FMO DATABASE

FMODB ID: 1N7QZ

Calculation Name: 3MYF-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3MYF

Chain ID: A

ChEMBL ID:
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UniProt ID:
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Base Structure: X-ray

Registration Date: 2023-09-21

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	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	117
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-940672.007151
FMO2-HF: Nuclear repulsion	893902.128415
FMO2-HF: Total energy	-46769.878736
FMO2-MP2: Total energy	-46902.635392

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:806:ASP)

Summations of interaction energy for fragment #1(A:806: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.
27.438	31.521	14.784	-9.622	-9.247	0.105

Interaction energy analysis for fragmet #1(A:806:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.846 / q_NPA : -0.932

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	808	HIS	0	-0.066	-0.047	1.736	-55.803	-54.466	14.479	-8.508	-7.308	0.101
4	A	809	THR	0	-0.018	0.019	2.626	-6.743	-4.369	0.308	-1.018	-1.665	0.004
5	A	810	LEU	0	-0.012	-0.017	4.102	-8.591	-8.230	-0.001	-0.071	-0.289	0.000
6	A	811	ASN	0	-0.010	0.005	4.708	1.013	0.914	-0.001	-0.021	0.120	0.000
7	A	812	TRP	0	0.061	0.013	7.338	-3.139	-3.139	0.000	0.000	0.000	0.000
8	A	813	ASP	-1	-0.830	-0.915	9.472	20.610	20.610	0.000	0.000	0.000	0.000
9	A	814	LEU	0	-0.075	-0.020	10.809	-1.900	-1.900	0.000	0.000	0.000	0.000
10	A	815	CYS	0	-0.002	0.016	11.492	-2.083	-2.083	0.000	0.000	0.000	0.000
11	A	816	LEU	0	0.013	0.003	13.188	-1.772	-1.772	0.000	0.000	0.000	0.000
12	A	817	THR	0	-0.042	-0.010	15.185	-1.485	-1.485	0.000	0.000	0.000	0.000
13	A	818	GLN	0	0.021	0.013	14.168	-0.827	-0.827	0.000	0.000	0.000	0.000
14	A	819	ALA	0	0.012	0.021	17.384	-0.925	-0.925	0.000	0.000	0.000	0.000
15	A	820	ASN	0	-0.048	-0.037	19.207	-1.285	-1.285	0.000	0.000	0.000	0.000
16	A	821	HIS	0	0.015	-0.010	18.766	-0.449	-0.449	0.000	0.000	0.000	0.000
17	A	822	LYS	1	0.846	0.938	19.824	-12.529	-12.529	0.000	0.000	0.000	0.000
18	A	823	SER	0	0.049	0.004	17.351	0.058	0.058	0.000	0.000	0.000	0.000
19	A	824	ASN	0	0.020	0.005	18.108	0.519	0.519	0.000	0.000	0.000	0.000
20	A	825	LEU	0	0.023	0.011	20.339	0.005	0.005	0.000	0.000	0.000	0.000
21	A	826	ALA	0	0.041	0.024	15.430	0.187	0.187	0.000	0.000	0.000	0.000
22	A	827	LEU	0	0.013	-0.006	14.224	0.607	0.607	0.000	0.000	0.000	0.000
23	A	828	GLU	-1	-0.935	-0.955	16.462	13.149	13.149	0.000	0.000	0.000	0.000
24	A	829	MET	0	-0.011	-0.014	17.251	-0.159	-0.159	0.000	0.000	0.000	0.000
25	A	830	LEU	0	0.017	0.003	11.370	0.349	0.349	0.000	0.000	0.000	0.000
26	A	831	LYS	1	0.930	0.966	14.923	-13.366	-13.366	0.000	0.000	0.000	0.000
27	A	832	MET	0	-0.026	-0.009	17.516	-0.182	-0.182	0.000	0.000	0.000	0.000
28	A	833	LEU	0	0.018	0.011	12.693	-0.131	-0.131	0.000	0.000	0.000	0.000
29	A	834	LEU	0	-0.009	-0.009	13.607	0.026	0.026	0.000	0.000	0.000	0.000
30	A	835	ASP	-1	-0.960	-0.980	15.947	12.834	12.834	0.000	0.000	0.000	0.000
31	A	836	SER	0	-0.066	-0.039	18.208	-0.320	-0.320	0.000	0.000	0.000	0.000
32	A	837	LEU	0	-0.007	-0.012	12.860	-0.123	-0.123	0.000	0.000	0.000	0.000
33	A	838	PRO	0	0.025	0.022	17.095	-0.064	-0.064	0.000	0.000	0.000	0.000
34	A	839	GLU	-1	-0.888	-0.945	18.956	11.773	11.773	0.000	0.000	0.000	0.000
35	A	840	THR	0	-0.074	-0.036	17.923	-0.445	-0.445	0.000	0.000	0.000	0.000
36	A	841	VAL	0	0.017	0.008	15.672	-0.071	-0.071	0.000	0.000	0.000	0.000
37	A	842	GLU	-1	-0.885	-0.929	18.582	12.492	12.492	0.000	0.000	0.000	0.000
38	A	843	LYS	1	0.899	0.950	22.186	-12.947	-12.947	0.000	0.000	0.000	0.000
39	A	844	ILE	0	-0.023	-0.009	17.911	-0.356	-0.356	0.000	0.000	0.000	0.000
40	A	845	GLN	0	0.013	-0.003	18.833	-0.678	-0.678	0.000	0.000	0.000	0.000
41	A	846	THR	0	-0.020	-0.011	22.015	-0.508	-0.508	0.000	0.000	0.000	0.000
42	A	847	ALA	0	-0.010	-0.014	24.612	-0.437	-0.437	0.000	0.000	0.000	0.000
43	A	848	LEU	0	0.005	-0.004	20.594	-0.332	-0.332	0.000	0.000	0.000	0.000
44	A	849	GLY	0	-0.016	0.006	24.479	-0.273	-0.273	0.000	0.000	0.000	0.000
45	A	850	GLN	0	-0.085	-0.053	27.004	-0.319	-0.319	0.000	0.000	0.000	0.000
46	A	851	ASN	0	-0.015	0.005	28.127	-0.123	-0.123	0.000	0.000	0.000	0.000
47	A	852	ASP	-1	-0.859	-0.896	28.370	10.064	10.064	0.000	0.000	0.000	0.000
48	A	853	GLN	0	0.019	-0.021	28.178	0.386	0.386	0.000	0.000	0.000	0.000
49	A	854	ALA	0	-0.033	-0.023	28.247	0.303	0.303	0.000	0.000	0.000	0.000
50	A	855	THR	0	-0.020	-0.034	26.523	0.161	0.161	0.000	0.000	0.000	0.000
51	A	856	MET	0	0.020	0.030	22.448	0.605	0.605	0.000	0.000	0.000	0.000
52	A	857	LEU	0	-0.014	0.002	24.005	0.468	0.468	0.000	0.000	0.000	0.000
53	A	858	SER	0	-0.044	-0.030	24.977	0.465	0.465	0.000	0.000	0.000	0.000
54	A	859	THR	0	-0.030	-0.026	22.096	0.349	0.349	0.000	0.000	0.000	0.000
55	A	860	ILE	0	0.064	0.035	18.844	0.573	0.573	0.000	0.000	0.000	0.000
56	A	861	HIS	0	-0.085	-0.040	20.467	0.288	0.288	0.000	0.000	0.000	0.000
57	A	862	LYS	1	0.913	0.951	22.225	-11.507	-11.507	0.000	0.000	0.000	0.000
58	A	863	LEU	0	0.031	0.030	15.040	0.190	0.190	0.000	0.000	0.000	0.000
59	A	864	HIS	0	-0.033	-0.028	17.337	1.443	1.443	0.000	0.000	0.000	0.000
60	A	865	GLY	0	0.005	0.004	18.397	0.477	0.477	0.000	0.000	0.000	0.000
61	A	866	ALA	0	0.026	0.005	17.395	0.167	0.167	0.000	0.000	0.000	0.000
62	A	867	SER	0	-0.040	-0.025	13.703	0.767	0.767	0.000	0.000	0.000	0.000
63	A	868	CYS	0	-0.046	-0.016	14.426	1.071	1.071	0.000	0.000	0.000	0.000
64	A	869	TYR	0	-0.109	-0.055	16.779	-0.402	-0.402	0.000	0.000	0.000	0.000
65	A	870	CYS	0	-0.006	0.007	12.988	-0.572	-0.572	0.000	0.000	0.000	0.000
66	A	871	GLY	0	0.001	-0.008	10.986	1.228	1.228	0.000	0.000	0.000	0.000
67	A	872	VAL	0	0.015	0.018	8.423	2.855	2.855	0.000	0.000	0.000	0.000
68	A	873	PRO	0	-0.027	-0.020	7.263	-2.418	-2.418	0.000	0.000	0.000	0.000
69	A	874	THR	0	0.026	0.020	6.066	-4.397	-4.397	0.000	0.000	0.000	0.000
70	A	875	THR	0	0.080	0.034	9.032	-3.264	-3.264	0.000	0.000	0.000	0.000
71	A	876	GLN	0	-0.014	-0.006	11.569	-3.309	-3.309	0.000	0.000	0.000	0.000
72	A	877	ARG	1	0.848	0.926	9.966	-28.985	-28.985	0.000	0.000	0.000	0.000
73	A	878	LEU	0	0.033	0.027	10.787	-1.639	-1.639	0.000	0.000	0.000	0.000
74	A	879	CYS	0	-0.016	-0.008	14.505	-1.829	-1.829	0.000	0.000	0.000	0.000
75	A	880	GLN	0	-0.018	0.004	16.890	-1.001	-1.001	0.000	0.000	0.000	0.000
76	A	881	GLU	-1	-0.851	-0.923	15.856	19.382	19.382	0.000	0.000	0.000	0.000
77	A	882	ILE	0	0.041	0.023	16.818	-1.231	-1.231	0.000	0.000	0.000	0.000
78	A	883	GLU	-1	-0.787	-0.886	20.362	12.735	12.735	0.000	0.000	0.000	0.000
79	A	884	SER	0	-0.117	-0.082	22.179	-1.044	-1.044	0.000	0.000	0.000	0.000
80	A	885	ALA	0	0.005	0.000	23.241	-0.725	-0.725	0.000	0.000	0.000	0.000
81	A	886	LEU	0	0.059	0.031	23.506	-0.666	-0.666	0.000	0.000	0.000	0.000
82	A	887	LYS	1	0.863	0.937	26.065	-12.774	-12.774	0.000	0.000	0.000	0.000
83	A	888	ARG	1	0.854	0.935	24.167	-13.081	-13.081	0.000	0.000	0.000	0.000
84	A	889	GLN	0	-0.027	-0.017	29.572	-0.171	-0.171	0.000	0.000	0.000	0.000
85	A	890	THR	0	-0.027	0.010	26.363	-0.072	-0.072	0.000	0.000	0.000	0.000
86	A	891	PRO	0	0.047	0.035	27.653	0.177	0.177	0.000	0.000	0.000	0.000
87	A	892	VAL	0	0.034	-0.011	24.115	0.335	0.335	0.000	0.000	0.000	0.000
88	A	893	GLU	-1	-0.940	-0.958	24.329	11.135	11.135	0.000	0.000	0.000	0.000
89	A	894	ASP	-1	-0.920	-0.961	25.038	11.608	11.608	0.000	0.000	0.000	0.000
90	A	895	LEU	0	-0.077	-0.041	21.264	0.438	0.438	0.000	0.000	0.000	0.000
91	A	896	GLU	-1	-0.915	-0.952	20.155	14.593	14.593	0.000	0.000	0.000	0.000
92	A	897	PRO	0	-0.024	-0.013	18.253	0.815	0.815	0.000	0.000	0.000	0.000
93	A	898	GLU	-1	-0.822	-0.921	15.822	17.609	17.609	0.000	0.000	0.000	0.000
94	A	899	ILE	0	-0.022	-0.020	15.484	1.258	1.258	0.000	0.000	0.000	0.000
95	A	900	LEU	0	-0.038	-0.019	16.147	0.826	0.826	0.000	0.000	0.000	0.000
96	A	901	GLU	-1	-0.919	-0.954	10.921	27.881	27.881	0.000	0.000	0.000	0.000
97	A	902	LEU	0	-0.015	-0.019	11.282	2.362	2.362	0.000	0.000	0.000	0.000
98	A	903	LEU	0	-0.039	-0.027	12.438	1.014	1.014	0.000	0.000	0.000	0.000
99	A	904	ASP	-1	-0.921	-0.959	8.996	31.275	31.275	0.000	0.000	0.000	0.000
100	A	905	GLU	-1	-0.846	-0.948	6.364	49.717	49.717	0.000	0.000	0.000	0.000
101	A	906	LEU	0	-0.022	-0.021	8.621	1.282	1.282	0.000	0.000	0.000	0.000
102	A	907	THR	0	0.029	0.033	10.706	-0.888	-0.888	0.000	0.000	0.000	0.000
103	A	908	LYS	1	0.895	0.952	4.679	-45.022	-44.912	-0.001	-0.004	-0.105	0.000
104	A	909	VAL	0	-0.007	0.000	6.562	0.833	0.833	0.000	0.000	0.000	0.000
105	A	910	GLU	-1	-0.907	-0.961	8.091	18.302	18.302	0.000	0.000	0.000	0.000
106	A	911	SER	0	-0.076	-0.037	8.141	-1.356	-1.356	0.000	0.000	0.000	0.000
107	A	912	ALA	0	0.042	0.018	5.259	-1.133	-1.133	0.000	0.000	0.000	0.000
108	A	913	VAL	0	0.036	0.007	6.776	-1.276	-1.276	0.000	0.000	0.000	0.000
109	A	914	LYS	1	0.955	0.976	9.835	-19.214	-19.214	0.000	0.000	0.000	0.000
110	A	915	GLN	0	-0.053	-0.004	6.416	0.632	0.632	0.000	0.000	0.000	0.000
111	A	916	VAL	0	0.013	-0.008	7.258	-1.257	-1.257	0.000	0.000	0.000	0.000
112	A	917	LEU	0	-0.046	-0.022	9.930	-1.452	-1.452	0.000	0.000	0.000	0.000
113	A	918	SER	0	-0.035	-0.025	12.942	-1.419	-1.419	0.000	0.000	0.000	0.000
114	A	919	GLN	0	-0.055	-0.009	9.784	0.303	0.303	0.000	0.000	0.000	0.000
115	A	920	LEU	0	-0.023	-0.023	12.383	-0.863	-0.863	0.000	0.000	0.000	0.000
116	A	921	SER	0	-0.089	-0.010	15.145	-0.885	-0.885	0.000	0.000	0.000	0.000
117	A	922	ALA	0	0.011	0.002	17.798	-0.339	-0.339	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:806:ASP)