FMO DATABASE

FMODB ID: 49LNN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-492613.712279
FMO2-HF: Nuclear repulsion	462178.166376
FMO2-HF: Total energy	-30435.545903
FMO2-MP2: Total energy	-30523.808221

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.
-69.692	-70.951	38.28	-18.995	-18.03	0.185

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 : -0.829 / q_NPA : -0.908

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	113	VAL	0	0.098	0.034	2.500	6.575	8.849	1.249	-1.498	-2.025	-0.015
4	B	114	SER	0	-0.004	0.004	4.995	3.532	3.717	-0.001	-0.007	-0.177	0.000
5	B	115	LYS	1	0.784	0.854	1.683	-134.475	-138.058	23.763	-11.380	-8.801	0.127
6	B	116	TRP	0	-0.046	0.010	2.523	1.485	5.737	1.428	-2.079	-3.602	0.019
7	B	117	SER	0	-0.006	-0.026	3.825	-14.790	-14.605	0.009	0.004	-0.199	0.001
8	B	118	PRO	0	0.074	0.006	6.211	-0.748	-0.748	0.000	0.000	0.000	0.000
9	B	119	SER	0	-0.025	-0.005	8.727	-2.650	-2.650	0.000	0.000	0.000	0.000
10	B	120	GLN	0	-0.005	0.011	1.755	-16.386	-20.958	11.832	-4.035	-3.226	0.053
11	B	121	VAL	0	0.026	0.033	7.205	-1.889	-1.889	0.000	0.000	0.000	0.000
12	B	122	VAL	0	-0.011	-0.010	9.531	-2.484	-2.484	0.000	0.000	0.000	0.000
13	B	123	ASP	-1	-0.877	-0.942	9.784	24.774	24.774	0.000	0.000	0.000	0.000
14	B	124	TRP	0	-0.001	-0.001	9.573	-1.146	-1.146	0.000	0.000	0.000	0.000
15	B	125	MET	0	-0.007	-0.002	11.465	-1.579	-1.579	0.000	0.000	0.000	0.000
16	B	126	LYS	1	0.845	0.921	13.981	-22.356	-22.356	0.000	0.000	0.000	0.000
17	B	127	GLY	0	-0.062	-0.011	14.816	-0.935	-0.935	0.000	0.000	0.000	0.000
18	B	128	LEU	0	-0.049	-0.011	15.122	-0.575	-0.575	0.000	0.000	0.000	0.000
19	B	129	ASP	-1	-0.840	-0.930	18.079	13.173	13.173	0.000	0.000	0.000	0.000
20	B	130	ASP	-1	-0.869	-0.941	21.929	12.603	12.603	0.000	0.000	0.000	0.000
21	B	131	CYS	0	-0.099	-0.047	24.064	-0.079	-0.079	0.000	0.000	0.000	0.000
22	B	132	LEU	0	0.006	0.005	20.208	-0.318	-0.318	0.000	0.000	0.000	0.000
23	B	133	GLN	0	0.043	0.013	18.802	0.800	0.800	0.000	0.000	0.000	0.000
24	B	134	GLN	0	-0.126	-0.061	21.521	-0.084	-0.084	0.000	0.000	0.000	0.000
25	B	135	TYR	0	-0.044	-0.046	20.678	-0.276	-0.276	0.000	0.000	0.000	0.000
26	B	136	ILE	0	0.035	0.032	16.490	0.518	0.518	0.000	0.000	0.000	0.000
27	B	137	LYS	1	0.895	0.952	18.046	-12.123	-12.123	0.000	0.000	0.000	0.000
28	B	138	ASN	0	-0.041	-0.022	19.880	-0.049	-0.049	0.000	0.000	0.000	0.000
29	B	139	PHE	0	0.115	0.049	14.515	0.164	0.164	0.000	0.000	0.000	0.000
30	B	140	GLU	-1	-0.870	-0.943	15.305	18.908	18.908	0.000	0.000	0.000	0.000
31	B	141	ARG	1	0.748	0.861	16.369	-13.291	-13.291	0.000	0.000	0.000	0.000
32	B	142	GLU	-1	-0.819	-0.902	17.905	14.793	14.793	0.000	0.000	0.000	0.000
33	B	143	LYS	1	0.772	0.890	13.754	-18.066	-18.066	0.000	0.000	0.000	0.000
34	B	144	ILE	0	0.030	0.026	12.519	1.202	1.202	0.000	0.000	0.000	0.000
35	B	145	SER	0	-0.004	-0.026	8.831	2.121	2.121	0.000	0.000	0.000	0.000
36	B	146	GLY	0	0.065	0.009	7.021	-2.273	-2.273	0.000	0.000	0.000	0.000
37	B	147	ASP	-1	-0.856	-0.898	8.082	22.128	22.128	0.000	0.000	0.000	0.000
38	B	148	GLN	0	0.045	0.036	9.855	-0.660	-0.660	0.000	0.000	0.000	0.000
39	B	149	LEU	0	0.007	0.017	10.282	-1.450	-1.450	0.000	0.000	0.000	0.000
40	B	150	LEU	0	-0.038	-0.032	8.400	-1.396	-1.396	0.000	0.000	0.000	0.000
41	B	151	ARG	1	0.751	0.855	12.291	-22.538	-22.538	0.000	0.000	0.000	0.000
42	B	152	ILE	0	-0.017	0.020	15.262	-1.002	-1.002	0.000	0.000	0.000	0.000
43	B	153	THR	0	-0.021	-0.041	17.187	-0.798	-0.798	0.000	0.000	0.000	0.000
44	B	154	HIS	0	-0.007	-0.031	20.960	0.376	0.376	0.000	0.000	0.000	0.000
45	B	155	GLN	0	-0.060	-0.033	24.007	-0.436	-0.436	0.000	0.000	0.000	0.000
46	B	156	GLU	-1	-0.793	-0.875	19.260	15.942	15.942	0.000	0.000	0.000	0.000
47	B	157	LEU	0	-0.024	-0.009	19.076	0.180	0.180	0.000	0.000	0.000	0.000
48	B	158	GLU	-1	-0.908	-0.939	22.257	10.667	10.667	0.000	0.000	0.000	0.000
49	B	159	ASP	-1	-0.879	-0.927	23.634	11.905	11.905	0.000	0.000	0.000	0.000
50	B	160	LEU	0	-0.107	-0.040	18.290	0.086	0.086	0.000	0.000	0.000	0.000
51	B	161	GLY	0	-0.056	-0.032	22.488	0.174	0.174	0.000	0.000	0.000	0.000
52	B	162	VAL	0	-0.026	-0.012	21.989	-0.368	-0.368	0.000	0.000	0.000	0.000
53	B	163	SER	0	0.038	0.020	25.310	-0.083	-0.083	0.000	0.000	0.000	0.000
54	B	164	ARG	1	0.913	0.953	28.642	-10.372	-10.372	0.000	0.000	0.000	0.000
55	B	165	ILE	0	0.130	0.055	27.845	0.306	0.306	0.000	0.000	0.000	0.000
56	B	166	GLY	0	0.000	0.005	27.494	0.232	0.232	0.000	0.000	0.000	0.000
57	B	167	HIS	0	-0.012	-0.008	24.953	0.266	0.266	0.000	0.000	0.000	0.000
58	B	168	GLN	0	-0.039	-0.037	23.365	0.524	0.524	0.000	0.000	0.000	0.000
59	B	169	GLU	-1	-0.855	-0.926	22.554	12.437	12.437	0.000	0.000	0.000	0.000
60	B	170	LEU	0	0.001	0.017	22.470	0.235	0.235	0.000	0.000	0.000	0.000
61	B	171	ILE	0	-0.014	-0.004	17.666	0.667	0.667	0.000	0.000	0.000	0.000
62	B	172	LEU	0	0.019	-0.004	18.066	0.955	0.955	0.000	0.000	0.000	0.000
63	B	173	GLU	-1	-0.920	-0.945	18.771	13.353	13.353	0.000	0.000	0.000	0.000
64	B	174	ALA	0	-0.007	-0.005	16.134	0.513	0.513	0.000	0.000	0.000	0.000
65	B	175	VAL	0	-0.009	-0.022	13.596	1.362	1.362	0.000	0.000	0.000	0.000
66	B	176	ASP	-1	-0.882	-0.929	14.211	16.235	16.235	0.000	0.000	0.000	0.000
67	B	177	LEU	0	-0.051	-0.031	14.947	0.410	0.410	0.000	0.000	0.000	0.000
68	B	178	LEU	0	-0.043	-0.014	8.312	0.921	0.921	0.000	0.000	0.000	0.000
69	B	179	CYS	0	-0.008	-0.004	10.376	1.752	1.752	0.000	0.000	0.000	0.000
70	B	180	ALA	0	0.018	-0.002	12.097	0.423	0.423	0.000	0.000	0.000	0.000
71	B	181	LEU	0	-0.014	-0.007	9.000	0.026	0.026	0.000	0.000	0.000	0.000
72	B	182	ASN	0	-0.043	0.000	6.947	3.897	3.897	0.000	0.000	0.000	0.000
73	B	183	TYR	0	-0.076	-0.045	8.510	1.692	1.692	0.000	0.000	0.000	0.000
74	B	184	GLY	0	-0.010	0.008	10.602	-1.013	-1.013	0.000	0.000	0.000	0.000
75	B	185	LEU	0	-0.076	-0.030	12.044	-1.316	-1.316	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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