FMO DATABASE

FMODB ID: 9Y5G2

Calculation Name: 3GQH-A-Xray312

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GQH

Chain ID: A

ChEMBL ID:

UniProt ID: P20345

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	163
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1406192.519995
FMO2-HF: Nuclear repulsion	1344571.367031
FMO2-HF: Total energy	-61621.152963
FMO2-MP2: Total energy	-61806.159684

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:692:ASP )

Summations of interaction energy for fragment #1(A:692:ASP )

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.
-55.392	-51.549	35.276	-18.689	-20.43	0.09

Interaction energy analysis for fragmet #1(A:692:ASP )

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 : 0.020

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	694	ALA	0	0.049	0.025	3.649	3.962	6.124	0.012	-0.926	-1.249	0.000
4	A	695	GLU	-1	-0.940	-0.965	5.540	-2.035	-1.985	0.000	-0.004	-0.046	0.000
5	A	696	TYR	0	0.002	0.000	8.697	1.606	1.606	0.000	0.000	0.000	0.000
6	A	697	PHE	0	0.012	0.001	9.576	-0.718	-0.718	0.000	0.000	0.000	0.000
7	A	698	GLU	-1	-0.885	-0.948	13.118	1.683	1.683	0.000	0.000	0.000	0.000
8	A	699	SER	0	-0.009	-0.022	15.867	-0.095	-0.095	0.000	0.000	0.000	0.000
9	A	700	LEU	0	-0.027	-0.032	17.003	-0.267	-0.267	0.000	0.000	0.000	0.000
10	A	701	GLY	0	-0.027	-0.018	20.196	-0.159	-0.159	0.000	0.000	0.000	0.000
11	A	702	GLY	0	0.004	0.005	20.193	-0.094	-0.094	0.000	0.000	0.000	0.000
12	A	703	GLN	0	-0.074	-0.035	19.931	0.024	0.024	0.000	0.000	0.000	0.000
13	A	704	VAL	0	0.021	0.013	14.928	0.109	0.109	0.000	0.000	0.000	0.000
14	A	705	ILE	0	-0.029	-0.012	13.071	-0.270	-0.270	0.000	0.000	0.000	0.000
15	A	706	GLU	-1	-0.916	-0.972	12.724	3.354	3.354	0.000	0.000	0.000	0.000
16	A	707	THR	0	0.027	0.010	8.748	0.597	0.597	0.000	0.000	0.000	0.000
17	A	708	GLY	0	0.058	0.020	8.480	-1.352	-1.352	0.000	0.000	0.000	0.000
18	A	709	TYR	0	-0.067	-0.020	9.760	-0.974	-0.974	0.000	0.000	0.000	0.000
19	A	710	LEU	0	0.014	0.011	10.215	0.961	0.961	0.000	0.000	0.000	0.000
20	A	711	VAL	0	-0.004	-0.012	10.101	-0.586	-0.586	0.000	0.000	0.000	0.000
21	A	712	THR	0	0.009	-0.020	12.762	-0.189	-0.189	0.000	0.000	0.000	0.000
22	A	713	LEU	0	-0.022	-0.017	14.923	0.137	0.137	0.000	0.000	0.000	0.000
23	A	714	GLU	-1	-0.854	-0.921	17.198	0.895	0.895	0.000	0.000	0.000	0.000
24	A	715	LYS	1	0.909	0.943	20.729	-0.907	-0.907	0.000	0.000	0.000	0.000
25	A	716	GLY	0	0.002	0.006	19.472	-0.017	-0.017	0.000	0.000	0.000	0.000
26	A	717	LYS	1	0.874	0.975	17.422	-1.230	-1.230	0.000	0.000	0.000	0.000
27	A	718	ILE	0	0.023	0.015	11.773	-0.086	-0.086	0.000	0.000	0.000	0.000
28	A	719	ARG	1	0.740	0.815	15.633	-1.503	-1.503	0.000	0.000	0.000	0.000
29	A	720	LYS	1	0.936	0.976	15.186	-2.175	-2.175	0.000	0.000	0.000	0.000
30	A	721	ALA	0	-0.013	0.004	15.145	-0.259	-0.259	0.000	0.000	0.000	0.000
31	A	722	GLU	-1	-0.852	-0.929	16.844	1.466	1.466	0.000	0.000	0.000	0.000
32	A	723	LYS	1	0.995	0.973	20.084	-0.775	-0.775	0.000	0.000	0.000	0.000
33	A	724	GLY	0	-0.005	0.007	21.469	-0.037	-0.037	0.000	0.000	0.000	0.000
34	A	725	GLU	-1	-0.790	-0.834	19.080	1.237	1.237	0.000	0.000	0.000	0.000
35	A	726	LYS	1	0.959	0.967	16.304	-0.496	-0.496	0.000	0.000	0.000	0.000
36	A	727	ILE	0	0.041	0.041	11.196	0.191	0.191	0.000	0.000	0.000	0.000
37	A	728	ILE	0	-0.052	-0.027	10.897	-0.255	-0.255	0.000	0.000	0.000	0.000
38	A	729	GLY	0	0.057	0.027	7.847	-0.173	-0.173	0.000	0.000	0.000	0.000
39	A	730	VAL	0	-0.056	-0.010	5.735	-1.311	-1.311	0.000	0.000	0.000	0.000
40	A	731	ILE	0	-0.055	-0.001	5.681	3.785	3.785	0.000	0.000	0.000	0.000
41	A	732	SER	0	-0.021	-0.036	1.735	-17.749	-21.797	13.180	-5.731	-3.401	0.058
42	A	733	GLU	-1	-0.895	-0.968	4.788	3.120	3.097	0.000	-0.010	0.033	0.000
43	A	734	THR	0	-0.055	-0.042	1.730	-15.354	-20.882	12.905	-4.547	-2.830	0.039
44	A	735	ALA	0	-0.050	-0.004	2.543	-10.426	-6.824	3.545	-3.268	-3.878	0.011
45	A	736	GLY	0	-0.007	0.006	2.848	-2.874	-3.247	0.137	1.123	-0.888	0.002
46	A	737	PHE	0	-0.061	-0.033	4.355	2.193	2.459	0.000	-0.044	-0.222	0.000
47	A	738	VAL	0	0.032	0.018	6.077	0.584	0.584	0.000	0.000	0.000	0.000
48	A	739	LEU	0	0.009	0.004	8.477	-0.455	-0.455	0.000	0.000	0.000	0.000
49	A	740	GLY	0	0.048	0.008	11.471	0.624	0.624	0.000	0.000	0.000	0.000
50	A	741	GLU	-1	-0.896	-0.949	14.131	1.293	1.293	0.000	0.000	0.000	0.000
51	A	742	SER	0	-0.037	-0.028	15.265	0.011	0.011	0.000	0.000	0.000	0.000
52	A	743	SER	0	-0.016	0.009	16.318	-0.078	-0.078	0.000	0.000	0.000	0.000
53	A	744	PHE	0	0.026	-0.004	17.181	0.121	0.121	0.000	0.000	0.000	0.000
54	A	745	GLU	-1	-0.899	-0.927	21.582	0.691	0.691	0.000	0.000	0.000	0.000
55	A	746	TRP	0	-0.049	-0.048	23.547	-0.047	-0.047	0.000	0.000	0.000	0.000
56	A	747	GLN	0	0.029	0.012	26.762	-0.003	-0.003	0.000	0.000	0.000	0.000
57	A	748	GLY	0	0.015	0.018	26.927	0.007	0.007	0.000	0.000	0.000	0.000
58	A	749	ALA	0	0.036	0.008	27.824	-0.030	-0.030	0.000	0.000	0.000	0.000
59	A	750	VAL	0	-0.046	-0.017	28.000	-0.033	-0.033	0.000	0.000	0.000	0.000
60	A	751	LEU	0	0.022	0.006	28.876	0.032	0.032	0.000	0.000	0.000	0.000
61	A	752	LYS	1	0.904	0.955	23.211	-0.183	-0.183	0.000	0.000	0.000	0.000
62	A	753	ASN	0	0.045	0.015	27.209	0.037	0.037	0.000	0.000	0.000	0.000
63	A	754	GLU	-1	-0.887	-0.944	27.380	0.059	0.059	0.000	0.000	0.000	0.000
64	A	755	PHE	0	-0.011	-0.008	24.520	0.029	0.029	0.000	0.000	0.000	0.000
65	A	756	GLY	0	-0.006	0.000	22.835	-0.018	-0.018	0.000	0.000	0.000	0.000
66	A	757	GLY	0	-0.029	-0.004	23.412	-0.028	-0.028	0.000	0.000	0.000	0.000
67	A	758	ILE	0	-0.004	-0.007	24.411	0.054	0.054	0.000	0.000	0.000	0.000
68	A	759	ILE	0	0.005	0.008	27.359	-0.047	-0.047	0.000	0.000	0.000	0.000
69	A	760	TYR	0	-0.046	-0.048	27.062	-0.008	-0.008	0.000	0.000	0.000	0.000
70	A	761	GLU	-1	-0.831	-0.917	32.734	-0.079	-0.079	0.000	0.000	0.000	0.000
71	A	762	GLU	-1	-0.964	-0.985	36.158	-0.210	-0.210	0.000	0.000	0.000	0.000
72	A	763	VAL	0	-0.013	-0.004	38.149	0.020	0.020	0.000	0.000	0.000	0.000
73	A	764	THR	0	-0.013	-0.018	40.246	-0.024	-0.024	0.000	0.000	0.000	0.000
74	A	765	THR	0	-0.038	-0.023	42.109	0.013	0.013	0.000	0.000	0.000	0.000
75	A	766	GLU	-1	-0.926	-0.976	44.714	-0.124	-0.124	0.000	0.000	0.000	0.000
76	A	767	ASP	-1	-0.883	-0.927	46.420	-0.166	-0.166	0.000	0.000	0.000	0.000
77	A	768	GLY	0	-0.050	-0.024	46.176	-0.005	-0.005	0.000	0.000	0.000	0.000
78	A	769	VAL	0	-0.042	-0.019	40.482	-0.013	-0.013	0.000	0.000	0.000	0.000
79	A	770	LYS	1	0.961	0.984	39.607	0.206	0.206	0.000	0.000	0.000	0.000
80	A	771	PHE	0	-0.034	-0.015	35.615	-0.027	-0.027	0.000	0.000	0.000	0.000
81	A	772	LYS	1	0.947	0.984	29.019	0.380	0.380	0.000	0.000	0.000	0.000
82	A	773	ARG	1	0.901	0.949	33.490	0.085	0.085	0.000	0.000	0.000	0.000
83	A	774	PRO	0	-0.025	0.000	30.128	0.007	0.007	0.000	0.000	0.000	0.000
84	A	775	LEU	0	0.046	0.030	32.183	0.010	0.010	0.000	0.000	0.000	0.000
85	A	776	PRO	0	0.013	0.004	32.799	0.016	0.016	0.000	0.000	0.000	0.000
86	A	777	ASN	0	-0.037	-0.018	30.651	-0.029	-0.029	0.000	0.000	0.000	0.000
87	A	778	PRO	0	-0.004	-0.006	33.748	0.009	0.009	0.000	0.000	0.000	0.000
88	A	779	ASP	-1	-0.902	-0.945	33.510	0.220	0.220	0.000	0.000	0.000	0.000
89	A	780	PHE	0	-0.126	-0.046	29.854	0.029	0.029	0.000	0.000	0.000	0.000
90	A	781	ASP	-1	-0.796	-0.928	32.901	0.292	0.292	0.000	0.000	0.000	0.000
91	A	782	PRO	0	-0.073	-0.028	32.992	0.027	0.027	0.000	0.000	0.000	0.000
92	A	783	ASN	0	-0.050	-0.015	34.161	0.013	0.013	0.000	0.000	0.000	0.000
93	A	784	LYS	1	0.904	0.958	32.680	-0.402	-0.402	0.000	0.000	0.000	0.000
94	A	785	ASN	0	0.004	-0.003	28.594	-0.022	-0.022	0.000	0.000	0.000	0.000
95	A	786	TYR	0	0.027	0.009	21.673	0.021	0.021	0.000	0.000	0.000	0.000
96	A	787	ILE	0	-0.023	0.002	21.627	-0.027	-0.027	0.000	0.000	0.000	0.000
97	A	788	PRO	0	0.044	0.017	19.156	0.045	0.045	0.000	0.000	0.000	0.000
98	A	789	ARG	1	0.852	0.920	15.782	-1.000	-1.000	0.000	0.000	0.000	0.000
99	A	790	SER	0	0.042	0.034	14.529	0.237	0.237	0.000	0.000	0.000	0.000
100	A	791	GLN	0	-0.069	-0.031	15.516	0.219	0.219	0.000	0.000	0.000	0.000
101	A	792	ARG	1	0.867	0.952	17.532	-1.314	-1.314	0.000	0.000	0.000	0.000
102	A	793	ARG	1	0.993	0.985	16.724	-1.428	-1.428	0.000	0.000	0.000	0.000
103	A	794	GLU	-1	-0.853	-0.922	16.227	1.866	1.866	0.000	0.000	0.000	0.000
104	A	795	TRP	0	-0.033	-0.006	14.282	0.088	0.088	0.000	0.000	0.000	0.000
105	A	796	HIS	0	-0.003	0.017	10.441	0.158	0.158	0.000	0.000	0.000	0.000
106	A	797	VAL	0	0.048	0.023	5.119	-0.736	-0.712	0.000	-0.002	-0.022	0.000
107	A	798	VAL	0	-0.009	-0.004	6.504	2.124	2.124	0.000	0.000	0.000	0.000
108	A	799	GLY	0	0.022	0.002	2.873	-0.694	0.682	0.498	-0.786	-1.088	0.006
109	A	800	LEU	0	-0.019	-0.025	3.617	-5.004	-4.878	0.027	0.147	-0.300	0.002
110	A	801	LEU	0	0.005	0.012	3.421	-1.414	-0.961	0.003	-0.084	-0.372	0.000
111	A	802	GLY	0	-0.030	-0.024	2.496	-11.788	-9.290	2.309	-2.468	-2.338	-0.026
112	A	803	GLN	0	-0.025	-0.005	3.529	4.597	5.090	0.038	-0.027	-0.504	-0.001
113	A	804	ILE	0	0.013	0.012	2.439	-3.067	-0.359	2.622	-2.046	-3.284	-0.001
114	A	805	ALA	0	0.014	0.014	4.533	-2.866	-2.809	0.000	-0.016	-0.041	0.000
115	A	806	VAL	0	-0.001	-0.005	7.761	1.568	1.568	0.000	0.000	0.000	0.000
116	A	807	ARG	1	0.844	0.922	10.250	-4.329	-4.329	0.000	0.000	0.000	0.000
117	A	808	ILE	0	-0.009	0.003	13.674	-0.092	-0.092	0.000	0.000	0.000	0.000
118	A	809	ASP	-1	-0.684	-0.836	16.457	1.067	1.067	0.000	0.000	0.000	0.000
119	A	810	GLU	-1	-1.002	-1.012	20.193	0.763	0.763	0.000	0.000	0.000	0.000
120	A	811	THR	0	-0.075	-0.056	21.765	-0.119	-0.119	0.000	0.000	0.000	0.000
121	A	812	VAL	0	0.004	0.018	15.793	-0.095	-0.095	0.000	0.000	0.000	0.000
122	A	813	LYS	1	0.921	0.962	18.799	-0.410	-0.410	0.000	0.000	0.000	0.000
123	A	814	GLN	0	-0.023	-0.033	16.232	0.048	0.048	0.000	0.000	0.000	0.000
124	A	815	GLY	0	-0.037	-0.023	16.039	-0.045	-0.045	0.000	0.000	0.000	0.000
125	A	816	HIS	0	-0.052	-0.012	17.405	-0.090	-0.090	0.000	0.000	0.000	0.000
126	A	817	SER	0	-0.021	-0.002	15.439	-0.028	-0.028	0.000	0.000	0.000	0.000
127	A	818	ILE	0	-0.056	-0.030	11.949	0.161	0.161	0.000	0.000	0.000	0.000
128	A	819	ASP	-1	-0.838	-0.900	16.270	0.729	0.729	0.000	0.000	0.000	0.000
129	A	820	ALA	0	-0.021	-0.029	15.671	0.208	0.208	0.000	0.000	0.000	0.000
130	A	821	VAL	0	-0.014	-0.012	17.594	-0.200	-0.200	0.000	0.000	0.000	0.000
131	A	822	GLY	0	0.037	0.025	19.324	0.098	0.098	0.000	0.000	0.000	0.000
132	A	823	GLY	0	-0.053	-0.038	15.338	0.198	0.198	0.000	0.000	0.000	0.000
133	A	824	VAL	0	-0.061	-0.022	14.204	0.530	0.530	0.000	0.000	0.000	0.000
134	A	825	ALA	0	0.018	0.001	14.114	-0.203	-0.203	0.000	0.000	0.000	0.000
135	A	826	THR	0	-0.051	-0.032	16.073	-0.118	-0.118	0.000	0.000	0.000	0.000
136	A	827	ASP	-1	-0.935	-0.982	18.422	0.494	0.494	0.000	0.000	0.000	0.000
137	A	828	GLY	0	0.009	-0.005	19.210	0.026	0.026	0.000	0.000	0.000	0.000
138	A	829	ASP	-1	-0.897	-0.957	19.000	0.244	0.244	0.000	0.000	0.000	0.000
139	A	830	ASN	0	-0.103	-0.053	13.852	-0.182	-0.182	0.000	0.000	0.000	0.000
140	A	831	PHE	0	-0.003	-0.008	10.510	0.183	0.183	0.000	0.000	0.000	0.000
141	A	832	ILE	0	0.031	0.029	11.353	-0.114	-0.114	0.000	0.000	0.000	0.000
142	A	833	VAL	0	-0.016	0.004	11.270	0.003	0.003	0.000	0.000	0.000	0.000
143	A	834	GLN	0	-0.011	-0.019	8.844	-0.672	-0.672	0.000	0.000	0.000	0.000
144	A	835	GLU	-1	-0.925	-0.975	12.387	-0.311	-0.311	0.000	0.000	0.000	0.000
145	A	836	ILE	0	0.008	0.013	13.211	0.329	0.329	0.000	0.000	0.000	0.000
146	A	837	THR	0	0.008	0.008	12.388	-0.092	-0.092	0.000	0.000	0.000	0.000
147	A	838	THR	0	-0.079	-0.032	15.401	0.003	0.003	0.000	0.000	0.000	0.000
148	A	839	PRO	0	0.054	0.022	17.512	0.121	0.121	0.000	0.000	0.000	0.000
149	A	840	TYR	0	0.023	0.030	20.257	0.045	0.045	0.000	0.000	0.000	0.000
150	A	841	THR	0	-0.001	0.001	21.501	-0.134	-0.134	0.000	0.000	0.000	0.000
151	A	842	LYS	1	1.019	0.989	24.026	-0.694	-0.694	0.000	0.000	0.000	0.000
152	A	843	GLU	-1	-0.961	-0.985	26.660	0.803	0.803	0.000	0.000	0.000	0.000
153	A	844	LYS	1	0.894	0.976	19.756	-1.590	-1.590	0.000	0.000	0.000	0.000
154	A	845	GLY	0	-0.050	-0.023	22.114	0.102	0.102	0.000	0.000	0.000	0.000
155	A	846	TYR	0	-0.027	-0.024	15.850	0.036	0.036	0.000	0.000	0.000	0.000
156	A	847	GLY	0	0.030	0.018	17.932	-0.142	-0.142	0.000	0.000	0.000	0.000
157	A	848	VAL	0	-0.050	-0.031	11.785	0.330	0.330	0.000	0.000	0.000	0.000
158	A	849	ALA	0	0.020	0.016	12.570	-0.480	-0.480	0.000	0.000	0.000	0.000
159	A	850	ILE	0	-0.003	0.012	7.161	0.914	0.914	0.000	0.000	0.000	0.000
160	A	851	VAL	0	0.032	0.005	7.805	-0.740	-0.740	0.000	0.000	0.000	0.000
161	A	852	LEU	0	-0.043	-0.015	6.460	-0.204	-0.204	0.000	0.000	0.000	0.000
162	A	853	VAL	0	-0.001	0.002	5.444	0.448	0.448	0.000	0.000	0.000	0.000
163	A	854	LYS	0	0.079	0.036	6.569	0.432	0.432	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:692:ASP )