FMO DATABASE

FMODB ID: LJGG9

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:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
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
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-365194.22839
FMO2-HF: Nuclear repulsion	338871.471364
FMO2-HF: Total energy	-26322.757027
FMO2-MP2: Total energy	-26400.355823

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.
-7.909	-1.913	0.659	-2.383	-4.273	-0.005

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 : 0.066 / q_NPA : 0.029

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].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	67	LEU	0	-0.013	0.010	3.377	-1.525	1.297	0.007	-1.220	-1.610	0.004
4	A	68	SER	0	0.012	0.001	4.533	0.387	0.497	-0.001	-0.019	-0.090	0.000
5	A	69	ALA	0	0.011	-0.003	8.276	-0.088	-0.088	0.000	0.000	0.000	0.000
6	A	70	CYS	0	-0.025	-0.023	11.298	0.003	0.003	0.000	0.000	0.000	0.000
7	A	71	GLU	-1	-0.823	-0.933	6.793	-1.379	-1.379	0.000	0.000	0.000	0.000
8	A	72	VAL	0	-0.009	-0.001	7.332	0.007	0.007	0.000	0.000	0.000	0.000
9	A	73	ALA	0	0.046	0.041	9.437	0.125	0.125	0.000	0.000	0.000	0.000
10	A	74	VAL	0	-0.016	-0.012	12.410	0.091	0.091	0.000	0.000	0.000	0.000
11	A	75	LEU	0	-0.024	-0.020	7.042	0.086	0.086	0.000	0.000	0.000	0.000
12	A	76	ASP	-1	-0.826	-0.913	11.184	-0.504	-0.504	0.000	0.000	0.000	0.000
13	A	77	LEU	0	-0.050	-0.012	13.048	0.090	0.090	0.000	0.000	0.000	0.000
14	A	78	TYR	0	-0.054	-0.055	12.940	0.054	0.054	0.000	0.000	0.000	0.000
15	A	79	GLU	-1	-0.940	-0.962	12.187	-0.122	-0.122	0.000	0.000	0.000	0.000
16	A	80	GLN	0	-0.021	-0.022	14.672	0.072	0.072	0.000	0.000	0.000	0.000
17	A	81	SER	0	-0.083	-0.047	17.766	0.033	0.033	0.000	0.000	0.000	0.000
18	A	82	ASN	0	-0.102	-0.053	17.534	0.037	0.037	0.000	0.000	0.000	0.000
19	A	83	ILE	0	-0.058	-0.021	14.923	0.030	0.030	0.000	0.000	0.000	0.000
20	A	84	ARG	1	0.953	0.961	12.885	-0.184	-0.184	0.000	0.000	0.000	0.000
21	A	85	ILE	0	0.005	0.012	9.071	0.029	0.029	0.000	0.000	0.000	0.000
22	A	86	PRO	0	-0.018	-0.008	9.808	0.069	0.069	0.000	0.000	0.000	0.000
23	A	87	SER	0	0.044	0.024	6.082	-0.073	-0.073	0.000	0.000	0.000	0.000
24	A	88	ASP	-1	-0.883	-0.939	5.843	-0.368	-0.368	0.000	0.000	0.000	0.000
25	A	89	ILE	0	-0.021	-0.012	8.224	-0.098	-0.098	0.000	0.000	0.000	0.000
26	A	90	ILE	0	-0.011	0.001	2.933	-0.569	-0.045	0.163	-0.123	-0.563	0.000
27	A	91	GLU	-1	-0.858	-0.950	2.851	-4.340	-2.580	0.249	-0.814	-1.196	-0.009
28	A	92	ASP	-1	-0.870	-0.916	5.131	-0.155	-0.153	-0.001	-0.001	0.001	0.000
29	A	93	LEU	0	-0.037	-0.014	7.272	0.117	0.117	0.000	0.000	0.000	0.000
30	A	94	VAL	0	0.003	0.003	2.720	-0.683	0.095	0.242	-0.206	-0.815	0.000
31	A	95	ASN	0	-0.099	-0.066	6.107	0.393	0.393	0.000	0.000	0.000	0.000
32	A	96	GLN	0	-0.082	-0.038	8.244	0.168	0.168	0.000	0.000	0.000	0.000
33	A	97	ARG	1	0.849	0.936	8.305	0.630	0.630	0.000	0.000	0.000	0.000
34	A	98	LEU	0	0.005	0.014	10.864	0.057	0.057	0.000	0.000	0.000	0.000
35	A	99	GLN	0	-0.064	-0.040	12.574	-0.038	-0.038	0.000	0.000	0.000	0.000
36	A	100	SER	0	-0.022	-0.023	15.312	-0.014	-0.014	0.000	0.000	0.000	0.000
37	A	101	GLU	-1	-0.888	-0.955	15.060	-0.444	-0.444	0.000	0.000	0.000	0.000
38	A	102	GLN	0	0.010	-0.017	16.118	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	103	GLU	-1	-0.822	-0.871	15.928	-0.332	-0.332	0.000	0.000	0.000	0.000
40	A	104	VAL	0	0.052	0.022	11.070	0.013	0.013	0.000	0.000	0.000	0.000
41	A	105	LEU	0	0.022	0.024	13.591	0.002	0.002	0.000	0.000	0.000	0.000
42	A	106	ASN	0	0.021	0.004	15.921	0.028	0.028	0.000	0.000	0.000	0.000
43	A	107	TYR	0	0.023	0.028	11.048	0.024	0.024	0.000	0.000	0.000	0.000
44	A	108	ILE	0	0.048	0.027	10.819	0.024	0.024	0.000	0.000	0.000	0.000
45	A	109	GLU	-1	-0.768	-0.829	13.805	-0.173	-0.173	0.000	0.000	0.000	0.000
46	A	110	THR	0	-0.058	-0.031	16.820	0.046	0.046	0.000	0.000	0.000	0.000
47	A	111	GLN	0	-0.023	-0.026	12.325	0.067	0.067	0.000	0.000	0.000	0.000
48	A	112	ARG	1	0.821	0.873	14.582	0.229	0.229	0.000	0.000	0.000	0.000
49	A	113	THR	0	-0.056	-0.037	16.209	0.046	0.046	0.000	0.000	0.000	0.000
50	A	114	TYR	0	-0.019	-0.026	15.515	0.023	0.023	0.000	0.000	0.000	0.000
51	A	115	TRP	0	0.084	0.025	12.305	0.056	0.056	0.000	0.000	0.000	0.000
52	A	116	LYS	1	0.855	0.958	17.029	0.129	0.129	0.000	0.000	0.000	0.000
53	A	117	LEU	0	0.003	-0.007	20.067	0.016	0.016	0.000	0.000	0.000	0.000
54	A	118	GLU	-1	-0.817	-0.865	18.007	-0.014	-0.014	0.000	0.000	0.000	0.000
55	A	119	ASN	0	-0.045	-0.043	17.057	0.032	0.032	0.000	0.000	0.000	0.000
56	A	120	GLN	0	-0.038	0.001	21.091	0.003	0.003	0.000	0.000	0.000	0.000
57	A	121	LYS	1	0.796	0.894	22.142	0.026	0.026	0.000	0.000	0.000	0.000
58	A	122	LYS	1	0.962	0.977	25.916	-0.005	-0.005	0.000	0.000	0.000	0.000
59	A	123	LEU	0	-0.004	-0.002	25.835	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	124	TYR	0	-0.004	-0.002	28.301	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	125	ARG	1	0.971	0.974	29.760	-0.038	-0.038	0.000	0.000	0.000	0.000
62	A	126	GLY	0	0.043	0.039	32.513	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	127	SER	0	-0.012	-0.021	33.290	0.005	0.005	0.000	0.000	0.000	0.000
64	A	128	LEU	0	-0.032	0.000	34.813	0.000	0.000	0.000	0.000	0.000	0.000

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