FMO DATABASE

FMODB ID: G5VJ1

Calculation Name: 3D3M-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3D3M

Chain ID: A

ChEMBL ID:

UniProt ID: P78344

Base Structure: X-ray

Registration Date: 2023-09-23

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	161
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1754456.18894
FMO2-HF: Nuclear repulsion	1688732.962055
FMO2-HF: Total energy	-65723.226885
FMO2-MP2: Total energy	-65917.174814

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:730:LEU)

Summations of interaction energy for fragment #1(A:730: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.
-25.764	-16.261	4.993	-5.074	-9.424	0.003

Interaction energy analysis for fragmet #1(A:730:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.049 / q_NPA : 0.008

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	A	732	LYS	1	0.997	0.989	3.207	-7.440	-4.785	0.126	-1.307	-1.475	0.009
4	A	733	LEU	0	-0.007	0.013	2.293	-6.031	-4.160	2.743	-2.017	-2.597	0.004
5	A	734	GLU	-1	-0.730	-0.860	3.591	-1.875	-1.413	0.005	-0.115	-0.352	0.000
6	A	735	LYS	1	0.702	0.843	5.436	-1.211	-1.211	0.000	0.000	0.000	0.000
7	A	736	GLU	-1	-0.816	-0.886	7.245	0.735	0.735	0.000	0.000	0.000	0.000
8	A	737	LEU	0	0.044	0.027	7.283	-0.270	-0.270	0.000	0.000	0.000	0.000
9	A	738	LEU	0	0.013	0.015	9.160	-0.146	-0.146	0.000	0.000	0.000	0.000
10	A	739	LYS	1	0.792	0.878	11.347	-0.964	-0.964	0.000	0.000	0.000	0.000
11	A	740	GLN	0	-0.047	-0.050	12.120	-0.168	-0.168	0.000	0.000	0.000	0.000
12	A	741	ILE	0	0.001	0.003	12.092	-0.064	-0.064	0.000	0.000	0.000	0.000
13	A	742	LYS	1	0.933	0.965	15.276	-0.248	-0.248	0.000	0.000	0.000	0.000
14	A	743	LEU	0	-0.066	-0.030	16.046	-0.013	-0.013	0.000	0.000	0.000	0.000
15	A	744	ASP	-1	-0.794	-0.876	18.099	0.097	0.097	0.000	0.000	0.000	0.000
16	A	745	PRO	0	-0.010	0.016	18.212	-0.003	-0.003	0.000	0.000	0.000	0.000
17	A	746	SER	0	0.027	0.015	19.359	-0.046	-0.046	0.000	0.000	0.000	0.000
18	A	747	PRO	0	0.043	0.006	18.090	0.008	0.008	0.000	0.000	0.000	0.000
19	A	748	GLN	0	-0.030	-0.014	17.610	0.000	0.000	0.000	0.000	0.000	0.000
20	A	749	THR	0	-0.041	-0.039	17.437	-0.007	-0.007	0.000	0.000	0.000	0.000
21	A	750	ILE	0	0.011	0.027	12.868	0.031	0.031	0.000	0.000	0.000	0.000
22	A	751	TYR	0	-0.023	-0.013	13.256	0.026	0.026	0.000	0.000	0.000	0.000
23	A	752	LYS	1	0.923	0.970	13.973	-0.124	-0.124	0.000	0.000	0.000	0.000
24	A	753	TRP	0	0.060	0.022	7.972	0.046	0.046	0.000	0.000	0.000	0.000
25	A	754	ILE	0	0.037	0.013	8.758	0.086	0.086	0.000	0.000	0.000	0.000
26	A	755	LYS	1	0.822	0.912	10.229	0.009	0.009	0.000	0.000	0.000	0.000
27	A	756	ASP	-1	-0.904	-0.962	12.747	0.104	0.104	0.000	0.000	0.000	0.000
28	A	757	ASN	0	-0.083	-0.034	10.089	0.135	0.135	0.000	0.000	0.000	0.000
29	A	758	ILE	0	-0.034	0.003	5.093	0.273	0.273	0.000	0.000	0.000	0.000
30	A	759	SER	0	0.014	0.007	7.730	-0.195	-0.195	0.000	0.000	0.000	0.000
31	A	760	PRO	0	0.112	0.042	7.697	-0.210	-0.210	0.000	0.000	0.000	0.000
32	A	761	LYS	1	0.917	0.957	8.921	0.287	0.287	0.000	0.000	0.000	0.000
33	A	762	LEU	0	0.001	-0.006	2.989	-0.821	-0.032	0.122	-0.161	-0.750	0.000
34	A	763	HIS	0	-0.059	-0.035	5.450	-0.371	-0.371	0.000	0.000	0.000	0.000
35	A	764	VAL	0	0.051	0.025	7.914	0.056	0.056	0.000	0.000	0.000	0.000
36	A	765	ASP	-1	-0.850	-0.914	3.052	-6.882	-5.551	0.188	-0.673	-0.847	-0.006
37	A	766	LYS	1	0.877	0.931	6.376	0.947	0.947	0.000	0.000	0.000	0.000
38	A	767	GLY	0	0.006	0.009	2.732	-0.006	0.348	0.201	-0.193	-0.362	-0.001
39	A	768	PHE	0	-0.045	-0.032	2.691	-1.625	-0.348	0.318	-0.350	-1.244	-0.001
40	A	769	VAL	0	0.036	0.019	3.482	0.851	0.812	0.022	0.132	-0.116	0.000
41	A	770	ASN	0	-0.038	-0.011	5.923	0.344	0.344	0.000	0.000	0.000	0.000
42	A	771	ILE	0	0.005	0.009	2.476	-0.282	0.521	1.268	-0.390	-1.681	-0.002
43	A	772	LEU	0	-0.035	0.006	5.911	0.591	0.591	0.000	0.000	0.000	0.000
44	A	773	MET	0	0.016	0.003	7.951	0.283	0.283	0.000	0.000	0.000	0.000
45	A	774	THR	0	0.007	-0.010	8.868	0.215	0.215	0.000	0.000	0.000	0.000
46	A	775	SER	0	-0.048	-0.031	8.649	0.249	0.249	0.000	0.000	0.000	0.000
47	A	776	PHE	0	0.006	0.000	11.309	0.106	0.106	0.000	0.000	0.000	0.000
48	A	777	LEU	0	-0.009	0.004	13.719	0.062	0.062	0.000	0.000	0.000	0.000
49	A	778	GLN	0	0.000	-0.003	11.507	0.132	0.132	0.000	0.000	0.000	0.000
50	A	779	TYR	0	-0.071	-0.051	15.403	0.039	0.039	0.000	0.000	0.000	0.000
51	A	780	ILE	0	0.053	0.023	17.282	0.021	0.021	0.000	0.000	0.000	0.000
52	A	781	SER	0	0.003	-0.004	19.067	0.004	0.004	0.000	0.000	0.000	0.000
53	A	782	SER	0	-0.093	-0.048	19.453	0.025	0.025	0.000	0.000	0.000	0.000
54	A	783	GLU	-1	-0.863	-0.907	21.251	0.069	0.069	0.000	0.000	0.000	0.000
55	A	784	VAL	0	-0.039	-0.007	23.407	0.001	0.001	0.000	0.000	0.000	0.000
56	A	785	ASN	0	-0.091	-0.052	24.444	0.005	0.005	0.000	0.000	0.000	0.000
57	A	786	PRO	0	0.061	0.058	24.875	0.003	0.003	0.000	0.000	0.000	0.000
58	A	787	PRO	0	-0.012	-0.036	24.376	-0.007	-0.007	0.000	0.000	0.000	0.000
59	A	788	SER	0	-0.050	0.002	27.512	0.006	0.006	0.000	0.000	0.000	0.000
60	A	796	ALA	0	-0.040	-0.038	30.897	-0.004	-0.004	0.000	0.000	0.000	0.000
61	A	797	PRO	0	0.001	0.012	28.467	0.006	0.006	0.000	0.000	0.000	0.000
62	A	798	SER	0	0.011	-0.002	31.136	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	799	LYS	1	0.923	0.923	32.376	0.026	0.026	0.000	0.000	0.000	0.000
64	A	800	GLU	-1	-0.765	-0.860	32.933	-0.033	-0.033	0.000	0.000	0.000	0.000
65	A	801	GLN	0	0.011	0.015	28.791	-0.006	-0.006	0.000	0.000	0.000	0.000
66	A	802	LEU	0	-0.022	-0.016	28.215	-0.008	-0.008	0.000	0.000	0.000	0.000
67	A	803	GLU	-1	-0.964	-0.976	28.418	-0.055	-0.055	0.000	0.000	0.000	0.000
68	A	804	GLN	0	0.017	-0.003	26.267	-0.007	-0.007	0.000	0.000	0.000	0.000
69	A	805	GLU	-1	-0.769	-0.850	23.293	-0.128	-0.128	0.000	0.000	0.000	0.000
70	A	806	LYS	1	0.954	0.977	23.844	0.108	0.108	0.000	0.000	0.000	0.000
71	A	807	GLN	0	0.015	0.008	24.969	-0.013	-0.013	0.000	0.000	0.000	0.000
72	A	808	LEU	0	0.019	0.014	21.553	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	809	LEU	0	0.016	0.018	18.508	-0.012	-0.012	0.000	0.000	0.000	0.000
74	A	810	LEU	0	0.002	-0.004	20.907	-0.020	-0.020	0.000	0.000	0.000	0.000
75	A	811	SER	0	-0.094	-0.048	21.749	0.001	0.001	0.000	0.000	0.000	0.000
76	A	812	PHE	0	0.017	-0.019	16.850	0.000	0.000	0.000	0.000	0.000	0.000
77	A	813	LYS	1	0.865	0.950	17.554	0.153	0.153	0.000	0.000	0.000	0.000
78	A	814	PRO	0	0.000	0.000	18.689	-0.032	-0.032	0.000	0.000	0.000	0.000
79	A	815	VAL	0	-0.016	-0.003	13.691	-0.016	-0.016	0.000	0.000	0.000	0.000
80	A	816	MET	0	-0.017	-0.005	13.922	-0.069	-0.069	0.000	0.000	0.000	0.000
81	A	817	GLN	0	0.031	-0.010	14.842	-0.046	-0.046	0.000	0.000	0.000	0.000
82	A	818	LYS	1	0.882	0.965	15.616	0.243	0.243	0.000	0.000	0.000	0.000
83	A	819	PHE	0	-0.039	-0.049	10.860	0.000	0.000	0.000	0.000	0.000	0.000
84	A	820	LEU	0	-0.010	0.002	12.170	-0.093	-0.093	0.000	0.000	0.000	0.000
85	A	821	HIS	0	-0.055	-0.025	14.833	0.012	0.012	0.000	0.000	0.000	0.000
86	A	822	ASP	-1	-0.845	-0.907	17.534	-0.345	-0.345	0.000	0.000	0.000	0.000
87	A	823	HIS	0	-0.022	-0.004	14.418	-0.060	-0.060	0.000	0.000	0.000	0.000
88	A	824	VAL	0	0.074	0.030	15.641	-0.069	-0.069	0.000	0.000	0.000	0.000
89	A	825	ASP	-1	-0.817	-0.915	12.886	-0.901	-0.901	0.000	0.000	0.000	0.000
90	A	826	LEU	0	-0.014	0.005	9.525	-0.119	-0.119	0.000	0.000	0.000	0.000
91	A	827	GLN	0	-0.020	-0.033	12.294	-0.029	-0.029	0.000	0.000	0.000	0.000
92	A	828	VAL	0	0.013	0.016	14.337	0.014	0.014	0.000	0.000	0.000	0.000
93	A	829	SER	0	-0.012	-0.015	9.245	0.008	0.008	0.000	0.000	0.000	0.000
94	A	830	ALA	0	0.012	0.010	11.330	-0.044	-0.044	0.000	0.000	0.000	0.000
95	A	831	LEU	0	0.017	0.021	12.572	0.059	0.059	0.000	0.000	0.000	0.000
96	A	832	TYR	0	-0.032	-0.047	12.229	0.075	0.075	0.000	0.000	0.000	0.000
97	A	833	ALA	0	0.013	0.005	10.446	0.038	0.038	0.000	0.000	0.000	0.000
98	A	834	LEU	0	0.012	0.020	12.271	0.103	0.103	0.000	0.000	0.000	0.000
99	A	835	GLN	0	-0.036	-0.033	15.741	0.068	0.068	0.000	0.000	0.000	0.000
100	A	836	VAL	0	0.005	0.000	12.069	0.070	0.070	0.000	0.000	0.000	0.000
101	A	837	HIS	0	0.016	0.017	14.334	0.058	0.058	0.000	0.000	0.000	0.000
102	A	838	CYS	0	-0.051	-0.035	15.559	0.075	0.075	0.000	0.000	0.000	0.000
103	A	839	TYR	0	-0.015	-0.014	16.777	0.041	0.041	0.000	0.000	0.000	0.000
104	A	840	ASN	0	-0.014	-0.025	13.438	0.047	0.047	0.000	0.000	0.000	0.000
105	A	841	SER	0	-0.049	0.000	17.910	0.047	0.047	0.000	0.000	0.000	0.000
106	A	842	ASN	0	-0.068	-0.048	20.981	0.001	0.001	0.000	0.000	0.000	0.000
107	A	843	PHE	0	-0.072	-0.037	20.396	0.012	0.012	0.000	0.000	0.000	0.000
108	A	844	PRO	0	0.080	0.057	23.154	0.008	0.008	0.000	0.000	0.000	0.000
109	A	845	LYS	1	1.020	0.995	26.177	0.075	0.075	0.000	0.000	0.000	0.000
110	A	846	GLY	0	-0.037	-0.028	28.532	0.005	0.005	0.000	0.000	0.000	0.000
111	A	847	MET	0	-0.021	-0.001	20.239	0.001	0.001	0.000	0.000	0.000	0.000
112	A	848	LEU	0	0.063	0.040	20.406	-0.009	-0.009	0.000	0.000	0.000	0.000
113	A	849	LEU	0	0.019	0.011	23.130	-0.012	-0.012	0.000	0.000	0.000	0.000
114	A	850	ARG	1	0.808	0.874	25.060	0.120	0.120	0.000	0.000	0.000	0.000
115	A	851	PHE	0	0.002	-0.012	19.362	0.001	0.001	0.000	0.000	0.000	0.000
116	A	852	PHE	0	0.039	0.019	20.010	-0.016	-0.016	0.000	0.000	0.000	0.000
117	A	853	VAL	0	0.004	0.008	23.079	-0.003	-0.003	0.000	0.000	0.000	0.000
118	A	854	HIS	0	-0.033	-0.031	22.785	0.004	0.004	0.000	0.000	0.000	0.000
119	A	855	PHE	0	-0.022	-0.028	16.408	-0.002	-0.002	0.000	0.000	0.000	0.000
120	A	856	TYR	0	-0.033	-0.020	21.524	-0.009	-0.009	0.000	0.000	0.000	0.000
121	A	857	ASP	-1	-0.911	-0.951	24.337	-0.156	-0.156	0.000	0.000	0.000	0.000
122	A	858	MET	0	-0.156	-0.079	21.612	0.017	0.017	0.000	0.000	0.000	0.000
123	A	859	GLU	-1	-0.849	-0.916	23.317	-0.191	-0.191	0.000	0.000	0.000	0.000
124	A	860	ILE	0	-0.058	-0.026	17.157	-0.011	-0.011	0.000	0.000	0.000	0.000
125	A	861	ILE	0	-0.074	-0.030	16.086	-0.055	-0.055	0.000	0.000	0.000	0.000
126	A	862	GLU	-1	-0.826	-0.903	19.786	-0.314	-0.314	0.000	0.000	0.000	0.000
127	A	863	GLU	-1	-0.822	-0.915	22.312	-0.229	-0.229	0.000	0.000	0.000	0.000
128	A	864	GLU	-1	-0.843	-0.937	22.862	-0.287	-0.287	0.000	0.000	0.000	0.000
129	A	865	ALA	0	-0.006	0.002	18.236	-0.020	-0.020	0.000	0.000	0.000	0.000
130	A	866	PHE	0	0.002	-0.022	19.769	-0.024	-0.024	0.000	0.000	0.000	0.000
131	A	867	LEU	0	-0.012	0.002	21.812	-0.005	-0.005	0.000	0.000	0.000	0.000
132	A	868	ALA	0	0.010	0.005	19.350	-0.001	-0.001	0.000	0.000	0.000	0.000
133	A	869	TRP	0	-0.034	-0.025	16.409	0.019	0.019	0.000	0.000	0.000	0.000
134	A	870	LYS	1	0.792	0.875	19.096	0.231	0.231	0.000	0.000	0.000	0.000
135	A	871	GLU	-1	-0.848	-0.916	22.526	-0.240	-0.240	0.000	0.000	0.000	0.000
136	A	872	ASP	-1	-0.800	-0.836	16.571	-0.540	-0.540	0.000	0.000	0.000	0.000
137	A	873	ILE	0	-0.054	-0.034	19.808	0.017	0.017	0.000	0.000	0.000	0.000
138	A	874	THR	0	-0.085	-0.059	16.108	-0.024	-0.024	0.000	0.000	0.000	0.000
139	A	875	GLN	0	-0.045	-0.010	11.268	-0.171	-0.171	0.000	0.000	0.000	0.000
140	A	876	GLU	-1	-0.926	-0.960	13.857	-0.365	-0.365	0.000	0.000	0.000	0.000
141	A	877	PHE	0	-0.038	-0.012	9.006	-0.033	-0.033	0.000	0.000	0.000	0.000
142	A	878	PRO	0	0.010	0.012	14.314	0.044	0.044	0.000	0.000	0.000	0.000
143	A	879	GLY	0	0.027	0.000	17.393	-0.020	-0.020	0.000	0.000	0.000	0.000
144	A	880	LYS	1	0.919	0.976	18.668	0.414	0.414	0.000	0.000	0.000	0.000
145	A	881	GLY	0	0.053	0.023	20.654	0.012	0.012	0.000	0.000	0.000	0.000
146	A	882	LYS	1	0.922	0.961	23.836	0.145	0.145	0.000	0.000	0.000	0.000
147	A	883	ALA	0	0.016	0.021	21.170	0.012	0.012	0.000	0.000	0.000	0.000
148	A	884	LEU	0	0.057	0.021	23.068	0.011	0.011	0.000	0.000	0.000	0.000
149	A	885	PHE	0	-0.063	-0.022	25.157	0.013	0.013	0.000	0.000	0.000	0.000
150	A	886	GLN	0	-0.084	-0.068	24.135	0.016	0.016	0.000	0.000	0.000	0.000
151	A	887	VAL	0	0.016	0.013	23.961	0.011	0.011	0.000	0.000	0.000	0.000
152	A	888	ASN	0	0.034	0.014	27.201	-0.007	-0.007	0.000	0.000	0.000	0.000
153	A	889	GLN	0	-0.017	0.016	29.123	0.001	0.001	0.000	0.000	0.000	0.000
154	A	890	TRP	0	0.001	0.003	24.829	0.003	0.003	0.000	0.000	0.000	0.000
155	A	891	LEU	0	0.040	0.003	24.214	-0.002	-0.002	0.000	0.000	0.000	0.000
156	A	892	THR	0	-0.022	-0.015	28.410	-0.001	-0.001	0.000	0.000	0.000	0.000
157	A	893	TRP	0	-0.042	-0.022	31.637	0.010	0.010	0.000	0.000	0.000	0.000
158	A	894	LEU	0	-0.039	-0.005	26.453	0.001	0.001	0.000	0.000	0.000	0.000
159	A	895	GLU	-1	-0.908	-0.950	29.534	-0.210	-0.210	0.000	0.000	0.000	0.000
160	A	896	THR	0	-0.090	-0.028	31.160	0.010	0.010	0.000	0.000	0.000	0.000
161	A	897	ALA	0	-0.052	-0.036	34.960	0.004	0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:730:LEU)