FMO DATABASE

FMODB ID: 3QZZL

Calculation Name: 2BNK-A-Xray372

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: 2023-03-13

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	64
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-363824.028895
FMO2-HF: Nuclear repulsion	337501.726326
FMO2-HF: Total energy	-26322.302569
FMO2-MP2: Total energy	-26399.94917

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:65:VAL)

Summations of interaction energy for fragment #1(A:65: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.
-6.664	-1.039	0.397	-2.174	-3.846	-0.002

Interaction energy analysis for fragmet #1(A:65:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.056 / q_NPA : 0.020

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	67	LEU	0	-0.022	-0.007	3.239	-1.784	1.128	0.016	-1.223	-1.705	0.005
4	A	68	SER	0	0.034	0.025	4.845	0.438	0.562	-0.001	-0.016	-0.107	0.000
5	A	69	ALA	0	-0.005	-0.007	8.209	-0.112	-0.112	0.000	0.000	0.000	0.000
6	A	70	CYS	0	0.001	0.003	11.303	0.025	0.025	0.000	0.000	0.000	0.000
7	A	71	GLU	-1	-0.847	-0.956	7.065	-1.269	-1.269	0.000	0.000	0.000	0.000
8	A	72	VAL	0	-0.006	-0.006	7.289	0.048	0.048	0.000	0.000	0.000	0.000
9	A	73	ALA	0	0.078	0.059	9.336	0.103	0.103	0.000	0.000	0.000	0.000
10	A	74	VAL	0	-0.047	-0.032	12.526	0.088	0.088	0.000	0.000	0.000	0.000
11	A	75	LEU	0	-0.040	-0.040	6.669	0.082	0.082	0.000	0.000	0.000	0.000
12	A	76	ASP	-1	-0.854	-0.920	10.833	-0.372	-0.372	0.000	0.000	0.000	0.000
13	A	77	LEU	0	-0.029	-0.011	12.957	0.075	0.075	0.000	0.000	0.000	0.000
14	A	78	TYR	0	-0.065	-0.074	12.763	0.041	0.041	0.000	0.000	0.000	0.000
15	A	79	GLU	-1	-0.966	-0.969	12.138	-0.042	-0.042	0.000	0.000	0.000	0.000
16	A	80	GLN	0	-0.018	-0.010	14.600	0.053	0.053	0.000	0.000	0.000	0.000
17	A	81	SER	0	-0.095	-0.039	17.659	0.016	0.016	0.000	0.000	0.000	0.000
18	A	82	ASN	0	-0.086	-0.049	17.862	0.027	0.027	0.000	0.000	0.000	0.000
19	A	83	ILE	0	-0.026	-0.001	14.685	0.021	0.021	0.000	0.000	0.000	0.000
20	A	84	ARG	1	0.954	0.971	13.088	-0.267	-0.267	0.000	0.000	0.000	0.000
21	A	85	ILE	0	-0.007	0.001	8.948	-0.007	-0.007	0.000	0.000	0.000	0.000
22	A	86	PRO	0	-0.003	-0.003	9.784	0.093	0.093	0.000	0.000	0.000	0.000
23	A	87	SER	0	0.058	0.021	6.236	-0.078	-0.078	0.000	0.000	0.000	0.000
24	A	88	ASP	-1	-0.912	-0.953	6.072	-0.070	-0.070	0.000	0.000	0.000	0.000
25	A	89	ILE	0	-0.022	-0.020	8.216	-0.097	-0.097	0.000	0.000	0.000	0.000
26	A	90	ILE	0	-0.010	0.001	2.966	-0.588	-0.122	0.202	-0.121	-0.546	0.000
27	A	91	GLU	-1	-0.886	-0.954	3.086	-2.925	-1.514	0.099	-0.640	-0.871	-0.006
28	A	92	ASP	-1	-0.927	-0.956	5.063	-0.241	-0.240	-0.001	-0.001	0.002	0.000
29	A	93	LEU	0	0.000	0.003	7.393	0.099	0.099	0.000	0.000	0.000	0.000
30	A	94	VAL	0	0.054	0.034	2.963	-0.662	0.049	0.082	-0.173	-0.619	-0.001
31	A	95	ASN	0	-0.095	-0.049	6.286	0.221	0.221	0.000	0.000	0.000	0.000
32	A	96	GLN	0	-0.074	-0.045	8.660	0.147	0.147	0.000	0.000	0.000	0.000
33	A	97	ARG	1	0.845	0.930	9.146	0.567	0.567	0.000	0.000	0.000	0.000
34	A	98	LEU	0	0.019	0.017	11.301	0.060	0.060	0.000	0.000	0.000	0.000
35	A	99	GLN	0	-0.039	-0.024	12.822	-0.046	-0.046	0.000	0.000	0.000	0.000
36	A	100	SER	0	-0.088	-0.061	15.490	0.015	0.015	0.000	0.000	0.000	0.000
37	A	101	GLU	-1	-0.878	-0.935	15.264	-0.405	-0.405	0.000	0.000	0.000	0.000
38	A	102	GLN	0	0.015	-0.018	16.712	0.004	0.004	0.000	0.000	0.000	0.000
39	A	103	GLU	-1	-0.840	-0.895	16.378	-0.299	-0.299	0.000	0.000	0.000	0.000
40	A	104	VAL	0	0.044	0.024	11.697	0.019	0.019	0.000	0.000	0.000	0.000
41	A	105	LEU	0	0.034	0.035	14.228	0.009	0.009	0.000	0.000	0.000	0.000
42	A	106	ASN	0	0.008	-0.008	16.086	0.027	0.027	0.000	0.000	0.000	0.000
43	A	107	TYR	0	0.038	0.033	11.064	0.023	0.023	0.000	0.000	0.000	0.000
44	A	108	ILE	0	0.072	0.022	10.745	0.032	0.032	0.000	0.000	0.000	0.000
45	A	109	GLU	-1	-0.771	-0.822	13.590	-0.092	-0.092	0.000	0.000	0.000	0.000
46	A	110	THR	0	-0.051	-0.028	17.032	0.039	0.039	0.000	0.000	0.000	0.000
47	A	111	GLN	0	-0.011	-0.002	12.407	0.052	0.052	0.000	0.000	0.000	0.000
48	A	112	ARG	1	0.835	0.894	14.607	0.144	0.144	0.000	0.000	0.000	0.000
49	A	113	THR	0	-0.080	-0.039	16.566	0.034	0.034	0.000	0.000	0.000	0.000
50	A	114	TYR	0	-0.030	-0.028	15.609	0.017	0.017	0.000	0.000	0.000	0.000
51	A	115	TRP	0	0.072	0.011	12.503	0.041	0.041	0.000	0.000	0.000	0.000
52	A	116	LYS	1	0.880	0.959	17.286	0.068	0.068	0.000	0.000	0.000	0.000
53	A	117	LEU	0	-0.005	-0.019	20.418	0.011	0.011	0.000	0.000	0.000	0.000
54	A	118	GLU	-1	-0.791	-0.852	18.300	0.014	0.014	0.000	0.000	0.000	0.000
55	A	119	ASN	0	-0.066	-0.042	17.294	0.026	0.026	0.000	0.000	0.000	0.000
56	A	120	GLN	0	-0.057	-0.019	21.338	0.001	0.001	0.000	0.000	0.000	0.000
57	A	121	LYS	1	0.809	0.907	22.255	-0.006	-0.006	0.000	0.000	0.000	0.000
58	A	122	LYS	1	0.967	0.987	25.899	-0.023	-0.023	0.000	0.000	0.000	0.000
59	A	123	LEU	0	0.017	0.004	25.895	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	124	TYR	0	-0.019	-0.013	28.568	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	125	ARG	1	0.977	0.977	30.409	-0.053	-0.053	0.000	0.000	0.000	0.000
62	A	126	GLY	0	0.029	0.034	32.481	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	127	SER	0	-0.019	-0.026	32.921	0.003	0.003	0.000	0.000	0.000	0.000
64	A	128	LEU	0	-0.007	0.014	34.258	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:65:VAL)