FMO DATABASE

FMODB ID: 17RQZ

Calculation Name: 1B72-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1B72

Chain ID: B

ChEMBL ID:

UniProt ID: P14653

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	73
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-480667.223407
FMO2-HF: Nuclear repulsion	450759.675776
FMO2-HF: Total energy	-29907.547631
FMO2-MP2: Total energy	-29996.379523

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:235:ARG)

Summations of interaction energy for fragment #1(B:235:ARG)

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.
113.709	116.343	3.882	-2.808	-3.708	-0.024

Interaction energy analysis for fragmet #1(B:235:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.032 / q_NPA : 1.006

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	237	ARG	1	0.933	0.960	2.209	10.824	13.273	3.883	-2.791	-3.540	-0.024
4	B	238	ARG	1	0.973	0.978	4.520	40.171	40.356	-0.001	-0.017	-0.168	0.000
5	B	239	ASN	0	0.008	0.010	6.417	-1.560	-1.560	0.000	0.000	0.000	0.000
6	B	240	PHE	0	0.041	0.022	7.959	-1.204	-1.204	0.000	0.000	0.000	0.000
7	B	241	ASN	0	0.037	0.021	11.465	0.669	0.669	0.000	0.000	0.000	0.000
8	B	242	LYS	1	1.006	1.002	14.682	13.715	13.715	0.000	0.000	0.000	0.000
9	B	243	GLN	0	0.079	0.029	17.771	0.251	0.251	0.000	0.000	0.000	0.000
10	B	244	ALA	0	0.035	0.016	14.729	0.302	0.302	0.000	0.000	0.000	0.000
11	B	245	THR	0	-0.037	-0.034	14.809	0.519	0.519	0.000	0.000	0.000	0.000
12	B	246	GLU	-1	-0.880	-0.926	17.171	-12.311	-12.311	0.000	0.000	0.000	0.000
13	B	247	ILE	0	0.060	0.029	19.450	0.442	0.442	0.000	0.000	0.000	0.000
14	B	248	LEU	0	-0.043	-0.024	14.776	0.218	0.218	0.000	0.000	0.000	0.000
15	B	249	ASN	0	0.016	-0.007	19.367	0.116	0.116	0.000	0.000	0.000	0.000
16	B	250	GLU	-1	-0.871	-0.916	21.633	-11.062	-11.062	0.000	0.000	0.000	0.000
17	B	251	TYR	0	0.019	0.005	22.223	0.415	0.415	0.000	0.000	0.000	0.000
18	B	252	PHE	0	-0.065	-0.045	21.509	0.221	0.221	0.000	0.000	0.000	0.000
19	B	253	TYR	0	-0.038	-0.077	23.116	0.290	0.290	0.000	0.000	0.000	0.000
20	B	254	SER	0	0.068	0.065	26.622	0.483	0.483	0.000	0.000	0.000	0.000
21	B	255	HIS	1	0.814	0.883	26.407	11.668	11.668	0.000	0.000	0.000	0.000
22	B	256	LEU	0	0.048	0.034	26.707	-0.187	-0.187	0.000	0.000	0.000	0.000
23	B	257	SER	0	-0.012	-0.003	28.384	-0.159	-0.159	0.000	0.000	0.000	0.000
24	B	258	ASN	0	0.000	-0.013	28.349	0.016	0.016	0.000	0.000	0.000	0.000
25	B	259	PRO	0	-0.028	0.020	23.512	-0.227	-0.227	0.000	0.000	0.000	0.000
26	B	260	TYR	0	-0.076	-0.069	22.828	-0.901	-0.901	0.000	0.000	0.000	0.000
27	B	261	PRO	0	-0.033	0.010	20.789	0.326	0.326	0.000	0.000	0.000	0.000
28	B	262	SER	0	0.037	-0.030	22.913	-0.543	-0.543	0.000	0.000	0.000	0.000
29	B	263	GLU	-1	-0.818	-0.938	21.157	-14.842	-14.842	0.000	0.000	0.000	0.000
30	B	264	GLU	-1	-0.787	-0.844	21.977	-11.819	-11.819	0.000	0.000	0.000	0.000
31	B	265	ALA	0	0.011	0.006	23.401	-0.280	-0.280	0.000	0.000	0.000	0.000
32	B	266	LYS	1	0.802	0.905	18.277	15.370	15.370	0.000	0.000	0.000	0.000
33	B	267	GLU	-1	-0.919	-0.964	18.789	-15.538	-15.538	0.000	0.000	0.000	0.000
34	B	268	GLU	-1	-0.907	-0.944	19.755	-12.327	-12.327	0.000	0.000	0.000	0.000
35	B	269	LEU	0	-0.037	-0.033	18.700	-0.218	-0.218	0.000	0.000	0.000	0.000
36	B	270	ALA	0	0.007	0.006	15.715	-0.504	-0.504	0.000	0.000	0.000	0.000
37	B	271	LYS	1	0.968	0.987	16.467	13.065	13.065	0.000	0.000	0.000	0.000
38	B	272	LYS	1	0.869	0.943	18.936	12.454	12.454	0.000	0.000	0.000	0.000
39	B	273	CYS	0	-0.081	-0.028	15.347	0.093	0.093	0.000	0.000	0.000	0.000
40	B	274	GLY	0	-0.007	0.011	15.137	-0.562	-0.562	0.000	0.000	0.000	0.000
41	B	275	ILE	0	-0.087	-0.043	11.009	-1.996	-1.996	0.000	0.000	0.000	0.000
42	B	276	THR	0	0.033	0.008	9.717	1.200	1.200	0.000	0.000	0.000	0.000
43	B	277	VAL	0	0.163	0.070	12.309	-0.292	-0.292	0.000	0.000	0.000	0.000
44	B	278	SER	0	0.012	0.002	10.581	1.018	1.018	0.000	0.000	0.000	0.000
45	B	279	GLN	0	-0.013	-0.012	6.319	1.737	1.737	0.000	0.000	0.000	0.000
46	B	280	VAL	0	0.065	0.050	10.628	0.334	0.334	0.000	0.000	0.000	0.000
47	B	281	SER	0	0.000	-0.010	14.286	1.333	1.333	0.000	0.000	0.000	0.000
48	B	282	ASN	0	-0.009	-0.015	8.974	1.959	1.959	0.000	0.000	0.000	0.000
49	B	283	TRP	0	-0.034	0.006	12.464	0.310	0.310	0.000	0.000	0.000	0.000
50	B	284	PHE	0	0.067	0.024	14.123	0.851	0.851	0.000	0.000	0.000	0.000
51	B	285	GLY	0	-0.018	0.007	15.762	0.926	0.926	0.000	0.000	0.000	0.000
52	B	286	ASN	0	-0.050	-0.049	10.861	1.081	1.081	0.000	0.000	0.000	0.000
53	B	287	LYS	1	0.799	0.912	15.306	15.737	15.737	0.000	0.000	0.000	0.000
54	B	288	ARG	1	0.961	0.989	18.323	15.538	15.538	0.000	0.000	0.000	0.000
55	B	289	ILE	0	-0.038	-0.016	17.878	0.766	0.766	0.000	0.000	0.000	0.000
56	B	290	ARG	1	0.935	0.946	12.281	20.883	20.883	0.000	0.000	0.000	0.000
57	B	291	TYR	0	0.066	0.053	19.871	0.437	0.437	0.000	0.000	0.000	0.000
58	B	292	LYS	1	0.971	0.976	22.510	13.066	13.066	0.000	0.000	0.000	0.000
59	B	293	LYS	1	0.903	0.955	21.346	13.044	13.044	0.000	0.000	0.000	0.000
60	B	294	ASN	0	-0.066	-0.040	24.151	0.445	0.445	0.000	0.000	0.000	0.000
61	B	295	ILE	0	0.098	0.058	25.839	-0.179	-0.179	0.000	0.000	0.000	0.000
62	B	296	GLY	0	0.036	0.020	27.763	-0.042	-0.042	0.000	0.000	0.000	0.000
63	B	297	LYS	1	0.920	0.966	21.873	13.470	13.470	0.000	0.000	0.000	0.000
64	B	298	PHE	0	-0.037	-0.024	20.393	-0.552	-0.552	0.000	0.000	0.000	0.000
65	B	299	GLN	0	0.041	0.031	25.893	-0.260	-0.260	0.000	0.000	0.000	0.000
66	B	300	GLU	-1	-0.892	-0.933	28.220	-10.697	-10.697	0.000	0.000	0.000	0.000
67	B	301	GLU	-1	-0.800	-0.863	22.199	-14.113	-14.113	0.000	0.000	0.000	0.000
68	B	302	ALA	0	-0.009	-0.034	26.597	0.002	0.002	0.000	0.000	0.000	0.000
69	B	303	ASN	0	-0.034	-0.028	28.375	0.240	0.240	0.000	0.000	0.000	0.000
70	B	304	ILE	0	-0.033	0.000	26.994	0.203	0.203	0.000	0.000	0.000	0.000
71	B	305	TYR	0	-0.117	-0.071	23.420	-0.163	-0.163	0.000	0.000	0.000	0.000
72	B	306	ALA	0	-0.032	0.009	28.336	0.013	0.013	0.000	0.000	0.000	0.000
73	B	307	ALA	0	0.000	0.006	30.563	0.026	0.026	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:235:ARG)