FMO DATABASE

FMODB ID: 8951Y

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

Total energy (hartree)

FMO2-HF: Electronic energy	-947043.256008
FMO2-HF: Nuclear repulsion	900272.549402
FMO2-HF: Total energy	-46770.706606
FMO2-MP2: Total energy	-46903.423648

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.
19.115	19.321	21.726	-11.169	-10.762	0.119

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 : -0.825 / q_NPA : -0.912

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	-0.053	-0.044	1.787	-61.775	-64.092	21.552	-10.162	-9.073	0.115
4	A	809	THR	0	-0.040	-0.008	2.806	-12.433	-10.324	0.177	-0.826	-1.459	0.004
5	A	810	LEU	0	-0.040	-0.032	4.152	-8.225	-7.764	-0.001	-0.149	-0.311	0.000
6	A	811	ASN	0	0.002	0.005	4.770	1.913	1.869	-0.001	-0.024	0.069	0.000
7	A	812	TRP	0	0.073	0.025	7.500	-3.683	-3.683	0.000	0.000	0.000	0.000
8	A	813	ASP	-1	-0.832	-0.925	9.717	22.733	22.733	0.000	0.000	0.000	0.000
9	A	814	LEU	0	-0.043	0.004	10.467	-2.025	-2.025	0.000	0.000	0.000	0.000
10	A	815	CYS	0	-0.017	0.016	11.706	-2.065	-2.065	0.000	0.000	0.000	0.000
11	A	816	LEU	0	-0.011	-0.001	13.383	-1.887	-1.887	0.000	0.000	0.000	0.000
12	A	817	THR	0	-0.028	-0.031	15.404	-1.569	-1.569	0.000	0.000	0.000	0.000
13	A	818	GLN	0	0.006	0.012	14.416	-0.746	-0.746	0.000	0.000	0.000	0.000
14	A	819	ALA	0	-0.004	0.005	17.424	-1.070	-1.070	0.000	0.000	0.000	0.000
15	A	820	ASN	0	-0.039	-0.024	19.290	-1.468	-1.468	0.000	0.000	0.000	0.000
16	A	821	HIS	0	-0.002	-0.014	17.966	-0.638	-0.638	0.000	0.000	0.000	0.000
17	A	822	LYS	1	0.852	0.938	20.125	-12.451	-12.451	0.000	0.000	0.000	0.000
18	A	823	SER	0	0.076	0.023	17.723	0.060	0.060	0.000	0.000	0.000	0.000
19	A	824	ASN	0	-0.014	-0.007	18.135	0.647	0.647	0.000	0.000	0.000	0.000
20	A	825	LEU	0	0.022	0.010	20.157	-0.030	-0.030	0.000	0.000	0.000	0.000
21	A	826	ALA	0	0.032	0.020	14.941	0.184	0.184	0.000	0.000	0.000	0.000
22	A	827	LEU	0	0.018	-0.002	14.292	0.589	0.589	0.000	0.000	0.000	0.000
23	A	828	GLU	-1	-0.860	-0.905	16.371	13.107	13.107	0.000	0.000	0.000	0.000
24	A	829	MET	0	-0.003	-0.009	16.734	-0.229	-0.229	0.000	0.000	0.000	0.000
25	A	830	LEU	0	0.028	0.012	10.820	0.293	0.293	0.000	0.000	0.000	0.000
26	A	831	LYS	1	0.832	0.901	14.359	-13.191	-13.191	0.000	0.000	0.000	0.000
27	A	832	MET	0	-0.027	-0.016	16.957	-0.203	-0.203	0.000	0.000	0.000	0.000
28	A	833	LEU	0	0.024	0.016	12.424	-0.157	-0.157	0.000	0.000	0.000	0.000
29	A	834	LEU	0	-0.019	-0.016	13.006	-0.048	-0.048	0.000	0.000	0.000	0.000
30	A	835	ASP	-1	-0.963	-0.980	15.380	12.689	12.689	0.000	0.000	0.000	0.000
31	A	836	SER	0	-0.029	-0.023	18.048	-0.259	-0.259	0.000	0.000	0.000	0.000
32	A	837	LEU	0	-0.006	0.011	12.727	-0.079	-0.079	0.000	0.000	0.000	0.000
33	A	838	PRO	0	0.029	0.015	16.917	-0.176	-0.176	0.000	0.000	0.000	0.000
34	A	839	GLU	-1	-0.817	-0.887	18.946	11.499	11.499	0.000	0.000	0.000	0.000
35	A	840	THR	0	-0.068	-0.049	18.312	-0.552	-0.552	0.000	0.000	0.000	0.000
36	A	841	VAL	0	-0.010	-0.007	15.526	-0.023	-0.023	0.000	0.000	0.000	0.000
37	A	842	GLU	-1	-0.856	-0.900	18.443	11.978	11.978	0.000	0.000	0.000	0.000
38	A	843	LYS	1	0.816	0.885	21.951	-12.348	-12.348	0.000	0.000	0.000	0.000
39	A	844	ILE	0	0.007	0.006	18.013	-0.314	-0.314	0.000	0.000	0.000	0.000
40	A	845	GLN	0	-0.008	-0.006	19.682	-0.222	-0.222	0.000	0.000	0.000	0.000
41	A	846	THR	0	-0.009	-0.021	22.115	-0.472	-0.472	0.000	0.000	0.000	0.000
42	A	847	ALA	0	-0.045	-0.026	24.555	-0.429	-0.429	0.000	0.000	0.000	0.000
43	A	848	LEU	0	0.003	-0.006	21.337	-0.273	-0.273	0.000	0.000	0.000	0.000
44	A	849	GLY	0	-0.010	0.003	24.838	-0.329	-0.329	0.000	0.000	0.000	0.000
45	A	850	GLN	0	-0.081	-0.053	27.357	-0.364	-0.364	0.000	0.000	0.000	0.000
46	A	851	ASN	0	-0.012	-0.024	28.368	-0.091	-0.091	0.000	0.000	0.000	0.000
47	A	852	ASP	-1	-0.840	-0.878	28.616	10.047	10.047	0.000	0.000	0.000	0.000
48	A	853	GLN	0	0.028	-0.023	27.873	0.554	0.554	0.000	0.000	0.000	0.000
49	A	854	ALA	0	-0.046	-0.015	28.208	0.248	0.248	0.000	0.000	0.000	0.000
50	A	855	THR	0	-0.034	-0.054	26.167	0.193	0.193	0.000	0.000	0.000	0.000
51	A	856	MET	0	0.034	0.049	22.288	0.632	0.632	0.000	0.000	0.000	0.000
52	A	857	LEU	0	-0.017	0.007	23.668	0.494	0.494	0.000	0.000	0.000	0.000
53	A	858	SER	0	-0.029	-0.028	24.761	0.376	0.376	0.000	0.000	0.000	0.000
54	A	859	THR	0	-0.037	-0.033	21.911	0.209	0.209	0.000	0.000	0.000	0.000
55	A	860	ILE	0	0.078	0.038	18.742	0.519	0.519	0.000	0.000	0.000	0.000
56	A	861	HIS	0	-0.080	-0.046	20.141	0.381	0.381	0.000	0.000	0.000	0.000
57	A	862	LYS	1	0.868	0.929	21.983	-11.553	-11.553	0.000	0.000	0.000	0.000
58	A	863	LEU	0	0.042	0.030	14.946	0.229	0.229	0.000	0.000	0.000	0.000
59	A	864	HIS	0	-0.028	-0.022	17.121	1.452	1.452	0.000	0.000	0.000	0.000
60	A	865	GLY	0	0.022	0.020	18.192	0.573	0.573	0.000	0.000	0.000	0.000
61	A	866	ALA	0	0.024	0.008	17.603	0.152	0.152	0.000	0.000	0.000	0.000
62	A	867	SER	0	-0.019	-0.029	13.622	0.788	0.788	0.000	0.000	0.000	0.000
63	A	868	CYS	0	-0.066	-0.031	14.331	1.211	1.211	0.000	0.000	0.000	0.000
64	A	869	TYR	0	-0.075	-0.035	16.687	-0.548	-0.548	0.000	0.000	0.000	0.000
65	A	870	CYS	0	-0.004	-0.001	12.780	-0.559	-0.559	0.000	0.000	0.000	0.000
66	A	871	GLY	0	0.016	0.009	11.012	1.196	1.196	0.000	0.000	0.000	0.000
67	A	872	VAL	0	0.003	0.007	8.449	2.974	2.974	0.000	0.000	0.000	0.000
68	A	873	PRO	0	-0.002	-0.005	7.139	-2.110	-2.110	0.000	0.000	0.000	0.000
69	A	874	THR	0	-0.011	-0.009	6.322	-3.275	-3.275	0.000	0.000	0.000	0.000
70	A	875	THR	0	0.064	0.030	9.070	-3.367	-3.367	0.000	0.000	0.000	0.000
71	A	876	GLN	0	-0.014	-0.006	11.131	-1.762	-1.762	0.000	0.000	0.000	0.000
72	A	877	ARG	1	0.764	0.863	9.811	-28.618	-28.618	0.000	0.000	0.000	0.000
73	A	878	LEU	0	0.029	0.026	11.290	-1.815	-1.815	0.000	0.000	0.000	0.000
74	A	879	CYS	0	-0.052	-0.020	14.641	-1.796	-1.796	0.000	0.000	0.000	0.000
75	A	880	GLN	0	-0.023	-0.003	16.984	-1.156	-1.156	0.000	0.000	0.000	0.000
76	A	881	GLU	-1	-0.822	-0.907	15.469	19.804	19.804	0.000	0.000	0.000	0.000
77	A	882	ILE	0	0.048	0.024	16.938	-1.179	-1.179	0.000	0.000	0.000	0.000
78	A	883	GLU	-1	-0.751	-0.857	20.506	12.364	12.364	0.000	0.000	0.000	0.000
79	A	884	SER	0	-0.096	-0.073	22.113	-1.063	-1.063	0.000	0.000	0.000	0.000
80	A	885	ALA	0	-0.044	-0.019	23.045	-0.654	-0.654	0.000	0.000	0.000	0.000
81	A	886	LEU	0	0.054	0.030	23.456	-0.603	-0.603	0.000	0.000	0.000	0.000
82	A	887	LYS	1	0.773	0.883	24.716	-13.312	-13.312	0.000	0.000	0.000	0.000
83	A	888	ARG	1	0.867	0.944	23.510	-13.288	-13.288	0.000	0.000	0.000	0.000
84	A	889	GLN	0	-0.037	-0.014	29.516	-0.208	-0.208	0.000	0.000	0.000	0.000
85	A	890	THR	0	0.027	0.025	26.536	-0.184	-0.184	0.000	0.000	0.000	0.000
86	A	891	PRO	0	-0.012	0.007	27.878	0.228	0.228	0.000	0.000	0.000	0.000
87	A	892	VAL	0	0.031	0.005	24.722	0.379	0.379	0.000	0.000	0.000	0.000
88	A	893	GLU	-1	-0.907	-0.936	24.783	10.836	10.836	0.000	0.000	0.000	0.000
89	A	894	ASP	-1	-0.923	-0.963	25.616	11.384	11.384	0.000	0.000	0.000	0.000
90	A	895	LEU	0	-0.070	-0.031	21.666	0.424	0.424	0.000	0.000	0.000	0.000
91	A	896	GLU	-1	-0.917	-0.950	20.509	14.077	14.077	0.000	0.000	0.000	0.000
92	A	897	PRO	0	-0.026	-0.014	18.348	0.755	0.755	0.000	0.000	0.000	0.000
93	A	898	GLU	-1	-0.825	-0.924	15.855	17.188	17.188	0.000	0.000	0.000	0.000
94	A	899	ILE	0	0.001	-0.009	15.790	1.156	1.156	0.000	0.000	0.000	0.000
95	A	900	LEU	0	-0.021	-0.009	16.695	0.569	0.569	0.000	0.000	0.000	0.000
96	A	901	GLU	-1	-0.853	-0.908	11.097	27.372	27.372	0.000	0.000	0.000	0.000
97	A	902	LEU	0	-0.005	-0.005	11.731	2.177	2.177	0.000	0.000	0.000	0.000
98	A	903	LEU	0	0.000	-0.001	12.546	0.731	0.731	0.000	0.000	0.000	0.000
99	A	904	ASP	-1	-0.844	-0.905	9.742	30.145	30.145	0.000	0.000	0.000	0.000
100	A	905	GLU	-1	-0.803	-0.887	5.942	46.163	46.163	0.000	0.000	0.000	0.000
101	A	906	LEU	0	-0.006	-0.019	8.318	1.263	1.263	0.000	0.000	0.000	0.000
102	A	907	THR	0	-0.024	-0.007	10.850	-0.890	-0.890	0.000	0.000	0.000	0.000
103	A	908	LYS	1	0.782	0.881	5.093	-38.449	-38.449	0.000	0.000	0.000	0.000
104	A	909	VAL	0	-0.009	-0.009	6.829	0.479	0.479	0.000	0.000	0.000	0.000
105	A	910	GLU	-1	-0.825	-0.911	8.188	17.153	17.153	0.000	0.000	0.000	0.000
106	A	911	SER	0	-0.073	-0.026	7.537	-1.320	-1.320	0.000	0.000	0.000	0.000
107	A	912	ALA	0	0.034	0.011	4.487	-0.803	-0.806	-0.001	-0.008	0.012	0.000
108	A	913	VAL	0	0.026	0.003	6.158	-0.839	-0.839	0.000	0.000	0.000	0.000
109	A	914	LYS	1	0.877	0.935	9.387	-19.888	-19.888	0.000	0.000	0.000	0.000
110	A	915	GLN	0	-0.052	-0.005	6.672	1.063	1.063	0.000	0.000	0.000	0.000
111	A	916	VAL	0	0.025	0.000	7.144	-1.211	-1.211	0.000	0.000	0.000	0.000
112	A	917	LEU	0	-0.002	-0.008	9.839	-1.493	-1.493	0.000	0.000	0.000	0.000
113	A	918	SER	0	-0.055	-0.035	12.734	-1.481	-1.481	0.000	0.000	0.000	0.000
114	A	919	GLN	0	-0.059	-0.007	9.977	0.618	0.618	0.000	0.000	0.000	0.000
115	A	920	LEU	0	-0.041	-0.023	12.068	-0.700	-0.700	0.000	0.000	0.000	0.000
116	A	921	SER	0	-0.069	-0.025	15.260	-0.864	-0.864	0.000	0.000	0.000	0.000
117	A	922	ALA	0	-0.017	-0.008	17.710	-0.321	-0.321	0.000	0.000	0.000	0.000

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