FMO DATABASE

FMODB ID: J3YY9

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	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	64
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-363393.134974
FMO2-HF: Nuclear repulsion	337071.487113
FMO2-HF: Total energy	-26321.647861
FMO2-MP2: Total energy	-26399.35438

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.
-3.761	0.273	0.246	-1.165	-3.113	-0.001

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 : 0.036 / 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

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	0.004	0.002	3.476	-1.074	0.998	0.013	-0.630	-1.455	0.002
4	A	68	SER	0	0.030	0.027	4.753	-0.441	-0.333	-0.001	-0.013	-0.094	0.000
5	A	69	ALA	0	0.001	-0.007	8.129	0.039	0.039	0.000	0.000	0.000	0.000
6	A	70	CYS	0	-0.004	-0.008	11.382	0.004	0.004	0.000	0.000	0.000	0.000
7	A	71	GLU	-1	-0.862	-0.951	7.174	0.460	0.460	0.000	0.000	0.000	0.000
8	A	72	VAL	0	0.008	-0.002	7.712	0.056	0.056	0.000	0.000	0.000	0.000
9	A	73	ALA	0	0.063	0.052	10.076	-0.021	-0.021	0.000	0.000	0.000	0.000
10	A	74	VAL	0	-0.040	-0.023	12.810	-0.025	-0.025	0.000	0.000	0.000	0.000
11	A	75	LEU	0	-0.031	-0.038	6.878	-0.009	-0.009	0.000	0.000	0.000	0.000
12	A	76	ASP	-1	-0.860	-0.927	11.318	0.269	0.269	0.000	0.000	0.000	0.000
13	A	77	LEU	0	-0.030	-0.013	13.650	-0.046	-0.046	0.000	0.000	0.000	0.000
14	A	78	TYR	0	-0.072	-0.047	13.291	-0.032	-0.032	0.000	0.000	0.000	0.000
15	A	79	GLU	-1	-0.971	-0.973	12.501	0.193	0.193	0.000	0.000	0.000	0.000
16	A	80	GLN	0	0.008	0.001	15.068	-0.044	-0.044	0.000	0.000	0.000	0.000
17	A	81	SER	0	-0.085	-0.030	17.981	-0.026	-0.026	0.000	0.000	0.000	0.000
18	A	82	ASN	0	-0.081	-0.045	17.971	-0.007	-0.007	0.000	0.000	0.000	0.000
19	A	83	ILE	0	-0.034	-0.007	14.975	-0.016	-0.016	0.000	0.000	0.000	0.000
20	A	84	ARG	1	0.959	0.973	13.231	-0.072	-0.072	0.000	0.000	0.000	0.000
21	A	85	ILE	0	-0.012	-0.003	9.116	-0.046	-0.046	0.000	0.000	0.000	0.000
22	A	86	PRO	0	-0.009	-0.002	9.853	0.030	0.030	0.000	0.000	0.000	0.000
23	A	87	SER	0	0.065	0.013	6.139	0.069	0.069	0.000	0.000	0.000	0.000
24	A	88	ASP	-1	-0.900	-0.943	6.143	-0.130	-0.130	0.000	0.000	0.000	0.000
25	A	89	ILE	0	-0.042	-0.025	8.244	-0.040	-0.040	0.000	0.000	0.000	0.000
26	A	90	ILE	0	-0.010	0.001	3.143	-0.318	0.112	0.095	-0.090	-0.436	0.000
27	A	91	GLU	-1	-0.900	-0.957	3.591	-1.851	-1.162	0.012	-0.252	-0.448	-0.002
28	A	92	ASP	-1	-0.966	-0.980	5.046	0.006	0.017	-0.001	0.000	-0.009	0.000
29	A	93	LEU	0	-0.006	-0.009	7.073	0.037	0.037	0.000	0.000	0.000	0.000
30	A	94	VAL	0	0.053	0.036	2.802	-0.700	0.024	0.128	-0.180	-0.671	-0.001
31	A	95	ASN	0	-0.092	-0.046	6.284	0.020	0.020	0.000	0.000	0.000	0.000
32	A	96	GLN	0	-0.064	-0.037	8.551	0.015	0.015	0.000	0.000	0.000	0.000
33	A	97	ARG	1	0.864	0.940	8.422	-0.078	-0.078	0.000	0.000	0.000	0.000
34	A	98	LEU	0	0.023	0.019	11.012	-0.013	-0.013	0.000	0.000	0.000	0.000
35	A	99	GLN	0	-0.023	-0.015	12.769	0.010	0.010	0.000	0.000	0.000	0.000
36	A	100	SER	0	-0.077	-0.017	15.436	-0.006	-0.006	0.000	0.000	0.000	0.000
37	A	101	GLU	-1	-0.903	-0.953	15.163	0.155	0.155	0.000	0.000	0.000	0.000
38	A	102	GLN	0	0.050	-0.010	16.596	0.016	0.016	0.000	0.000	0.000	0.000
39	A	103	GLU	-1	-0.880	-0.942	16.361	0.086	0.086	0.000	0.000	0.000	0.000
40	A	104	VAL	0	0.035	0.026	11.720	-0.006	-0.006	0.000	0.000	0.000	0.000
41	A	105	LEU	0	0.043	0.034	14.130	0.005	0.005	0.000	0.000	0.000	0.000
42	A	106	ASN	0	0.007	-0.008	16.248	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	107	TYR	0	0.037	0.035	10.867	-0.015	-0.015	0.000	0.000	0.000	0.000
44	A	108	ILE	0	0.065	0.019	11.101	-0.017	-0.017	0.000	0.000	0.000	0.000
45	A	109	GLU	-1	-0.851	-0.932	13.708	0.094	0.094	0.000	0.000	0.000	0.000
46	A	110	THR	0	-0.036	-0.012	16.901	-0.017	-0.017	0.000	0.000	0.000	0.000
47	A	111	GLN	0	0.015	0.005	12.351	-0.014	-0.014	0.000	0.000	0.000	0.000
48	A	112	ARG	1	0.897	0.960	14.673	-0.138	-0.138	0.000	0.000	0.000	0.000
49	A	113	THR	0	-0.089	-0.039	16.625	-0.014	-0.014	0.000	0.000	0.000	0.000
50	A	114	TYR	0	-0.016	-0.001	15.710	-0.008	-0.008	0.000	0.000	0.000	0.000
51	A	115	TRP	0	0.080	0.013	12.530	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	116	LYS	1	0.907	0.961	17.343	-0.058	-0.058	0.000	0.000	0.000	0.000
53	A	117	LEU	0	-0.021	-0.023	20.486	-0.005	-0.005	0.000	0.000	0.000	0.000
54	A	118	GLU	-1	-0.922	-0.952	18.440	0.005	0.005	0.000	0.000	0.000	0.000
55	A	119	ASN	0	-0.060	-0.036	17.333	-0.008	-0.008	0.000	0.000	0.000	0.000
56	A	120	GLN	0	-0.045	-0.017	21.408	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	121	LYS	1	0.889	0.967	22.854	-0.014	-0.014	0.000	0.000	0.000	0.000
58	A	122	LYS	1	0.972	0.993	25.954	-0.009	-0.009	0.000	0.000	0.000	0.000
59	A	123	LEU	0	0.031	0.006	26.308	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	124	TYR	0	-0.029	-0.015	28.625	0.001	0.001	0.000	0.000	0.000	0.000
61	A	125	ARG	1	0.953	0.973	30.085	-0.008	-0.008	0.000	0.000	0.000	0.000
62	A	126	GLY	0	0.026	0.026	32.536	0.000	0.000	0.000	0.000	0.000	0.000
63	A	127	SER	0	0.006	-0.016	32.330	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	128	LEU	0	-0.012	0.013	34.332	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)