FMO DATABASE

FMODB ID: 4J8QN

Calculation Name: 3BPQ-B-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: 3BPQ

Chain ID: B

ChEMBL ID:
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UniProt ID: P0CL56

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	86
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-635818.841903
FMO2-HF: Nuclear repulsion	600862.679927
FMO2-HF: Total energy	-34956.161976
FMO2-MP2: Total energy	-35060.967673

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(B:3:VAL)

Summations of interaction energy for fragment #1(B:3:VAL)

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.
-11.07	-2.888	10.002	-5.565	-12.619	-0.013

Interaction energy analysis for fragmet #1(B:3:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.006 / q_NPA : 0.001

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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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	B	5	PHE	0	0.011	-0.001	2.364	-2.146	0.839	1.814	-1.707	-3.092	0.004
4	B	6	ALA	0	-0.006	0.009	5.811	0.009	0.009	0.000	0.000	0.000	0.000
5	B	7	LYS	1	1.020	0.987	9.322	-0.012	-0.012	0.000	0.000	0.000	0.000
6	B	8	THR	0	-0.012	-0.015	12.116	-0.017	-0.017	0.000	0.000	0.000	0.000
7	B	9	PHE	0	0.089	0.061	7.774	-0.002	-0.002	0.000	0.000	0.000	0.000
8	B	10	VAL	0	0.068	0.027	10.173	-0.014	-0.014	0.000	0.000	0.000	0.000
9	B	11	LYS	1	0.901	0.945	12.269	-0.016	-0.016	0.000	0.000	0.000	0.000
10	B	12	ASP	-1	-0.713	-0.826	12.963	0.042	0.042	0.000	0.000	0.000	0.000
11	B	13	LEU	0	0.009	0.004	10.056	-0.006	-0.006	0.000	0.000	0.000	0.000
12	B	14	LYS	1	0.837	0.912	13.813	0.039	0.039	0.000	0.000	0.000	0.000
13	B	15	HIS	0	0.037	0.035	17.073	-0.003	-0.003	0.000	0.000	0.000	0.000
14	B	16	VAL	0	-0.068	-0.013	14.087	0.001	0.001	0.000	0.000	0.000	0.000
15	B	17	PRO	0	0.021	0.018	17.044	-0.010	-0.010	0.000	0.000	0.000	0.000
16	B	18	GLY	0	0.069	0.015	17.097	-0.006	-0.006	0.000	0.000	0.000	0.000
17	B	19	HIS	0	0.048	0.016	16.610	-0.018	-0.018	0.000	0.000	0.000	0.000
18	B	20	ILE	0	-0.013	-0.009	14.460	-0.009	-0.009	0.000	0.000	0.000	0.000
19	B	21	ARG	1	0.956	0.979	12.605	0.082	0.082	0.000	0.000	0.000	0.000
20	B	22	LYS	1	0.974	0.991	11.706	0.105	0.105	0.000	0.000	0.000	0.000
21	B	23	ARG	1	0.965	0.983	12.401	0.061	0.061	0.000	0.000	0.000	0.000
22	B	24	ILE	0	0.006	0.001	8.039	-0.019	-0.019	0.000	0.000	0.000	0.000
23	B	25	LYS	1	0.953	0.996	7.814	0.340	0.340	0.000	0.000	0.000	0.000
24	B	26	LEU	0	0.015	0.006	7.810	-0.093	-0.093	0.000	0.000	0.000	0.000
25	B	27	ILE	0	-0.056	-0.015	5.854	-0.047	-0.047	0.000	0.000	0.000	0.000
26	B	28	ILE	0	-0.010	-0.013	2.454	-0.826	-0.111	0.401	-0.200	-0.916	0.000
27	B	29	GLU	-1	-0.864	-0.966	4.278	-1.472	-1.271	0.000	-0.028	-0.172	0.000
28	B	30	GLU	-1	-0.880	-0.923	6.792	-0.762	-0.762	0.000	0.000	0.000	0.000
29	B	31	CYS	0	-0.059	-0.022	2.850	0.190	-0.844	2.995	-0.416	-1.545	-0.001
30	B	32	GLN	0	-0.044	-0.007	3.360	-2.308	-1.184	0.053	-0.342	-0.835	-0.002
31	B	33	ASN	0	-0.078	-0.049	4.214	0.344	0.460	0.000	-0.012	-0.105	0.000
32	B	34	SER	0	0.030	0.018	6.888	0.166	0.166	0.000	0.000	0.000	0.000
33	B	35	ASN	0	-0.046	-0.019	3.795	-0.241	0.229	0.002	-0.106	-0.366	-0.001
34	B	36	SER	0	-0.011	-0.002	5.302	0.542	0.569	-0.001	0.000	-0.025	0.000
35	B	37	LEU	0	-0.022	-0.041	4.959	-0.107	-0.107	0.000	0.000	0.000	0.000
36	B	38	ASN	0	-0.042	-0.040	8.061	0.048	0.048	0.000	0.000	0.000	0.000
37	B	39	ASP	-1	-0.817	-0.906	11.736	-0.078	-0.078	0.000	0.000	0.000	0.000
38	B	40	LEU	0	-0.034	0.006	8.809	0.014	0.014	0.000	0.000	0.000	0.000
39	B	41	LYS	1	0.961	1.000	11.980	0.239	0.239	0.000	0.000	0.000	0.000
40	B	42	LEU	0	-0.076	-0.046	8.663	0.010	0.010	0.000	0.000	0.000	0.000
41	B	43	ASP	-1	-0.728	-0.818	13.370	0.017	0.017	0.000	0.000	0.000	0.000
42	B	44	ILE	0	-0.008	-0.009	9.673	0.017	0.017	0.000	0.000	0.000	0.000
43	B	45	LYS	1	0.912	0.951	13.744	-0.069	-0.069	0.000	0.000	0.000	0.000
44	B	46	LYS	1	1.006	1.019	14.391	-0.141	-0.141	0.000	0.000	0.000	0.000
45	B	47	ILE	0	-0.060	-0.027	14.684	-0.022	-0.022	0.000	0.000	0.000	0.000
46	B	48	LYS	1	0.964	0.971	17.427	-0.050	-0.050	0.000	0.000	0.000	0.000
47	B	49	GLY	0	0.049	0.018	20.763	-0.002	-0.002	0.000	0.000	0.000	0.000
48	B	50	TYR	0	0.026	0.031	17.295	0.000	0.000	0.000	0.000	0.000	0.000
49	B	51	HIS	0	0.028	0.008	16.521	-0.014	-0.014	0.000	0.000	0.000	0.000
50	B	52	ASN	0	-0.015	-0.004	11.942	-0.020	-0.020	0.000	0.000	0.000	0.000
51	B	53	TYR	0	0.023	0.019	11.564	0.024	0.024	0.000	0.000	0.000	0.000
52	B	54	TYR	0	0.027	0.004	10.064	-0.058	-0.058	0.000	0.000	0.000	0.000
53	B	55	ARG	1	0.810	0.879	11.649	-0.026	-0.026	0.000	0.000	0.000	0.000
54	B	56	ILE	0	0.038	0.032	8.127	-0.017	-0.017	0.000	0.000	0.000	0.000
55	B	57	ARG	1	0.868	0.924	12.432	-0.004	-0.004	0.000	0.000	0.000	0.000
56	B	58	VAL	0	-0.010	-0.014	11.881	-0.018	-0.018	0.000	0.000	0.000	0.000
57	B	59	GLY	0	0.004	-0.001	15.220	-0.001	-0.001	0.000	0.000	0.000	0.000
58	B	60	ASN	0	-0.001	-0.017	18.957	0.010	0.010	0.000	0.000	0.000	0.000
59	B	61	TYR	0	0.006	0.007	15.421	0.004	0.004	0.000	0.000	0.000	0.000
60	B	62	SER	0	-0.022	-0.004	14.768	-0.004	-0.004	0.000	0.000	0.000	0.000
61	B	63	ILE	0	-0.006	-0.004	8.184	-0.008	-0.008	0.000	0.000	0.000	0.000
62	B	64	GLY	0	-0.020	-0.009	11.357	0.000	0.000	0.000	0.000	0.000	0.000
63	B	65	ILE	0	-0.004	-0.016	6.038	0.002	0.002	0.000	0.000	0.000	0.000
64	B	66	GLU	-1	-0.781	-0.864	8.039	0.302	0.302	0.000	0.000	0.000	0.000
65	B	67	VAL	0	0.000	0.001	6.854	0.113	0.113	0.000	0.000	0.000	0.000
66	B	68	ASN	0	-0.024	-0.012	7.633	-0.188	-0.188	0.000	0.000	0.000	0.000
67	B	69	GLY	0	0.031	0.009	8.828	0.166	0.166	0.000	0.000	0.000	0.000
68	B	70	ASP	-1	-0.843	-0.924	8.580	0.600	0.600	0.000	0.000	0.000	0.000
69	B	71	THR	0	-0.036	-0.001	4.073	0.307	0.461	0.000	-0.017	-0.136	0.000
70	B	72	ILE	0	0.012	0.014	2.250	-1.972	-1.036	1.358	-0.539	-1.756	0.000
71	B	73	ILE	0	-0.022	-0.014	2.480	-1.908	-0.295	1.899	-1.679	-1.834	-0.017
72	B	74	PHE	0	0.034	0.004	2.319	-1.636	-0.761	1.481	-0.519	-1.837	0.004
73	B	75	ARG	1	0.830	0.873	5.792	-0.436	-0.436	0.000	0.000	0.000	0.000
74	B	76	ARG	1	0.761	0.834	9.365	-0.110	-0.110	0.000	0.000	0.000	0.000
75	B	77	VAL	0	-0.024	-0.001	11.157	0.014	0.014	0.000	0.000	0.000	0.000
76	B	78	LEU	0	0.015	0.013	12.882	-0.015	-0.015	0.000	0.000	0.000	0.000
77	B	79	HIS	0	0.043	0.016	16.634	0.002	0.002	0.000	0.000	0.000	0.000
78	B	80	ARG	1	0.992	0.976	19.714	-0.001	-0.001	0.000	0.000	0.000	0.000
79	B	81	LYS	1	0.955	0.974	21.760	0.012	0.012	0.000	0.000	0.000	0.000
80	B	82	SER	0	0.017	0.002	20.561	-0.001	-0.001	0.000	0.000	0.000	0.000
81	B	83	ILE	0	-0.031	-0.018	17.960	0.005	0.005	0.000	0.000	0.000	0.000
82	B	84	TYR	0	-0.018	-0.012	21.376	0.003	0.003	0.000	0.000	0.000	0.000
83	B	85	ASP	-1	-0.867	-0.914	24.192	0.023	0.023	0.000	0.000	0.000	0.000
84	B	86	TYR	0	-0.064	-0.036	19.681	0.005	0.005	0.000	0.000	0.000	0.000
85	B	87	PHE	0	-0.057	-0.014	23.250	0.006	0.006	0.000	0.000	0.000	0.000
86	B	88	PRO	0	0.042	0.034	25.486	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:3:VAL)