FMO DATABASE

FMODB ID: Z691N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1028779.990131
FMO2-HF: Nuclear repulsion	978134.1852
FMO2-HF: Total energy	-50645.804931
FMO2-MP2: Total energy	-50790.70602

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.
-3.427	-0.807	0.015	-1.233	-1.402	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 : 0.017 / q_NPA : 0.007

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	-0.902	-0.947	3.455	-4.309	-1.689	0.015	-1.233	-1.402	0.002
4	A	6	LEU	0	-0.054	-0.008	5.452	0.548	0.548	0.000	0.000	0.000	0.000
5	A	7	HIS	0	0.010	0.004	7.888	0.162	0.162	0.000	0.000	0.000	0.000
6	A	8	VAL	0	0.017	0.010	11.257	0.103	0.103	0.000	0.000	0.000	0.000
7	A	9	LYS	1	0.874	0.943	13.905	0.439	0.439	0.000	0.000	0.000	0.000
8	A	10	THR	0	0.023	0.003	17.435	0.012	0.012	0.000	0.000	0.000	0.000
9	A	11	VAL	0	-0.041	-0.007	20.474	0.009	0.009	0.000	0.000	0.000	0.000
10	A	12	LYS	1	0.875	0.909	23.942	0.191	0.191	0.000	0.000	0.000	0.000
11	A	13	ARG	1	0.881	0.923	27.070	0.160	0.160	0.000	0.000	0.000	0.000
12	A	14	GLY	0	-0.042	-0.012	29.583	0.003	0.003	0.000	0.000	0.000	0.000
13	A	15	GLU	-1	-0.786	-0.867	25.910	-0.197	-0.197	0.000	0.000	0.000	0.000
14	A	16	ASN	0	-0.060	-0.024	27.086	0.017	0.017	0.000	0.000	0.000	0.000
15	A	17	VAL	0	-0.004	0.004	21.518	-0.014	-0.014	0.000	0.000	0.000	0.000
16	A	18	THR	0	0.035	0.013	20.588	0.023	0.023	0.000	0.000	0.000	0.000
17	A	19	MET	0	-0.040	-0.003	16.213	-0.053	-0.053	0.000	0.000	0.000	0.000
18	A	20	GLU	-1	-0.867	-0.916	16.176	-0.272	-0.272	0.000	0.000	0.000	0.000
19	A	21	CYS	0	-0.050	-0.012	11.675	0.046	0.046	0.000	0.000	0.000	0.000
20	A	22	SER	0	-0.046	-0.017	14.273	0.013	0.013	0.000	0.000	0.000	0.000
21	A	23	MET	0	0.017	0.025	15.724	0.039	0.039	0.000	0.000	0.000	0.000
22	A	24	SER	0	0.017	0.006	16.685	0.037	0.037	0.000	0.000	0.000	0.000
23	A	25	LYS	1	0.906	0.939	11.236	0.049	0.049	0.000	0.000	0.000	0.000
24	A	26	VAL	0	0.000	0.016	14.632	0.058	0.058	0.000	0.000	0.000	0.000
25	A	27	THR	0	-0.027	-0.012	16.126	0.003	0.003	0.000	0.000	0.000	0.000
26	A	28	ASN	0	-0.044	-0.013	18.621	-0.048	-0.048	0.000	0.000	0.000	0.000
27	A	29	LYS	1	0.940	0.944	20.262	-0.020	-0.020	0.000	0.000	0.000	0.000
28	A	30	ASN	0	-0.073	-0.041	21.366	-0.024	-0.024	0.000	0.000	0.000	0.000
29	A	31	ASN	0	-0.045	-0.026	18.777	-0.028	-0.028	0.000	0.000	0.000	0.000
30	A	32	LEU	0	-0.017	0.011	15.661	0.016	0.016	0.000	0.000	0.000	0.000
31	A	33	ALA	0	-0.022	-0.026	16.451	-0.016	-0.016	0.000	0.000	0.000	0.000
32	A	34	TRP	0	-0.014	-0.010	13.905	-0.017	-0.017	0.000	0.000	0.000	0.000
33	A	35	TYR	0	-0.002	-0.010	13.972	0.034	0.034	0.000	0.000	0.000	0.000
34	A	36	ARG	1	0.831	0.927	15.184	0.114	0.114	0.000	0.000	0.000	0.000
35	A	37	GLN	0	-0.009	-0.020	12.191	0.007	0.007	0.000	0.000	0.000	0.000
36	A	38	SER	0	0.065	0.035	16.007	-0.033	-0.033	0.000	0.000	0.000	0.000
37	A	39	PHE	0	0.036	0.016	16.656	0.012	0.012	0.000	0.000	0.000	0.000
38	A	40	GLY	0	0.032	0.027	17.226	0.028	0.028	0.000	0.000	0.000	0.000
39	A	41	LYS	1	0.844	0.918	17.328	0.164	0.164	0.000	0.000	0.000	0.000
40	A	42	VAL	0	0.059	0.034	15.230	-0.022	-0.022	0.000	0.000	0.000	0.000
41	A	43	PRO	0	0.002	-0.002	12.175	0.005	0.005	0.000	0.000	0.000	0.000
42	A	44	GLN	0	-0.034	-0.003	15.362	0.043	0.043	0.000	0.000	0.000	0.000
43	A	45	TYR	0	0.004	-0.004	18.005	-0.013	-0.013	0.000	0.000	0.000	0.000
44	A	46	PHE	0	-0.039	-0.010	19.207	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	47	VAL	0	0.014	0.000	20.240	0.005	0.005	0.000	0.000	0.000	0.000
46	A	48	ARG	1	0.933	0.977	20.040	-0.025	-0.025	0.000	0.000	0.000	0.000
47	A	49	TYR	0	0.051	0.019	21.253	-0.010	-0.010	0.000	0.000	0.000	0.000
48	A	50	TYR	0	-0.064	-0.037	23.083	0.015	0.015	0.000	0.000	0.000	0.000
49	A	51	SER	0	0.027	0.027	26.769	-0.008	-0.008	0.000	0.000	0.000	0.000
50	A	52	SER	0	-0.032	-0.019	29.064	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	53	ASN	0	0.023	0.001	30.435	0.001	0.001	0.000	0.000	0.000	0.000
52	A	54	SER	0	0.003	0.021	29.506	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	55	GLY	0	0.067	0.033	26.807	-0.008	-0.008	0.000	0.000	0.000	0.000
54	A	56	TYR	0	-0.022	-0.022	24.394	0.003	0.003	0.000	0.000	0.000	0.000
55	A	57	LYS	1	0.852	0.907	25.313	0.007	0.007	0.000	0.000	0.000	0.000
56	A	58	PHE	0	0.024	0.004	23.932	0.003	0.003	0.000	0.000	0.000	0.000
57	A	59	ALA	0	-0.005	0.002	23.402	0.011	0.011	0.000	0.000	0.000	0.000
58	A	60	GLU	-1	-0.819	-0.907	25.484	-0.011	-0.011	0.000	0.000	0.000	0.000
59	A	61	GLY	0	-0.037	0.000	27.452	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	62	PHE	0	-0.044	-0.019	25.851	-0.008	-0.008	0.000	0.000	0.000	0.000
61	A	63	LYS	1	0.966	0.972	28.037	0.062	0.062	0.000	0.000	0.000	0.000
62	A	64	ASP	-1	-0.766	-0.873	28.181	-0.109	-0.109	0.000	0.000	0.000	0.000
63	A	65	SER	0	0.012	-0.003	29.236	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	66	ARG	1	0.717	0.843	26.765	0.138	0.138	0.000	0.000	0.000	0.000
65	A	67	PHE	0	-0.016	-0.005	22.080	-0.010	-0.010	0.000	0.000	0.000	0.000
66	A	68	SER	0	-0.023	-0.013	25.572	0.012	0.012	0.000	0.000	0.000	0.000
67	A	69	MET	0	-0.034	-0.021	20.081	-0.007	-0.007	0.000	0.000	0.000	0.000
68	A	70	THR	0	-0.016	-0.003	23.734	0.015	0.015	0.000	0.000	0.000	0.000
69	A	71	VAL	0	-0.039	-0.015	22.930	-0.009	-0.009	0.000	0.000	0.000	0.000
70	A	72	ASN	0	0.018	-0.002	23.687	0.004	0.004	0.000	0.000	0.000	0.000
71	A	73	ASP	-1	-0.826	-0.916	23.279	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	74	GLN	0	-0.040	-0.014	21.129	0.016	0.016	0.000	0.000	0.000	0.000
73	A	75	LYS	1	0.774	0.870	19.412	0.197	0.197	0.000	0.000	0.000	0.000
74	A	76	PHE	0	0.079	0.016	17.377	0.031	0.031	0.000	0.000	0.000	0.000
75	A	77	ASP	-1	-0.741	-0.857	18.791	-0.222	-0.222	0.000	0.000	0.000	0.000
76	A	78	LEU	0	0.020	0.016	18.067	0.026	0.026	0.000	0.000	0.000	0.000
77	A	79	ASN	0	-0.015	-0.006	20.871	-0.013	-0.013	0.000	0.000	0.000	0.000
78	A	80	ILE	0	0.009	0.006	21.327	0.011	0.011	0.000	0.000	0.000	0.000
79	A	81	ILE	0	-0.003	0.000	25.349	-0.009	-0.009	0.000	0.000	0.000	0.000
80	A	82	GLY	0	0.037	0.011	28.956	0.006	0.006	0.000	0.000	0.000	0.000
81	A	83	ALA	0	-0.051	-0.014	25.482	0.005	0.005	0.000	0.000	0.000	0.000
82	A	84	ARG	1	0.809	0.866	26.839	0.130	0.130	0.000	0.000	0.000	0.000
83	A	85	GLU	-1	-0.817	-0.933	25.253	-0.147	-0.147	0.000	0.000	0.000	0.000
84	A	86	ASP	-1	-0.782	-0.856	23.996	-0.156	-0.156	0.000	0.000	0.000	0.000
85	A	87	ASP	-1	-0.806	-0.866	22.707	-0.169	-0.169	0.000	0.000	0.000	0.000
86	A	88	GLY	0	0.024	0.032	20.160	-0.022	-0.022	0.000	0.000	0.000	0.000
87	A	89	GLY	0	-0.039	-0.037	17.100	0.030	0.030	0.000	0.000	0.000	0.000
88	A	90	GLU	-1	-0.850	-0.911	10.464	-0.747	-0.747	0.000	0.000	0.000	0.000
89	A	91	TYR	0	-0.058	-0.051	13.273	0.090	0.090	0.000	0.000	0.000	0.000
90	A	92	PHE	0	0.030	0.007	8.208	-0.069	-0.069	0.000	0.000	0.000	0.000
91	A	94	GLY	0	0.050	0.005	11.037	0.000	0.000	0.000	0.000	0.000	0.000
92	A	95	GLU	-1	-0.778	-0.872	12.481	0.167	0.167	0.000	0.000	0.000	0.000
93	A	96	VAL	0	-0.008	-0.004	13.770	0.068	0.068	0.000	0.000	0.000	0.000
94	A	97	GLU	-1	-0.834	-0.911	15.282	0.451	0.451	0.000	0.000	0.000	0.000
95	A	98	GLY	0	0.052	0.034	15.438	0.071	0.071	0.000	0.000	0.000	0.000
96	A	99	ILE	0	-0.045	-0.032	16.822	-0.042	-0.042	0.000	0.000	0.000	0.000
97	A	100	ILE	0	0.003	0.003	11.460	0.013	0.013	0.000	0.000	0.000	0.000
98	A	101	ILE	0	-0.020	0.002	11.126	-0.037	-0.037	0.000	0.000	0.000	0.000
99	A	102	LYS	1	0.810	0.901	9.093	-0.499	-0.499	0.000	0.000	0.000	0.000
100	A	103	PHE	0	0.014	-0.020	7.133	-0.090	-0.090	0.000	0.000	0.000	0.000
101	A	104	THR	0	0.001	0.006	7.206	0.045	0.045	0.000	0.000	0.000	0.000
102	A	105	SER	0	-0.049	-0.036	9.102	-0.128	-0.128	0.000	0.000	0.000	0.000
103	A	106	GLY	0	0.076	0.026	9.934	0.096	0.096	0.000	0.000	0.000	0.000
104	A	107	THR	0	-0.098	-0.059	10.681	-0.092	-0.092	0.000	0.000	0.000	0.000
105	A	108	ARG	1	0.876	0.941	11.273	0.775	0.775	0.000	0.000	0.000	0.000
106	A	109	LEU	0	-0.015	0.005	13.821	-0.012	-0.012	0.000	0.000	0.000	0.000
107	A	110	GLN	0	0.003	-0.014	16.586	-0.011	-0.011	0.000	0.000	0.000	0.000
108	A	111	PHE	0	0.023	-0.006	19.354	0.000	0.000	0.000	0.000	0.000	0.000
109	A	112	GLU	-1	-0.752	-0.877	23.143	-0.194	-0.194	0.000	0.000	0.000	0.000
110	A	113	GLY	0	-0.030	0.008	24.675	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	114	SER	0	-0.073	-0.052	25.788	0.010	0.010	0.000	0.000	0.000	0.000
112	A	115	ASN	0	-0.035	-0.059	29.504	0.005	0.005	0.000	0.000	0.000	0.000
113	A	116	GLU	-1	-0.833	-0.887	31.848	-0.153	-0.153	0.000	0.000	0.000	0.000
114	A	117	GLY	0	0.008	0.030	35.157	0.007	0.007	0.000	0.000	0.000	0.000
115	A	118	SER	0	-0.047	-0.028	38.706	0.002	0.002	0.000	0.000	0.000	0.000
116	A	119	LYS	1	0.901	0.937	40.816	0.086	0.086	0.000	0.000	0.000	0.000
117	A	120	SER	0	0.001	0.002	39.707	0.005	0.005	0.000	0.000	0.000	0.000
118	A	121	SER	0	0.002	-0.003	36.738	-0.004	-0.004	0.000	0.000	0.000	0.000
119	A	122	ASP	-1	-0.923	-0.949	36.277	-0.106	-0.106	0.000	0.000	0.000	0.000
120	A	123	GLY	0	0.005	-0.007	36.674	0.005	0.005	0.000	0.000	0.000	0.000
121	A	124	GLU	-1	-0.934	-0.966	32.984	-0.144	-0.144	0.000	0.000	0.000	0.000
122	A	125	GLY	0	-0.014	0.015	33.028	-0.009	-0.009	0.000	0.000	0.000	0.000
123	A	126	SER	0	0.052	-0.007	30.273	-0.003	-0.003	0.000	0.000	0.000	0.000
124	A	127	SER	0	-0.088	-0.031	25.827	-0.019	-0.019	0.000	0.000	0.000	0.000
125	A	128	CYS	0	-0.042	-0.005	25.841	-0.004	-0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:ILE)