FMO DATABASE

FMODB ID: LJ3Y9

Calculation Name: 4YII-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4YII

Chain ID: A

ChEMBL ID:

UniProt ID: Q9UJX6

Base Structure: X-ray

Registration Date: 2023-06-19

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	72
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-482724.037279
FMO2-HF: Nuclear repulsion	453056.955113
FMO2-HF: Total energy	-29667.082166
FMO2-MP2: Total energy	-29753.448886

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(A:747:LYS)

Summations of interaction energy for fragment #1(A:747:LYS)

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.
-225.662	-213.587	23.521	-16.613	-18.98	-0.157

Interaction energy analysis for fragmet #1(A:747:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.912 / q_NPA : 0.950

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	A	749	GLU	-1	-0.898	-0.957	3.583	-30.271	-28.544	-0.005	-0.692	-1.030	0.002
4	A	750	GLU	-1	-0.871	-0.929	1.791	-123.668	-122.299	19.154	-10.412	-10.110	-0.103
5	A	751	LEU	0	0.004	-0.003	2.442	5.447	6.877	1.642	-0.618	-2.454	0.000
6	A	752	LEU	0	0.016	0.001	4.900	6.228	6.346	-0.001	-0.007	-0.109	0.000
7	A	753	LEU	0	0.020	0.029	7.329	3.956	3.956	0.000	0.000	0.000	0.000
8	A	754	PHE	0	0.020	-0.007	3.003	6.775	7.195	0.028	-0.080	-0.368	0.000
9	A	755	TRP	0	-0.050	-0.030	8.654	3.218	3.218	0.000	0.000	0.000	0.000
10	A	756	THR	0	0.047	0.037	11.136	2.833	2.833	0.000	0.000	0.000	0.000
11	A	757	TYR	0	-0.005	-0.013	11.590	1.866	1.866	0.000	0.000	0.000	0.000
12	A	758	ILE	0	-0.025	-0.009	10.041	1.663	1.663	0.000	0.000	0.000	0.000
13	A	759	GLN	0	0.005	-0.006	14.039	0.921	0.921	0.000	0.000	0.000	0.000
14	A	760	ALA	0	0.041	0.038	16.675	1.335	1.335	0.000	0.000	0.000	0.000
15	A	761	MET	0	-0.023	-0.003	13.157	1.169	1.169	0.000	0.000	0.000	0.000
16	A	762	LEU	0	-0.022	-0.023	17.166	0.950	0.950	0.000	0.000	0.000	0.000
17	A	763	THR	0	-0.050	-0.014	19.947	0.951	0.951	0.000	0.000	0.000	0.000
18	A	764	ASN	0	-0.084	-0.060	21.317	1.249	1.249	0.000	0.000	0.000	0.000
19	A	765	LEU	0	-0.049	-0.024	20.232	0.506	0.506	0.000	0.000	0.000	0.000
20	A	766	GLU	-1	-0.836	-0.879	23.355	-12.061	-12.061	0.000	0.000	0.000	0.000
21	A	767	SER	0	-0.090	-0.075	21.816	-0.295	-0.295	0.000	0.000	0.000	0.000
22	A	768	LEU	0	-0.035	-0.012	17.802	0.049	0.049	0.000	0.000	0.000	0.000
23	A	769	SER	0	0.075	0.037	19.100	-0.436	-0.436	0.000	0.000	0.000	0.000
24	A	770	LEU	0	0.047	0.006	12.280	-0.524	-0.524	0.000	0.000	0.000	0.000
25	A	771	ASP	-1	-0.890	-0.938	14.572	-19.019	-19.019	0.000	0.000	0.000	0.000
26	A	772	ARG	1	0.926	0.955	16.014	14.113	14.113	0.000	0.000	0.000	0.000
27	A	773	ILE	0	0.037	0.026	11.855	-0.406	-0.406	0.000	0.000	0.000	0.000
28	A	774	TYR	0	0.030	0.007	9.186	-1.857	-1.857	0.000	0.000	0.000	0.000
29	A	775	ASN	0	-0.032	-0.025	12.010	-0.638	-0.638	0.000	0.000	0.000	0.000
30	A	776	MET	0	0.034	0.007	14.529	0.040	0.040	0.000	0.000	0.000	0.000
31	A	777	LEU	0	0.011	0.013	8.440	-0.044	-0.044	0.000	0.000	0.000	0.000
32	A	778	ARG	1	0.956	0.985	9.681	26.677	26.677	0.000	0.000	0.000	0.000
33	A	779	MET	0	-0.045	-0.012	11.355	0.356	0.356	0.000	0.000	0.000	0.000
34	A	780	PHE	0	-0.012	-0.006	13.391	0.957	0.957	0.000	0.000	0.000	0.000
35	A	781	VAL	0	-0.022	-0.009	7.587	0.422	0.422	0.000	0.000	0.000	0.000
36	A	782	VAL	0	-0.014	0.002	6.675	0.140	0.140	0.000	0.000	0.000	0.000
37	A	783	THR	0	-0.115	-0.064	8.783	1.283	1.283	0.000	0.000	0.000	0.000
38	A	784	GLY	0	0.017	0.024	11.538	2.192	2.192	0.000	0.000	0.000	0.000
39	A	785	PRO	0	-0.004	-0.031	12.326	-1.051	-1.051	0.000	0.000	0.000	0.000
40	A	786	ALA	0	-0.029	-0.009	8.888	0.351	0.351	0.000	0.000	0.000	0.000
41	A	787	LEU	0	-0.036	0.003	8.908	-1.503	-1.503	0.000	0.000	0.000	0.000
42	A	788	ALA	0	0.008	0.012	4.514	-2.809	-2.737	-0.001	-0.002	-0.068	0.000
43	A	789	GLU	-1	-0.867	-0.940	3.280	-40.892	-40.557	0.005	-0.080	-0.260	0.000
44	A	790	ILE	0	-0.086	-0.046	2.374	-31.572	-29.874	2.459	-1.950	-2.207	-0.027
45	A	791	ASP	-1	-0.830	-0.918	4.295	-31.048	-30.969	-0.001	-0.016	-0.062	0.000
46	A	792	LEU	0	0.004	-0.010	7.139	-0.847	-0.847	0.000	0.000	0.000	0.000
47	A	793	GLN	0	-0.006	-0.009	9.740	0.104	0.104	0.000	0.000	0.000	0.000
48	A	794	GLU	-1	-0.830	-0.914	2.862	-90.965	-86.138	0.241	-2.756	-2.312	-0.029
49	A	795	LEU	0	-0.003	0.010	7.016	1.575	1.575	0.000	0.000	0.000	0.000
50	A	796	GLN	0	-0.034	-0.026	8.055	3.901	3.901	0.000	0.000	0.000	0.000
51	A	797	GLY	0	0.029	0.014	10.338	1.847	1.847	0.000	0.000	0.000	0.000
52	A	798	TYR	0	0.019	-0.006	7.391	2.918	2.918	0.000	0.000	0.000	0.000
53	A	799	LEU	0	0.009	-0.005	9.583	2.281	2.281	0.000	0.000	0.000	0.000
54	A	800	GLN	0	0.004	-0.004	12.649	1.283	1.283	0.000	0.000	0.000	0.000
55	A	801	LYS	1	0.791	0.883	11.026	22.014	22.014	0.000	0.000	0.000	0.000
56	A	802	LYS	1	0.949	0.983	10.643	26.214	26.214	0.000	0.000	0.000	0.000
57	A	803	VAL	0	-0.027	-0.009	14.637	1.131	1.131	0.000	0.000	0.000	0.000
58	A	804	ARG	1	0.886	0.948	13.898	20.081	20.081	0.000	0.000	0.000	0.000
59	A	805	ASP	-1	-0.833	-0.887	15.322	-17.579	-17.579	0.000	0.000	0.000	0.000
60	A	806	GLN	0	-0.060	-0.029	18.432	0.648	0.648	0.000	0.000	0.000	0.000
61	A	807	GLN	0	-0.011	-0.004	15.128	-0.558	-0.558	0.000	0.000	0.000	0.000
62	A	808	LEU	0	-0.046	-0.026	14.582	-0.240	-0.240	0.000	0.000	0.000	0.000
63	A	809	VAL	0	0.041	0.024	18.784	0.379	0.379	0.000	0.000	0.000	0.000
64	A	810	TYR	0	-0.004	-0.002	19.233	-0.212	-0.212	0.000	0.000	0.000	0.000
65	A	811	SER	0	-0.003	-0.015	21.464	0.461	0.461	0.000	0.000	0.000	0.000
66	A	812	ALA	0	0.017	-0.001	24.700	-0.124	-0.124	0.000	0.000	0.000	0.000
67	A	813	GLY	0	0.009	0.016	23.042	0.059	0.059	0.000	0.000	0.000	0.000
68	A	814	VAL	0	-0.063	-0.024	20.667	-0.717	-0.717	0.000	0.000	0.000	0.000
69	A	815	TYR	0	0.001	-0.012	15.901	0.008	0.008	0.000	0.000	0.000	0.000
70	A	816	ARG	1	0.960	0.980	19.598	12.918	12.918	0.000	0.000	0.000	0.000
71	A	817	LEU	0	-0.010	0.010	18.576	-0.599	-0.599	0.000	0.000	0.000	0.000
72	A	818	PRO	0	-0.011	0.008	21.025	0.804	0.804	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:747:LYS)