FMO DATABASE

FMODB ID: QY3KY

Calculation Name: 3B5N-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3B5N

Chain ID: C

ChEMBL ID:

UniProt ID: P40357

Base Structure: X-ray

Registration Date: 2023-09-20

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	70
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-280606.423749
FMO2-HF: Nuclear repulsion	253004.079322
FMO2-HF: Total energy	-27602.344427
FMO2-MP2: Total energy	-27680.410251

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(C:431:GLY)

Summations of interaction energy for fragment #1(C:431: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.
-1.196	1.439	0.034	-1.173	-1.497	0.004

Interaction energy analysis for fragmet #1(C:431:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.063 / q_NPA : 0.028

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	C	433	ILE	0	0.043	0.039	3.424	-3.040	-1.108	0.012	-0.984	-0.961	0.004
4	C	434	LYS	1	0.915	0.960	3.342	0.294	0.784	0.023	-0.117	-0.397	0.000
5	C	435	PHE	0	0.043	0.017	4.301	0.432	0.645	-0.001	-0.072	-0.139	0.000
6	C	436	THR	0	0.065	0.020	6.191	0.378	0.378	0.000	0.000	0.000	0.000
7	C	437	LYS	1	0.972	0.977	8.083	0.173	0.173	0.000	0.000	0.000	0.000
8	C	438	GLN	0	0.010	0.007	7.414	0.017	0.017	0.000	0.000	0.000	0.000
9	C	439	SER	0	0.019	0.007	10.270	0.095	0.095	0.000	0.000	0.000	0.000
10	C	440	SER	0	-0.009	0.000	12.255	0.069	0.069	0.000	0.000	0.000	0.000
11	C	441	VAL	0	-0.021	-0.005	13.476	0.028	0.028	0.000	0.000	0.000	0.000
12	C	442	ALA	0	-0.011	-0.009	14.622	0.027	0.027	0.000	0.000	0.000	0.000
13	C	443	SER	0	0.012	0.012	16.350	0.023	0.023	0.000	0.000	0.000	0.000
14	C	444	THR	0	0.006	-0.006	18.102	0.014	0.014	0.000	0.000	0.000	0.000
15	C	445	ARG	1	0.952	0.973	16.625	0.192	0.192	0.000	0.000	0.000	0.000
16	C	446	ASN	0	-0.002	-0.004	20.819	0.008	0.008	0.000	0.000	0.000	0.000
17	C	447	THR	0	0.020	0.010	22.316	0.010	0.010	0.000	0.000	0.000	0.000
18	C	448	LEU	0	-0.001	0.007	24.009	0.006	0.006	0.000	0.000	0.000	0.000
19	C	449	LYS	1	0.954	0.978	24.526	0.090	0.090	0.000	0.000	0.000	0.000
20	C	450	MET	0	0.017	0.008	25.269	0.005	0.005	0.000	0.000	0.000	0.000
21	C	451	ALA	0	0.007	0.014	28.439	0.005	0.005	0.000	0.000	0.000	0.000
22	C	452	GLN	0	0.026	0.003	29.032	0.001	0.001	0.000	0.000	0.000	0.000
23	C	453	ASP	-1	-0.902	-0.946	30.828	-0.047	-0.047	0.000	0.000	0.000	0.000
24	C	454	ALA	0	-0.034	-0.026	32.871	0.003	0.003	0.000	0.000	0.000	0.000
25	C	455	GLU	-1	-0.920	-0.954	34.451	-0.026	-0.026	0.000	0.000	0.000	0.000
26	C	456	ARG	1	0.897	0.955	33.961	0.041	0.041	0.000	0.000	0.000	0.000
27	C	457	ALA	0	-0.022	-0.018	37.537	0.002	0.002	0.000	0.000	0.000	0.000
28	C	458	GLY	0	0.032	0.016	38.875	0.002	0.002	0.000	0.000	0.000	0.000
29	C	459	MET	0	0.029	0.007	40.218	0.002	0.002	0.000	0.000	0.000	0.000
30	C	460	ASN	0	-0.012	-0.007	42.093	0.001	0.001	0.000	0.000	0.000	0.000
31	C	461	THR	0	-0.046	-0.022	42.899	0.001	0.001	0.000	0.000	0.000	0.000
32	C	462	LEU	0	0.021	0.003	43.925	0.001	0.001	0.000	0.000	0.000	0.000
33	C	463	GLY	0	0.015	0.024	46.537	0.001	0.001	0.000	0.000	0.000	0.000
34	C	464	MET	0	-0.049	-0.030	45.887	0.001	0.001	0.000	0.000	0.000	0.000
35	C	465	LEU	0	0.003	-0.001	47.970	0.001	0.001	0.000	0.000	0.000	0.000
36	C	466	GLY	0	0.018	0.020	50.920	0.001	0.001	0.000	0.000	0.000	0.000
37	C	467	HIS	0	-0.006	-0.007	52.556	0.000	0.000	0.000	0.000	0.000	0.000
38	C	468	GLN	0	0.004	-0.015	51.702	0.001	0.001	0.000	0.000	0.000	0.000
39	C	469	SER	0	0.007	0.010	55.133	0.001	0.001	0.000	0.000	0.000	0.000
40	C	470	GLU	-1	-0.923	-0.958	56.952	-0.009	-0.009	0.000	0.000	0.000	0.000
41	C	471	GLN	0	-0.070	-0.037	57.036	0.000	0.000	0.000	0.000	0.000	0.000
42	C	472	LEU	0	-0.018	-0.024	57.604	0.000	0.000	0.000	0.000	0.000	0.000
43	C	473	ASN	0	0.074	0.051	61.055	0.001	0.001	0.000	0.000	0.000	0.000
44	C	474	ASN	0	-0.031	-0.006	63.101	0.001	0.001	0.000	0.000	0.000	0.000
45	C	475	VAL	0	-0.073	-0.038	63.324	0.000	0.000	0.000	0.000	0.000	0.000
46	C	476	GLU	-1	-0.901	-0.959	63.202	-0.006	-0.006	0.000	0.000	0.000	0.000
47	C	477	GLY	0	0.051	0.035	66.825	0.000	0.000	0.000	0.000	0.000	0.000
48	C	478	ASN	0	-0.019	-0.024	68.356	0.000	0.000	0.000	0.000	0.000	0.000
49	C	479	LEU	0	-0.045	-0.023	67.341	0.000	0.000	0.000	0.000	0.000	0.000
50	C	480	ASP	-1	-0.878	-0.937	70.731	-0.004	-0.004	0.000	0.000	0.000	0.000
51	C	481	LEU	0	-0.032	-0.011	72.927	0.000	0.000	0.000	0.000	0.000	0.000
52	C	482	MET	0	0.024	-0.003	71.844	0.000	0.000	0.000	0.000	0.000	0.000
53	C	483	LYS	1	0.869	0.952	70.750	0.005	0.005	0.000	0.000	0.000	0.000
54	C	484	VAL	0	-0.022	-0.009	76.997	0.000	0.000	0.000	0.000	0.000	0.000
55	C	485	GLN	0	-0.007	-0.021	78.161	0.000	0.000	0.000	0.000	0.000	0.000
56	C	486	ASN	0	0.046	0.013	77.924	0.000	0.000	0.000	0.000	0.000	0.000
57	C	487	LYS	1	0.941	0.995	79.629	0.003	0.003	0.000	0.000	0.000	0.000
58	C	488	VAL	0	0.006	0.007	83.403	0.000	0.000	0.000	0.000	0.000	0.000
59	C	489	ALA	0	-0.024	-0.022	83.897	0.000	0.000	0.000	0.000	0.000	0.000
60	C	490	ASP	-1	-0.888	-0.940	84.190	-0.003	-0.003	0.000	0.000	0.000	0.000
61	C	491	GLU	-1	-0.973	-0.989	86.745	-0.003	-0.003	0.000	0.000	0.000	0.000
62	C	492	LYS	1	0.920	0.962	88.999	0.004	0.004	0.000	0.000	0.000	0.000
63	C	493	VAL	0	0.012	0.009	87.441	0.000	0.000	0.000	0.000	0.000	0.000
64	C	494	ALA	0	-0.018	-0.007	90.642	0.000	0.000	0.000	0.000	0.000	0.000
65	C	495	GLU	-1	-0.941	-0.974	92.532	-0.003	-0.003	0.000	0.000	0.000	0.000
66	C	496	LEU	0	0.021	-0.001	91.825	0.000	0.000	0.000	0.000	0.000	0.000
67	C	497	LYS	1	0.922	0.967	94.103	0.003	0.003	0.000	0.000	0.000	0.000
68	C	498	LYS	1	0.898	0.952	96.056	0.002	0.002	0.000	0.000	0.000	0.000
69	C	499	LEU	0	-0.049	-0.020	97.996	0.000	0.000	0.000	0.000	0.000	0.000
70	C	500	GLN	0	-0.068	-0.013	97.826	0.000	0.000	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(C:431:GLY)