FMO DATABASE

FMODB ID: YZ672

Calculation Name: 4A9A-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4A9A

Chain ID: D

ChEMBL ID:

UniProt ID: P39729

Base Structure: X-ray

Registration Date: 2023-06-21

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	86
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-435149.948552
FMO2-HF: Nuclear repulsion	401611.302548
FMO2-HF: Total energy	-33538.646004
FMO2-MP2: Total energy	-33637.977459

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(D:214:LEU)

Summations of interaction energy for fragment #1(D:214:LEU)

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.
-0.808	3.76	0.669	-2.243	-2.994	-0.003

Interaction energy analysis for fragmet #1(D:214:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.002 / q_NPA : 0.007

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	D	216	LYS	1	0.903	0.943	2.953	-0.450	3.093	0.275	-1.870	-1.948	-0.001
4	D	217	GLN	0	0.035	0.010	2.508	-0.501	0.524	0.394	-0.373	-1.046	-0.002
5	D	218	PRO	0	-0.023	0.012	6.031	0.078	0.078	0.000	0.000	0.000	0.000
6	D	219	LYS	1	0.924	0.946	9.069	0.258	0.258	0.000	0.000	0.000	0.000
7	D	220	ILE	0	0.038	0.034	11.126	-0.010	-0.010	0.000	0.000	0.000	0.000
8	D	221	THR	0	-0.035	-0.044	13.269	0.023	0.023	0.000	0.000	0.000	0.000
9	D	222	LEU	0	-0.022	-0.028	16.316	0.018	0.018	0.000	0.000	0.000	0.000
10	D	223	GLU	-1	-0.836	-0.929	17.989	0.038	0.038	0.000	0.000	0.000	0.000
11	D	224	GLU	-1	-0.767	-0.853	16.245	-0.065	-0.065	0.000	0.000	0.000	0.000
12	D	225	PHE	0	-0.027	-0.023	13.429	0.022	0.022	0.000	0.000	0.000	0.000
13	D	226	ILE	0	-0.052	-0.031	16.116	0.023	0.023	0.000	0.000	0.000	0.000
14	D	227	GLU	-1	-0.942	-0.963	19.565	0.030	0.030	0.000	0.000	0.000	0.000
15	D	228	THR	0	-0.029	-0.008	17.792	-0.013	-0.013	0.000	0.000	0.000	0.000
16	D	229	GLU	-1	-0.887	-0.922	13.095	0.002	0.002	0.000	0.000	0.000	0.000
17	D	230	ARG	1	0.952	0.976	14.665	-0.157	-0.157	0.000	0.000	0.000	0.000
18	D	231	GLY	0	-0.055	-0.034	16.216	0.024	0.024	0.000	0.000	0.000	0.000
19	D	232	LYS	1	0.842	0.907	14.022	0.034	0.034	0.000	0.000	0.000	0.000
20	D	233	LEU	0	-0.055	-0.010	11.395	0.022	0.022	0.000	0.000	0.000	0.000
21	D	234	ASP	-1	-0.742	-0.844	14.632	0.227	0.227	0.000	0.000	0.000	0.000
22	D	235	LYS	1	0.976	0.964	16.669	-0.132	-0.132	0.000	0.000	0.000	0.000
23	D	236	SER	0	-0.064	-0.040	19.142	0.005	0.005	0.000	0.000	0.000	0.000
24	D	237	LYS	1	0.825	0.896	16.058	-0.268	-0.268	0.000	0.000	0.000	0.000
25	D	238	LEU	0	-0.011	0.017	15.171	0.066	0.066	0.000	0.000	0.000	0.000
26	D	239	THR	0	0.006	-0.010	15.083	-0.046	-0.046	0.000	0.000	0.000	0.000
27	D	240	PRO	0	0.000	0.010	16.826	0.013	0.013	0.000	0.000	0.000	0.000
28	D	241	ILE	0	0.022	0.017	16.054	0.020	0.020	0.000	0.000	0.000	0.000
29	D	242	THR	0	0.011	-0.002	18.577	-0.039	-0.039	0.000	0.000	0.000	0.000
30	D	243	ILE	0	0.057	0.012	19.251	0.033	0.033	0.000	0.000	0.000	0.000
31	D	244	ALA	0	0.021	0.021	19.832	0.018	0.018	0.000	0.000	0.000	0.000
32	D	245	ASN	0	0.031	0.002	15.733	0.026	0.026	0.000	0.000	0.000	0.000
33	D	246	PHE	0	0.059	0.033	14.735	0.081	0.081	0.000	0.000	0.000	0.000
34	D	247	ALA	0	0.030	0.017	14.928	0.041	0.041	0.000	0.000	0.000	0.000
35	D	248	GLN	0	-0.025	-0.019	13.995	0.030	0.030	0.000	0.000	0.000	0.000
36	D	249	TRP	0	0.028	0.022	8.420	0.017	0.017	0.000	0.000	0.000	0.000
37	D	250	LYS	1	0.899	0.946	10.520	-0.381	-0.381	0.000	0.000	0.000	0.000
38	D	251	LYS	1	0.845	0.915	12.243	-0.803	-0.803	0.000	0.000	0.000	0.000
39	D	252	ASP	-1	-0.794	-0.890	8.041	1.034	1.034	0.000	0.000	0.000	0.000
40	D	253	HIS	0	0.003	0.018	7.746	0.040	0.040	0.000	0.000	0.000	0.000
41	D	254	VAL	0	-0.008	-0.020	9.041	-0.030	-0.030	0.000	0.000	0.000	0.000
42	D	255	ILE	0	0.035	0.017	9.936	-0.070	-0.070	0.000	0.000	0.000	0.000
43	D	256	ALA	0	0.012	0.013	5.211	-0.080	-0.080	0.000	0.000	0.000	0.000
44	D	257	LYS	1	0.909	0.968	7.220	-0.442	-0.442	0.000	0.000	0.000	0.000
45	D	258	ILE	0	-0.002	-0.013	9.471	-0.124	-0.124	0.000	0.000	0.000	0.000
46	D	259	ASN	0	0.029	-0.002	8.409	-0.174	-0.174	0.000	0.000	0.000	0.000
47	D	260	ALA	0	-0.041	-0.011	6.752	-0.154	-0.154	0.000	0.000	0.000	0.000
48	D	261	GLU	-1	-0.827	-0.926	8.814	0.072	0.072	0.000	0.000	0.000	0.000
49	D	262	LYS	1	0.830	0.919	12.225	-0.183	-0.183	0.000	0.000	0.000	0.000
50	D	263	LYS	1	0.972	1.001	9.035	0.587	0.587	0.000	0.000	0.000	0.000
51	D	264	LEU	0	-0.017	-0.015	12.553	-0.034	-0.034	0.000	0.000	0.000	0.000
52	D	265	SER	0	0.011	0.007	15.771	0.011	0.011	0.000	0.000	0.000	0.000
53	D	266	SER	0	-0.021	0.013	17.788	-0.003	-0.003	0.000	0.000	0.000	0.000
54	D	267	LYS	1	0.890	0.937	19.333	0.136	0.136	0.000	0.000	0.000	0.000
55	D	268	ARG	1	0.867	0.924	22.056	-0.006	-0.006	0.000	0.000	0.000	0.000
56	D	269	LYS	1	0.970	0.979	24.541	0.053	0.053	0.000	0.000	0.000	0.000
57	D	270	PRO	0	0.010	0.001	27.662	0.005	0.005	0.000	0.000	0.000	0.000
58	D	271	THR	0	0.010	-0.020	28.261	-0.002	-0.002	0.000	0.000	0.000	0.000
59	D	272	GLY	0	0.067	0.024	30.988	0.000	0.000	0.000	0.000	0.000	0.000
60	D	273	ARG	1	1.005	1.002	29.695	-0.044	-0.044	0.000	0.000	0.000	0.000
61	D	274	GLU	-1	-0.763	-0.843	27.699	0.014	0.014	0.000	0.000	0.000	0.000
62	D	275	ILE	0	-0.023	-0.006	32.349	-0.001	-0.001	0.000	0.000	0.000	0.000
63	D	276	ILE	0	0.040	0.011	35.288	0.000	0.000	0.000	0.000	0.000	0.000
64	D	277	LEU	0	-0.006	0.001	33.222	0.001	0.001	0.000	0.000	0.000	0.000
65	D	278	LYS	1	0.767	0.863	34.242	-0.005	-0.005	0.000	0.000	0.000	0.000
66	D	279	MET	0	-0.014	-0.019	36.461	-0.001	-0.001	0.000	0.000	0.000	0.000
67	D	280	SER	0	-0.053	-0.027	39.428	0.000	0.000	0.000	0.000	0.000	0.000
68	D	281	ALA	0	-0.038	-0.001	38.242	0.002	0.002	0.000	0.000	0.000	0.000
69	D	282	GLU	-1	-0.826	-0.875	39.749	0.007	0.007	0.000	0.000	0.000	0.000
70	D	320	ASP	-1	-0.908	-0.959	37.579	0.070	0.070	0.000	0.000	0.000	0.000
71	D	321	GLY	0	-0.042	-0.019	38.858	-0.003	-0.003	0.000	0.000	0.000	0.000
72	D	322	GLY	0	-0.044	-0.011	40.540	-0.004	-0.004	0.000	0.000	0.000	0.000
73	D	323	ILE	0	-0.048	-0.034	35.047	0.003	0.003	0.000	0.000	0.000	0.000
74	D	324	LYS	1	0.907	0.939	29.692	-0.116	-0.116	0.000	0.000	0.000	0.000
75	D	325	ASP	-1	-0.865	-0.931	32.271	0.077	0.077	0.000	0.000	0.000	0.000
76	D	326	TYR	0	-0.033	-0.027	26.885	0.008	0.008	0.000	0.000	0.000	0.000
77	D	327	GLY	0	0.040	0.030	27.877	0.009	0.009	0.000	0.000	0.000	0.000
78	D	328	ASP	-1	-0.922	-0.943	25.608	0.114	0.114	0.000	0.000	0.000	0.000
79	D	329	GLY	0	-0.039	-0.018	23.640	0.003	0.003	0.000	0.000	0.000	0.000
80	D	330	SER	0	-0.108	-0.075	22.002	0.022	0.022	0.000	0.000	0.000	0.000
81	D	331	ASN	0	-0.065	-0.049	22.185	-0.005	-0.005	0.000	0.000	0.000	0.000
82	D	332	PRO	0	0.033	0.044	22.281	-0.010	-0.010	0.000	0.000	0.000	0.000
83	D	333	THR	0	-0.005	-0.009	25.068	0.012	0.012	0.000	0.000	0.000	0.000
84	D	334	PHE	0	-0.027	-0.033	23.453	-0.007	-0.007	0.000	0.000	0.000	0.000
85	D	335	ASP	-1	-0.860	-0.906	28.760	0.133	0.133	0.000	0.000	0.000	0.000
86	D	336	ILE	0	-0.014	0.001	31.997	-0.007	-0.007	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(D:214:LEU)