FMO DATABASE

FMODB ID: 3JLGL

Calculation Name: 1BGF-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 1BGF

Chain ID: A

ChEMBL ID:
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UniProt ID: P42228

Base Structure: X-ray

Registration Date: 2023-09-23

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	124
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1101123.457814
FMO2-HF: Nuclear repulsion	1050239.048268
FMO2-HF: Total energy	-50884.409546
FMO2-MP2: Total energy	-51032.438754

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:0:GLY)

Summations of interaction energy for fragment #1(A:0:GLY)

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.
0.758	2.09	-0.028	-0.653	-0.652	0

Interaction energy analysis for fragmet #1(A:0:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.013 / q_NPA : -0.019

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].
3	A	2	SER	0	0.003	0.003	3.773	-0.086	1.246	-0.028	-0.653	-0.652
4	A	3	GLN	0	-0.025	-0.040	6.939	0.395	0.395	0.000	0.000	0.000
5	A	4	TRP	0	-0.013	-0.026	9.639	0.109	0.109	0.000	0.000	0.000
6	A	5	ASN	0	-0.042	-0.020	6.125	0.354	0.354	0.000	0.000	0.000
7	A	6	GLN	0	0.021	0.007	6.385	0.222	0.222	0.000	0.000	0.000
8	A	7	VAL	0	0.025	0.008	9.781	0.003	0.003	0.000	0.000	0.000
9	A	8	GLN	0	-0.055	-0.031	11.062	-0.049	-0.049	0.000	0.000	0.000
10	A	9	GLN	0	-0.077	-0.030	9.352	-0.020	-0.020	0.000	0.000	0.000
11	A	10	LEU	0	-0.037	0.006	12.508	0.008	0.008	0.000	0.000	0.000
12	A	11	GLU	-1	-0.830	-0.905	15.758	0.129	0.129	0.000	0.000	0.000
13	A	12	ILE	0	0.054	0.011	19.101	-0.005	-0.005	0.000	0.000	0.000
14	A	13	LYS	1	0.813	0.878	20.649	-0.161	-0.161	0.000	0.000	0.000
15	A	14	PHE	0	0.028	0.024	17.683	-0.006	-0.006	0.000	0.000	0.000
16	A	15	LEU	0	-0.007	0.000	20.128	-0.010	-0.010	0.000	0.000	0.000
17	A	16	GLU	-1	-0.959	-0.980	22.101	0.050	0.050	0.000	0.000	0.000
18	A	17	GLN	0	-0.004	-0.005	23.344	-0.002	-0.002	0.000	0.000	0.000
19	A	18	VAL	0	0.004	-0.002	19.967	-0.001	-0.001	0.000	0.000	0.000
20	A	19	ASP	-1	-0.938	-0.952	23.402	-0.009	-0.009	0.000	0.000	0.000
21	A	20	GLN	0	-0.005	-0.013	26.215	-0.010	-0.010	0.000	0.000	0.000
22	A	21	PHE	0	-0.084	-0.043	23.359	-0.001	-0.001	0.000	0.000	0.000
23	A	22	TYR	0	-0.040	-0.019	18.978	-0.012	-0.012	0.000	0.000	0.000
24	A	23	ASP	-1	-0.702	-0.844	25.606	-0.022	-0.022	0.000	0.000	0.000
25	A	24	ASP	-1	-0.933	-0.965	27.942	-0.043	-0.043	0.000	0.000	0.000
26	A	25	ASN	0	-0.163	-0.106	28.197	-0.010	-0.010	0.000	0.000	0.000
27	A	26	PHE	0	0.011	-0.021	18.875	-0.012	-0.012	0.000	0.000	0.000
28	A	27	PRO	0	0.074	0.059	24.455	0.006	0.006	0.000	0.000	0.000
29	A	28	MET	0	0.072	0.020	19.946	-0.016	-0.016	0.000	0.000	0.000
30	A	29	GLU	-1	-0.862	-0.936	19.925	-0.107	-0.107	0.000	0.000	0.000
31	A	30	ILE	0	-0.024	-0.013	19.954	-0.028	-0.028	0.000	0.000	0.000
32	A	31	ARG	1	0.718	0.836	12.683	0.097	0.097	0.000	0.000	0.000
33	A	32	HIS	0	0.016	0.005	14.895	-0.032	-0.032	0.000	0.000	0.000
34	A	33	LEU	0	-0.053	-0.033	14.934	-0.058	-0.058	0.000	0.000	0.000
35	A	34	LEU	0	-0.038	-0.010	15.780	-0.046	-0.046	0.000	0.000	0.000
36	A	35	ALA	0	0.011	0.028	11.961	0.006	0.006	0.000	0.000	0.000
37	A	36	GLN	0	0.013	-0.011	7.671	-0.244	-0.244	0.000	0.000	0.000
38	A	37	TRP	0	0.046	0.041	11.573	0.055	0.055	0.000	0.000	0.000
39	A	38	ILE	0	0.030	0.005	15.077	0.043	0.043	0.000	0.000	0.000
40	A	39	GLU	-1	-0.723	-0.848	9.860	-0.293	-0.293	0.000	0.000	0.000
41	A	40	THR	0	-0.063	-0.030	12.830	0.009	0.009	0.000	0.000	0.000
42	A	41	GLN	0	-0.066	-0.034	14.328	0.045	0.045	0.000	0.000	0.000
43	A	42	ASP	-1	-0.866	-0.925	17.760	-0.013	-0.013	0.000	0.000	0.000
44	A	43	TRP	0	-0.014	-0.041	17.834	0.008	0.008	0.000	0.000	0.000
45	A	44	GLU	-1	-0.761	-0.882	19.239	0.009	0.009	0.000	0.000	0.000
46	A	45	VAL	0	-0.004	0.012	22.968	0.004	0.004	0.000	0.000	0.000
47	A	46	ALA	0	-0.044	-0.022	24.243	0.000	0.000	0.000	0.000	0.000
48	A	47	SER	0	-0.074	-0.046	25.744	0.002	0.002	0.000	0.000	0.000
49	A	48	ASN	0	-0.064	-0.032	27.583	0.005	0.005	0.000	0.000	0.000
50	A	49	ASN	0	0.033	0.012	28.845	-0.002	-0.002	0.000	0.000	0.000
51	A	50	GLU	-1	-0.835	-0.921	29.934	-0.032	-0.032	0.000	0.000	0.000
52	A	51	THR	0	0.004	0.011	31.328	-0.004	-0.004	0.000	0.000	0.000
53	A	52	MET	0	-0.021	-0.014	24.670	-0.004	-0.004	0.000	0.000	0.000
54	A	53	ALA	0	0.019	0.020	26.852	-0.009	-0.009	0.000	0.000	0.000
55	A	54	THR	0	-0.048	-0.033	27.770	-0.006	-0.006	0.000	0.000	0.000
56	A	55	ILE	0	0.003	0.002	25.671	-0.007	-0.007	0.000	0.000	0.000
57	A	56	LEU	0	0.007	0.007	21.780	-0.011	-0.011	0.000	0.000	0.000
58	A	57	LEU	0	0.011	0.017	24.195	-0.013	-0.013	0.000	0.000	0.000
59	A	58	GLN	0	-0.001	-0.013	26.601	-0.001	-0.001	0.000	0.000	0.000
60	A	59	ASN	0	0.001	-0.008	22.778	-0.004	-0.004	0.000	0.000	0.000
61	A	60	LEU	0	0.018	0.027	21.274	-0.016	-0.016	0.000	0.000	0.000
62	A	61	LEU	0	-0.049	-0.039	23.367	-0.010	-0.010	0.000	0.000	0.000
63	A	62	ILE	0	-0.009	0.010	23.992	-0.002	-0.002	0.000	0.000	0.000
64	A	63	GLN	0	-0.009	-0.014	18.164	-0.035	-0.035	0.000	0.000	0.000
65	A	64	LEU	0	-0.002	0.002	21.950	-0.012	-0.012	0.000	0.000	0.000
66	A	65	ASP	-1	-0.818	-0.904	23.811	-0.114	-0.114	0.000	0.000	0.000
67	A	66	GLU	-1	-0.886	-0.934	20.723	-0.225	-0.225	0.000	0.000	0.000
68	A	67	GLN	0	-0.017	-0.010	17.969	-0.014	-0.014	0.000	0.000	0.000
69	A	68	LEU	0	-0.028	-0.016	22.119	0.006	0.006	0.000	0.000	0.000
70	A	69	GLY	0	0.011	0.025	25.499	0.008	0.008	0.000	0.000	0.000
71	A	70	ARG	1	0.867	0.921	16.155	0.336	0.336	0.000	0.000	0.000
72	A	71	VAL	0	0.037	0.010	22.523	0.006	0.006	0.000	0.000	0.000
73	A	72	SER	0	-0.060	-0.050	24.565	0.018	0.018	0.000	0.000	0.000
74	A	73	LYS	1	0.910	0.964	24.886	0.167	0.167	0.000	0.000	0.000
75	A	74	GLU	-1	-0.872	-0.928	20.424	-0.239	-0.239	0.000	0.000	0.000
76	A	75	LYS	1	0.903	0.958	25.411	0.106	0.106	0.000	0.000	0.000
77	A	76	ASN	0	0.056	0.037	22.895	0.021	0.021	0.000	0.000	0.000
78	A	77	LEU	0	0.016	-0.015	26.612	0.001	0.001	0.000	0.000	0.000
79	A	78	LEU	0	0.042	0.030	26.192	0.002	0.002	0.000	0.000	0.000
80	A	79	LEU	0	0.062	0.027	21.586	0.003	0.003	0.000	0.000	0.000
81	A	80	ILE	0	-0.004	0.009	26.043	0.002	0.002	0.000	0.000	0.000
82	A	81	HIS	0	-0.029	-0.010	28.545	0.009	0.009	0.000	0.000	0.000
83	A	82	ASN	0	-0.021	-0.027	27.278	0.008	0.008	0.000	0.000	0.000
84	A	83	LEU	0	0.062	0.027	23.152	0.004	0.004	0.000	0.000	0.000
85	A	84	LYS	1	0.919	0.969	27.349	0.095	0.095	0.000	0.000	0.000
86	A	85	ARG	1	0.849	0.924	30.783	0.059	0.059	0.000	0.000	0.000
87	A	86	ILE	0	0.070	0.042	25.521	0.004	0.004	0.000	0.000	0.000
88	A	87	ARG	1	0.854	0.912	29.042	0.100	0.100	0.000	0.000	0.000
89	A	88	LYS	1	0.926	0.965	29.878	0.060	0.060	0.000	0.000	0.000
90	A	89	VAL	0	0.019	0.013	31.013	0.003	0.003	0.000	0.000	0.000
91	A	90	LEU	0	0.050	0.014	25.819	0.003	0.003	0.000	0.000	0.000
92	A	91	GLN	0	-0.017	-0.010	30.303	0.001	0.001	0.000	0.000	0.000
93	A	92	GLY	0	0.018	0.022	33.015	0.003	0.003	0.000	0.000	0.000
94	A	93	LYS	1	0.847	0.927	30.304	0.042	0.042	0.000	0.000	0.000
95	A	94	PHE	0	-0.051	-0.032	31.344	0.002	0.002	0.000	0.000	0.000
96	A	95	HIS	0	-0.069	-0.039	32.771	0.002	0.002	0.000	0.000	0.000
97	A	96	GLY	0	-0.003	0.013	35.348	0.003	0.003	0.000	0.000	0.000
98	A	97	ASN	0	0.003	-0.006	33.420	0.001	0.001	0.000	0.000	0.000
99	A	98	PRO	0	0.060	0.022	29.897	0.000	0.000	0.000	0.000	0.000
100	A	99	MET	0	0.030	0.013	28.855	-0.003	-0.003	0.000	0.000	0.000
101	A	100	HIS	0	-0.016	0.001	28.811	0.003	0.003	0.000	0.000	0.000
102	A	101	VAL	0	0.004	0.001	25.390	0.002	0.002	0.000	0.000	0.000
103	A	102	ALA	0	-0.004	0.015	24.441	-0.002	-0.002	0.000	0.000	0.000
104	A	103	VAL	0	0.031	0.029	24.229	0.004	0.004	0.000	0.000	0.000
105	A	104	VAL	0	-0.033	-0.011	24.797	0.007	0.007	0.000	0.000	0.000
106	A	105	ILE	0	-0.009	0.000	19.726	0.005	0.005	0.000	0.000	0.000
107	A	106	SER	0	0.010	-0.008	20.432	0.006	0.006	0.000	0.000	0.000
108	A	107	ASN	0	-0.081	-0.052	20.886	0.020	0.020	0.000	0.000	0.000
109	A	108	CYS	0	-0.010	0.022	20.119	0.011	0.011	0.000	0.000	0.000
110	A	109	LEU	0	0.044	0.017	14.863	0.015	0.015	0.000	0.000	0.000
111	A	110	ARG	1	0.947	0.966	16.919	-0.043	-0.043	0.000	0.000	0.000
112	A	111	GLU	-1	-0.751	-0.840	19.243	0.113	0.113	0.000	0.000	0.000
113	A	112	GLU	-1	-0.759	-0.838	14.942	0.017	0.017	0.000	0.000	0.000
114	A	113	ARG	1	0.840	0.927	14.300	-0.033	-0.033	0.000	0.000	0.000
115	A	114	ARG	1	0.761	0.851	16.153	-0.076	-0.076	0.000	0.000	0.000
116	A	115	ILE	0	-0.012	-0.014	17.922	0.018	0.018	0.000	0.000	0.000
117	A	116	LEU	0	-0.038	-0.029	11.894	0.019	0.019	0.000	0.000	0.000
118	A	117	ALA	0	-0.045	-0.010	15.594	0.040	0.040	0.000	0.000	0.000
119	A	118	ALA	0	-0.050	-0.026	17.334	-0.002	-0.002	0.000	0.000	0.000
120	A	119	ALA	0	-0.016	0.010	16.813	-0.017	-0.017	0.000	0.000	0.000
121	A	120	ASN	0	-0.019	-0.012	18.577	0.024	0.024	0.000	0.000	0.000
122	A	121	MET	0	0.005	-0.004	12.013	0.021	0.021	0.000	0.000	0.000
123	A	122	PRO	0	-0.031	0.001	16.940	-0.023	-0.023	0.000	0.000	0.000
124	A	123	ILE	0	0.007	0.003	17.048	0.054	0.054	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:GLY)