FMO DATABASE

FMODB ID: KR633

Calculation Name: 2BNK-A-Xray308

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2BNK

Chain ID: A

ChEMBL ID:

UniProt ID: P16517

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	66
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-367409.173243
FMO2-HF: Nuclear repulsion	340916.564879
FMO2-HF: Total energy	-26492.608365
FMO2-MP2: Total energy	-26570.856378

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:64:ACE )

Summations of interaction energy for fragment #1(A:64:ACE )

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.
1.275	2.109	-0.003	-0.33	-0.501	0

Interaction energy analysis for fragmet #1(A:64:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : -0.004

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].
3	A	66	ASN	0	-0.093	-0.030	3.881	1.231	1.905	-0.004	-0.303	-0.367
4	A	67	LEU	0	-0.004	-0.001	4.475	-0.004	0.090	0.000	-0.012	-0.082
5	A	68	SER	0	0.032	0.027	6.784	0.127	0.127	0.000	0.000	0.000
6	A	69	ALA	0	0.001	-0.007	9.571	0.093	0.093	0.000	0.000	0.000
7	A	70	CYS	0	-0.002	-0.008	12.281	0.034	0.034	0.000	0.000	0.000
8	A	71	GLU	-1	-0.863	-0.951	9.176	-0.140	-0.140	0.000	0.000	0.000
9	A	72	VAL	0	0.004	-0.004	7.314	0.061	0.061	0.000	0.000	0.000
10	A	73	ALA	0	0.067	0.054	9.316	0.074	0.074	0.000	0.000	0.000
11	A	74	VAL	0	-0.038	-0.022	12.379	-0.001	-0.001	0.000	0.000	0.000
12	A	75	LEU	0	-0.034	-0.039	6.051	0.001	0.001	0.000	0.000	0.000
13	A	76	ASP	-1	-0.859	-0.926	9.904	0.704	0.704	0.000	0.000	0.000
14	A	77	LEU	0	-0.029	-0.013	11.798	-0.035	-0.035	0.000	0.000	0.000
15	A	78	TYR	0	-0.074	-0.048	11.860	-0.040	-0.040	0.000	0.000	0.000
16	A	79	GLU	-1	-0.970	-0.972	10.361	0.710	0.710	0.000	0.000	0.000
17	A	80	GLN	0	0.007	0.000	12.820	-0.066	-0.066	0.000	0.000	0.000
18	A	81	SER	0	-0.084	-0.030	16.009	-0.050	-0.050	0.000	0.000	0.000
19	A	82	ASN	0	-0.082	-0.045	15.848	-0.005	-0.005	0.000	0.000	0.000
20	A	83	ILE	0	-0.034	-0.007	13.986	-0.035	-0.035	0.000	0.000	0.000
21	A	84	ARG	1	0.962	0.974	11.455	-0.240	-0.240	0.000	0.000	0.000
22	A	85	ILE	0	-0.015	-0.004	8.962	-0.080	-0.080	0.000	0.000	0.000
23	A	86	PRO	0	-0.013	-0.004	9.284	0.067	0.067	0.000	0.000	0.000
24	A	87	SER	0	0.068	0.014	6.847	0.058	0.058	0.000	0.000	0.000
25	A	88	ASP	-1	-0.898	-0.941	8.150	-0.307	-0.307	0.000	0.000	0.000
26	A	89	ILE	0	-0.041	-0.025	10.724	-0.025	-0.025	0.000	0.000	0.000
27	A	90	ILE	0	-0.014	-0.001	3.995	-0.032	0.034	0.001	-0.015	-0.052
28	A	91	GLU	-1	-0.895	-0.955	7.304	-1.092	-1.092	0.000	0.000	0.000
29	A	92	ASP	-1	-0.967	-0.979	9.059	-0.231	-0.231	0.000	0.000	0.000
30	A	93	LEU	0	-0.005	-0.009	8.366	0.057	0.057	0.000	0.000	0.000
31	A	94	VAL	0	0.052	0.036	6.765	0.029	0.029	0.000	0.000	0.000
32	A	95	ASN	0	-0.092	-0.046	9.944	-0.003	-0.003	0.000	0.000	0.000
33	A	96	GLN	0	-0.066	-0.039	13.100	0.073	0.073	0.000	0.000	0.000
34	A	97	ARG	1	0.864	0.940	13.627	0.271	0.271	0.000	0.000	0.000
35	A	98	LEU	0	0.025	0.020	14.716	0.028	0.028	0.000	0.000	0.000
36	A	99	GLN	0	-0.025	-0.017	15.437	-0.006	-0.006	0.000	0.000	0.000
37	A	100	SER	0	-0.076	-0.016	17.950	0.018	0.018	0.000	0.000	0.000
38	A	101	GLU	-1	-0.905	-0.955	16.109	0.133	0.133	0.000	0.000	0.000
39	A	102	GLN	0	0.052	-0.009	17.279	0.016	0.016	0.000	0.000	0.000
40	A	103	GLU	-1	-0.879	-0.941	18.232	-0.030	-0.030	0.000	0.000	0.000
41	A	104	VAL	0	0.030	0.025	12.295	-0.008	-0.008	0.000	0.000	0.000
42	A	105	LEU	0	0.046	0.035	15.108	-0.005	-0.005	0.000	0.000	0.000
43	A	106	ASN	0	0.010	-0.006	16.428	0.006	0.006	0.000	0.000	0.000
44	A	107	TYR	0	0.040	0.036	13.274	-0.011	-0.011	0.000	0.000	0.000
45	A	108	ILE	0	0.062	0.018	11.389	-0.009	-0.009	0.000	0.000	0.000
46	A	109	GLU	-1	-0.849	-0.931	14.452	0.089	0.089	0.000	0.000	0.000
47	A	110	THR	0	-0.035	-0.011	17.824	-0.003	-0.003	0.000	0.000	0.000
48	A	111	GLN	0	0.016	0.005	14.567	0.003	0.003	0.000	0.000	0.000
49	A	112	ARG	1	0.894	0.959	14.541	-0.125	-0.125	0.000	0.000	0.000
50	A	113	THR	0	-0.089	-0.039	17.257	0.000	0.000	0.000	0.000	0.000
51	A	114	TYR	0	-0.014	0.000	17.916	-0.002	-0.002	0.000	0.000	0.000
52	A	115	TRP	0	0.078	0.012	14.852	0.014	0.014	0.000	0.000	0.000
53	A	116	LYS	1	0.907	0.961	18.706	-0.033	-0.033	0.000	0.000	0.000
54	A	117	LEU	0	-0.020	-0.022	21.210	-0.001	-0.001	0.000	0.000	0.000
55	A	118	GLU	-1	-0.923	-0.953	20.614	-0.046	-0.046	0.000	0.000	0.000
56	A	119	ASN	0	-0.061	-0.036	18.173	-0.005	-0.005	0.000	0.000	0.000
57	A	120	GLN	0	-0.044	-0.017	22.484	0.002	0.002	0.000	0.000	0.000
58	A	121	LYS	1	0.888	0.967	25.245	0.034	0.034	0.000	0.000	0.000
59	A	122	LYS	1	0.972	0.993	27.611	0.007	0.007	0.000	0.000	0.000
60	A	123	LEU	0	0.032	0.006	27.734	-0.003	-0.003	0.000	0.000	0.000
61	A	124	TYR	0	-0.029	-0.015	30.078	0.004	0.004	0.000	0.000	0.000
62	A	125	ARG	1	0.952	0.973	30.602	-0.001	-0.001	0.000	0.000	0.000
63	A	126	GLY	0	0.029	0.027	33.802	0.002	0.002	0.000	0.000	0.000
64	A	127	SER	0	0.018	-0.015	32.770	0.000	0.000	0.000	0.000	0.000
65	A	128	LEU	0	-0.073	-0.024	34.812	0.001	0.001	0.000	0.000	0.000
66	A	129	NME	0	0.044	0.033	35.543	0.002	0.002	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:64:ACE )