FMO DATABASE

FMODB ID: 491ZN

Calculation Name: 3HM0-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: 3HM0

Chain ID: A

ChEMBL ID:
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UniProt ID: A0A0H3

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1103752.138179
FMO2-HF: Nuclear repulsion	1052930.01446
FMO2-HF: Total energy	-50822.123719
FMO2-MP2: Total energy	-50972.179014

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:13:ASN)

Summations of interaction energy for fragment #1(A:13:ASN)

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.
-4.446	-3.113	9.528	-4.599	-6.261	-0.02

Interaction energy analysis for fragmet #1(A:13:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.038 / q_NPA : -0.026

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	15	PHE	0	-0.045	-0.033	3.828	-0.897	0.558	-0.023	-0.695	-0.737	0.003
4	A	16	HIS	0	-0.044	-0.017	6.198	1.293	1.293	0.000	0.000	0.000	0.000
5	A	17	ASP	-1	-0.819	-0.919	8.963	-0.252	-0.252	0.000	0.000	0.000	0.000
6	A	18	PHE	0	0.004	0.001	12.479	0.099	0.099	0.000	0.000	0.000	0.000
7	A	19	GLN	0	0.030	0.002	15.525	-0.093	-0.093	0.000	0.000	0.000	0.000
8	A	20	ALA	0	-0.030	-0.007	19.000	0.029	0.029	0.000	0.000	0.000	0.000
9	A	21	ARG	1	0.910	0.967	21.613	-0.077	-0.077	0.000	0.000	0.000	0.000
10	A	22	VAL	0	-0.018	0.015	24.821	-0.002	-0.002	0.000	0.000	0.000	0.000
11	A	23	TYR	0	0.026	0.006	26.715	0.011	0.011	0.000	0.000	0.000	0.000
12	A	24	VAL	0	0.078	0.013	29.983	-0.011	-0.011	0.000	0.000	0.000	0.000
13	A	25	ALA	0	-0.013	-0.002	30.027	-0.009	-0.009	0.000	0.000	0.000	0.000
14	A	26	ASP	-1	-0.813	-0.902	26.162	-0.034	-0.034	0.000	0.000	0.000	0.000
15	A	27	THR	0	-0.058	-0.013	28.212	-0.021	-0.021	0.000	0.000	0.000	0.000
16	A	28	ASP	-1	-0.760	-0.883	30.768	-0.121	-0.121	0.000	0.000	0.000	0.000
17	A	29	PHE	0	-0.038	-0.033	33.022	0.003	0.003	0.000	0.000	0.000	0.000
18	A	30	SER	0	-0.097	-0.047	32.480	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	31	GLY	0	0.011	0.005	34.257	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	32	VAL	0	-0.053	-0.021	28.876	0.003	0.003	0.000	0.000	0.000	0.000
21	A	33	VAL	0	-0.058	-0.024	24.308	0.009	0.009	0.000	0.000	0.000	0.000
22	A	34	TYR	0	0.028	0.014	27.378	-0.023	-0.023	0.000	0.000	0.000	0.000
23	A	35	HIS	0	0.006	-0.013	25.117	-0.022	-0.022	0.000	0.000	0.000	0.000
24	A	36	ALA	0	0.029	0.001	23.575	-0.021	-0.021	0.000	0.000	0.000	0.000
25	A	37	ARG	1	0.909	0.954	23.401	0.045	0.045	0.000	0.000	0.000	0.000
26	A	38	TYR	0	0.052	0.031	19.793	0.012	0.012	0.000	0.000	0.000	0.000
27	A	39	LEU	0	-0.010	-0.016	18.677	-0.022	-0.022	0.000	0.000	0.000	0.000
28	A	40	GLU	-1	-0.908	-0.940	18.819	-0.023	-0.023	0.000	0.000	0.000	0.000
29	A	41	PHE	0	-0.037	-0.018	18.604	0.039	0.039	0.000	0.000	0.000	0.000
30	A	42	PHE	0	0.013	-0.013	13.871	0.020	0.020	0.000	0.000	0.000	0.000
31	A	43	GLU	-1	-0.946	-0.965	14.295	0.074	0.074	0.000	0.000	0.000	0.000
32	A	44	ARG	1	0.979	0.991	15.853	0.013	0.013	0.000	0.000	0.000	0.000
33	A	45	GLY	0	0.023	0.020	13.062	0.088	0.088	0.000	0.000	0.000	0.000
34	A	46	ARG	1	0.895	0.943	11.115	0.364	0.364	0.000	0.000	0.000	0.000
35	A	47	SER	0	-0.006	-0.016	12.192	0.180	0.180	0.000	0.000	0.000	0.000
36	A	48	GLU	-1	-0.819	-0.900	14.078	0.585	0.585	0.000	0.000	0.000	0.000
37	A	49	PHE	0	0.005	0.021	4.994	-0.118	-0.021	-0.001	-0.001	-0.095	0.000
38	A	50	LEU	0	-0.032	-0.032	10.750	0.259	0.259	0.000	0.000	0.000	0.000
39	A	51	ARG	1	0.828	0.903	12.486	-0.446	-0.446	0.000	0.000	0.000	0.000
40	A	52	ASP	-1	-0.859	-0.915	10.721	1.327	1.327	0.000	0.000	0.000	0.000
41	A	53	THR	0	-0.145	-0.060	8.883	0.179	0.179	0.000	0.000	0.000	0.000
42	A	54	GLY	0	0.032	-0.001	11.945	-0.076	-0.076	0.000	0.000	0.000	0.000
43	A	55	PHE	0	-0.049	-0.014	14.135	-0.116	-0.116	0.000	0.000	0.000	0.000
44	A	56	ASN	0	0.054	0.037	16.271	-0.061	-0.061	0.000	0.000	0.000	0.000
45	A	57	ASN	0	0.065	0.002	18.122	-0.023	-0.023	0.000	0.000	0.000	0.000
46	A	58	THR	0	0.006	0.003	20.228	-0.027	-0.027	0.000	0.000	0.000	0.000
47	A	59	LEU	0	-0.011	-0.001	19.561	-0.025	-0.025	0.000	0.000	0.000	0.000
48	A	60	LEU	0	0.021	0.031	16.903	-0.025	-0.025	0.000	0.000	0.000	0.000
49	A	61	ALA	0	0.032	0.032	21.466	-0.034	-0.034	0.000	0.000	0.000	0.000
50	A	62	SER	0	-0.078	-0.062	24.530	-0.024	-0.024	0.000	0.000	0.000	0.000
51	A	63	GLY	0	0.025	0.004	25.870	-0.021	-0.021	0.000	0.000	0.000	0.000
52	A	64	VAL	0	-0.048	-0.012	23.341	-0.008	-0.008	0.000	0.000	0.000	0.000
53	A	65	GLU	-1	-0.925	-0.968	21.117	0.427	0.427	0.000	0.000	0.000	0.000
54	A	66	GLY	0	-0.040	-0.009	24.478	-0.011	-0.011	0.000	0.000	0.000	0.000
55	A	67	GLU	-1	-0.771	-0.868	25.859	0.077	0.077	0.000	0.000	0.000	0.000
56	A	68	LYS	1	0.918	0.974	25.646	-0.103	-0.103	0.000	0.000	0.000	0.000
57	A	69	LEU	0	-0.037	-0.034	20.967	-0.023	-0.023	0.000	0.000	0.000	0.000
58	A	70	PHE	0	0.012	0.002	20.799	0.026	0.026	0.000	0.000	0.000	0.000
59	A	71	PHE	0	0.034	0.010	14.002	-0.039	-0.039	0.000	0.000	0.000	0.000
60	A	72	VAL	0	-0.023	-0.011	17.472	-0.013	-0.013	0.000	0.000	0.000	0.000
61	A	73	VAL	0	0.003	0.004	16.243	-0.034	-0.034	0.000	0.000	0.000	0.000
62	A	74	ARG	1	0.880	0.938	16.832	0.216	0.216	0.000	0.000	0.000	0.000
63	A	75	HIS	0	0.058	0.027	15.554	0.074	0.074	0.000	0.000	0.000	0.000
64	A	76	MET	0	-0.033	-0.018	15.368	-0.027	-0.027	0.000	0.000	0.000	0.000
65	A	77	GLU	-1	-0.928	-0.946	15.901	-0.672	-0.672	0.000	0.000	0.000	0.000
66	A	78	ILE	0	-0.029	-0.021	16.190	-0.080	-0.080	0.000	0.000	0.000	0.000
67	A	79	ASN	0	0.014	0.017	18.100	0.074	0.074	0.000	0.000	0.000	0.000
68	A	80	PHE	0	0.020	-0.012	19.618	-0.014	-0.014	0.000	0.000	0.000	0.000
69	A	81	SER	0	-0.058	-0.017	20.820	0.000	0.000	0.000	0.000	0.000	0.000
70	A	82	ARG	1	0.923	0.949	21.576	0.380	0.380	0.000	0.000	0.000	0.000
71	A	83	PRO	0	0.011	0.015	23.775	-0.014	-0.014	0.000	0.000	0.000	0.000
72	A	84	ALA	0	0.002	0.001	23.606	0.005	0.005	0.000	0.000	0.000	0.000
73	A	85	GLN	0	0.044	0.001	25.629	0.015	0.015	0.000	0.000	0.000	0.000
74	A	86	ILE	0	0.033	0.004	28.126	0.008	0.008	0.000	0.000	0.000	0.000
75	A	87	ASP	-1	-0.875	-0.945	29.567	0.015	0.015	0.000	0.000	0.000	0.000
76	A	88	ASN	0	-0.056	-0.006	25.052	-0.010	-0.010	0.000	0.000	0.000	0.000
77	A	89	LEU	0	-0.009	-0.002	22.571	0.009	0.009	0.000	0.000	0.000	0.000
78	A	90	LEU	0	-0.030	-0.020	19.722	-0.028	-0.028	0.000	0.000	0.000	0.000
79	A	91	THR	0	0.007	0.008	15.046	0.075	0.075	0.000	0.000	0.000	0.000
80	A	92	ILE	0	-0.041	-0.020	13.091	-0.110	-0.110	0.000	0.000	0.000	0.000
81	A	93	LYS	1	0.852	0.934	10.017	0.425	0.425	0.000	0.000	0.000	0.000
82	A	94	THR	0	0.051	0.029	7.824	-0.379	-0.379	0.000	0.000	0.000	0.000
83	A	95	ARG	1	0.915	0.981	2.117	6.262	6.690	3.895	-1.401	-2.922	0.009
84	A	96	ILE	0	0.013	0.016	3.455	-1.292	-0.785	0.003	-0.159	-0.350	0.000
85	A	97	SER	0	-0.025	-0.023	1.949	-10.814	-12.044	5.655	-2.327	-2.098	-0.032
86	A	98	ARG	1	0.949	0.974	4.284	2.209	2.285	-0.001	-0.016	-0.059	0.000
87	A	99	LEU	0	0.074	0.046	7.187	0.256	0.256	0.000	0.000	0.000	0.000
88	A	100	GLN	0	0.029	-0.010	9.132	-0.053	-0.053	0.000	0.000	0.000	0.000
89	A	101	GLY	0	0.005	0.008	12.857	0.019	0.019	0.000	0.000	0.000	0.000
90	A	102	ALA	0	-0.011	0.000	14.940	0.060	0.060	0.000	0.000	0.000	0.000
91	A	103	ARG	1	0.871	0.933	13.858	0.358	0.358	0.000	0.000	0.000	0.000
92	A	104	PHE	0	-0.019	-0.020	8.389	0.063	0.063	0.000	0.000	0.000	0.000
93	A	105	PHE	0	-0.007	0.002	8.381	0.081	0.081	0.000	0.000	0.000	0.000
94	A	106	MET	0	0.023	0.020	6.658	-0.658	-0.658	0.000	0.000	0.000	0.000
95	A	107	GLU	-1	-0.930	-0.958	6.647	-3.491	-3.491	0.000	0.000	0.000	0.000
96	A	108	GLN	0	-0.034	-0.054	7.874	-0.018	-0.018	0.000	0.000	0.000	0.000
97	A	109	TYR	0	-0.026	-0.022	8.684	0.105	0.105	0.000	0.000	0.000	0.000
98	A	110	ILE	0	0.024	0.023	13.133	0.116	0.116	0.000	0.000	0.000	0.000
99	A	111	LEU	0	0.019	-0.001	14.414	-0.046	-0.046	0.000	0.000	0.000	0.000
100	A	112	HIS	0	-0.002	0.005	18.394	0.076	0.076	0.000	0.000	0.000	0.000
101	A	113	GLY	0	0.037	0.017	21.309	-0.010	-0.010	0.000	0.000	0.000	0.000
102	A	114	GLU	-1	-0.926	-0.964	19.363	-0.170	-0.170	0.000	0.000	0.000	0.000
103	A	115	SER	0	-0.056	-0.019	20.268	-0.065	-0.065	0.000	0.000	0.000	0.000
104	A	116	MET	0	0.013	0.012	13.915	0.016	0.016	0.000	0.000	0.000	0.000
105	A	117	LEU	0	-0.029	-0.008	18.905	0.018	0.018	0.000	0.000	0.000	0.000
106	A	118	VAL	0	0.054	0.037	17.780	-0.006	-0.006	0.000	0.000	0.000	0.000
107	A	119	THR	0	-0.050	-0.030	14.129	-0.065	-0.065	0.000	0.000	0.000	0.000
108	A	120	ALA	0	0.022	0.000	13.301	0.076	0.076	0.000	0.000	0.000	0.000
109	A	121	LYS	1	0.920	0.980	10.762	1.248	1.248	0.000	0.000	0.000	0.000
110	A	122	VAL	0	-0.006	0.003	11.142	0.203	0.203	0.000	0.000	0.000	0.000
111	A	123	GLU	-1	-0.819	-0.899	11.216	-0.718	-0.718	0.000	0.000	0.000	0.000
112	A	124	ILE	0	-0.009	-0.001	11.718	0.115	0.115	0.000	0.000	0.000	0.000
113	A	125	ALA	0	-0.012	-0.013	13.847	-0.008	-0.008	0.000	0.000	0.000	0.000
114	A	126	LEU	0	0.012	0.007	16.552	0.032	0.032	0.000	0.000	0.000	0.000
115	A	127	ILE	0	-0.035	-0.022	18.337	-0.025	-0.025	0.000	0.000	0.000	0.000
116	A	128	ASN	0	0.017	0.002	22.122	0.009	0.009	0.000	0.000	0.000	0.000
117	A	129	GLU	-1	-0.897	-0.949	25.257	0.067	0.067	0.000	0.000	0.000	0.000
118	A	130	GLU	-1	-0.865	-0.932	28.206	0.044	0.044	0.000	0.000	0.000	0.000
119	A	131	GLY	0	-0.031	-0.015	25.953	-0.015	-0.015	0.000	0.000	0.000	0.000
120	A	132	LYS	1	0.806	0.913	25.912	-0.053	-0.053	0.000	0.000	0.000	0.000
121	A	133	PRO	0	-0.018	-0.010	21.949	0.016	0.016	0.000	0.000	0.000	0.000
122	A	134	ARG	1	0.822	0.890	20.948	-0.058	-0.058	0.000	0.000	0.000	0.000
123	A	135	ARG	1	0.920	0.956	17.765	-0.002	-0.002	0.000	0.000	0.000	0.000
124	A	136	LEU	0	-0.015	-0.022	11.974	0.015	0.015	0.000	0.000	0.000	0.000
125	A	137	PRO	0	0.045	0.039	15.669	-0.006	-0.006	0.000	0.000	0.000	0.000
126	A	138	LYS	1	0.963	0.989	13.228	-0.601	-0.601	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:13:ASN)