FMO DATABASE

FMODB ID: YZRL2

Calculation Name: 1BII-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1BII

Chain ID: B

ChEMBL ID:

UniProt ID: P01887

Base Structure: X-ray

Registration Date: 2023-06-26

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	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	98
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-776098.335479
FMO2-HF: Nuclear repulsion	734116.157602
FMO2-HF: Total energy	-41982.177877
FMO2-MP2: Total energy	-42101.04684

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(B:301:ILE)

Summations of interaction energy for fragment #1(B:301:ILE)

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.
-4.18	-1.094	0.109	-1.162	-2.033	0

Interaction energy analysis for fragmet #1(B:301:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / q_NPA : -0.013

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	B	303	LYS	1	0.899	0.949	3.790	-2.953	-1.087	-0.022	-0.829	-1.014	0.002
4	B	304	THR	0	0.052	0.014	6.386	-0.500	-0.500	0.000	0.000	0.000	0.000
5	B	305	PRO	0	0.009	0.018	10.108	0.072	0.072	0.000	0.000	0.000	0.000
6	B	306	GLN	0	-0.025	0.002	12.259	-0.114	-0.114	0.000	0.000	0.000	0.000
7	B	307	ILE	0	-0.010	-0.015	15.173	-0.036	-0.036	0.000	0.000	0.000	0.000
8	B	308	GLN	0	-0.009	0.004	18.323	0.015	0.015	0.000	0.000	0.000	0.000
9	B	309	VAL	0	0.012	-0.006	21.593	-0.012	-0.012	0.000	0.000	0.000	0.000
10	B	310	TYR	0	-0.007	-0.008	22.914	0.005	0.005	0.000	0.000	0.000	0.000
11	B	311	SER	0	0.018	-0.008	27.530	-0.004	-0.004	0.000	0.000	0.000	0.000
12	B	312	ARG	1	0.934	0.967	28.993	-0.037	-0.037	0.000	0.000	0.000	0.000
13	B	313	HIS	0	0.008	0.016	30.803	0.005	0.005	0.000	0.000	0.000	0.000
14	B	314	PRO	0	0.059	0.038	34.228	0.001	0.001	0.000	0.000	0.000	0.000
15	B	315	PRO	0	-0.019	-0.005	34.241	-0.005	-0.005	0.000	0.000	0.000	0.000
16	B	316	GLU	-1	-0.884	-0.943	36.739	0.035	0.035	0.000	0.000	0.000	0.000
17	B	317	ASN	0	0.000	0.012	40.235	0.000	0.000	0.000	0.000	0.000	0.000
18	B	318	GLY	0	0.012	0.020	41.686	-0.001	-0.001	0.000	0.000	0.000	0.000
19	B	319	LYS	1	0.861	0.926	40.594	-0.027	-0.027	0.000	0.000	0.000	0.000
20	B	320	PRO	0	0.037	0.014	38.873	0.002	0.002	0.000	0.000	0.000	0.000
21	B	321	ASN	0	-0.006	0.005	33.828	0.004	0.004	0.000	0.000	0.000	0.000
22	B	322	ILE	0	0.001	-0.012	29.353	-0.004	-0.004	0.000	0.000	0.000	0.000
23	B	323	LEU	0	-0.010	0.009	27.685	0.006	0.006	0.000	0.000	0.000	0.000
24	B	324	ASN	0	-0.018	-0.021	24.528	-0.012	-0.012	0.000	0.000	0.000	0.000
25	B	325	CYS	0	-0.051	-0.019	21.102	-0.004	-0.004	0.000	0.000	0.000	0.000
26	B	326	TYR	0	0.003	0.014	18.156	-0.001	-0.001	0.000	0.000	0.000	0.000
27	B	327	VAL	0	0.007	0.001	13.947	0.021	0.021	0.000	0.000	0.000	0.000
28	B	328	THR	0	0.055	0.016	13.476	0.006	0.006	0.000	0.000	0.000	0.000
29	B	329	GLN	0	-0.037	-0.035	10.446	-0.020	-0.020	0.000	0.000	0.000	0.000
30	B	330	PHE	0	-0.009	0.011	8.254	0.269	0.269	0.000	0.000	0.000	0.000
31	B	331	HIS	0	0.039	0.035	3.240	-1.566	-0.346	0.131	-0.333	-1.019	-0.002
32	B	332	PRO	0	-0.005	-0.015	5.523	0.075	0.075	0.000	0.000	0.000	0.000
33	B	333	PRO	0	0.055	0.008	6.183	0.244	0.244	0.000	0.000	0.000	0.000
34	B	334	HIS	0	0.017	0.031	9.356	0.093	0.093	0.000	0.000	0.000	0.000
35	B	335	ILE	0	0.003	0.001	11.249	-0.003	-0.003	0.000	0.000	0.000	0.000
36	B	336	GLU	-1	-0.992	-0.995	13.731	-0.089	-0.089	0.000	0.000	0.000	0.000
37	B	337	ILE	0	0.045	0.030	16.724	0.022	0.022	0.000	0.000	0.000	0.000
38	B	338	GLN	0	0.020	0.026	19.684	-0.006	-0.006	0.000	0.000	0.000	0.000
39	B	339	MET	0	0.031	0.032	23.344	0.009	0.009	0.000	0.000	0.000	0.000
40	B	340	LEU	0	-0.036	-0.023	25.846	-0.009	-0.009	0.000	0.000	0.000	0.000
41	B	341	LYS	1	1.004	0.999	28.789	-0.005	-0.005	0.000	0.000	0.000	0.000
42	B	342	ASN	0	-0.031	-0.032	32.388	-0.002	-0.002	0.000	0.000	0.000	0.000
43	B	343	GLY	0	0.019	0.012	30.910	-0.003	-0.003	0.000	0.000	0.000	0.000
44	B	344	LYS	1	0.928	0.970	31.153	0.003	0.003	0.000	0.000	0.000	0.000
45	B	345	LYS	1	0.955	0.973	25.695	0.046	0.046	0.000	0.000	0.000	0.000
46	B	346	ILE	0	-0.043	-0.023	29.153	-0.002	-0.002	0.000	0.000	0.000	0.000
47	B	347	PRO	0	-0.018	-0.014	29.228	-0.003	-0.003	0.000	0.000	0.000	0.000
48	B	348	LYS	1	0.952	0.985	30.079	-0.004	-0.004	0.000	0.000	0.000	0.000
49	B	349	VAL	0	-0.034	0.003	24.880	0.007	0.007	0.000	0.000	0.000	0.000
50	B	350	GLU	-1	-0.914	-0.940	26.203	-0.010	-0.010	0.000	0.000	0.000	0.000
51	B	351	MET	0	-0.017	-0.019	19.231	0.011	0.011	0.000	0.000	0.000	0.000
52	B	352	SER	0	-0.052	-0.032	21.372	-0.007	-0.007	0.000	0.000	0.000	0.000
53	B	353	ASP	-1	-0.844	-0.906	19.083	0.072	0.072	0.000	0.000	0.000	0.000
54	B	354	MET	0	0.008	0.013	15.258	0.007	0.007	0.000	0.000	0.000	0.000
55	B	355	SER	0	-0.014	-0.006	14.676	-0.019	-0.019	0.000	0.000	0.000	0.000
56	B	356	PHE	0	-0.004	-0.014	10.600	-0.006	-0.006	0.000	0.000	0.000	0.000
57	B	357	SER	0	0.040	0.017	11.691	-0.046	-0.046	0.000	0.000	0.000	0.000
58	B	358	LYS	1	0.953	0.970	12.033	-0.182	-0.182	0.000	0.000	0.000	0.000
59	B	359	ASP	-1	-0.841	-0.869	10.598	0.756	0.756	0.000	0.000	0.000	0.000
60	B	360	TRP	0	-0.024	-0.017	7.258	0.175	0.175	0.000	0.000	0.000	0.000
61	B	361	SER	0	-0.134	-0.077	7.331	-0.071	-0.071	0.000	0.000	0.000	0.000
62	B	362	PHE	0	0.031	-0.006	6.668	-0.174	-0.174	0.000	0.000	0.000	0.000
63	B	363	TYR	0	-0.057	-0.031	10.336	0.077	0.077	0.000	0.000	0.000	0.000
64	B	364	ILE	0	-0.029	-0.007	13.712	-0.046	-0.046	0.000	0.000	0.000	0.000
65	B	365	LEU	0	0.004	0.015	16.859	0.023	0.023	0.000	0.000	0.000	0.000
66	B	366	ALA	0	0.002	0.000	20.543	-0.017	-0.017	0.000	0.000	0.000	0.000
67	B	367	HIS	0	0.001	-0.017	22.561	0.012	0.012	0.000	0.000	0.000	0.000
68	B	368	THR	0	-0.030	-0.046	26.292	-0.009	-0.009	0.000	0.000	0.000	0.000
69	B	369	GLU	-1	-0.898	-0.950	29.717	0.015	0.015	0.000	0.000	0.000	0.000
70	B	370	PHE	0	-0.085	-0.048	32.659	-0.002	-0.002	0.000	0.000	0.000	0.000
71	B	371	THR	0	0.029	0.007	35.163	0.002	0.002	0.000	0.000	0.000	0.000
72	B	372	PRO	0	-0.034	0.013	36.375	-0.001	-0.001	0.000	0.000	0.000	0.000
73	B	373	THR	0	0.002	-0.026	37.574	-0.002	-0.002	0.000	0.000	0.000	0.000
74	B	374	GLU	-1	-0.870	-0.937	39.009	0.036	0.036	0.000	0.000	0.000	0.000
75	B	375	THR	0	-0.005	-0.001	40.574	0.000	0.000	0.000	0.000	0.000	0.000
76	B	376	ASP	-1	-0.934	-0.938	36.461	0.016	0.016	0.000	0.000	0.000	0.000
77	B	377	THR	0	0.035	0.029	31.970	0.004	0.004	0.000	0.000	0.000	0.000
78	B	378	TYR	0	0.017	-0.011	30.102	-0.007	-0.007	0.000	0.000	0.000	0.000
79	B	379	ALA	0	0.014	0.009	26.781	0.006	0.006	0.000	0.000	0.000	0.000
80	B	381	ARG	1	0.885	0.929	21.537	0.026	0.026	0.000	0.000	0.000	0.000
81	B	382	VAL	0	0.040	0.017	15.277	-0.012	-0.012	0.000	0.000	0.000	0.000
82	B	383	LYS	1	0.952	0.969	16.364	0.093	0.093	0.000	0.000	0.000	0.000
83	B	384	HIS	0	0.064	0.044	7.852	0.061	0.061	0.000	0.000	0.000	0.000
84	B	385	ASP	-1	-0.836	-0.918	8.769	-0.474	-0.474	0.000	0.000	0.000	0.000
85	B	386	SER	0	-0.116	-0.067	7.415	-0.007	-0.007	0.000	0.000	0.000	0.000
86	B	387	MET	0	-0.069	-0.041	8.351	0.111	0.111	0.000	0.000	0.000	0.000
87	B	388	ALA	0	-0.006	0.012	11.828	-0.043	-0.043	0.000	0.000	0.000	0.000
88	B	389	GLU	-1	-0.919	-0.962	14.208	-0.053	-0.053	0.000	0.000	0.000	0.000
89	B	390	PRO	0	-0.065	-0.034	16.271	0.015	0.015	0.000	0.000	0.000	0.000
90	B	391	LYS	1	1.006	1.006	17.668	-0.134	-0.134	0.000	0.000	0.000	0.000
91	B	392	THR	0	-0.028	-0.021	19.273	-0.005	-0.005	0.000	0.000	0.000	0.000
92	B	393	VAL	0	-0.021	-0.005	20.988	0.008	0.008	0.000	0.000	0.000	0.000
93	B	394	TYR	0	0.003	-0.025	23.827	-0.011	-0.011	0.000	0.000	0.000	0.000
94	B	395	TRP	0	-0.029	-0.019	27.204	0.004	0.004	0.000	0.000	0.000	0.000
95	B	396	ASP	-1	-0.879	-0.934	28.822	0.078	0.078	0.000	0.000	0.000	0.000
96	B	397	ARG	1	0.844	0.891	30.185	-0.040	-0.040	0.000	0.000	0.000	0.000
97	B	398	ASP	-1	-0.946	-0.964	32.751	0.066	0.066	0.000	0.000	0.000	0.000
98	B	399	MET	0	-0.022	0.007	26.096	0.006	0.006	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(B:301:ILE)