FMO DATABASE

FMODB ID: G56M1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-941747.265102
FMO2-HF: Nuclear repulsion	894976.679913
FMO2-HF: Total energy	-46770.58519
FMO2-MP2: Total energy	-46903.352109

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.
21.969	24.167	18.383	-10.47	-10.109	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 : -0.835 / q_NPA : -0.921

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	-0.048	-0.040	1.757	-60.667	-61.188	18.153	-9.294	-8.338	0.111
4	A	809	THR	0	-0.053	-0.013	2.686	-11.635	-9.179	0.232	-1.080	-1.607	0.008
5	A	810	LEU	0	-0.019	-0.019	4.236	-8.807	-8.460	-0.001	-0.076	-0.270	0.000
6	A	811	ASN	0	-0.003	0.005	4.790	1.313	1.229	-0.001	-0.020	0.106	0.000
7	A	812	TRP	0	0.073	0.020	7.428	-3.552	-3.552	0.000	0.000	0.000	0.000
8	A	813	ASP	-1	-0.845	-0.924	9.563	22.164	22.164	0.000	0.000	0.000	0.000
9	A	814	LEU	0	-0.038	-0.001	10.591	-2.091	-2.091	0.000	0.000	0.000	0.000
10	A	815	CYS	0	-0.014	0.012	11.580	-2.032	-2.032	0.000	0.000	0.000	0.000
11	A	816	LEU	0	0.020	0.003	13.272	-1.854	-1.854	0.000	0.000	0.000	0.000
12	A	817	THR	0	-0.046	-0.027	15.280	-1.543	-1.543	0.000	0.000	0.000	0.000
13	A	818	GLN	0	0.004	0.006	14.306	-0.759	-0.759	0.000	0.000	0.000	0.000
14	A	819	ALA	0	-0.001	0.015	17.485	-0.971	-0.971	0.000	0.000	0.000	0.000
15	A	820	ASN	0	-0.034	-0.029	19.291	-1.338	-1.338	0.000	0.000	0.000	0.000
16	A	821	HIS	0	0.002	-0.012	18.423	-0.521	-0.521	0.000	0.000	0.000	0.000
17	A	822	LYS	1	0.848	0.936	19.919	-12.579	-12.579	0.000	0.000	0.000	0.000
18	A	823	SER	0	0.063	0.012	17.567	0.086	0.086	0.000	0.000	0.000	0.000
19	A	824	ASN	0	-0.008	-0.006	18.180	0.540	0.540	0.000	0.000	0.000	0.000
20	A	825	LEU	0	0.037	0.016	20.404	0.007	0.007	0.000	0.000	0.000	0.000
21	A	826	ALA	0	0.039	0.028	15.489	0.164	0.164	0.000	0.000	0.000	0.000
22	A	827	LEU	0	0.032	0.004	14.170	0.599	0.599	0.000	0.000	0.000	0.000
23	A	828	GLU	-1	-0.867	-0.905	16.520	13.155	13.155	0.000	0.000	0.000	0.000
24	A	829	MET	0	-0.009	-0.017	17.248	-0.223	-0.223	0.000	0.000	0.000	0.000
25	A	830	LEU	0	0.014	0.007	11.517	0.299	0.299	0.000	0.000	0.000	0.000
26	A	831	LYS	1	0.845	0.910	14.964	-13.252	-13.252	0.000	0.000	0.000	0.000
27	A	832	MET	0	-0.039	-0.021	17.544	-0.229	-0.229	0.000	0.000	0.000	0.000
28	A	833	LEU	0	0.019	0.014	12.858	-0.136	-0.136	0.000	0.000	0.000	0.000
29	A	834	LEU	0	-0.016	-0.014	13.720	0.031	0.031	0.000	0.000	0.000	0.000
30	A	835	ASP	-1	-0.960	-0.977	16.073	12.773	12.773	0.000	0.000	0.000	0.000
31	A	836	SER	0	-0.043	-0.026	18.408	-0.334	-0.334	0.000	0.000	0.000	0.000
32	A	837	LEU	0	0.000	-0.005	12.975	-0.126	-0.126	0.000	0.000	0.000	0.000
33	A	838	PRO	0	0.023	0.019	17.215	-0.076	-0.076	0.000	0.000	0.000	0.000
34	A	839	GLU	-1	-0.802	-0.882	19.065	11.674	11.674	0.000	0.000	0.000	0.000
35	A	840	THR	0	-0.063	-0.040	18.284	-0.443	-0.443	0.000	0.000	0.000	0.000
36	A	841	VAL	0	0.006	0.003	15.707	-0.028	-0.028	0.000	0.000	0.000	0.000
37	A	842	GLU	-1	-0.876	-0.927	18.648	12.233	12.233	0.000	0.000	0.000	0.000
38	A	843	LYS	1	0.811	0.877	22.249	-12.652	-12.652	0.000	0.000	0.000	0.000
39	A	844	ILE	0	-0.014	-0.006	18.155	-0.313	-0.313	0.000	0.000	0.000	0.000
40	A	845	GLN	0	0.000	-0.010	19.603	-0.434	-0.434	0.000	0.000	0.000	0.000
41	A	846	THR	0	-0.021	0.001	22.305	-0.498	-0.498	0.000	0.000	0.000	0.000
42	A	847	ALA	0	-0.019	-0.019	24.906	-0.425	-0.425	0.000	0.000	0.000	0.000
43	A	848	LEU	0	0.006	-0.005	21.055	-0.302	-0.302	0.000	0.000	0.000	0.000
44	A	849	GLY	0	-0.013	0.006	24.913	-0.264	-0.264	0.000	0.000	0.000	0.000
45	A	850	GLN	0	-0.080	-0.052	27.454	-0.342	-0.342	0.000	0.000	0.000	0.000
46	A	851	ASN	0	-0.027	-0.011	28.561	-0.077	-0.077	0.000	0.000	0.000	0.000
47	A	852	ASP	-1	-0.865	-0.893	28.786	9.981	9.981	0.000	0.000	0.000	0.000
48	A	853	GLN	0	0.019	-0.024	28.580	0.492	0.492	0.000	0.000	0.000	0.000
49	A	854	ALA	0	-0.029	-0.022	28.626	0.308	0.308	0.000	0.000	0.000	0.000
50	A	855	THR	0	-0.012	-0.030	26.651	0.183	0.183	0.000	0.000	0.000	0.000
51	A	856	MET	0	0.031	0.042	22.847	0.618	0.618	0.000	0.000	0.000	0.000
52	A	857	LEU	0	-0.010	0.004	24.091	0.492	0.492	0.000	0.000	0.000	0.000
53	A	858	SER	0	-0.018	-0.016	25.026	0.376	0.376	0.000	0.000	0.000	0.000
54	A	859	THR	0	-0.044	-0.043	22.404	0.346	0.346	0.000	0.000	0.000	0.000
55	A	860	ILE	0	0.061	0.037	19.156	0.610	0.610	0.000	0.000	0.000	0.000
56	A	861	HIS	0	-0.085	-0.044	20.525	0.330	0.330	0.000	0.000	0.000	0.000
57	A	862	LYS	1	0.890	0.939	22.301	-11.398	-11.398	0.000	0.000	0.000	0.000
58	A	863	LEU	0	0.040	0.033	15.020	0.197	0.197	0.000	0.000	0.000	0.000
59	A	864	HIS	0	-0.014	-0.020	17.428	1.469	1.469	0.000	0.000	0.000	0.000
60	A	865	GLY	0	0.013	0.020	18.477	0.526	0.526	0.000	0.000	0.000	0.000
61	A	866	ALA	0	0.027	0.005	17.565	0.192	0.192	0.000	0.000	0.000	0.000
62	A	867	SER	0	-0.032	-0.029	13.894	0.754	0.754	0.000	0.000	0.000	0.000
63	A	868	CYS	0	-0.061	-0.027	14.525	1.138	1.138	0.000	0.000	0.000	0.000
64	A	869	TYR	0	-0.096	-0.049	16.875	-0.374	-0.374	0.000	0.000	0.000	0.000
65	A	870	CYS	0	-0.019	-0.009	13.124	-0.624	-0.624	0.000	0.000	0.000	0.000
66	A	871	GLY	0	0.021	0.012	11.059	1.230	1.230	0.000	0.000	0.000	0.000
67	A	872	VAL	0	0.015	0.014	8.656	3.037	3.037	0.000	0.000	0.000	0.000
68	A	873	PRO	0	-0.013	-0.011	7.082	-2.457	-2.457	0.000	0.000	0.000	0.000
69	A	874	THR	0	0.012	0.008	6.112	-3.405	-3.405	0.000	0.000	0.000	0.000
70	A	875	THR	0	0.069	0.028	8.949	-3.392	-3.392	0.000	0.000	0.000	0.000
71	A	876	GLN	0	-0.011	0.001	11.604	-2.212	-2.212	0.000	0.000	0.000	0.000
72	A	877	ARG	1	0.784	0.878	10.160	-28.513	-28.513	0.000	0.000	0.000	0.000
73	A	878	LEU	0	0.015	0.020	11.092	-1.702	-1.702	0.000	0.000	0.000	0.000
74	A	879	CYS	0	-0.043	-0.027	14.728	-1.817	-1.817	0.000	0.000	0.000	0.000
75	A	880	GLN	0	-0.025	0.002	16.790	-1.194	-1.194	0.000	0.000	0.000	0.000
76	A	881	GLU	-1	-0.823	-0.904	15.703	19.800	19.800	0.000	0.000	0.000	0.000
77	A	882	ILE	0	0.042	0.023	17.085	-1.207	-1.207	0.000	0.000	0.000	0.000
78	A	883	GLU	-1	-0.757	-0.853	20.624	12.481	12.481	0.000	0.000	0.000	0.000
79	A	884	SER	0	-0.103	-0.074	22.023	-1.020	-1.020	0.000	0.000	0.000	0.000
80	A	885	ALA	0	-0.015	-0.011	23.389	-0.693	-0.693	0.000	0.000	0.000	0.000
81	A	886	LEU	0	0.066	0.036	23.823	-0.637	-0.637	0.000	0.000	0.000	0.000
82	A	887	LYS	1	0.777	0.880	25.260	-13.131	-13.131	0.000	0.000	0.000	0.000
83	A	888	ARG	1	0.858	0.944	24.186	-13.109	-13.109	0.000	0.000	0.000	0.000
84	A	889	GLN	0	-0.036	-0.016	29.813	-0.196	-0.196	0.000	0.000	0.000	0.000
85	A	890	THR	0	0.017	0.013	26.437	-0.133	-0.133	0.000	0.000	0.000	0.000
86	A	891	PRO	0	-0.002	0.020	27.933	0.198	0.198	0.000	0.000	0.000	0.000
87	A	892	VAL	0	0.034	-0.003	24.618	0.350	0.350	0.000	0.000	0.000	0.000
88	A	893	GLU	-1	-0.891	-0.935	24.654	11.009	11.009	0.000	0.000	0.000	0.000
89	A	894	ASP	-1	-0.919	-0.959	25.325	11.497	11.497	0.000	0.000	0.000	0.000
90	A	895	LEU	0	-0.084	-0.042	21.601	0.421	0.421	0.000	0.000	0.000	0.000
91	A	896	GLU	-1	-0.925	-0.954	20.450	14.369	14.369	0.000	0.000	0.000	0.000
92	A	897	PRO	0	-0.015	-0.009	18.511	0.773	0.773	0.000	0.000	0.000	0.000
93	A	898	GLU	-1	-0.833	-0.929	16.075	17.363	17.363	0.000	0.000	0.000	0.000
94	A	899	ILE	0	-0.013	-0.016	15.804	1.249	1.249	0.000	0.000	0.000	0.000
95	A	900	LEU	0	-0.021	-0.010	16.556	0.784	0.784	0.000	0.000	0.000	0.000
96	A	901	GLU	-1	-0.855	-0.912	11.157	27.807	27.807	0.000	0.000	0.000	0.000
97	A	902	LEU	0	-0.015	-0.015	11.672	2.237	2.237	0.000	0.000	0.000	0.000
98	A	903	LEU	0	-0.023	-0.020	12.802	0.990	0.990	0.000	0.000	0.000	0.000
99	A	904	ASP	-1	-0.865	-0.928	9.445	30.833	30.833	0.000	0.000	0.000	0.000
100	A	905	GLU	-1	-0.800	-0.890	6.298	48.610	48.610	0.000	0.000	0.000	0.000
101	A	906	LEU	0	-0.016	-0.016	8.668	1.264	1.264	0.000	0.000	0.000	0.000
102	A	907	THR	0	-0.001	0.013	10.921	-0.967	-0.967	0.000	0.000	0.000	0.000
103	A	908	LYS	1	0.810	0.895	5.254	-40.646	-40.646	0.000	0.000	0.000	0.000
104	A	909	VAL	0	-0.005	-0.004	6.683	0.983	0.983	0.000	0.000	0.000	0.000
105	A	910	GLU	-1	-0.835	-0.911	8.216	17.377	17.377	0.000	0.000	0.000	0.000
106	A	911	SER	0	-0.079	-0.035	7.987	-1.548	-1.548	0.000	0.000	0.000	0.000
107	A	912	ALA	0	0.030	0.015	5.241	-0.945	-0.945	0.000	0.000	0.000	0.000
108	A	913	VAL	0	0.038	0.008	6.758	-1.045	-1.045	0.000	0.000	0.000	0.000
109	A	914	LYS	1	0.879	0.928	9.844	-19.928	-19.928	0.000	0.000	0.000	0.000
110	A	915	GLN	0	-0.055	-0.001	6.465	0.726	0.726	0.000	0.000	0.000	0.000
111	A	916	VAL	0	0.009	-0.012	7.284	-1.201	-1.201	0.000	0.000	0.000	0.000
112	A	917	LEU	0	-0.018	-0.010	9.962	-1.359	-1.359	0.000	0.000	0.000	0.000
113	A	918	SER	0	-0.040	-0.024	12.965	-1.445	-1.445	0.000	0.000	0.000	0.000
114	A	919	GLN	0	-0.064	-0.012	9.756	0.375	0.375	0.000	0.000	0.000	0.000
115	A	920	LEU	0	-0.027	-0.022	11.995	-0.835	-0.835	0.000	0.000	0.000	0.000
116	A	921	SER	0	-0.087	-0.025	15.191	-0.873	-0.873	0.000	0.000	0.000	0.000
117	A	922	ALA	0	0.003	0.003	17.836	-0.335	-0.335	0.000	0.000	0.000	0.000

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