FMO DATABASE

FMODB ID: 89QRY

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	OptAll
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	-1759301.59568
FMO2-HF: Nuclear repulsion	1693577.371417
FMO2-HF: Total energy	-65724.224263
FMO2-MP2: Total energy	-65917.904522

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.
-23.466	-14.419	6.376	-5.052	-10.37	-0.017

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 : 0.035 / q_NPA : 0.015

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	0.991	0.987	3.492	-5.565	-3.656	0.016	-0.877	-1.048	0.004
4	A	733	LEU	0	-0.001	0.001	2.340	-4.430	-2.805	2.184	-1.577	-2.232	0.003
5	A	734	GLU	-1	-0.743	-0.864	3.693	-1.870	-1.285	0.003	-0.230	-0.358	0.001
6	A	735	LYS	1	0.745	0.865	5.656	-0.960	-0.960	0.000	0.000	0.000	0.000
7	A	736	GLU	-1	-0.801	-0.865	7.553	0.772	0.772	0.000	0.000	0.000	0.000
8	A	737	LEU	0	0.018	0.014	6.992	-0.250	-0.250	0.000	0.000	0.000	0.000
9	A	738	LEU	0	0.027	0.010	9.018	-0.137	-0.137	0.000	0.000	0.000	0.000
10	A	739	LYS	1	0.809	0.891	11.317	-0.890	-0.890	0.000	0.000	0.000	0.000
11	A	740	GLN	0	-0.048	-0.051	12.124	-0.160	-0.160	0.000	0.000	0.000	0.000
12	A	741	ILE	0	-0.008	-0.008	11.683	-0.063	-0.063	0.000	0.000	0.000	0.000
13	A	742	LYS	1	0.907	0.952	14.991	-0.204	-0.204	0.000	0.000	0.000	0.000
14	A	743	LEU	0	-0.083	-0.021	15.913	-0.005	-0.005	0.000	0.000	0.000	0.000
15	A	744	ASP	-1	-0.800	-0.895	17.868	0.096	0.096	0.000	0.000	0.000	0.000
16	A	745	PRO	0	0.031	0.030	18.098	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	746	SER	0	0.004	0.003	19.432	-0.046	-0.046	0.000	0.000	0.000	0.000
18	A	747	PRO	0	0.034	0.008	17.954	0.012	0.012	0.000	0.000	0.000	0.000
19	A	748	GLN	0	-0.033	-0.014	17.602	0.000	0.000	0.000	0.000	0.000	0.000
20	A	749	THR	0	-0.033	-0.039	17.634	-0.007	-0.007	0.000	0.000	0.000	0.000
21	A	750	ILE	0	0.016	0.026	12.979	0.034	0.034	0.000	0.000	0.000	0.000
22	A	751	TYR	0	-0.007	-0.001	13.282	0.026	0.026	0.000	0.000	0.000	0.000
23	A	752	LYS	1	0.919	0.965	14.070	-0.141	-0.141	0.000	0.000	0.000	0.000
24	A	753	TRP	0	0.020	0.009	7.778	0.043	0.043	0.000	0.000	0.000	0.000
25	A	754	ILE	0	0.026	0.001	8.921	0.086	0.086	0.000	0.000	0.000	0.000
26	A	755	LYS	1	0.818	0.895	10.218	-0.028	-0.028	0.000	0.000	0.000	0.000
27	A	756	ASP	-1	-0.874	-0.930	12.881	0.100	0.100	0.000	0.000	0.000	0.000
28	A	757	ASN	0	-0.080	-0.034	10.622	0.113	0.113	0.000	0.000	0.000	0.000
29	A	758	ILE	0	-0.026	0.002	5.267	0.304	0.304	0.000	0.000	0.000	0.000
30	A	759	SER	0	0.008	0.009	7.775	-0.191	-0.191	0.000	0.000	0.000	0.000
31	A	760	PRO	0	0.091	0.032	7.865	-0.226	-0.226	0.000	0.000	0.000	0.000
32	A	761	LYS	1	0.903	0.946	9.050	0.305	0.305	0.000	0.000	0.000	0.000
33	A	762	LEU	0	0.008	0.003	3.124	-0.708	-0.066	0.065	-0.128	-0.579	0.000
34	A	763	HIS	0	-0.040	-0.019	5.584	-0.336	-0.336	0.000	0.000	0.000	0.000
35	A	764	VAL	0	0.044	0.017	8.063	0.095	0.095	0.000	0.000	0.000	0.000
36	A	765	ASP	-1	-0.839	-0.908	2.789	-9.296	-7.045	0.593	-1.278	-1.566	-0.014
37	A	766	LYS	1	0.887	0.932	6.201	1.028	1.028	0.000	0.000	0.000	0.000
38	A	767	GLY	0	0.003	-0.003	2.269	0.128	0.333	1.314	-0.783	-0.736	-0.003
39	A	768	PHE	0	-0.041	-0.036	2.646	-0.999	0.083	0.666	0.006	-1.754	-0.004
40	A	769	VAL	0	0.041	0.021	3.275	1.076	0.814	0.049	0.349	-0.136	0.000
41	A	770	ASN	0	-0.053	-0.009	5.675	0.380	0.380	0.000	0.000	0.000	0.000
42	A	771	ILE	0	0.015	0.005	2.570	-0.704	0.306	1.486	-0.534	-1.961	-0.004
43	A	772	LEU	0	-0.025	0.010	5.987	0.555	0.555	0.000	0.000	0.000	0.000
44	A	773	MET	0	0.020	0.014	7.890	0.243	0.243	0.000	0.000	0.000	0.000
45	A	774	THR	0	0.001	-0.013	8.560	0.199	0.199	0.000	0.000	0.000	0.000
46	A	775	SER	0	-0.056	-0.038	8.609	0.230	0.230	0.000	0.000	0.000	0.000
47	A	776	PHE	0	0.023	0.002	11.230	0.095	0.095	0.000	0.000	0.000	0.000
48	A	777	LEU	0	0.001	0.018	13.721	0.055	0.055	0.000	0.000	0.000	0.000
49	A	778	GLN	0	0.000	0.003	11.230	0.120	0.120	0.000	0.000	0.000	0.000
50	A	779	TYR	0	-0.093	-0.062	15.221	0.038	0.038	0.000	0.000	0.000	0.000
51	A	780	ILE	0	0.061	0.031	16.946	0.016	0.016	0.000	0.000	0.000	0.000
52	A	781	SER	0	-0.012	-0.019	18.432	0.005	0.005	0.000	0.000	0.000	0.000
53	A	782	SER	0	-0.102	-0.064	19.226	0.025	0.025	0.000	0.000	0.000	0.000
54	A	783	GLU	-1	-0.841	-0.884	21.172	0.071	0.071	0.000	0.000	0.000	0.000
55	A	784	VAL	0	-0.032	-0.003	23.280	0.001	0.001	0.000	0.000	0.000	0.000
56	A	785	ASN	0	-0.096	-0.061	24.175	0.001	0.001	0.000	0.000	0.000	0.000
57	A	786	PRO	0	0.056	0.050	24.465	0.004	0.004	0.000	0.000	0.000	0.000
58	A	787	PRO	0	-0.024	-0.027	24.073	-0.006	-0.006	0.000	0.000	0.000	0.000
59	A	788	SER	0	-0.031	0.001	27.173	0.003	0.003	0.000	0.000	0.000	0.000
60	A	796	ALA	0	-0.050	-0.043	30.693	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	797	PRO	0	0.021	0.020	27.815	0.006	0.006	0.000	0.000	0.000	0.000
62	A	798	SER	0	0.001	-0.020	30.550	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	799	LYS	1	0.910	0.921	32.073	0.021	0.021	0.000	0.000	0.000	0.000
64	A	800	GLU	-1	-0.772	-0.850	32.667	-0.027	-0.027	0.000	0.000	0.000	0.000
65	A	801	GLN	0	0.036	0.033	28.548	-0.006	-0.006	0.000	0.000	0.000	0.000
66	A	802	LEU	0	-0.024	-0.019	27.836	-0.008	-0.008	0.000	0.000	0.000	0.000
67	A	803	GLU	-1	-0.911	-0.944	28.261	-0.048	-0.048	0.000	0.000	0.000	0.000
68	A	804	GLN	0	0.004	-0.012	26.083	-0.010	-0.010	0.000	0.000	0.000	0.000
69	A	805	GLU	-1	-0.744	-0.834	23.056	-0.110	-0.110	0.000	0.000	0.000	0.000
70	A	806	LYS	1	0.882	0.950	23.468	0.109	0.109	0.000	0.000	0.000	0.000
71	A	807	GLN	0	-0.030	-0.024	24.776	-0.013	-0.013	0.000	0.000	0.000	0.000
72	A	808	LEU	0	0.001	0.007	21.567	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	809	LEU	0	0.004	0.014	17.996	-0.009	-0.009	0.000	0.000	0.000	0.000
74	A	810	LEU	0	0.018	0.002	20.433	-0.021	-0.021	0.000	0.000	0.000	0.000
75	A	811	SER	0	-0.096	-0.057	21.743	0.000	0.000	0.000	0.000	0.000	0.000
76	A	812	PHE	0	0.022	-0.008	16.820	0.002	0.002	0.000	0.000	0.000	0.000
77	A	813	LYS	1	0.848	0.937	17.590	0.143	0.143	0.000	0.000	0.000	0.000
78	A	814	PRO	0	0.003	-0.003	18.549	-0.032	-0.032	0.000	0.000	0.000	0.000
79	A	815	VAL	0	-0.027	-0.011	13.644	-0.023	-0.023	0.000	0.000	0.000	0.000
80	A	816	MET	0	-0.021	-0.007	13.682	-0.062	-0.062	0.000	0.000	0.000	0.000
81	A	817	GLN	0	0.057	0.008	14.398	-0.045	-0.045	0.000	0.000	0.000	0.000
82	A	818	LYS	1	0.766	0.903	15.209	0.253	0.253	0.000	0.000	0.000	0.000
83	A	819	PHE	0	-0.027	-0.030	10.708	0.013	0.013	0.000	0.000	0.000	0.000
84	A	820	LEU	0	0.005	0.002	11.960	-0.114	-0.114	0.000	0.000	0.000	0.000
85	A	821	HIS	0	0.028	0.018	14.691	0.020	0.020	0.000	0.000	0.000	0.000
86	A	822	ASP	-1	-0.838	-0.907	17.396	-0.344	-0.344	0.000	0.000	0.000	0.000
87	A	823	HIS	0	-0.038	-0.011	13.851	-0.068	-0.068	0.000	0.000	0.000	0.000
88	A	824	VAL	0	0.075	0.035	15.076	-0.077	-0.077	0.000	0.000	0.000	0.000
89	A	825	ASP	-1	-0.817	-0.902	12.546	-0.881	-0.881	0.000	0.000	0.000	0.000
90	A	826	LEU	0	-0.028	-0.012	9.434	-0.113	-0.113	0.000	0.000	0.000	0.000
91	A	827	GLN	0	-0.011	-0.033	11.897	-0.027	-0.027	0.000	0.000	0.000	0.000
92	A	828	VAL	0	0.024	0.025	13.937	0.017	0.017	0.000	0.000	0.000	0.000
93	A	829	SER	0	-0.008	-0.010	8.704	0.020	0.020	0.000	0.000	0.000	0.000
94	A	830	ALA	0	0.006	0.007	10.473	-0.058	-0.058	0.000	0.000	0.000	0.000
95	A	831	LEU	0	0.011	0.014	12.160	0.067	0.067	0.000	0.000	0.000	0.000
96	A	832	TYR	0	-0.026	-0.048	11.714	0.075	0.075	0.000	0.000	0.000	0.000
97	A	833	ALA	0	-0.007	0.004	10.105	0.032	0.032	0.000	0.000	0.000	0.000
98	A	834	LEU	0	-0.009	0.002	11.724	0.099	0.099	0.000	0.000	0.000	0.000
99	A	835	GLN	0	-0.036	-0.030	15.280	0.059	0.059	0.000	0.000	0.000	0.000
100	A	836	VAL	0	0.017	0.005	11.289	0.065	0.065	0.000	0.000	0.000	0.000
101	A	837	HIS	0	0.007	0.005	13.843	0.053	0.053	0.000	0.000	0.000	0.000
102	A	838	CYS	0	-0.026	-0.014	15.104	0.065	0.065	0.000	0.000	0.000	0.000
103	A	839	TYR	0	-0.020	-0.013	16.331	0.036	0.036	0.000	0.000	0.000	0.000
104	A	840	ASN	0	-0.010	-0.015	13.174	0.043	0.043	0.000	0.000	0.000	0.000
105	A	841	SER	0	-0.032	-0.007	17.605	0.041	0.041	0.000	0.000	0.000	0.000
106	A	842	ASN	0	-0.047	-0.032	20.520	0.000	0.000	0.000	0.000	0.000	0.000
107	A	843	PHE	0	-0.019	-0.013	19.780	0.007	0.007	0.000	0.000	0.000	0.000
108	A	844	PRO	0	0.053	0.038	22.676	0.008	0.008	0.000	0.000	0.000	0.000
109	A	845	LYS	1	0.977	0.975	25.759	0.063	0.063	0.000	0.000	0.000	0.000
110	A	846	GLY	0	0.011	0.006	27.825	0.005	0.005	0.000	0.000	0.000	0.000
111	A	847	MET	0	-0.032	-0.005	19.959	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	848	LEU	0	0.041	0.030	19.717	-0.008	-0.008	0.000	0.000	0.000	0.000
113	A	849	LEU	0	0.026	0.016	22.630	-0.013	-0.013	0.000	0.000	0.000	0.000
114	A	850	ARG	1	0.803	0.869	24.780	0.103	0.103	0.000	0.000	0.000	0.000
115	A	851	PHE	0	0.016	-0.006	19.288	0.000	0.000	0.000	0.000	0.000	0.000
116	A	852	PHE	0	0.022	0.005	19.368	-0.017	-0.017	0.000	0.000	0.000	0.000
117	A	853	VAL	0	0.014	0.015	22.684	-0.005	-0.005	0.000	0.000	0.000	0.000
118	A	854	HIS	0	-0.045	-0.039	22.377	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	855	PHE	0	-0.015	-0.037	16.090	-0.005	-0.005	0.000	0.000	0.000	0.000
120	A	856	TYR	0	-0.036	-0.020	21.228	-0.009	-0.009	0.000	0.000	0.000	0.000
121	A	857	ASP	-1	-0.860	-0.933	24.184	-0.136	-0.136	0.000	0.000	0.000	0.000
122	A	858	MET	0	-0.102	-0.052	21.709	0.018	0.018	0.000	0.000	0.000	0.000
123	A	859	GLU	-1	-0.846	-0.909	22.769	-0.181	-0.181	0.000	0.000	0.000	0.000
124	A	860	ILE	0	-0.069	-0.025	16.781	-0.015	-0.015	0.000	0.000	0.000	0.000
125	A	861	ILE	0	-0.082	-0.037	15.739	-0.058	-0.058	0.000	0.000	0.000	0.000
126	A	862	GLU	-1	-0.805	-0.888	19.379	-0.307	-0.307	0.000	0.000	0.000	0.000
127	A	863	GLU	-1	-0.833	-0.914	21.957	-0.211	-0.211	0.000	0.000	0.000	0.000
128	A	864	GLU	-1	-0.845	-0.936	22.510	-0.272	-0.272	0.000	0.000	0.000	0.000
129	A	865	ALA	0	-0.011	0.002	17.897	-0.019	-0.019	0.000	0.000	0.000	0.000
130	A	866	PHE	0	-0.010	-0.027	19.303	-0.022	-0.022	0.000	0.000	0.000	0.000
131	A	867	LEU	0	0.009	0.016	21.427	-0.003	-0.003	0.000	0.000	0.000	0.000
132	A	868	ALA	0	0.001	-0.006	19.120	0.001	0.001	0.000	0.000	0.000	0.000
133	A	869	TRP	0	-0.031	-0.028	15.845	0.020	0.020	0.000	0.000	0.000	0.000
134	A	870	LYS	1	0.755	0.861	18.654	0.218	0.218	0.000	0.000	0.000	0.000
135	A	871	GLU	-1	-0.780	-0.875	22.118	-0.219	-0.219	0.000	0.000	0.000	0.000
136	A	872	ASP	-1	-0.796	-0.837	16.123	-0.500	-0.500	0.000	0.000	0.000	0.000
137	A	873	ILE	0	-0.042	-0.026	19.413	0.018	0.018	0.000	0.000	0.000	0.000
138	A	874	THR	0	-0.079	-0.059	15.757	-0.013	-0.013	0.000	0.000	0.000	0.000
139	A	875	GLN	0	-0.062	-0.030	10.832	-0.199	-0.199	0.000	0.000	0.000	0.000
140	A	876	GLU	-1	-0.927	-0.957	13.456	-0.343	-0.343	0.000	0.000	0.000	0.000
141	A	877	PHE	0	-0.011	0.002	8.292	0.045	0.045	0.000	0.000	0.000	0.000
142	A	878	PRO	0	0.012	0.009	13.680	0.042	0.042	0.000	0.000	0.000	0.000
143	A	879	GLY	0	0.032	0.000	16.825	-0.014	-0.014	0.000	0.000	0.000	0.000
144	A	880	LYS	1	0.864	0.955	18.198	0.385	0.385	0.000	0.000	0.000	0.000
145	A	881	GLY	0	0.048	0.025	20.055	0.009	0.009	0.000	0.000	0.000	0.000
146	A	882	LYS	1	0.885	0.930	23.343	0.119	0.119	0.000	0.000	0.000	0.000
147	A	883	ALA	0	-0.005	0.013	20.442	0.010	0.010	0.000	0.000	0.000	0.000
148	A	884	LEU	0	0.060	0.028	22.436	0.011	0.011	0.000	0.000	0.000	0.000
149	A	885	PHE	0	-0.059	-0.023	24.467	0.012	0.012	0.000	0.000	0.000	0.000
150	A	886	GLN	0	-0.088	-0.062	23.758	0.015	0.015	0.000	0.000	0.000	0.000
151	A	887	VAL	0	0.006	0.003	23.381	0.008	0.008	0.000	0.000	0.000	0.000
152	A	888	ASN	0	0.063	0.028	26.731	-0.008	-0.008	0.000	0.000	0.000	0.000
153	A	889	GLN	0	-0.026	0.011	28.529	0.002	0.002	0.000	0.000	0.000	0.000
154	A	890	TRP	0	0.008	0.002	24.372	0.003	0.003	0.000	0.000	0.000	0.000
155	A	891	LEU	0	0.041	0.005	23.910	-0.002	-0.002	0.000	0.000	0.000	0.000
156	A	892	THR	0	-0.026	-0.020	28.047	-0.002	-0.002	0.000	0.000	0.000	0.000
157	A	893	TRP	0	-0.039	0.002	31.467	0.009	0.009	0.000	0.000	0.000	0.000
158	A	894	LEU	0	-0.047	-0.009	25.748	0.001	0.001	0.000	0.000	0.000	0.000
159	A	895	GLU	-1	-0.905	-0.943	28.975	-0.199	-0.199	0.000	0.000	0.000	0.000
160	A	896	THR	0	-0.125	-0.071	30.810	0.010	0.010	0.000	0.000	0.000	0.000
161	A	897	ALA	0	-0.006	-0.013	34.638	0.003	0.003	0.000	0.000	0.000	0.000

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