FMO DATABASE

FMODB ID: MV7LZ

Calculation Name: 3DB0-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: 3DB0

Chain ID: A

ChEMBL ID:
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UniProt ID: Q926Z8

Base Structure: X-ray

Registration Date: 2023-09-20

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	126
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1046567.700184
FMO2-HF: Nuclear repulsion	996491.319325
FMO2-HF: Total energy	-50076.380859
FMO2-MP2: Total energy	-50223.365523

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:1:MET)

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

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.
1.883	5.008	0.119	-0.7	-2.546	0.001

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.031 / q_NPA : -0.036

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	3	ASN	0	-0.003	-0.021	3.512	2.246	3.708	0.013	-0.304	-1.171	0.001
4	A	4	GLU	-1	-0.924	-0.948	3.336	0.229	0.994	0.034	-0.184	-0.616	0.000
5	A	5	LEU	0	-0.025	-0.017	3.506	0.215	1.113	0.072	-0.212	-0.759	0.000
6	A	6	GLU	-1	-0.893	-0.951	5.893	-1.026	-1.026	0.000	0.000	0.000	0.000
7	A	7	ASP	-1	-0.882	-0.932	8.054	-0.005	-0.005	0.000	0.000	0.000	0.000
8	A	8	LYS	1	0.827	0.921	8.437	0.264	0.264	0.000	0.000	0.000	0.000
9	A	9	ILE	0	0.037	0.003	8.776	0.190	0.190	0.000	0.000	0.000	0.000
10	A	10	LEU	0	0.026	0.015	12.012	0.112	0.112	0.000	0.000	0.000	0.000
11	A	11	ALA	0	0.041	0.030	13.432	0.079	0.079	0.000	0.000	0.000	0.000
12	A	12	ILE	0	-0.062	-0.029	13.217	0.064	0.064	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.024	-0.012	15.901	0.037	0.037	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.898	-0.949	17.132	-0.170	-0.170	0.000	0.000	0.000	0.000
15	A	15	GLN	0	-0.099	-0.042	17.317	0.045	0.045	0.000	0.000	0.000	0.000
16	A	16	HIS	1	0.739	0.838	19.312	0.080	0.080	0.000	0.000	0.000	0.000
17	A	17	GLN	0	0.050	0.027	22.514	-0.016	-0.016	0.000	0.000	0.000	0.000
18	A	18	VAL	0	-0.038	0.007	25.204	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	19	GLY	0	0.038	0.013	23.346	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	20	VAL	0	-0.060	-0.025	23.317	0.012	0.012	0.000	0.000	0.000	0.000
21	A	21	LEU	0	0.013	0.011	23.403	-0.022	-0.022	0.000	0.000	0.000	0.000
22	A	22	THR	0	-0.055	-0.045	23.601	0.018	0.018	0.000	0.000	0.000	0.000
23	A	23	SER	0	0.001	-0.012	25.220	-0.017	-0.017	0.000	0.000	0.000	0.000
24	A	24	VAL	0	0.012	0.000	27.359	0.011	0.011	0.000	0.000	0.000	0.000
25	A	25	GLN	0	-0.009	0.000	29.877	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	26	GLY	0	-0.004	0.002	33.488	0.008	0.008	0.000	0.000	0.000	0.000
27	A	27	ASP	-1	-0.905	-0.963	32.844	-0.103	-0.103	0.000	0.000	0.000	0.000
28	A	28	PHE	0	0.004	-0.004	33.532	0.006	0.006	0.000	0.000	0.000	0.000
29	A	29	PRO	0	-0.027	-0.002	29.314	-0.008	-0.008	0.000	0.000	0.000	0.000
30	A	30	HIS	0	-0.007	0.001	29.942	0.011	0.011	0.000	0.000	0.000	0.000
31	A	31	ALA	0	-0.004	-0.015	28.399	-0.013	-0.013	0.000	0.000	0.000	0.000
32	A	32	ARG	1	0.938	0.974	28.621	0.141	0.141	0.000	0.000	0.000	0.000
33	A	33	TYR	0	0.014	0.019	27.164	-0.010	-0.010	0.000	0.000	0.000	0.000
34	A	34	MET	0	-0.029	-0.006	26.908	0.007	0.007	0.000	0.000	0.000	0.000
35	A	35	THR	0	0.045	0.019	27.252	0.003	0.003	0.000	0.000	0.000	0.000
36	A	36	PHE	0	-0.031	-0.021	23.326	-0.009	-0.009	0.000	0.000	0.000	0.000
37	A	37	LEU	0	0.055	0.029	24.741	0.010	0.010	0.000	0.000	0.000	0.000
38	A	38	HIS	0	-0.045	-0.044	18.250	0.019	0.019	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.824	-0.889	21.053	-0.235	-0.235	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.013	0.012	16.884	-0.039	-0.039	0.000	0.000	0.000	0.000
41	A	41	LEU	0	0.020	0.003	11.810	0.073	0.073	0.000	0.000	0.000	0.000
42	A	42	THR	0	-0.067	-0.022	16.203	0.005	0.005	0.000	0.000	0.000	0.000
43	A	43	LEU	0	-0.008	-0.002	18.631	0.036	0.036	0.000	0.000	0.000	0.000
44	A	44	TYR	0	-0.003	-0.011	21.850	0.003	0.003	0.000	0.000	0.000	0.000
45	A	45	THR	0	-0.021	-0.032	25.625	0.014	0.014	0.000	0.000	0.000	0.000
46	A	46	PRO	0	0.051	0.050	28.039	-0.004	-0.004	0.000	0.000	0.000	0.000
47	A	47	SER	0	-0.041	-0.040	31.815	0.004	0.004	0.000	0.000	0.000	0.000
48	A	48	GLY	0	0.008	0.003	33.955	0.000	0.000	0.000	0.000	0.000	0.000
49	A	49	LYS	1	0.934	0.963	37.361	0.073	0.073	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.712	-0.828	39.533	-0.076	-0.076	0.000	0.000	0.000	0.000
51	A	51	LEU	0	-0.050	-0.010	36.862	0.003	0.003	0.000	0.000	0.000	0.000
52	A	52	PRO	0	-0.030	-0.014	40.295	0.000	0.000	0.000	0.000	0.000	0.000
53	A	53	LYS	1	0.859	0.917	43.215	0.065	0.065	0.000	0.000	0.000	0.000
54	A	54	THR	0	-0.071	-0.049	45.147	0.001	0.001	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.995	-1.001	41.711	-0.080	-0.080	0.000	0.000	0.000	0.000
56	A	56	GLU	-1	-0.927	-0.951	40.374	-0.106	-0.106	0.000	0.000	0.000	0.000
57	A	57	VAL	0	0.005	0.004	35.734	0.002	0.002	0.000	0.000	0.000	0.000
58	A	58	ARG	1	0.944	0.965	35.054	0.124	0.124	0.000	0.000	0.000	0.000
59	A	59	ARG	1	0.903	0.947	28.346	0.186	0.186	0.000	0.000	0.000	0.000
60	A	60	ASN	0	0.035	0.014	27.972	-0.017	-0.017	0.000	0.000	0.000	0.000
61	A	61	PRO	0	-0.026	-0.003	25.773	0.008	0.008	0.000	0.000	0.000	0.000
62	A	62	HIS	0	0.003	0.007	22.616	-0.029	-0.029	0.000	0.000	0.000	0.000
63	A	63	VAL	0	-0.033	-0.011	21.923	0.029	0.029	0.000	0.000	0.000	0.000
64	A	64	CYS	0	-0.031	-0.019	18.914	-0.028	-0.028	0.000	0.000	0.000	0.000
65	A	65	VAL	0	0.013	0.012	19.564	0.036	0.036	0.000	0.000	0.000	0.000
66	A	66	LEU	0	-0.010	0.014	18.636	-0.021	-0.021	0.000	0.000	0.000	0.000
67	A	67	ILE	0	0.029	0.001	18.594	0.020	0.020	0.000	0.000	0.000	0.000
68	A	68	GLY	0	0.056	0.026	18.251	-0.006	-0.006	0.000	0.000	0.000	0.000
69	A	69	TYR	0	-0.048	-0.016	20.004	0.027	0.027	0.000	0.000	0.000	0.000
70	A	70	ASP	-1	-0.789	-0.861	21.641	-0.010	-0.010	0.000	0.000	0.000	0.000
71	A	71	SER	0	-0.056	-0.029	22.873	0.009	0.009	0.000	0.000	0.000	0.000
72	A	72	PRO	0	-0.003	-0.009	22.786	0.000	0.000	0.000	0.000	0.000	0.000
73	A	73	GLY	0	-0.024	-0.008	21.060	0.018	0.018	0.000	0.000	0.000	0.000
74	A	74	SER	0	-0.043	-0.016	18.955	0.008	0.008	0.000	0.000	0.000	0.000
75	A	75	ALA	0	0.018	0.020	13.728	0.004	0.004	0.000	0.000	0.000	0.000
76	A	76	PHE	0	-0.063	-0.040	15.741	-0.037	-0.037	0.000	0.000	0.000	0.000
77	A	77	LEU	0	0.024	0.014	12.583	0.003	0.003	0.000	0.000	0.000	0.000
78	A	78	GLU	-1	-0.807	-0.886	14.113	-0.234	-0.234	0.000	0.000	0.000	0.000
79	A	79	ILE	0	0.008	-0.004	14.121	-0.080	-0.080	0.000	0.000	0.000	0.000
80	A	80	ASN	0	-0.014	-0.009	15.084	0.104	0.104	0.000	0.000	0.000	0.000
81	A	81	GLY	0	0.071	0.027	16.635	-0.080	-0.080	0.000	0.000	0.000	0.000
82	A	82	LEU	0	-0.020	0.011	19.215	0.051	0.051	0.000	0.000	0.000	0.000
83	A	83	ALA	0	0.006	-0.001	22.523	-0.003	-0.003	0.000	0.000	0.000	0.000
84	A	84	SER	0	-0.057	-0.037	25.316	0.010	0.010	0.000	0.000	0.000	0.000
85	A	85	LEU	0	0.008	0.007	28.196	0.000	0.000	0.000	0.000	0.000	0.000
86	A	86	GLU	-1	-0.810	-0.903	28.173	-0.228	-0.228	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.868	-0.941	30.617	-0.126	-0.126	0.000	0.000	0.000	0.000
88	A	88	ASP	-1	-0.879	-0.910	31.573	-0.145	-0.145	0.000	0.000	0.000	0.000
89	A	89	GLU	-1	-0.763	-0.883	33.511	-0.116	-0.116	0.000	0.000	0.000	0.000
90	A	90	SER	0	-0.049	-0.038	32.986	0.009	0.009	0.000	0.000	0.000	0.000
91	A	91	ILE	0	-0.064	-0.027	28.515	0.002	0.002	0.000	0.000	0.000	0.000
92	A	92	LYS	1	0.811	0.890	31.222	0.123	0.123	0.000	0.000	0.000	0.000
93	A	93	GLU	-1	-0.877	-0.938	33.408	-0.085	-0.085	0.000	0.000	0.000	0.000
94	A	94	ARG	1	0.818	0.899	25.095	0.198	0.198	0.000	0.000	0.000	0.000
95	A	95	ILE	0	-0.014	-0.008	28.581	0.002	0.002	0.000	0.000	0.000	0.000
96	A	96	TRP	0	0.078	0.039	31.399	0.006	0.006	0.000	0.000	0.000	0.000
97	A	97	GLU	-1	-0.848	-0.919	32.984	-0.077	-0.077	0.000	0.000	0.000	0.000
98	A	98	ASN	0	-0.110	-0.077	30.102	0.012	0.012	0.000	0.000	0.000	0.000
99	A	99	ILE	0	-0.050	-0.028	30.878	0.004	0.004	0.000	0.000	0.000	0.000
100	A	100	SER	0	-0.066	-0.029	33.313	0.006	0.006	0.000	0.000	0.000	0.000
101	A	101	LYS	1	0.803	0.917	32.406	0.076	0.076	0.000	0.000	0.000	0.000
102	A	102	ASP	-1	-0.960	-0.981	37.900	-0.043	-0.043	0.000	0.000	0.000	0.000
103	A	103	TRP	0	-0.037	-0.016	40.680	0.000	0.000	0.000	0.000	0.000	0.000
104	A	104	PHE	0	-0.044	-0.025	41.417	-0.003	-0.003	0.000	0.000	0.000	0.000
105	A	105	GLN	0	-0.122	-0.067	42.610	0.005	0.005	0.000	0.000	0.000	0.000
106	A	106	GLY	0	0.084	0.062	40.401	0.000	0.000	0.000	0.000	0.000	0.000
107	A	107	GLU	-1	-0.907	-0.956	39.820	-0.068	-0.068	0.000	0.000	0.000	0.000
108	A	108	ASP	-1	-0.875	-0.952	39.238	-0.097	-0.097	0.000	0.000	0.000	0.000
109	A	109	SER	0	0.035	-0.001	37.107	0.002	0.002	0.000	0.000	0.000	0.000
110	A	110	PRO	0	-0.055	-0.017	38.980	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	111	SER	0	-0.071	-0.053	40.706	0.006	0.006	0.000	0.000	0.000	0.000
112	A	112	PHE	0	-0.045	0.004	33.906	0.000	0.000	0.000	0.000	0.000	0.000
113	A	113	VAL	0	0.018	0.023	34.368	-0.006	-0.006	0.000	0.000	0.000	0.000
114	A	114	VAL	0	0.045	0.017	29.251	0.000	0.000	0.000	0.000	0.000	0.000
115	A	115	ILE	0	-0.086	-0.042	26.792	-0.005	-0.005	0.000	0.000	0.000	0.000
116	A	116	LYS	1	0.898	0.937	24.216	0.268	0.268	0.000	0.000	0.000	0.000
117	A	117	ILE	0	-0.031	-0.037	20.431	0.005	0.005	0.000	0.000	0.000	0.000
118	A	118	VAL	0	0.037	0.027	18.854	-0.018	-0.018	0.000	0.000	0.000	0.000
119	A	119	PRO	0	-0.012	-0.005	14.820	0.020	0.020	0.000	0.000	0.000	0.000
120	A	120	GLU	-1	-0.926	-0.967	15.358	-0.497	-0.497	0.000	0.000	0.000	0.000
121	A	121	GLN	0	-0.034	-0.027	11.192	-0.045	-0.045	0.000	0.000	0.000	0.000
122	A	122	ILE	0	0.039	0.022	10.512	0.133	0.133	0.000	0.000	0.000	0.000
123	A	123	ARG	1	0.787	0.890	9.378	0.199	0.199	0.000	0.000	0.000	0.000
124	A	124	ILE	0	0.043	0.022	8.421	0.045	0.045	0.000	0.000	0.000	0.000
125	A	125	LEU	0	-0.073	-0.028	11.080	0.142	0.142	0.000	0.000	0.000	0.000
126	A	126	ASN	0	0.028	0.007	13.616	-0.052	-0.052	0.000	0.000	0.000	0.000

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