	0.000	0.000	0.000
19	A	21	CYS	0	-0.097	-0.015	11.664	0.053	0.053	0.000	0.000	0.000	0.000
20	A	22	SER	0	-0.027	-0.029	14.369	0.017	0.017	0.000	0.000	0.000	0.000
21	A	23	MET	0	0.061	0.041	15.846	0.035	0.035	0.000	0.000	0.000	0.000
22	A	24	SER	0	0.009	0.005	15.859	0.033	0.033	0.000	0.000	0.000	0.000
23	A	25	LYS	1	0.878	0.939	10.899	-0.061	-0.061	0.000	0.000	0.000	0.000
24	A	26	VAL	0	-0.004	0.012	14.448	0.052	0.052	0.000	0.000	0.000	0.000
25	A	27	THR	0	-0.010	-0.009	16.146	0.015	0.015	0.000	0.000	0.000	0.000
26	A	28	ASN	0	0.011	0.015	18.489	-0.048	-0.048	0.000	0.000	0.000	0.000
27	A	29	LYS	1	0.937	0.976	20.615	-0.024	-0.024	0.000	0.000	0.000	0.000
28	A	30	ASN	0	-0.092	-0.044	21.638	-0.029	-0.029	0.000	0.000	0.000	0.000
29	A	31	ASN	0	-0.096	-0.063	18.776	-0.028	-0.028	0.000	0.000	0.000	0.000
30	A	32	LEU	0	0.003	0.021	15.894	0.014	0.014	0.000	0.000	0.000	0.000
31	A	33	ALA	0	-0.027	-0.030	16.262	-0.009	-0.009	0.000	0.000	0.000	0.000
32	A	34	TRP	0	-0.005	0.001	14.446	-0.035	-0.035	0.000	0.000	0.000	0.000
33	A	35	TYR	0	-0.008	-0.035	14.745	0.048	0.048	0.000	0.000	0.000	0.000
34	A	36	ARG	1	0.910	0.985	15.588	0.158	0.158	0.000	0.000	0.000	0.000
35	A	37	GLN	0	-0.004	-0.014	12.659	-0.006	-0.006	0.000	0.000	0.000	0.000
36	A	38	SER	0	0.033	0.021	16.458	-0.030	-0.030	0.000	0.000	0.000	0.000
37	A	39	PHE	0	0.049	0.008	17.021	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	40	GLY	0	0.042	0.021	17.416	0.033	0.033	0.000	0.000	0.000	0.000
39	A	41	LYS	1	0.845	0.934	17.713	0.216	0.216	0.000	0.000	0.000	0.000
40	A	42	VAL	0	0.037	0.031	16.013	-0.024	-0.024	0.000	0.000	0.000	0.000
41	A	43	PRO	0	0.005	-0.010	12.814	0.011	0.011	0.000	0.000	0.000	0.000
42	A	44	GLN	0	-0.021	0.000	15.852	0.046	0.046	0.000	0.000	0.000	0.000
43	A	45	TYR	0	0.019	-0.005	18.164	-0.016	-0.016	0.000	0.000	0.000	0.000
44	A	46	PHE	0	-0.040	-0.017	19.324	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	47	VAL	0	0.012	0.010	20.645	0.008	0.008	0.000	0.000	0.000	0.000
46	A	48	ARG	1	0.951	1.005	20.590	-0.006	-0.006	0.000	0.000	0.000	0.000
47	A	49	TYR	0	0.055	0.030	21.598	-0.008	-0.008	0.000	0.000	0.000	0.000
48	A	50	TYR	0	-0.103	-0.049	23.329	0.011	0.011	0.000	0.000	0.000	0.000
49	A	51	SER	0	0.039	0.013	27.023	-0.006	-0.006	0.000	0.000	0.000	0.000
50	A	52	SER	0	-0.005	-0.002	29.477	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	53	ASN	0	0.010	0.007	30.851	0.003	0.003	0.000	0.000	0.000	0.000
52	A	54	SER	0	0.002	0.006	29.856	0.000	0.000	0.000	0.000	0.000	0.000
53	A	55	GLY	0	0.046	0.037	27.483	-0.006	-0.006	0.000	0.000	0.000	0.000
54	A	56	TYR	0	0.009	-0.022	24.751	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	57	LYS	1	0.860	0.925	25.651	0.029	0.029	0.000	0.000	0.000	0.000
56	A	58	PHE	0	0.027	0.005	24.188	0.003	0.003	0.000	0.000	0.000	0.000
57	A	59	ALA	0	-0.018	-0.002	23.727	0.013	0.013	0.000	0.000	0.000	0.000
58	A	60	GLU	-1	-0.850	-0.937	25.837	-0.028	-0.028	0.000	0.000	0.000	0.000
59	A	61	GLY	0	-0.023	0.011	27.826	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	62	PHE	0	-0.087	-0.050	26.409	-0.011	-0.011	0.000	0.000	0.000	0.000
61	A	63	LYS	1	0.987	0.985	28.915	0.080	0.080	0.000	0.000	0.000	0.000
62	A	64	ASP	-1	-0.794	-0.906	28.552	-0.134	-0.134	0.000	0.000	0.000	0.000
63	A	65	SER	0	0.030	0.022	29.822	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	66	ARG	1	0.744	0.842	27.166	0.161	0.161	0.000	0.000	0.000	0.000
65	A	67	PHE	0	-0.009	0.018	22.524	-0.011	-0.011	0.000	0.000	0.000	0.000
66	A	68	SER	0	-0.012	-0.011	25.946	0.013	0.013	0.000	0.000	0.000	0.000
67	A	69	MET	0	-0.004	-0.016	20.453	-0.011	-0.011	0.000	0.000	0.000	0.000
68	A	70	THR	0	-0.025	0.006	24.539	0.020	0.020	0.000	0.000	0.000	0.000
69	A	71	VAL	0	-0.010	-0.002	22.962	-0.011	-0.011	0.000	0.000	0.000	0.000
70	A	72	ASN	0	0.023	0.006	23.902	0.008	0.008	0.000	0.000	0.000	0.000
71	A	73	ASP	-1	-0.826	-0.923	24.048	0.005	0.005	0.000	0.000	0.000	0.000
72	A	74	GLN	0	-0.092	-0.032	21.296	0.020	0.020	0.000	0.000	0.000	0.000
73	A	75	LYS	1	0.768	0.841	19.731	0.195	0.195	0.000	0.000	0.000	0.000
74	A	76	PHE	0	0.054	-0.003	17.798	0.034	0.034	0.000	0.000	0.000	0.000
75	A	77	ASP	-1	-0.739	-0.863	19.039	-0.232	-0.232	0.000	0.000	0.000	0.000
76	A	78	LEU	0	-0.002	0.018	18.829	0.026	0.026	0.000	0.000	0.000	0.000
77	A	79	ASN	0	-0.033	-0.029	21.715	-0.003	-0.003	0.000	0.000	0.000	0.000
78	A	80	ILE	0	-0.004	-0.010	22.101	0.010	0.010	0.000	0.000	0.000	0.000
79	A	81	ILE	0	0.012	0.003	26.066	-0.007	-0.007	0.000	0.000	0.000	0.000
80	A	82	GLY	0	0.016	0.004	28.903	0.008	0.008	0.000	0.000	0.000	0.000
81	A	83	ALA	0	-0.142	-0.032	26.650	0.008	0.008	0.000	0.000	0.000	0.000
82	A	84	ARG	1	0.838	0.876	27.138	0.151	0.151	0.000	0.000	0.000	0.000
83	A	85	GLU	-1	-0.779	-0.912	25.465	-0.175	-0.175	0.000	0.000	0.000	0.000
84	A	86	ASP	-1	-0.808	-0.856	24.223	-0.192	-0.192	0.000	0.000	0.000	0.000
85	A	87	ASP	-1	-0.780	-0.867	23.020	-0.197	-0.197	0.000	0.000	0.000	0.000
86	A	88	GLY	0	0.007	0.025	20.946	-0.027	-0.027	0.000	0.000	0.000	0.000
87	A	89	GLY	0	-0.102	-0.055	17.993	0.029	0.029	0.000	0.000	0.000	0.000
88	A	90	GLU	-1	-0.867	-0.933	11.286	-0.858	-0.858	0.000	0.000	0.000	0.000
89	A	91	TYR	0	-0.071	-0.070	13.540	0.101	0.101	0.000	0.000	0.000	0.000
90	A	92	PHE	0	0.065	0.063	9.234	-0.077	-0.077	0.000	0.000	0.000	0.000
91	A	94	GLY	0	0.036	-0.005	11.363	-0.022	-0.022	0.000	0.000	0.000	0.000
92	A	95	GLU	-1	-0.782	-0.892	12.607	0.164	0.164	0.000	0.000	0.000	0.000
93	A	96	VAL	0	-0.021	-0.024	14.185	0.065	0.065	0.000	0.000	0.000	0.000
94	A	97	GLU	-1	-0.886	-0.935	15.044	0.434	0.434	0.000	0.000	0.000	0.000
95	A	98	GLY	0	0.076	0.042	15.445	0.061	0.061	0.000	0.000	0.000	0.000
96	A	99	ILE	0	-0.041	-0.030	17.051	-0.042	-0.042	0.000	0.000	0.000	0.000
97	A	100	ILE	0	0.041	0.025	11.420	0.012	0.012	0.000	0.000	0.000	0.000
98	A	101	ILE	0	-0.012	0.011	11.642	-0.024	-0.024	0.000	0.000	0.000	0.000
99	A	102	LYS	1	0.817	0.907	8.705	-0.505	-0.505	0.000	0.000	0.000	0.000
100	A	103	PHE	0	0.004	-0.027	7.549	-0.027	-0.027	0.000	0.000	0.000	0.000
101	A	104	THR	0	-0.005	0.018	7.240	-0.054	-0.054	0.000	0.000	0.000	0.000
102	A	105	SER	0	-0.007	-0.009	8.725	-0.142	-0.142	0.000	0.000	0.000	0.000
103	A	106	GLY	0	0.064	0.023	9.580	0.154	0.154	0.000	0.000	0.000	0.000
104	A	107	THR	0	-0.029	-0.048	10.746	-0.128	-0.128	0.000	0.000	0.000	0.000
105	A	108	ARG	1	0.878	0.950	11.297	0.892	0.892	0.000	0.000	0.000	0.000
106	A	109	LEU	0	-0.005	0.002	14.076	-0.004	-0.004	0.000	0.000	0.000	0.000
107	A	110	GLN	0	-0.036	-0.007	16.883	0.004	0.004	0.000	0.000	0.000	0.000
108	A	111	PHE	0	0.030	-0.044	19.756	-0.004	-0.004	0.000	0.000	0.000	0.000
109	A	112	GLU	-1	-0.748	-0.894	23.415	-0.225	-0.225	0.000	0.000	0.000	0.000
110	A	113	GLY	0	-0.003	0.019	24.780	-0.003	-0.003	0.000	0.000	0.000	0.000
111	A	114	SER	0	-0.010	-0.020	25.959	0.010	0.010	0.000	0.000	0.000	0.000
112	A	115	ASN	0	-0.034	-0.034	29.594	0.009	0.009	0.000	0.000	0.000	0.000
113	A	116	GLU	-1	-0.937	-0.960	32.411	-0.172	-0.172	0.000	0.000	0.000	0.000
114	A	117	GLY	0	0.028	0.028	35.578	0.006	0.006	0.000	0.000	0.000	0.000
115	A	118	SER	0	-0.054	-0.018	39.382	0.002	0.002	0.000	0.000	0.000	0.000
116	A	119	LYS	1	0.951	0.948	41.110	0.097	0.097	0.000	0.000	0.000	0.000
117	A	120	SER	0	0.007	0.010	39.580	0.004	0.004	0.000	0.000	0.000	0.000
118	A	121	SER	0	-0.027	-0.018	37.370	-0.005	-0.005	0.000	0.000	0.000	0.000
119	A	122	ASP	-1	-0.887	-0.934	36.171	-0.122	-0.122	0.000	0.000	0.000	0.000
120	A	123	GLY	0	-0.028	-0.017	36.426	0.006	0.006	0.000	0.000	0.000	0.000
121	A	124	GLU	-1	-0.952	-0.972	33.698	-0.159	-0.159	0.000	0.000	0.000	0.000
122	A	125	GLY	0	-0.037	0.021	33.312	-0.010	-0.010	0.000	0.000	0.000	0.000
123	A	126	SER	0	0.104	-0.004	30.646	-0.003	-0.003	0.000	0.000	0.000	0.000
124	A	127	SER	0	-0.129	-0.038	26.182	-0.020	-0.020	0.000	0.000	0.000	0.000
125	A	128	CYS	0	-0.006	0.003	25.833	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:3:ILE)