FMO DATABASE

FMODB ID: 52N9Z

Calculation Name: 3BS5-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BS5

Chain ID: B

ChEMBL ID:

UniProt ID: Q8ML92

Base Structure: X-ray

Registration Date: 2023-06-22

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	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	75
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-494038.119649
FMO2-HF: Nuclear repulsion	463602.438338
FMO2-HF: Total energy	-30435.681311
FMO2-MP2: Total energy	-30523.922415

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:111:GLU)

Summations of interaction energy for fragment #1(B:111:GLU)

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.
-72.314	-74.508	39.599	-18.98	-18.425	0.183

Interaction energy analysis for fragmet #1(B:111:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.813 / q_NPA : -0.898

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	B	113	VAL	0	0.092	0.031	2.623	7.131	9.679	0.790	-1.504	-1.835	-0.015
4	B	114	SER	0	0.014	0.007	5.037	3.604	3.769	-0.001	-0.006	-0.157	0.000
5	B	115	LYS	1	0.775	0.861	1.736	-138.986	-144.128	24.346	-10.860	-8.344	0.123
6	B	116	TRP	0	-0.052	-0.008	2.439	5.041	9.481	2.434	-2.521	-4.353	0.019
7	B	117	SER	0	-0.009	-0.033	3.668	-17.503	-17.331	0.020	0.095	-0.287	0.001
8	B	118	PRO	0	0.045	0.000	6.135	-0.789	-0.789	0.000	0.000	0.000	0.000
9	B	119	SER	0	-0.040	-0.010	8.798	-2.603	-2.603	0.000	0.000	0.000	0.000
10	B	120	GLN	0	0.002	0.023	1.765	-16.564	-20.941	12.010	-4.184	-3.449	0.055
11	B	121	VAL	0	0.028	0.031	7.246	-2.268	-2.268	0.000	0.000	0.000	0.000
12	B	122	VAL	0	0.011	-0.005	9.531	-2.551	-2.551	0.000	0.000	0.000	0.000
13	B	123	ASP	-1	-0.848	-0.928	10.195	24.149	24.149	0.000	0.000	0.000	0.000
14	B	124	TRP	0	-0.011	-0.001	9.482	-0.914	-0.914	0.000	0.000	0.000	0.000
15	B	125	MET	0	-0.003	0.002	11.421	-1.555	-1.555	0.000	0.000	0.000	0.000
16	B	126	LYS	1	0.823	0.912	14.276	-22.171	-22.171	0.000	0.000	0.000	0.000
17	B	127	GLY	0	-0.045	-0.007	14.810	-0.807	-0.807	0.000	0.000	0.000	0.000
18	B	128	LEU	0	-0.037	-0.007	15.170	-0.365	-0.365	0.000	0.000	0.000	0.000
19	B	129	ASP	-1	-0.848	-0.932	18.111	13.296	13.296	0.000	0.000	0.000	0.000
20	B	130	ASP	-1	-0.874	-0.941	21.967	12.593	12.593	0.000	0.000	0.000	0.000
21	B	131	CYS	0	-0.092	-0.047	24.228	-0.089	-0.089	0.000	0.000	0.000	0.000
22	B	132	LEU	0	0.008	0.011	20.163	-0.305	-0.305	0.000	0.000	0.000	0.000
23	B	133	GLN	0	0.019	-0.001	18.784	0.725	0.725	0.000	0.000	0.000	0.000
24	B	134	GLN	0	-0.125	-0.065	21.632	-0.123	-0.123	0.000	0.000	0.000	0.000
25	B	135	TYR	0	-0.019	-0.029	20.899	-0.373	-0.373	0.000	0.000	0.000	0.000
26	B	136	ILE	0	0.035	0.039	16.277	0.420	0.420	0.000	0.000	0.000	0.000
27	B	137	LYS	1	0.907	0.948	17.871	-12.141	-12.141	0.000	0.000	0.000	0.000
28	B	138	ASN	0	-0.061	-0.032	20.295	-0.362	-0.362	0.000	0.000	0.000	0.000
29	B	139	PHE	0	0.093	0.038	14.352	0.109	0.109	0.000	0.000	0.000	0.000
30	B	140	GLU	-1	-0.893	-0.956	15.420	18.957	18.957	0.000	0.000	0.000	0.000
31	B	141	ARG	1	0.752	0.868	16.443	-13.598	-13.598	0.000	0.000	0.000	0.000
32	B	142	GLU	-1	-0.810	-0.896	17.655	15.068	15.068	0.000	0.000	0.000	0.000
33	B	143	LYS	1	0.777	0.893	13.660	-17.837	-17.837	0.000	0.000	0.000	0.000
34	B	144	ILE	0	0.024	0.018	12.347	1.388	1.388	0.000	0.000	0.000	0.000
35	B	145	SER	0	0.008	-0.014	8.343	1.934	1.934	0.000	0.000	0.000	0.000
36	B	146	GLY	0	0.055	0.002	7.157	-2.754	-2.754	0.000	0.000	0.000	0.000
37	B	147	ASP	-1	-0.839	-0.883	8.094	22.957	22.957	0.000	0.000	0.000	0.000
38	B	148	GLN	0	0.034	0.034	9.854	-0.627	-0.627	0.000	0.000	0.000	0.000
39	B	149	LEU	0	0.011	0.010	10.185	-1.431	-1.431	0.000	0.000	0.000	0.000
40	B	150	LEU	0	-0.044	-0.031	8.339	-1.396	-1.396	0.000	0.000	0.000	0.000
41	B	151	ARG	1	0.737	0.837	12.271	-22.844	-22.844	0.000	0.000	0.000	0.000
42	B	152	ILE	0	-0.031	0.017	15.511	-1.038	-1.038	0.000	0.000	0.000	0.000
43	B	153	THR	0	-0.012	-0.036	17.453	-0.726	-0.726	0.000	0.000	0.000	0.000
44	B	154	HIS	0	-0.008	-0.030	21.202	0.374	0.374	0.000	0.000	0.000	0.000
45	B	155	GLN	0	-0.047	-0.021	24.250	-0.446	-0.446	0.000	0.000	0.000	0.000
46	B	156	GLU	-1	-0.793	-0.878	18.934	15.962	15.962	0.000	0.000	0.000	0.000
47	B	157	LEU	0	-0.018	-0.005	18.938	0.262	0.262	0.000	0.000	0.000	0.000
48	B	158	GLU	-1	-0.905	-0.936	22.107	10.722	10.722	0.000	0.000	0.000	0.000
49	B	159	ASP	-1	-0.878	-0.919	23.241	12.087	12.087	0.000	0.000	0.000	0.000
50	B	160	LEU	0	-0.096	-0.045	18.040	0.094	0.094	0.000	0.000	0.000	0.000
51	B	161	GLY	0	-0.032	-0.020	22.228	0.135	0.135	0.000	0.000	0.000	0.000
52	B	162	VAL	0	-0.026	-0.010	21.856	-0.443	-0.443	0.000	0.000	0.000	0.000
53	B	163	SER	0	0.006	0.000	25.226	-0.106	-0.106	0.000	0.000	0.000	0.000
54	B	164	ARG	1	0.909	0.959	28.395	-10.695	-10.695	0.000	0.000	0.000	0.000
55	B	165	ILE	0	0.134	0.054	27.719	0.303	0.303	0.000	0.000	0.000	0.000
56	B	166	GLY	0	-0.014	0.001	27.101	0.281	0.281	0.000	0.000	0.000	0.000
57	B	167	HIS	0	0.011	-0.001	24.604	0.180	0.180	0.000	0.000	0.000	0.000
58	B	168	GLN	0	-0.059	-0.044	23.132	0.614	0.614	0.000	0.000	0.000	0.000
59	B	169	GLU	-1	-0.850	-0.926	22.301	12.524	12.524	0.000	0.000	0.000	0.000
60	B	170	LEU	0	0.017	0.015	22.442	0.330	0.330	0.000	0.000	0.000	0.000
61	B	171	ILE	0	-0.022	-0.010	17.570	0.705	0.705	0.000	0.000	0.000	0.000
62	B	172	LEU	0	0.015	0.004	17.865	1.035	1.035	0.000	0.000	0.000	0.000
63	B	173	GLU	-1	-0.915	-0.947	18.473	13.436	13.436	0.000	0.000	0.000	0.000
64	B	174	ALA	0	-0.017	-0.009	15.951	0.552	0.552	0.000	0.000	0.000	0.000
65	B	175	VAL	0	-0.006	-0.017	13.730	1.409	1.409	0.000	0.000	0.000	0.000
66	B	176	ASP	-1	-0.877	-0.938	14.021	16.756	16.756	0.000	0.000	0.000	0.000
67	B	177	LEU	0	-0.048	-0.022	14.872	0.383	0.383	0.000	0.000	0.000	0.000
68	B	178	LEU	0	-0.031	-0.008	8.067	0.912	0.912	0.000	0.000	0.000	0.000
69	B	179	CYS	0	-0.023	-0.013	10.246	1.882	1.882	0.000	0.000	0.000	0.000
70	B	180	ALA	0	0.007	-0.010	12.154	0.404	0.404	0.000	0.000	0.000	0.000
71	B	181	LEU	0	-0.024	-0.014	8.969	0.050	0.050	0.000	0.000	0.000	0.000
72	B	182	ASN	0	-0.049	-0.012	6.794	4.018	4.018	0.000	0.000	0.000	0.000
73	B	183	TYR	0	-0.055	-0.036	8.640	1.774	1.774	0.000	0.000	0.000	0.000
74	B	184	GLY	0	-0.016	0.007	10.901	-1.043	-1.043	0.000	0.000	0.000	0.000
75	B	185	LEU	0	-0.065	-0.022	12.335	-1.417	-1.417	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:111:GLU)