FMO DATABASE

FMODB ID: K92R3

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

Total energy (hartree)

FMO2-HF: Electronic energy	-492642.929526
FMO2-HF: Nuclear repulsion	462207.723443
FMO2-HF: Total energy	-30435.206082
FMO2-MP2: Total energy	-30523.493132

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.
-48.415	-52.431	37.002	-17.083	-15.9	0.161

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 : -0.842 / q_NPA : -0.916

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	0.101	0.031	2.579	5.339	7.711	0.906	-1.436	-1.841	-0.014
4	B	114	SER	0	-0.005	0.001	5.141	2.863	3.044	-0.001	-0.007	-0.172	0.000
5	B	115	LYS	1	0.760	0.851	1.657	-124.730	-129.037	22.985	-10.300	-8.378	0.115
6	B	116	TRP	0	-0.003	0.024	2.891	2.159	5.444	0.390	-1.292	-2.383	0.011
7	B	117	SER	0	-0.015	-0.020	4.327	-12.708	-12.529	0.001	-0.041	-0.138	0.000
8	B	118	PRO	0	0.072	0.002	6.653	-0.595	-0.595	0.000	0.000	0.000	0.000
9	B	119	SER	0	-0.069	-0.022	8.978	-2.000	-2.000	0.000	0.000	0.000	0.000
10	B	120	GLN	0	0.058	0.032	1.720	-9.958	-15.684	12.721	-4.007	-2.988	0.049
11	B	121	VAL	0	0.021	0.029	7.176	-1.829	-1.829	0.000	0.000	0.000	0.000
12	B	122	VAL	0	-0.015	-0.011	9.669	-2.451	-2.451	0.000	0.000	0.000	0.000
13	B	123	ASP	-1	-0.933	-0.973	9.464	26.050	26.050	0.000	0.000	0.000	0.000
14	B	124	TRP	0	-0.015	-0.012	9.489	-1.193	-1.193	0.000	0.000	0.000	0.000
15	B	125	MET	0	-0.013	-0.002	11.370	-1.674	-1.674	0.000	0.000	0.000	0.000
16	B	126	LYS	1	0.919	0.960	14.400	-20.282	-20.282	0.000	0.000	0.000	0.000
17	B	127	GLY	0	-0.056	-0.005	14.751	-0.924	-0.924	0.000	0.000	0.000	0.000
18	B	128	LEU	0	-0.052	-0.014	15.134	-0.558	-0.558	0.000	0.000	0.000	0.000
19	B	129	ASP	-1	-0.840	-0.930	17.986	13.206	13.206	0.000	0.000	0.000	0.000
20	B	130	ASP	-1	-0.867	-0.937	21.828	12.612	12.612	0.000	0.000	0.000	0.000
21	B	131	CYS	0	-0.098	-0.050	23.978	-0.069	-0.069	0.000	0.000	0.000	0.000
22	B	132	LEU	0	0.015	0.005	19.904	-0.323	-0.323	0.000	0.000	0.000	0.000
23	B	133	GLN	0	0.036	0.008	18.685	0.798	0.798	0.000	0.000	0.000	0.000
24	B	134	GLN	0	-0.120	-0.058	21.541	-0.014	-0.014	0.000	0.000	0.000	0.000
25	B	135	TYR	0	-0.052	-0.079	20.748	-0.271	-0.271	0.000	0.000	0.000	0.000
26	B	136	ILE	0	0.040	0.031	16.738	0.493	0.493	0.000	0.000	0.000	0.000
27	B	137	LYS	1	0.907	0.955	18.221	-12.113	-12.113	0.000	0.000	0.000	0.000
28	B	138	ASN	0	-0.040	-0.018	20.123	-0.029	-0.029	0.000	0.000	0.000	0.000
29	B	139	PHE	0	0.108	0.048	14.889	0.122	0.122	0.000	0.000	0.000	0.000
30	B	140	GLU	-1	-0.887	-0.949	15.544	18.739	18.739	0.000	0.000	0.000	0.000
31	B	141	ARG	1	0.742	0.860	16.630	-13.278	-13.278	0.000	0.000	0.000	0.000
32	B	142	GLU	-1	-0.815	-0.903	18.447	14.642	14.642	0.000	0.000	0.000	0.000
33	B	143	LYS	1	0.769	0.891	14.260	-17.884	-17.884	0.000	0.000	0.000	0.000
34	B	144	ILE	0	0.052	0.036	12.872	1.122	1.122	0.000	0.000	0.000	0.000
35	B	145	SER	0	0.008	-0.002	9.483	1.679	1.679	0.000	0.000	0.000	0.000
36	B	146	GLY	0	0.080	0.018	7.121	-2.114	-2.114	0.000	0.000	0.000	0.000
37	B	147	ASP	-1	-0.919	-0.965	8.194	22.459	22.459	0.000	0.000	0.000	0.000
38	B	148	GLN	0	-0.004	-0.007	9.884	-1.304	-1.304	0.000	0.000	0.000	0.000
39	B	149	LEU	0	0.011	0.020	10.358	-1.377	-1.377	0.000	0.000	0.000	0.000
40	B	150	LEU	0	-0.041	-0.032	8.396	-1.353	-1.353	0.000	0.000	0.000	0.000
41	B	151	ARG	1	0.822	0.919	12.399	-21.428	-21.428	0.000	0.000	0.000	0.000
42	B	152	ILE	0	0.007	0.035	15.358	-0.987	-0.987	0.000	0.000	0.000	0.000
43	B	153	THR	0	0.007	0.004	17.296	-0.751	-0.751	0.000	0.000	0.000	0.000
44	B	154	HIS	0	0.002	-0.025	21.071	0.348	0.348	0.000	0.000	0.000	0.000
45	B	155	GLN	0	-0.033	-0.015	24.138	-0.385	-0.385	0.000	0.000	0.000	0.000
46	B	156	GLU	-1	-0.854	-0.934	18.922	15.801	15.801	0.000	0.000	0.000	0.000
47	B	157	LEU	0	-0.017	-0.004	19.301	0.164	0.164	0.000	0.000	0.000	0.000
48	B	158	GLU	-1	-0.938	-0.965	22.525	10.587	10.587	0.000	0.000	0.000	0.000
49	B	159	ASP	-1	-0.885	-0.932	23.976	11.890	11.890	0.000	0.000	0.000	0.000
50	B	160	LEU	0	-0.116	-0.047	18.655	0.069	0.069	0.000	0.000	0.000	0.000
51	B	161	GLY	0	-0.059	-0.038	22.866	0.170	0.170	0.000	0.000	0.000	0.000
52	B	162	VAL	0	-0.026	-0.006	22.265	-0.361	-0.361	0.000	0.000	0.000	0.000
53	B	163	SER	0	0.033	0.021	25.580	-0.078	-0.078	0.000	0.000	0.000	0.000
54	B	164	ARG	1	0.922	0.956	28.867	-10.280	-10.280	0.000	0.000	0.000	0.000
55	B	165	ILE	0	0.135	0.059	28.036	0.295	0.295	0.000	0.000	0.000	0.000
56	B	166	GLY	0	-0.004	0.000	27.673	0.228	0.228	0.000	0.000	0.000	0.000
57	B	167	HIS	0	-0.008	0.032	25.110	0.354	0.354	0.000	0.000	0.000	0.000
58	B	168	GLN	0	-0.026	-0.034	23.536	0.482	0.482	0.000	0.000	0.000	0.000
59	B	169	GLU	-1	-0.844	-0.922	22.738	12.362	12.362	0.000	0.000	0.000	0.000
60	B	170	LEU	0	-0.012	0.017	22.224	0.230	0.230	0.000	0.000	0.000	0.000
61	B	171	ILE	0	-0.017	-0.007	17.741	0.650	0.650	0.000	0.000	0.000	0.000
62	B	172	LEU	0	0.020	-0.003	18.134	0.934	0.934	0.000	0.000	0.000	0.000
63	B	173	GLU	-1	-0.921	-0.945	18.952	13.426	13.426	0.000	0.000	0.000	0.000
64	B	174	ALA	0	-0.004	-0.003	15.920	0.506	0.506	0.000	0.000	0.000	0.000
65	B	175	VAL	0	-0.015	-0.022	13.646	1.351	1.351	0.000	0.000	0.000	0.000
66	B	176	ASP	-1	-0.893	-0.934	14.370	16.043	16.043	0.000	0.000	0.000	0.000
67	B	177	LEU	0	-0.039	-0.029	14.805	0.420	0.420	0.000	0.000	0.000	0.000
68	B	178	LEU	0	-0.041	-0.010	8.322	0.886	0.886	0.000	0.000	0.000	0.000
69	B	179	CYS	0	-0.015	-0.009	10.259	1.645	1.645	0.000	0.000	0.000	0.000
70	B	180	ALA	0	0.012	-0.003	11.951	0.426	0.426	0.000	0.000	0.000	0.000
71	B	181	LEU	0	-0.010	-0.006	8.805	0.024	0.024	0.000	0.000	0.000	0.000
72	B	182	ASN	0	-0.014	0.015	6.799	3.954	3.954	0.000	0.000	0.000	0.000
73	B	183	TYR	0	-0.094	-0.051	8.357	1.671	1.671	0.000	0.000	0.000	0.000
74	B	184	GLY	0	-0.008	0.007	10.436	-0.985	-0.985	0.000	0.000	0.000	0.000
75	B	185	LEU	0	-0.074	-0.034	11.877	-1.328	-1.328	0.000	0.000	0.000	0.000

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