FMO DATABASE

FMODB ID: M3LVZ

Calculation Name: 3C8I-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: 3C8I

Chain ID: A

ChEMBL ID:
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UniProt ID: Q6NIK4

Base Structure: X-ray

Registration Date: 2023-03-14

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	127
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1044788.429192
FMO2-HF: Nuclear repulsion	995946.978561
FMO2-HF: Total energy	-48841.450631
FMO2-MP2: Total energy	-48983.735052

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:15:ASP)

Summations of interaction energy for fragment #1(A:15: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.
16.811	21.149	0.776	-1.703	-3.411	0.004

Interaction energy analysis for fragmet #1(A:15:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.905 / q_NPA : -0.963

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	17	VAL	0	0.016	0.005	3.880	1.850	3.910	-0.010	-0.761	-1.289	0.003
4	A	18	PRO	0	-0.027	0.004	6.352	-4.516	-4.516	0.000	0.000	0.000	0.000
5	A	19	ALA	0	0.019	-0.009	10.116	0.501	0.501	0.000	0.000	0.000	0.000
6	A	20	MET	0	-0.032	-0.013	12.276	-1.167	-1.167	0.000	0.000	0.000	0.000
7	A	21	ILE	0	-0.012	0.008	16.087	0.078	0.078	0.000	0.000	0.000	0.000
8	A	22	ALA	0	0.016	0.000	18.623	-0.331	-0.331	0.000	0.000	0.000	0.000
9	A	23	GLU	-1	-0.787	-0.866	20.431	11.984	11.984	0.000	0.000	0.000	0.000
10	A	24	VAL	0	-0.047	-0.028	22.534	0.458	0.458	0.000	0.000	0.000	0.000
11	A	25	ASN	0	-0.025	-0.008	25.200	-0.719	-0.719	0.000	0.000	0.000	0.000
12	A	26	PRO	0	0.009	-0.011	27.438	0.097	0.097	0.000	0.000	0.000	0.000
13	A	27	ARG	1	0.874	0.924	27.672	-9.932	-9.932	0.000	0.000	0.000	0.000
14	A	28	ASP	-1	-0.803	-0.873	23.300	12.108	12.108	0.000	0.000	0.000	0.000
15	A	29	MET	0	-0.004	0.021	18.842	-0.494	-0.494	0.000	0.000	0.000	0.000
16	A	30	VAL	0	0.006	0.015	18.270	0.362	0.362	0.000	0.000	0.000	0.000
17	A	31	VAL	0	0.003	0.010	13.958	-0.152	-0.152	0.000	0.000	0.000	0.000
18	A	32	MET	0	-0.002	0.019	14.323	0.132	0.132	0.000	0.000	0.000	0.000
19	A	33	ALA	0	-0.003	-0.008	9.248	0.145	0.145	0.000	0.000	0.000	0.000
20	A	34	LEU	0	-0.030	-0.004	9.600	-1.777	-1.777	0.000	0.000	0.000	0.000
21	A	35	VAL	0	0.020	0.002	5.932	4.759	4.759	0.000	0.000	0.000	0.000
22	A	36	ASN	0	0.067	0.021	4.112	-13.083	-12.813	0.000	-0.050	-0.220	0.000
23	A	37	THR	0	0.004	-0.031	5.606	4.180	4.180	0.000	0.000	0.000	0.000
24	A	38	ASN	0	-0.033	-0.010	8.009	-4.552	-4.552	0.000	0.000	0.000	0.000
25	A	39	VAL	0	-0.016	-0.007	7.005	4.500	4.500	0.000	0.000	0.000	0.000
26	A	40	ASP	-1	-0.848	-0.896	8.396	28.551	28.551	0.000	0.000	0.000	0.000
27	A	41	PRO	0	-0.038	-0.030	5.137	0.330	0.411	-0.001	-0.001	-0.079	0.000
28	A	42	THR	0	-0.080	-0.063	6.913	-0.468	-0.468	0.000	0.000	0.000	0.000
29	A	43	LEU	0	-0.017	0.006	10.334	-2.434	-2.434	0.000	0.000	0.000	0.000
30	A	44	PRO	0	-0.012	-0.023	9.868	2.546	2.546	0.000	0.000	0.000	0.000
31	A	45	PRO	0	-0.018	-0.006	7.520	-0.384	-0.384	0.000	0.000	0.000	0.000
32	A	46	ARG	1	0.847	0.937	8.887	-24.425	-24.425	0.000	0.000	0.000	0.000
33	A	47	TRP	0	-0.018	-0.013	6.713	2.040	2.040	0.000	0.000	0.000	0.000
34	A	48	ALA	0	0.020	0.020	9.691	-3.004	-3.004	0.000	0.000	0.000	0.000
35	A	49	LEU	0	-0.017	-0.006	10.531	2.143	2.143	0.000	0.000	0.000	0.000
36	A	50	ALA	0	0.030	0.022	10.282	-0.369	-0.369	0.000	0.000	0.000	0.000
37	A	51	THR	0	-0.071	-0.071	12.291	0.245	0.245	0.000	0.000	0.000	0.000
38	A	52	ARG	1	0.904	0.939	10.909	-20.580	-20.580	0.000	0.000	0.000	0.000
39	A	53	ASN	0	-0.036	-0.018	15.761	-0.243	-0.243	0.000	0.000	0.000	0.000
40	A	54	ILE	0	-0.009	-0.009	15.575	0.396	0.396	0.000	0.000	0.000	0.000
41	A	55	THR	0	0.034	0.014	19.001	-0.324	-0.324	0.000	0.000	0.000	0.000
42	A	56	ALA	0	0.009	-0.011	20.135	-0.405	-0.405	0.000	0.000	0.000	0.000
43	A	57	ILE	0	0.015	0.006	15.433	0.755	0.755	0.000	0.000	0.000	0.000
44	A	58	PRO	0	0.023	0.018	17.448	-0.428	-0.428	0.000	0.000	0.000	0.000
45	A	59	GLY	0	0.027	0.016	19.004	0.710	0.710	0.000	0.000	0.000	0.000
46	A	60	ILE	0	-0.086	-0.034	17.534	-0.039	-0.039	0.000	0.000	0.000	0.000
47	A	61	GLU	-1	-0.811	-0.908	21.527	12.325	12.325	0.000	0.000	0.000	0.000
48	A	62	GLY	0	-0.009	-0.016	25.269	-0.015	-0.015	0.000	0.000	0.000	0.000
49	A	63	ASP	-1	-0.877	-0.924	27.318	10.618	10.618	0.000	0.000	0.000	0.000
50	A	64	THR	0	-0.027	-0.026	22.489	0.139	0.139	0.000	0.000	0.000	0.000
51	A	65	ARG	1	0.833	0.937	22.902	-11.575	-11.575	0.000	0.000	0.000	0.000
52	A	66	LYS	1	0.870	0.921	23.662	-13.160	-13.160	0.000	0.000	0.000	0.000
53	A	67	VAL	0	0.045	0.009	22.513	0.595	0.595	0.000	0.000	0.000	0.000
54	A	68	GLY	0	0.001	-0.001	21.061	-0.466	-0.466	0.000	0.000	0.000	0.000
55	A	69	THR	0	-0.097	-0.061	19.424	0.206	0.206	0.000	0.000	0.000	0.000
56	A	70	ARG	1	0.830	0.902	15.723	-17.411	-17.411	0.000	0.000	0.000	0.000
57	A	71	ILE	0	0.031	0.007	12.486	-0.958	-0.958	0.000	0.000	0.000	0.000
58	A	72	PRO	0	-0.013	0.020	10.419	1.589	1.589	0.000	0.000	0.000	0.000
59	A	73	ALA	0	-0.001	-0.012	8.382	-2.051	-2.051	0.000	0.000	0.000	0.000
60	A	74	VAL	0	0.023	0.012	3.175	3.309	3.735	0.018	-0.151	-0.293	0.000
61	A	75	ALA	0	0.016	-0.002	2.279	-7.065	-5.962	0.766	-0.621	-1.249	0.002
62	A	76	VAL	0	-0.031	-0.013	3.995	1.270	1.668	0.003	-0.119	-0.281	-0.001
63	A	77	THR	0	0.013	0.017	4.909	-1.623	-1.623	0.000	0.000	0.000	0.000
64	A	78	GLY	0	-0.006	-0.006	7.437	-1.805	-1.805	0.000	0.000	0.000	0.000
65	A	79	GLN	0	-0.115	-0.080	11.287	-0.394	-0.394	0.000	0.000	0.000	0.000
66	A	80	ARG	1	0.818	0.885	11.801	-20.122	-20.122	0.000	0.000	0.000	0.000
67	A	81	SER	0	-0.076	-0.049	13.874	-1.578	-1.578	0.000	0.000	0.000	0.000
68	A	82	VAL	0	0.012	-0.009	15.526	1.019	1.019	0.000	0.000	0.000	0.000
69	A	83	GLY	0	-0.004	-0.005	17.960	-0.996	-0.996	0.000	0.000	0.000	0.000
70	A	84	ASN	0	-0.062	-0.028	19.771	-0.217	-0.217	0.000	0.000	0.000	0.000
71	A	85	GLN	0	0.020	0.016	14.051	-0.519	-0.519	0.000	0.000	0.000	0.000
72	A	86	ASP	-1	-0.778	-0.856	13.723	20.382	20.382	0.000	0.000	0.000	0.000
73	A	87	SER	0	0.038	0.004	11.083	1.623	1.623	0.000	0.000	0.000	0.000
74	A	88	TRP	0	0.028	0.003	6.559	-3.632	-3.632	0.000	0.000	0.000	0.000
75	A	89	ASP	-1	-0.818	-0.874	10.928	18.845	18.845	0.000	0.000	0.000	0.000
76	A	90	GLN	0	-0.002	-0.006	11.830	-0.540	-0.540	0.000	0.000	0.000	0.000
77	A	91	ILE	0	0.030	0.011	5.898	1.712	1.712	0.000	0.000	0.000	0.000
78	A	92	SER	0	0.003	0.009	8.670	-1.791	-1.791	0.000	0.000	0.000	0.000
79	A	93	PRO	0	0.022	0.020	8.018	1.970	1.970	0.000	0.000	0.000	0.000
80	A	94	MET	0	-0.018	-0.009	7.678	-3.526	-3.526	0.000	0.000	0.000	0.000
81	A	95	PRO	0	0.011	0.006	8.477	2.191	2.191	0.000	0.000	0.000	0.000
82	A	96	ILE	0	0.035	0.019	7.632	-0.900	-0.900	0.000	0.000	0.000	0.000
83	A	97	ALA	0	0.021	0.008	10.673	-0.994	-0.994	0.000	0.000	0.000	0.000
84	A	98	TRP	0	-0.067	-0.050	12.599	-0.775	-0.775	0.000	0.000	0.000	0.000
85	A	99	ALA	0	-0.038	-0.002	11.620	-0.627	-0.627	0.000	0.000	0.000	0.000
86	A	100	THR	0	0.007	-0.018	13.546	-1.232	-1.232	0.000	0.000	0.000	0.000
87	A	101	PRO	0	0.010	0.016	14.934	0.947	0.947	0.000	0.000	0.000	0.000
88	A	102	ASP	-1	-0.808	-0.877	17.445	15.395	15.395	0.000	0.000	0.000	0.000
89	A	103	SER	0	0.029	0.008	17.370	0.985	0.985	0.000	0.000	0.000	0.000
90	A	104	SER	0	-0.037	-0.036	18.321	0.272	0.272	0.000	0.000	0.000	0.000
91	A	105	VAL	0	-0.034	-0.024	12.415	0.962	0.962	0.000	0.000	0.000	0.000
92	A	106	ILE	0	-0.007	0.003	13.318	1.713	1.713	0.000	0.000	0.000	0.000
93	A	107	ALA	0	0.049	0.019	14.112	1.096	1.096	0.000	0.000	0.000	0.000
94	A	108	ARG	1	0.948	0.982	12.872	-20.159	-20.159	0.000	0.000	0.000	0.000
95	A	109	ALA	0	0.023	0.025	9.780	1.273	1.273	0.000	0.000	0.000	0.000
96	A	110	GLU	-1	-0.799	-0.902	10.582	21.126	21.126	0.000	0.000	0.000	0.000
97	A	111	SER	0	-0.103	-0.054	12.636	0.181	0.181	0.000	0.000	0.000	0.000
98	A	112	THR	0	-0.056	-0.038	8.290	-0.719	-0.719	0.000	0.000	0.000	0.000
99	A	113	ILE	0	-0.016	0.003	7.458	2.776	2.776	0.000	0.000	0.000	0.000
100	A	114	PRO	0	0.023	0.011	8.709	-2.960	-2.960	0.000	0.000	0.000	0.000
101	A	115	SER	0	-0.007	-0.016	11.661	-0.352	-0.352	0.000	0.000	0.000	0.000
102	A	116	GLU	-1	-0.798	-0.889	13.595	22.088	22.088	0.000	0.000	0.000	0.000
103	A	117	GLN	0	0.017	0.022	7.358	1.339	1.339	0.000	0.000	0.000	0.000
104	A	118	TRP	0	0.015	0.009	12.017	-0.841	-0.841	0.000	0.000	0.000	0.000
105	A	119	THR	0	-0.049	-0.032	14.141	-1.502	-1.502	0.000	0.000	0.000	0.000
106	A	120	THR	0	-0.039	-0.035	13.712	-1.355	-1.355	0.000	0.000	0.000	0.000
107	A	121	LEU	0	0.004	0.020	12.537	-0.931	-0.931	0.000	0.000	0.000	0.000
108	A	122	SER	0	-0.005	-0.007	14.977	-1.496	-1.496	0.000	0.000	0.000	0.000
109	A	123	LYS	1	0.880	0.930	18.535	-15.296	-15.296	0.000	0.000	0.000	0.000
110	A	124	ASN	0	-0.018	-0.018	16.689	-1.157	-1.157	0.000	0.000	0.000	0.000
111	A	125	LEU	0	0.034	0.021	18.002	-0.127	-0.127	0.000	0.000	0.000	0.000
112	A	126	ASN	0	-0.014	-0.020	19.499	0.218	0.218	0.000	0.000	0.000	0.000
113	A	127	LYS	1	0.907	0.955	19.242	-16.256	-16.256	0.000	0.000	0.000	0.000
114	A	128	LEU	0	0.014	0.005	19.748	0.316	0.316	0.000	0.000	0.000	0.000
115	A	129	ASP	-1	-0.821	-0.902	20.582	12.892	12.892	0.000	0.000	0.000	0.000
116	A	130	GLN	0	0.020	0.010	21.192	0.254	0.254	0.000	0.000	0.000	0.000
117	A	131	VAL	0	-0.033	-0.013	15.622	0.294	0.294	0.000	0.000	0.000	0.000
118	A	132	ARG	1	0.792	0.864	18.862	-12.967	-12.967	0.000	0.000	0.000	0.000
119	A	133	GLU	-1	-0.945	-0.958	21.011	11.871	11.871	0.000	0.000	0.000	0.000
120	A	134	THR	0	-0.092	-0.047	18.167	0.024	0.024	0.000	0.000	0.000	0.000
121	A	135	LYS	1	0.905	0.945	19.522	-14.391	-14.391	0.000	0.000	0.000	0.000
122	A	136	PHE	0	-0.037	-0.034	15.380	-0.605	-0.605	0.000	0.000	0.000	0.000
123	A	137	ASP	-1	-0.830	-0.860	14.985	17.531	17.531	0.000	0.000	0.000	0.000
124	A	138	LEU	0	-0.009	-0.006	10.573	1.735	1.735	0.000	0.000	0.000	0.000
125	A	139	LEU	0	-0.001	0.000	14.214	-1.096	-1.096	0.000	0.000	0.000	0.000
126	A	140	GLU	-1	-0.785	-0.860	12.798	23.259	23.259	0.000	0.000	0.000	0.000
127	A	141	LEU	0	-0.097	-0.046	13.291	-2.391	-2.391	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:15:ASP)