FMO DATABASE

FMODB ID: KGMK3

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

Total energy (hartree)

FMO2-HF: Electronic energy	-635480.349993
FMO2-HF: Nuclear repulsion	600524.572226
FMO2-HF: Total energy	-34955.777768
FMO2-MP2: Total energy	-35060.565102

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.
-8.83	-5.837	17.95	-6.881	-14.062	-0.009

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 : 0.027 / q_NPA : 0.008

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	B	5	PHE	0	0.012	0.003	2.804	-2.341	1.265	0.508	-1.619	-2.496	0.002
4	B	6	ALA	0	-0.006	0.008	5.609	0.046	0.046	0.000	0.000	0.000	0.000
5	B	7	LYS	1	1.013	0.985	9.180	0.088	0.088	0.000	0.000	0.000	0.000
6	B	8	THR	0	-0.014	-0.017	11.900	-0.017	-0.017	0.000	0.000	0.000	0.000
7	B	9	PHE	0	0.093	0.062	8.003	0.014	0.014	0.000	0.000	0.000	0.000
8	B	10	VAL	0	0.037	0.017	10.401	0.000	0.000	0.000	0.000	0.000	0.000
9	B	11	LYS	1	0.896	0.940	12.051	0.030	0.030	0.000	0.000	0.000	0.000
10	B	12	ASP	-1	-0.734	-0.858	12.864	0.043	0.043	0.000	0.000	0.000	0.000
11	B	13	LEU	0	-0.007	-0.008	10.072	0.005	0.005	0.000	0.000	0.000	0.000
12	B	14	LYS	1	0.880	0.938	13.808	0.095	0.095	0.000	0.000	0.000	0.000
13	B	15	HIS	0	0.045	0.037	17.108	0.000	0.000	0.000	0.000	0.000	0.000
14	B	16	VAL	0	-0.061	-0.010	14.292	0.008	0.008	0.000	0.000	0.000	0.000
15	B	17	PRO	0	0.022	0.021	17.183	-0.015	-0.015	0.000	0.000	0.000	0.000
16	B	18	GLY	0	0.072	0.012	17.200	-0.002	-0.002	0.000	0.000	0.000	0.000
17	B	19	HIS	0	0.043	0.013	16.684	-0.016	-0.016	0.000	0.000	0.000	0.000
18	B	20	ILE	0	-0.014	-0.006	14.203	-0.001	-0.001	0.000	0.000	0.000	0.000
19	B	21	ARG	1	0.963	0.976	12.706	0.121	0.121	0.000	0.000	0.000	0.000
20	B	22	LYS	1	0.963	0.987	11.775	0.084	0.084	0.000	0.000	0.000	0.000
21	B	23	ARG	1	0.968	0.982	12.412	-0.012	-0.012	0.000	0.000	0.000	0.000
22	B	24	ILE	0	0.011	0.002	8.066	0.005	0.005	0.000	0.000	0.000	0.000
23	B	25	LYS	1	0.984	1.003	7.850	0.346	0.346	0.000	0.000	0.000	0.000
24	B	26	LEU	0	0.018	0.010	7.781	-0.065	-0.065	0.000	0.000	0.000	0.000
25	B	27	ILE	0	-0.068	-0.022	5.795	-0.040	-0.040	0.000	0.000	0.000	0.000
26	B	28	ILE	0	-0.022	-0.016	2.337	-0.642	-0.040	0.618	-0.213	-1.006	0.000
27	B	29	GLU	-1	-0.914	-0.982	4.246	-1.344	-1.163	0.000	-0.024	-0.156	0.000
28	B	30	GLU	-1	-0.892	-0.937	6.679	-0.549	-0.549	0.000	0.000	0.000	0.000
29	B	31	CYS	0	-0.054	-0.023	2.735	1.071	-2.088	6.155	-0.953	-2.043	0.001
30	B	32	GLN	0	-0.043	0.002	3.068	-2.136	-1.272	0.053	-0.183	-0.734	-0.001
31	B	33	ASN	0	-0.062	-0.037	3.920	0.259	0.387	0.002	-0.009	-0.120	0.000
32	B	34	SER	0	0.035	0.024	7.458	0.185	0.185	0.000	0.000	0.000	0.000
33	B	35	ASN	0	-0.022	-0.008	3.699	-0.317	0.208	0.003	-0.126	-0.402	-0.001
34	B	36	SER	0	-0.010	0.000	5.484	0.519	0.519	0.000	0.000	0.000	0.000
35	B	37	LEU	0	-0.031	-0.048	4.683	-0.153	-0.072	-0.001	-0.006	-0.074	0.000
36	B	38	ASN	0	-0.004	-0.006	8.247	-0.001	-0.001	0.000	0.000	0.000	0.000
37	B	39	ASP	-1	-0.846	-0.934	11.841	0.035	0.035	0.000	0.000	0.000	0.000
38	B	40	LEU	0	-0.049	0.002	8.940	-0.005	-0.005	0.000	0.000	0.000	0.000
39	B	41	LYS	1	0.972	1.006	12.213	0.077	0.077	0.000	0.000	0.000	0.000
40	B	42	LEU	0	-0.073	-0.053	8.606	0.001	0.001	0.000	0.000	0.000	0.000
41	B	43	ASP	-1	-0.782	-0.878	13.361	0.092	0.092	0.000	0.000	0.000	0.000
42	B	44	ILE	0	0.002	-0.003	9.656	0.019	0.019	0.000	0.000	0.000	0.000
43	B	45	LYS	1	0.930	0.963	13.664	-0.157	-0.157	0.000	0.000	0.000	0.000
44	B	46	LYS	1	1.032	1.022	14.107	-0.195	-0.195	0.000	0.000	0.000	0.000
45	B	47	ILE	0	-0.083	-0.043	14.227	-0.029	-0.029	0.000	0.000	0.000	0.000
46	B	48	LYS	1	0.967	0.978	16.992	-0.093	-0.093	0.000	0.000	0.000	0.000
47	B	49	GLY	0	0.048	0.016	20.355	-0.003	-0.003	0.000	0.000	0.000	0.000
48	B	50	TYR	0	0.008	0.018	16.795	-0.003	-0.003	0.000	0.000	0.000	0.000
49	B	51	HIS	0	0.024	0.011	16.103	-0.006	-0.006	0.000	0.000	0.000	0.000
50	B	52	ASN	0	-0.020	-0.003	11.606	0.003	0.003	0.000	0.000	0.000	0.000
51	B	53	TYR	0	0.040	0.025	11.117	0.039	0.039	0.000	0.000	0.000	0.000
52	B	54	TYR	0	0.024	0.003	9.705	-0.064	-0.064	0.000	0.000	0.000	0.000
53	B	55	ARG	1	0.856	0.935	11.111	-0.126	-0.126	0.000	0.000	0.000	0.000
54	B	56	ILE	0	0.026	0.016	7.869	-0.022	-0.022	0.000	0.000	0.000	0.000
55	B	57	ARG	1	0.868	0.940	12.186	-0.087	-0.087	0.000	0.000	0.000	0.000
56	B	58	VAL	0	0.013	-0.001	11.761	-0.011	-0.011	0.000	0.000	0.000	0.000
57	B	59	GLY	0	-0.004	-0.006	15.039	-0.012	-0.012	0.000	0.000	0.000	0.000
58	B	60	ASN	0	-0.001	-0.011	18.779	0.012	0.012	0.000	0.000	0.000	0.000
59	B	61	TYR	0	0.006	0.006	15.174	-0.003	-0.003	0.000	0.000	0.000	0.000
60	B	62	SER	0	-0.023	-0.005	14.483	0.006	0.006	0.000	0.000	0.000	0.000
61	B	63	ILE	0	-0.009	0.000	7.808	-0.032	-0.032	0.000	0.000	0.000	0.000
62	B	64	GLY	0	-0.018	-0.010	10.858	0.014	0.014	0.000	0.000	0.000	0.000
63	B	65	ILE	0	0.005	-0.012	5.220	-0.027	-0.027	0.000	0.000	0.000	0.000
64	B	66	GLU	-1	-0.832	-0.894	7.290	0.279	0.279	0.000	0.000	0.000	0.000
65	B	67	VAL	0	-0.005	-0.001	6.749	0.128	0.128	0.000	0.000	0.000	0.000
66	B	68	ASN	0	-0.020	-0.008	7.623	-0.193	-0.193	0.000	0.000	0.000	0.000
67	B	69	GLY	0	0.033	0.010	8.829	0.158	0.158	0.000	0.000	0.000	0.000
68	B	70	ASP	-1	-0.845	-0.924	8.592	0.709	0.709	0.000	0.000	0.000	0.000
69	B	71	THR	0	-0.040	-0.005	3.960	0.308	0.489	0.000	-0.021	-0.160	0.000
70	B	72	ILE	0	0.021	0.016	2.345	-1.872	-1.208	1.883	-0.593	-1.955	0.002
71	B	73	ILE	0	-0.014	-0.012	2.464	-2.699	-0.847	2.259	-1.989	-2.123	-0.022
72	B	74	PHE	0	0.026	0.001	2.030	0.262	-2.270	6.470	-1.145	-2.793	0.010
73	B	75	ARG	1	0.841	0.888	5.816	-0.497	-0.497	0.000	0.000	0.000	0.000
74	B	76	ARG	1	0.779	0.863	9.401	-0.130	-0.130	0.000	0.000	0.000	0.000
75	B	77	VAL	0	-0.013	0.007	11.066	0.047	0.047	0.000	0.000	0.000	0.000
76	B	78	LEU	0	0.011	0.011	12.924	-0.029	-0.029	0.000	0.000	0.000	0.000
77	B	79	HIS	0	0.048	0.017	16.679	0.011	0.011	0.000	0.000	0.000	0.000
78	B	80	ARG	1	1.016	0.985	19.521	-0.040	-0.040	0.000	0.000	0.000	0.000
79	B	81	LYS	1	0.960	0.977	21.430	-0.003	-0.003	0.000	0.000	0.000	0.000
80	B	82	SER	0	0.019	0.001	20.649	-0.003	-0.003	0.000	0.000	0.000	0.000
81	B	83	ILE	0	-0.038	-0.022	17.870	0.003	0.003	0.000	0.000	0.000	0.000
82	B	84	TYR	0	-0.036	-0.019	21.114	0.004	0.004	0.000	0.000	0.000	0.000
83	B	85	ASP	-1	-0.869	-0.915	24.345	0.030	0.030	0.000	0.000	0.000	0.000
84	B	86	TYR	0	-0.071	-0.037	19.880	0.000	0.000	0.000	0.000	0.000	0.000
85	B	87	PHE	0	-0.054	-0.012	23.018	0.008	0.008	0.000	0.000	0.000	0.000
86	B	88	PRO	0	0.038	0.031	25.001	-0.002	-0.002	0.000	0.000	0.000	0.000

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