FMO DATABASE

FMODB ID: ZVYJN

Calculation Name: 2BK8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2BK8

Chain ID: A

ChEMBL ID:

UniProt ID: Q8WZ42

Base Structure: X-ray

Registration Date: 2023-09-21

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	97
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-702746.271257
FMO2-HF: Nuclear repulsion	663573.787963
FMO2-HF: Total energy	-39172.483295
FMO2-MP2: Total energy	-39285.393455

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:0:GLY)

Summations of interaction energy for fragment #1(A:0:GLY)

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.
5.195	-9.088	20.002	0.088	-5.808	-0.05

Interaction energy analysis for fragmet #1(A:0:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / 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	2	MET	0	-0.004	0.007	1.878	3.318	-9.221	11.422	4.813	-3.696	-0.042
4	A	3	VAL	0	-0.016	-0.007	3.973	-1.071	-1.088	0.000	0.004	0.013	0.000
5	A	4	SER	0	-0.055	-0.036	6.683	0.486	0.486	0.000	0.000	0.000	0.000
6	A	5	GLY	0	0.029	0.011	9.941	-0.106	-0.106	0.000	0.000	0.000	0.000
7	A	6	GLN	0	-0.034	-0.030	12.290	-0.011	-0.011	0.000	0.000	0.000	0.000
8	A	7	ILE	0	-0.005	0.006	15.960	0.048	0.048	0.000	0.000	0.000	0.000
9	A	8	MET	0	-0.030	-0.016	18.635	-0.030	-0.030	0.000	0.000	0.000	0.000
10	A	9	HIS	0	0.038	0.019	22.265	0.014	0.014	0.000	0.000	0.000	0.000
11	A	10	ALA	0	0.004	0.007	25.406	0.010	0.010	0.000	0.000	0.000	0.000
12	A	11	VAL	0	-0.028	-0.011	28.201	-0.009	-0.009	0.000	0.000	0.000	0.000
13	A	12	GLY	0	0.035	0.020	31.991	0.008	0.008	0.000	0.000	0.000	0.000
14	A	13	GLU	-1	-0.983	-0.993	33.270	0.032	0.032	0.000	0.000	0.000	0.000
15	A	14	GLU	-1	-0.840	-0.922	36.701	0.023	0.023	0.000	0.000	0.000	0.000
16	A	15	GLY	0	-0.018	-0.007	38.132	0.000	0.000	0.000	0.000	0.000	0.000
17	A	16	GLY	0	-0.009	0.009	35.979	0.004	0.004	0.000	0.000	0.000	0.000
18	A	17	HIS	0	-0.011	-0.013	30.921	0.002	0.002	0.000	0.000	0.000	0.000
19	A	18	VAL	0	-0.024	-0.001	27.475	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	19	LYS	1	0.939	0.975	24.028	-0.126	-0.126	0.000	0.000	0.000	0.000
21	A	20	TYR	0	-0.055	-0.036	20.910	-0.011	-0.011	0.000	0.000	0.000	0.000
22	A	21	VAL	0	-0.003	-0.011	17.556	0.019	0.019	0.000	0.000	0.000	0.000
23	A	22	CYS	0	-0.038	-0.011	13.790	-0.025	-0.025	0.000	0.000	0.000	0.000
24	A	23	LYS	1	0.869	0.921	10.848	-0.672	-0.672	0.000	0.000	0.000	0.000
25	A	24	ILE	0	0.000	-0.012	7.054	-0.129	-0.129	0.000	0.000	0.000	0.000
26	A	25	GLU	-1	-0.850	-0.897	5.804	1.079	1.079	0.000	0.000	0.000	0.000
27	A	26	ASN	0	-0.039	-0.042	2.011	-1.650	-4.053	8.577	-4.536	-1.638	-0.008
28	A	27	TYR	0	-0.023	-0.006	3.846	1.922	2.366	0.005	-0.162	-0.287	0.000
29	A	28	ASP	-1	-0.806	-0.881	5.589	3.683	3.683	0.000	0.000	0.000	0.000
30	A	29	GLN	0	-0.043	-0.047	8.024	-0.470	-0.470	0.000	0.000	0.000	0.000
31	A	30	SER	0	-0.018	-0.012	8.029	-0.351	-0.351	0.000	0.000	0.000	0.000
32	A	31	THR	0	-0.035	-0.017	7.925	-0.050	-0.050	0.000	0.000	0.000	0.000
33	A	32	GLN	0	-0.014	0.001	9.839	-0.084	-0.084	0.000	0.000	0.000	0.000
34	A	33	VAL	0	-0.009	-0.010	12.665	-0.060	-0.060	0.000	0.000	0.000	0.000
35	A	34	THR	0	-0.036	-0.008	14.739	-0.016	-0.016	0.000	0.000	0.000	0.000
36	A	35	TRP	0	0.060	0.014	17.606	-0.045	-0.045	0.000	0.000	0.000	0.000
37	A	36	TYR	0	-0.039	-0.032	18.417	-0.011	-0.011	0.000	0.000	0.000	0.000
38	A	37	PHE	0	0.009	0.028	22.724	0.001	0.001	0.000	0.000	0.000	0.000
39	A	38	GLY	0	0.024	0.009	25.912	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	39	VAL	0	-0.054	-0.042	25.129	-0.005	-0.005	0.000	0.000	0.000	0.000
41	A	40	ARG	1	0.922	0.970	26.354	-0.005	-0.005	0.000	0.000	0.000	0.000
42	A	41	GLN	0	0.055	0.030	21.979	-0.015	-0.015	0.000	0.000	0.000	0.000
43	A	42	LEU	0	-0.069	-0.027	23.402	0.001	0.001	0.000	0.000	0.000	0.000
44	A	43	GLU	-1	-0.932	-0.964	23.590	0.100	0.100	0.000	0.000	0.000	0.000
45	A	44	ASN	0	-0.012	-0.015	24.139	-0.012	-0.012	0.000	0.000	0.000	0.000
46	A	45	SER	0	-0.029	-0.012	27.229	-0.010	-0.010	0.000	0.000	0.000	0.000
47	A	46	GLU	-1	-0.937	-0.973	30.955	0.073	0.073	0.000	0.000	0.000	0.000
48	A	47	LYS	1	0.796	0.911	30.962	-0.052	-0.052	0.000	0.000	0.000	0.000
49	A	48	TYR	0	-0.023	-0.024	26.380	-0.005	-0.005	0.000	0.000	0.000	0.000
50	A	49	GLU	-1	-0.875	-0.928	26.058	0.163	0.163	0.000	0.000	0.000	0.000
51	A	50	ILE	0	-0.052	-0.041	20.632	0.003	0.003	0.000	0.000	0.000	0.000
52	A	51	THR	0	0.023	0.011	20.817	0.006	0.006	0.000	0.000	0.000	0.000
53	A	52	TYR	0	-0.008	-0.022	11.082	0.014	0.014	0.000	0.000	0.000	0.000
54	A	53	GLU	-1	-0.923	-0.957	16.160	0.428	0.428	0.000	0.000	0.000	0.000
55	A	54	ASP	-1	-0.888	-0.920	13.225	1.004	1.004	0.000	0.000	0.000	0.000
56	A	55	GLY	0	0.052	0.029	10.797	0.018	0.018	0.000	0.000	0.000	0.000
57	A	56	VAL	0	-0.049	-0.023	11.492	-0.115	-0.115	0.000	0.000	0.000	0.000
58	A	57	ALA	0	0.002	0.007	14.675	-0.020	-0.020	0.000	0.000	0.000	0.000
59	A	58	ILE	0	-0.022	-0.022	16.210	-0.044	-0.044	0.000	0.000	0.000	0.000
60	A	59	LEU	0	-0.005	0.016	19.913	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	60	TYR	0	0.023	-0.005	22.510	-0.007	-0.007	0.000	0.000	0.000	0.000
62	A	61	VAL	0	-0.018	-0.005	26.147	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	62	LYN	0	0.037	0.010	28.788	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	63	ASP	-1	-0.885	-0.938	32.398	0.058	0.058	0.000	0.000	0.000	0.000
65	A	64	ILE	0	-0.065	-0.015	31.137	-0.006	-0.006	0.000	0.000	0.000	0.000
66	A	65	THR	0	-0.007	-0.016	35.154	-0.005	-0.005	0.000	0.000	0.000	0.000
67	A	66	LYS	1	0.841	0.878	35.734	-0.014	-0.014	0.000	0.000	0.000	0.000
68	A	67	LEU	0	-0.045	-0.021	35.638	-0.005	-0.005	0.000	0.000	0.000	0.000
69	A	68	ASP	-1	-0.773	-0.867	31.487	0.035	0.035	0.000	0.000	0.000	0.000
70	A	69	ASP	-1	-0.769	-0.848	30.729	-0.006	-0.006	0.000	0.000	0.000	0.000
71	A	70	GLY	0	0.013	-0.007	29.600	-0.005	-0.005	0.000	0.000	0.000	0.000
72	A	71	THR	0	-0.045	-0.047	23.437	0.002	0.002	0.000	0.000	0.000	0.000
73	A	72	TYR	0	-0.033	-0.031	22.779	0.004	0.004	0.000	0.000	0.000	0.000
74	A	73	ARG	1	0.876	0.933	15.783	0.158	0.158	0.000	0.000	0.000	0.000
75	A	74	CYS	0	-0.023	0.001	14.775	0.033	0.033	0.000	0.000	0.000	0.000
76	A	75	LYS	1	0.788	0.864	14.188	0.139	0.139	0.000	0.000	0.000	0.000
77	A	76	VAL	0	0.025	0.000	9.206	0.084	0.084	0.000	0.000	0.000	0.000
78	A	77	VAL	0	0.006	-0.007	9.692	-0.193	-0.193	0.000	0.000	0.000	0.000
79	A	78	ASN	0	0.015	-0.010	3.769	-0.867	-0.802	-0.001	-0.014	-0.051	0.000
80	A	79	ASP	-1	-0.881	-0.935	7.889	0.100	0.100	0.000	0.000	0.000	0.000
81	A	80	TYR	0	-0.105	-0.050	4.156	-0.629	-0.462	-0.001	-0.017	-0.149	0.000
82	A	81	GLY	0	-0.010	-0.003	6.241	-0.350	-0.350	0.000	0.000	0.000	0.000
83	A	82	GLU	-1	-0.849	-0.901	7.694	0.047	0.047	0.000	0.000	0.000	0.000
84	A	83	ASP	-1	-0.764	-0.851	8.813	-0.735	-0.735	0.000	0.000	0.000	0.000
85	A	84	SER	0	-0.080	-0.045	10.602	0.189	0.189	0.000	0.000	0.000	0.000
86	A	85	SER	0	0.029	0.041	13.161	-0.053	-0.053	0.000	0.000	0.000	0.000
87	A	86	TYR	0	-0.033	-0.039	15.613	0.038	0.038	0.000	0.000	0.000	0.000
88	A	87	ALA	0	-0.009	0.006	19.458	0.001	0.001	0.000	0.000	0.000	0.000
89	A	88	GLU	-1	-0.753	-0.842	22.441	-0.041	-0.041	0.000	0.000	0.000	0.000
90	A	89	LEU	0	-0.017	0.022	26.245	0.012	0.012	0.000	0.000	0.000	0.000
91	A	90	PHE	0	-0.035	-0.027	28.869	-0.008	-0.008	0.000	0.000	0.000	0.000
92	A	91	VAL	0	0.041	0.018	32.310	0.007	0.007	0.000	0.000	0.000	0.000
93	A	92	LYS	1	0.956	0.963	35.554	-0.015	-0.015	0.000	0.000	0.000	0.000
94	A	93	GLY	0	-0.019	-0.026	38.977	0.002	0.002	0.000	0.000	0.000	0.000
95	A	94	VAL	0	-0.034	0.006	36.028	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	95	ARG	1	0.756	0.853	29.546	0.020	0.020	0.000	0.000	0.000	0.000
97	A	96	GLU	-1	-0.982	-0.982	37.522	-0.026	-0.026	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:0:GLY)