FMO DATABASE

FMODB ID: 2JG8R

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1028136.939636
FMO2-HF: Nuclear repulsion	977495.840645
FMO2-HF: Total energy	-50641.098991
FMO2-MP2: Total energy	-50786.506985

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.
-4.533	-2.926	-0.018	-0.63	-0.958	0.002

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 : -0.048 / q_NPA : -0.040

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	-0.950	-0.960	3.802	-4.926	-3.319	-0.018	-0.630	-0.958	0.002
4	A	6	LEU	0	-0.024	-0.009	6.270	0.713	0.713	0.000	0.000	0.000	0.000
5	A	7	HIS	0	0.007	0.007	8.684	0.041	0.041	0.000	0.000	0.000	0.000
6	A	8	VAL	0	0.007	-0.006	12.027	0.046	0.046	0.000	0.000	0.000	0.000
7	A	9	LYS	1	0.900	0.960	14.384	0.213	0.213	0.000	0.000	0.000	0.000
8	A	10	THR	0	-0.014	-0.006	17.912	-0.006	-0.006	0.000	0.000	0.000	0.000
9	A	11	VAL	0	-0.034	-0.010	20.862	0.012	0.012	0.000	0.000	0.000	0.000
10	A	12	LYS	1	0.950	1.038	24.265	0.118	0.118	0.000	0.000	0.000	0.000
11	A	13	ARG	1	0.884	0.922	27.279	0.149	0.149	0.000	0.000	0.000	0.000
12	A	14	GLY	0	-0.011	-0.017	29.667	0.006	0.006	0.000	0.000	0.000	0.000
13	A	15	GLU	-1	-0.870	-0.936	25.608	-0.124	-0.124	0.000	0.000	0.000	0.000
14	A	16	ASN	0	-0.030	-0.031	27.015	0.019	0.019	0.000	0.000	0.000	0.000
15	A	17	VAL	0	-0.003	0.015	21.046	-0.004	-0.004	0.000	0.000	0.000	0.000
16	A	18	THR	0	0.009	-0.001	21.189	0.003	0.003	0.000	0.000	0.000	0.000
17	A	19	MET	0	-0.064	-0.018	16.282	-0.025	-0.025	0.000	0.000	0.000	0.000
18	A	20	GLU	-1	-0.931	-0.960	16.782	0.052	0.052	0.000	0.000	0.000	0.000
19	A	21	CYS	0	-0.114	-0.019	11.926	0.087	0.087	0.000	0.000	0.000	0.000
20	A	22	SER	0	-0.049	-0.043	14.422	0.005	0.005	0.000	0.000	0.000	0.000
21	A	23	MET	0	0.049	0.035	15.899	0.040	0.040	0.000	0.000	0.000	0.000
22	A	24	SER	0	0.028	0.005	15.785	0.023	0.023	0.000	0.000	0.000	0.000
23	A	25	LYS	1	0.890	0.935	11.078	-0.935	-0.935	0.000	0.000	0.000	0.000
24	A	26	VAL	0	-0.029	0.022	14.929	0.055	0.055	0.000	0.000	0.000	0.000
25	A	27	THR	0	-0.019	0.010	15.995	-0.015	-0.015	0.000	0.000	0.000	0.000
26	A	28	ASN	0	0.007	0.001	18.523	-0.059	-0.059	0.000	0.000	0.000	0.000
27	A	29	LYS	1	0.980	0.990	20.637	-0.224	-0.224	0.000	0.000	0.000	0.000
28	A	30	ASN	0	-0.102	-0.041	21.662	-0.032	-0.032	0.000	0.000	0.000	0.000
29	A	31	ASN	0	-0.082	-0.052	18.798	-0.043	-0.043	0.000	0.000	0.000	0.000
30	A	32	LEU	0	-0.013	0.015	15.670	0.017	0.017	0.000	0.000	0.000	0.000
31	A	33	ALA	0	-0.045	-0.033	16.539	-0.033	-0.033	0.000	0.000	0.000	0.000
32	A	34	TRP	0	0.006	0.009	14.286	0.000	0.000	0.000	0.000	0.000	0.000
33	A	35	TYR	0	-0.016	-0.011	15.175	0.015	0.015	0.000	0.000	0.000	0.000
34	A	36	ARG	1	0.951	1.010	15.689	0.095	0.095	0.000	0.000	0.000	0.000
35	A	37	GLN	0	-0.044	-0.031	13.036	-0.021	-0.021	0.000	0.000	0.000	0.000
36	A	38	SER	0	0.030	0.018	16.574	-0.027	-0.027	0.000	0.000	0.000	0.000
37	A	39	PHE	0	0.049	0.002	17.267	-0.013	-0.013	0.000	0.000	0.000	0.000
38	A	40	GLY	0	0.027	0.023	17.362	0.030	0.030	0.000	0.000	0.000	0.000
39	A	41	LYS	1	0.890	0.957	17.744	0.192	0.192	0.000	0.000	0.000	0.000
40	A	42	VAL	0	0.012	0.028	16.304	-0.030	-0.030	0.000	0.000	0.000	0.000
41	A	43	PRO	0	0.029	-0.008	12.974	0.016	0.016	0.000	0.000	0.000	0.000
42	A	44	GLN	0	-0.002	0.003	15.998	0.037	0.037	0.000	0.000	0.000	0.000
43	A	45	TYR	0	0.005	-0.036	18.379	-0.004	-0.004	0.000	0.000	0.000	0.000
44	A	46	PHE	0	-0.053	-0.024	19.574	-0.010	-0.010	0.000	0.000	0.000	0.000
45	A	47	VAL	0	0.025	0.007	20.884	0.002	0.002	0.000	0.000	0.000	0.000
46	A	48	ARG	1	0.935	1.004	20.838	-0.072	-0.072	0.000	0.000	0.000	0.000
47	A	49	TYR	0	0.052	0.027	21.860	-0.010	-0.010	0.000	0.000	0.000	0.000
48	A	50	TYR	0	-0.115	-0.049	23.587	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	51	SER	0	0.036	-0.002	27.273	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	52	SER	0	-0.006	-0.001	29.552	-0.010	-0.010	0.000	0.000	0.000	0.000
51	A	53	ASN	0	0.027	0.023	30.885	0.011	0.011	0.000	0.000	0.000	0.000
52	A	54	SER	0	0.006	0.008	29.936	0.006	0.006	0.000	0.000	0.000	0.000
53	A	55	GLY	0	0.027	0.030	27.516	0.004	0.004	0.000	0.000	0.000	0.000
54	A	56	TYR	0	0.013	-0.023	25.098	0.006	0.006	0.000	0.000	0.000	0.000
55	A	57	LYS	1	0.938	0.974	25.902	-0.048	-0.048	0.000	0.000	0.000	0.000
56	A	58	PHE	0	0.047	0.014	23.986	0.007	0.007	0.000	0.000	0.000	0.000
57	A	59	ALA	0	-0.009	-0.006	24.041	0.007	0.007	0.000	0.000	0.000	0.000
58	A	60	GLU	-1	-0.924	-0.987	26.042	0.006	0.006	0.000	0.000	0.000	0.000
59	A	61	GLY	0	-0.035	0.015	28.074	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	62	PHE	0	-0.089	-0.052	25.867	-0.011	-0.011	0.000	0.000	0.000	0.000
61	A	63	LYS	1	0.971	0.982	29.129	0.042	0.042	0.000	0.000	0.000	0.000
62	A	64	ASP	-1	-0.849	-0.951	28.462	-0.070	-0.070	0.000	0.000	0.000	0.000
63	A	65	SER	0	0.045	0.026	29.708	0.002	0.002	0.000	0.000	0.000	0.000
64	A	66	ARG	1	0.770	0.881	27.097	0.086	0.086	0.000	0.000	0.000	0.000
65	A	67	PHE	0	0.002	0.036	22.572	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	68	SER	0	-0.022	-0.015	25.828	0.009	0.009	0.000	0.000	0.000	0.000
67	A	69	MET	0	0.015	-0.024	21.038	-0.009	-0.009	0.000	0.000	0.000	0.000
68	A	70	THR	0	-0.053	0.004	24.537	0.004	0.004	0.000	0.000	0.000	0.000
69	A	71	VAL	0	-0.017	-0.013	22.671	0.010	0.010	0.000	0.000	0.000	0.000
70	A	72	ASN	0	0.007	-0.012	23.956	0.006	0.006	0.000	0.000	0.000	0.000
71	A	73	ASP	-1	-0.870	-0.928	24.103	0.171	0.171	0.000	0.000	0.000	0.000
72	A	74	GLN	0	-0.081	-0.037	21.350	0.032	0.032	0.000	0.000	0.000	0.000
73	A	75	LYS	1	0.928	0.952	19.798	-0.075	-0.075	0.000	0.000	0.000	0.000
74	A	76	PHE	0	0.057	0.000	17.797	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	77	ASP	-1	-0.773	-0.891	19.075	0.073	0.073	0.000	0.000	0.000	0.000
76	A	78	LEU	0	-0.002	0.009	19.092	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	79	ASN	0	-0.019	-0.023	21.658	0.011	0.011	0.000	0.000	0.000	0.000
78	A	80	ILE	0	-0.002	-0.005	22.060	0.002	0.002	0.000	0.000	0.000	0.000
79	A	81	ILE	0	0.025	-0.006	25.985	-0.006	-0.006	0.000	0.000	0.000	0.000
80	A	82	GLY	0	0.014	0.001	28.763	0.001	0.001	0.000	0.000	0.000	0.000
81	A	83	ALA	0	-0.125	-0.022	26.550	0.001	0.001	0.000	0.000	0.000	0.000
82	A	84	ARG	1	0.931	0.952	27.111	0.089	0.089	0.000	0.000	0.000	0.000
83	A	85	GLU	-1	-0.789	-0.909	25.431	-0.136	-0.136	0.000	0.000	0.000	0.000
84	A	86	ASP	-1	-0.879	-0.888	24.153	-0.138	-0.138	0.000	0.000	0.000	0.000
85	A	87	ASP	-1	-0.798	-0.910	23.129	-0.113	-0.113	0.000	0.000	0.000	0.000
86	A	88	GLY	0	-0.002	0.031	20.860	-0.014	-0.014	0.000	0.000	0.000	0.000
87	A	89	GLY	0	-0.097	-0.054	17.906	0.016	0.016	0.000	0.000	0.000	0.000
88	A	90	GLU	-1	-0.923	-0.970	11.498	-0.753	-0.753	0.000	0.000	0.000	0.000
89	A	91	TYR	0	-0.077	-0.078	13.433	0.085	0.085	0.000	0.000	0.000	0.000
90	A	92	PHE	0	0.061	0.059	9.737	-0.018	-0.018	0.000	0.000	0.000	0.000
91	A	94	GLY	0	0.049	0.006	11.643	0.057	0.057	0.000	0.000	0.000	0.000
92	A	95	GLU	-1	-0.716	-0.885	12.834	0.370	0.370	0.000	0.000	0.000	0.000
93	A	96	VAL	0	-0.025	-0.020	14.324	0.055	0.055	0.000	0.000	0.000	0.000
94	A	97	GLU	-1	-0.966	-0.989	15.146	0.497	0.497	0.000	0.000	0.000	0.000
95	A	98	GLY	0	0.056	0.031	15.473	0.048	0.048	0.000	0.000	0.000	0.000
96	A	99	ILE	0	-0.023	-0.018	17.018	-0.037	-0.037	0.000	0.000	0.000	0.000
97	A	100	ILE	0	0.044	0.037	11.412	-0.010	-0.010	0.000	0.000	0.000	0.000
98	A	101	ILE	0	-0.010	-0.005	11.588	0.009	0.009	0.000	0.000	0.000	0.000
99	A	102	LYS	1	0.876	0.951	8.801	-0.615	-0.615	0.000	0.000	0.000	0.000
100	A	103	PHE	0	-0.002	-0.029	7.694	0.053	0.053	0.000	0.000	0.000	0.000
101	A	104	THR	0	-0.026	0.009	7.515	0.072	0.072	0.000	0.000	0.000	0.000
102	A	105	SER	0	0.001	-0.004	8.775	0.073	0.073	0.000	0.000	0.000	0.000
103	A	106	GLY	0	0.070	0.023	9.557	0.015	0.015	0.000	0.000	0.000	0.000
104	A	107	THR	0	-0.007	-0.033	10.684	-0.063	-0.063	0.000	0.000	0.000	0.000
105	A	108	ARG	1	0.946	0.999	11.752	0.772	0.772	0.000	0.000	0.000	0.000
106	A	109	LEU	0	0.012	0.009	14.026	0.013	0.013	0.000	0.000	0.000	0.000
107	A	110	GLN	0	-0.051	-0.010	17.229	-0.013	-0.013	0.000	0.000	0.000	0.000
108	A	111	PHE	0	0.010	-0.058	19.722	0.004	0.004	0.000	0.000	0.000	0.000
109	A	112	GLU	-1	-0.756	-0.921	23.384	-0.164	-0.164	0.000	0.000	0.000	0.000
110	A	113	GLY	0	-0.022	0.017	24.824	0.003	0.003	0.000	0.000	0.000	0.000
111	A	114	SER	0	-0.030	-0.043	25.927	0.005	0.005	0.000	0.000	0.000	0.000
112	A	115	ASN	0	0.007	-0.005	29.580	0.004	0.004	0.000	0.000	0.000	0.000
113	A	116	GLU	-1	-0.998	-0.984	32.902	-0.110	-0.110	0.000	0.000	0.000	0.000
114	A	117	GLY	0	0.048	0.035	35.571	0.005	0.005	0.000	0.000	0.000	0.000
115	A	118	SER	0	-0.060	-0.022	39.378	0.000	0.000	0.000	0.000	0.000	0.000
116	A	119	LYS	1	0.967	0.957	41.107	0.077	0.077	0.000	0.000	0.000	0.000
117	A	120	SER	0	0.014	0.008	40.574	0.001	0.001	0.000	0.000	0.000	0.000
118	A	121	SER	0	-0.032	-0.018	37.321	-0.005	-0.005	0.000	0.000	0.000	0.000
119	A	122	ASP	-1	-0.910	-0.943	36.042	-0.120	-0.120	0.000	0.000	0.000	0.000
120	A	123	GLY	0	-0.018	-0.010	36.134	0.007	0.007	0.000	0.000	0.000	0.000
121	A	124	GLU	-1	-0.946	-0.966	33.024	-0.156	-0.156	0.000	0.000	0.000	0.000
122	A	125	GLY	0	-0.043	0.008	32.873	-0.010	-0.010	0.000	0.000	0.000	0.000
123	A	126	SER	0	0.104	0.013	29.883	-0.003	-0.003	0.000	0.000	0.000	0.000
124	A	127	SER	0	-0.125	-0.044	26.017	-0.013	-0.013	0.000	0.000	0.000	0.000
125	A	128	CYS	0	-0.005	0.000	25.373	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)