FMO DATABASE

FMODB ID: YZ5G2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1105994.925998
FMO2-HF: Nuclear repulsion	1055171.860076
FMO2-HF: Total energy	-50823.065922
FMO2-MP2: Total energy	-50973.160425

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.
-6.908	-5.471	9.69	-5.219	-5.907	-0.028

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 : -0.036 / 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	15	PHE	0	-0.051	-0.032	3.848	1.209	2.726	-0.006	-0.684	-0.827	0.002
4	A	16	HIS	0	-0.017	-0.012	5.794	0.988	0.988	0.000	0.000	0.000	0.000
5	A	17	ASP	-1	-0.777	-0.879	8.493	0.562	0.562	0.000	0.000	0.000	0.000
6	A	18	PHE	0	0.027	0.020	11.994	0.013	0.013	0.000	0.000	0.000	0.000
7	A	19	GLN	0	-0.013	-0.026	15.055	-0.087	-0.087	0.000	0.000	0.000	0.000
8	A	20	ALA	0	-0.021	-0.005	18.621	0.005	0.005	0.000	0.000	0.000	0.000
9	A	21	ARG	1	0.817	0.907	21.594	-0.213	-0.213	0.000	0.000	0.000	0.000
10	A	22	VAL	0	-0.034	0.003	25.113	-0.002	-0.002	0.000	0.000	0.000	0.000
11	A	23	TYR	0	0.023	-0.001	26.565	0.003	0.003	0.000	0.000	0.000	0.000
12	A	24	VAL	0	0.057	0.011	30.033	-0.009	-0.009	0.000	0.000	0.000	0.000
13	A	25	ALA	0	0.003	0.008	30.467	-0.010	-0.010	0.000	0.000	0.000	0.000
14	A	26	ASP	-1	-0.795	-0.885	25.986	0.136	0.136	0.000	0.000	0.000	0.000
15	A	27	THR	0	-0.070	-0.036	27.981	-0.015	-0.015	0.000	0.000	0.000	0.000
16	A	28	ASP	-1	-0.782	-0.877	30.604	-0.019	-0.019	0.000	0.000	0.000	0.000
17	A	29	PHE	0	-0.023	-0.022	33.043	0.002	0.002	0.000	0.000	0.000	0.000
18	A	30	SER	0	-0.066	-0.047	32.553	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	31	GLY	0	-0.007	-0.001	34.259	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	32	VAL	0	-0.050	-0.020	28.864	0.009	0.009	0.000	0.000	0.000	0.000
21	A	33	VAL	0	-0.032	-0.023	24.171	0.003	0.003	0.000	0.000	0.000	0.000
22	A	34	TYR	0	0.047	0.027	26.994	-0.025	-0.025	0.000	0.000	0.000	0.000
23	A	35	HIS	0	0.004	-0.015	24.757	0.000	0.000	0.000	0.000	0.000	0.000
24	A	36	ALA	0	0.049	0.018	23.283	-0.007	-0.007	0.000	0.000	0.000	0.000
25	A	37	ARG	1	0.805	0.883	23.064	-0.097	-0.097	0.000	0.000	0.000	0.000
26	A	38	TYR	0	0.015	0.011	19.766	0.031	0.031	0.000	0.000	0.000	0.000
27	A	39	LEU	0	0.003	-0.002	18.488	0.013	0.013	0.000	0.000	0.000	0.000
28	A	40	GLU	-1	-0.801	-0.862	18.607	0.147	0.147	0.000	0.000	0.000	0.000
29	A	41	PHE	0	-0.031	-0.017	18.674	0.056	0.056	0.000	0.000	0.000	0.000
30	A	42	PHE	0	0.021	-0.006	14.009	0.062	0.062	0.000	0.000	0.000	0.000
31	A	43	GLU	-1	-0.908	-0.932	14.468	0.381	0.381	0.000	0.000	0.000	0.000
32	A	44	ARG	1	0.927	0.962	15.784	-0.150	-0.150	0.000	0.000	0.000	0.000
33	A	45	GLY	0	0.035	0.023	13.542	0.097	0.097	0.000	0.000	0.000	0.000
34	A	46	ARG	1	0.850	0.920	11.205	0.122	0.122	0.000	0.000	0.000	0.000
35	A	47	SER	0	-0.009	-0.036	12.548	0.154	0.154	0.000	0.000	0.000	0.000
36	A	48	GLU	-1	-0.799	-0.864	13.913	0.757	0.757	0.000	0.000	0.000	0.000
37	A	49	PHE	0	0.012	0.013	5.003	-0.120	-0.025	-0.001	0.000	-0.093	0.000
38	A	50	LEU	0	-0.019	-0.013	10.550	0.206	0.206	0.000	0.000	0.000	0.000
39	A	51	ARG	1	0.766	0.858	12.709	-0.714	-0.714	0.000	0.000	0.000	0.000
40	A	52	ASP	-1	-0.847	-0.912	10.988	1.725	1.725	0.000	0.000	0.000	0.000
41	A	53	THR	0	-0.090	-0.047	8.813	0.001	0.001	0.000	0.000	0.000	0.000
42	A	54	GLY	0	0.028	0.018	12.074	-0.126	-0.126	0.000	0.000	0.000	0.000
43	A	55	PHE	0	-0.027	-0.017	14.065	-0.159	-0.159	0.000	0.000	0.000	0.000
44	A	56	ASN	0	0.030	0.006	16.177	-0.081	-0.081	0.000	0.000	0.000	0.000
45	A	57	ASN	0	0.035	-0.012	17.833	-0.036	-0.036	0.000	0.000	0.000	0.000
46	A	58	THR	0	0.014	0.007	19.922	-0.044	-0.044	0.000	0.000	0.000	0.000
47	A	59	LEU	0	-0.002	0.015	19.293	-0.035	-0.035	0.000	0.000	0.000	0.000
48	A	60	LEU	0	0.000	0.020	17.110	-0.032	-0.032	0.000	0.000	0.000	0.000
49	A	61	ALA	0	0.042	0.027	21.695	-0.038	-0.038	0.000	0.000	0.000	0.000
50	A	62	SER	0	-0.074	-0.057	24.749	-0.031	-0.031	0.000	0.000	0.000	0.000
51	A	63	GLY	0	0.022	0.009	25.982	-0.019	-0.019	0.000	0.000	0.000	0.000
52	A	64	VAL	0	-0.043	-0.016	23.780	-0.012	-0.012	0.000	0.000	0.000	0.000
53	A	65	GLU	-1	-0.828	-0.913	20.608	0.349	0.349	0.000	0.000	0.000	0.000
54	A	66	GLY	0	-0.018	-0.003	24.558	-0.019	-0.019	0.000	0.000	0.000	0.000
55	A	67	GLU	-1	-0.766	-0.839	25.715	0.031	0.031	0.000	0.000	0.000	0.000
56	A	68	LYS	1	0.803	0.892	25.988	-0.091	-0.091	0.000	0.000	0.000	0.000
57	A	69	LEU	0	-0.044	-0.023	21.085	-0.026	-0.026	0.000	0.000	0.000	0.000
58	A	70	PHE	0	0.032	0.002	21.015	0.036	0.036	0.000	0.000	0.000	0.000
59	A	71	PHE	0	0.015	0.004	14.589	-0.054	-0.054	0.000	0.000	0.000	0.000
60	A	72	VAL	0	-0.014	-0.010	17.642	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	73	VAL	0	0.011	0.008	16.151	-0.034	-0.034	0.000	0.000	0.000	0.000
62	A	74	ARG	1	0.847	0.922	16.476	0.195	0.195	0.000	0.000	0.000	0.000
63	A	75	HIS	0	0.012	0.000	15.297	0.063	0.063	0.000	0.000	0.000	0.000
64	A	76	MET	0	-0.041	-0.025	14.723	0.013	0.013	0.000	0.000	0.000	0.000
65	A	77	GLU	-1	-0.867	-0.900	15.483	-0.629	-0.629	0.000	0.000	0.000	0.000
66	A	78	ILE	0	-0.011	-0.026	15.761	-0.026	-0.026	0.000	0.000	0.000	0.000
67	A	79	ASN	0	-0.005	0.007	17.821	0.051	0.051	0.000	0.000	0.000	0.000
68	A	80	PHE	0	0.031	-0.001	19.273	0.009	0.009	0.000	0.000	0.000	0.000
69	A	81	SER	0	-0.020	-0.012	20.912	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	82	ARG	1	0.895	0.937	21.719	0.167	0.167	0.000	0.000	0.000	0.000
71	A	83	PRO	0	0.018	0.028	23.728	0.004	0.004	0.000	0.000	0.000	0.000
72	A	84	ALA	0	0.018	0.011	23.682	0.011	0.011	0.000	0.000	0.000	0.000
73	A	85	GLN	0	-0.003	-0.012	25.711	-0.005	-0.005	0.000	0.000	0.000	0.000
74	A	86	ILE	0	0.052	0.011	28.290	0.017	0.017	0.000	0.000	0.000	0.000
75	A	87	ASP	-1	-0.852	-0.922	29.459	0.156	0.156	0.000	0.000	0.000	0.000
76	A	88	ASN	0	-0.016	0.009	25.232	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	89	LEU	0	0.027	0.013	22.255	0.006	0.006	0.000	0.000	0.000	0.000
78	A	90	LEU	0	-0.010	-0.001	20.013	-0.006	-0.006	0.000	0.000	0.000	0.000
79	A	91	THR	0	0.006	0.003	15.181	0.076	0.076	0.000	0.000	0.000	0.000
80	A	92	ILE	0	-0.035	-0.018	13.633	-0.105	-0.105	0.000	0.000	0.000	0.000
81	A	93	LYS	1	0.820	0.904	10.285	-0.513	-0.513	0.000	0.000	0.000	0.000
82	A	94	THR	0	0.008	-0.008	8.441	-0.527	-0.527	0.000	0.000	0.000	0.000
83	A	95	ARG	1	0.851	0.927	2.812	2.004	4.492	0.810	-1.080	-2.217	0.008
84	A	96	ILE	0	0.008	0.017	4.065	-2.306	-1.740	-0.001	-0.258	-0.308	-0.001
85	A	97	SER	0	-0.025	-0.014	1.815	-10.622	-13.940	8.889	-3.187	-2.384	-0.037
86	A	98	ARG	1	0.880	0.943	3.878	1.800	1.889	-0.001	-0.010	-0.078	0.000
87	A	99	LEU	0	0.035	0.021	6.775	0.448	0.448	0.000	0.000	0.000	0.000
88	A	100	GLN	0	0.030	0.002	8.993	-0.082	-0.082	0.000	0.000	0.000	0.000
89	A	101	GLY	0	0.015	0.007	12.752	0.072	0.072	0.000	0.000	0.000	0.000
90	A	102	ALA	0	-0.021	-0.012	14.816	0.083	0.083	0.000	0.000	0.000	0.000
91	A	103	ARG	1	0.832	0.898	13.928	0.445	0.445	0.000	0.000	0.000	0.000
92	A	104	PHE	0	0.004	-0.006	8.356	-0.022	-0.022	0.000	0.000	0.000	0.000
93	A	105	PHE	0	0.055	0.034	8.054	0.144	0.144	0.000	0.000	0.000	0.000
94	A	106	MET	0	0.033	0.017	6.254	-0.489	-0.489	0.000	0.000	0.000	0.000
95	A	107	GLU	-1	-0.832	-0.886	6.197	-3.193	-3.193	0.000	0.000	0.000	0.000
96	A	108	GLN	0	-0.014	-0.030	7.770	0.280	0.280	0.000	0.000	0.000	0.000
97	A	109	TYR	0	-0.036	-0.027	8.790	-0.098	-0.098	0.000	0.000	0.000	0.000
98	A	110	ILE	0	0.018	0.024	13.154	0.148	0.148	0.000	0.000	0.000	0.000
99	A	111	LEU	0	0.000	-0.007	14.635	-0.080	-0.080	0.000	0.000	0.000	0.000
100	A	112	HIS	0	0.009	0.006	18.717	0.068	0.068	0.000	0.000	0.000	0.000
101	A	113	GLY	0	0.061	0.034	21.600	-0.029	-0.029	0.000	0.000	0.000	0.000
102	A	114	GLU	-1	-0.901	-0.962	19.290	0.111	0.111	0.000	0.000	0.000	0.000
103	A	115	SER	0	-0.049	-0.013	20.264	-0.070	-0.070	0.000	0.000	0.000	0.000
104	A	116	MET	0	0.017	0.012	14.211	0.028	0.028	0.000	0.000	0.000	0.000
105	A	117	LEU	0	-0.044	-0.009	19.080	-0.020	-0.020	0.000	0.000	0.000	0.000
106	A	118	VAL	0	0.028	0.012	17.956	-0.032	-0.032	0.000	0.000	0.000	0.000
107	A	119	THR	0	-0.027	-0.011	14.272	0.007	0.007	0.000	0.000	0.000	0.000
108	A	120	ALA	0	0.008	0.007	13.192	0.008	0.008	0.000	0.000	0.000	0.000
109	A	121	LYS	1	0.876	0.945	9.697	1.345	1.345	0.000	0.000	0.000	0.000
110	A	122	VAL	0	0.003	0.002	10.666	0.172	0.172	0.000	0.000	0.000	0.000
111	A	123	GLU	-1	-0.811	-0.884	10.729	-0.781	-0.781	0.000	0.000	0.000	0.000
112	A	124	ILE	0	-0.007	-0.003	11.896	0.132	0.132	0.000	0.000	0.000	0.000
113	A	125	ALA	0	0.007	-0.002	13.636	-0.080	-0.080	0.000	0.000	0.000	0.000
114	A	126	LEU	0	0.008	0.010	16.211	0.058	0.058	0.000	0.000	0.000	0.000
115	A	127	ILE	0	-0.028	-0.011	18.278	-0.046	-0.046	0.000	0.000	0.000	0.000
116	A	128	ASN	0	0.019	-0.014	22.104	0.019	0.019	0.000	0.000	0.000	0.000
117	A	129	GLU	-1	-0.789	-0.862	25.280	0.081	0.081	0.000	0.000	0.000	0.000
118	A	130	GLU	-1	-0.833	-0.898	28.154	0.019	0.019	0.000	0.000	0.000	0.000
119	A	131	GLY	0	0.002	0.003	26.114	-0.015	-0.015	0.000	0.000	0.000	0.000
120	A	132	LYS	1	0.785	0.887	25.459	-0.016	-0.016	0.000	0.000	0.000	0.000
121	A	133	PRO	0	0.001	0.000	21.404	0.017	0.017	0.000	0.000	0.000	0.000
122	A	134	ARG	1	0.790	0.850	20.788	-0.011	-0.011	0.000	0.000	0.000	0.000
123	A	135	ARG	1	0.920	0.957	17.784	0.163	0.163	0.000	0.000	0.000	0.000
124	A	136	LEU	0	-0.012	-0.006	12.202	0.026	0.026	0.000	0.000	0.000	0.000
125	A	137	PRO	0	0.020	0.024	16.025	-0.032	-0.032	0.000	0.000	0.000	0.000
126	A	138	LYS	1	0.809	0.906	14.131	-0.304	-0.304	0.000	0.000	0.000	0.000

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