FMO DATABASE

FMODB ID: 5216Z

Calculation Name: 3HM0-A-Xray372

Preferred Name:
Warning: Undefined array key "pref_name" in /home/FMODBwui_src/fmodbwui/detail.php on line 446

Target Type:
Warning: Undefined array key "target_type" in /home/FMODBwui_src/fmodbwui/detail.php on line 447

Ligand Name:
Warning: Undefined variable $Ligand in /home/FMODBwui_src/fmodbwui/detail.php on line 448

Warning: Trying to access array offset on value of type null in /home/FMODBwui_src/fmodbwui/detail.php on line 448

Warning: Trying to access array offset on value of type null in /home/FMODBwui_src/fmodbwui/detail.php on line 448

ligand 3-letter code:
Warning: Undefined variable $Ligand in /home/FMODBwui_src/fmodbwui/detail.php on line 449

Warning: Trying to access array offset on value of type null in /home/FMODBwui_src/fmodbwui/detail.php on line 449

Warning: Trying to access array offset on value of type null in /home/FMODBwui_src/fmodbwui/detail.php on line 449

PDB ID: 3HM0

Chain ID: A

ChEMBL ID:
Warning: Undefined array key "chembl_id" in /home/FMODBwui_src/fmodbwui/detail.php on line 452

Warning: Undefined array key "chembl_id" in /home/FMODBwui_src/fmodbwui/detail.php on line 452

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	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	-1104364.354485
FMO2-HF: Nuclear repulsion	1053541.700149
FMO2-HF: Total energy	-50822.654336
FMO2-MP2: Total energy	-50972.723445

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.
-5.842	-2.762	5.85	-3.88	-5.05	-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 : -0.048 / q_NPA : -0.038

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

Sort

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	-0.042	-0.031	3.828	0.382	1.882	-0.021	-0.686	-0.792	0.002
4	A	16	HIS	0	-0.035	-0.022	5.772	1.180	1.180	0.000	0.000	0.000	0.000
5	A	17	ASP	-1	-0.795	-0.885	8.623	0.199	0.199	0.000	0.000	0.000	0.000
6	A	18	PHE	0	0.017	0.008	12.279	0.052	0.052	0.000	0.000	0.000	0.000
7	A	19	GLN	0	0.010	-0.008	15.203	-0.101	-0.101	0.000	0.000	0.000	0.000
8	A	20	ALA	0	-0.027	-0.005	18.793	0.014	0.014	0.000	0.000	0.000	0.000
9	A	21	ARG	1	0.866	0.946	21.646	-0.176	-0.176	0.000	0.000	0.000	0.000
10	A	22	VAL	0	-0.032	0.008	25.044	-0.002	-0.002	0.000	0.000	0.000	0.000
11	A	23	TYR	0	0.038	0.003	26.659	0.005	0.005	0.000	0.000	0.000	0.000
12	A	24	VAL	0	0.067	0.009	30.169	-0.010	-0.010	0.000	0.000	0.000	0.000
13	A	25	ALA	0	-0.008	0.005	30.249	-0.010	-0.010	0.000	0.000	0.000	0.000
14	A	26	ASP	-1	-0.800	-0.884	26.384	0.081	0.081	0.000	0.000	0.000	0.000
15	A	27	THR	0	-0.057	-0.021	28.344	-0.017	-0.017	0.000	0.000	0.000	0.000
16	A	28	ASP	-1	-0.761	-0.868	30.899	-0.052	-0.052	0.000	0.000	0.000	0.000
17	A	29	PHE	0	-0.028	-0.025	33.129	0.002	0.002	0.000	0.000	0.000	0.000
18	A	30	SER	0	-0.095	-0.060	32.687	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	31	GLY	0	0.004	0.001	34.350	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	32	VAL	0	-0.048	-0.018	28.964	0.007	0.007	0.000	0.000	0.000	0.000
21	A	33	VAL	0	-0.051	-0.026	24.395	0.006	0.006	0.000	0.000	0.000	0.000
22	A	34	TYR	0	0.032	0.020	27.464	-0.024	-0.024	0.000	0.000	0.000	0.000
23	A	35	HIS	0	0.004	-0.017	25.192	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	36	ALA	0	0.032	0.004	23.652	-0.011	-0.011	0.000	0.000	0.000	0.000
25	A	37	ARG	1	0.825	0.895	23.516	-0.055	-0.055	0.000	0.000	0.000	0.000
26	A	38	TYR	0	0.033	0.023	19.946	0.025	0.025	0.000	0.000	0.000	0.000
27	A	39	LEU	0	0.003	-0.008	18.786	0.003	0.003	0.000	0.000	0.000	0.000
28	A	40	GLU	-1	-0.820	-0.886	18.963	0.101	0.101	0.000	0.000	0.000	0.000
29	A	41	PHE	0	-0.024	-0.015	18.756	0.051	0.051	0.000	0.000	0.000	0.000
30	A	42	PHE	0	0.015	-0.012	14.074	0.051	0.051	0.000	0.000	0.000	0.000
31	A	43	GLU	-1	-0.909	-0.934	14.475	0.301	0.301	0.000	0.000	0.000	0.000
32	A	44	ARG	1	0.949	0.980	16.072	-0.106	-0.106	0.000	0.000	0.000	0.000
33	A	45	GLY	0	0.021	0.022	13.274	0.097	0.097	0.000	0.000	0.000	0.000
34	A	46	ARG	1	0.877	0.931	11.252	0.180	0.180	0.000	0.000	0.000	0.000
35	A	47	SER	0	-0.018	-0.039	12.418	0.180	0.180	0.000	0.000	0.000	0.000
36	A	48	GLU	-1	-0.804	-0.870	14.056	0.744	0.744	0.000	0.000	0.000	0.000
37	A	49	PHE	0	0.006	0.014	5.025	-0.157	-0.050	-0.001	-0.001	-0.105	0.000
38	A	50	LEU	0	-0.030	-0.030	10.547	0.196	0.196	0.000	0.000	0.000	0.000
39	A	51	ARG	1	0.798	0.868	12.445	-0.637	-0.637	0.000	0.000	0.000	0.000
40	A	52	ASP	-1	-0.868	-0.913	10.682	1.706	1.706	0.000	0.000	0.000	0.000
41	A	53	THR	0	-0.123	-0.047	8.861	0.110	0.110	0.000	0.000	0.000	0.000
42	A	54	GLY	0	0.033	0.004	12.070	-0.118	-0.118	0.000	0.000	0.000	0.000
43	A	55	PHE	0	-0.026	-0.012	14.337	-0.130	-0.130	0.000	0.000	0.000	0.000
44	A	56	ASN	0	0.037	0.023	16.350	-0.072	-0.072	0.000	0.000	0.000	0.000
45	A	57	ASN	0	0.050	-0.001	18.152	-0.030	-0.030	0.000	0.000	0.000	0.000
46	A	58	THR	0	0.022	0.012	20.337	-0.034	-0.034	0.000	0.000	0.000	0.000
47	A	59	LEU	0	-0.020	0.000	19.460	-0.029	-0.029	0.000	0.000	0.000	0.000
48	A	60	LEU	0	0.028	0.027	16.993	-0.031	-0.031	0.000	0.000	0.000	0.000
49	A	61	ALA	0	0.033	0.031	21.602	-0.039	-0.039	0.000	0.000	0.000	0.000
50	A	62	SER	0	-0.065	-0.046	24.742	-0.029	-0.029	0.000	0.000	0.000	0.000
51	A	63	GLY	0	0.031	0.009	26.039	-0.021	-0.021	0.000	0.000	0.000	0.000
52	A	64	VAL	0	-0.059	-0.020	23.760	-0.011	-0.011	0.000	0.000	0.000	0.000
53	A	65	GLU	-1	-0.941	-0.976	21.108	0.369	0.369	0.000	0.000	0.000	0.000
54	A	66	GLY	0	-0.033	-0.008	24.772	-0.017	-0.017	0.000	0.000	0.000	0.000
55	A	67	GLU	-1	-0.766	-0.847	25.685	0.050	0.050	0.000	0.000	0.000	0.000
56	A	68	LYS	1	0.806	0.897	25.819	-0.098	-0.098	0.000	0.000	0.000	0.000
57	A	69	LEU	0	-0.051	-0.037	20.932	-0.025	-0.025	0.000	0.000	0.000	0.000
58	A	70	PHE	0	0.011	-0.003	20.987	0.033	0.033	0.000	0.000	0.000	0.000
59	A	71	PHE	0	0.035	0.012	14.598	-0.045	-0.045	0.000	0.000	0.000	0.000
60	A	72	VAL	0	-0.012	-0.007	17.574	-0.011	-0.011	0.000	0.000	0.000	0.000
61	A	73	VAL	0	0.006	0.008	16.258	-0.034	-0.034	0.000	0.000	0.000	0.000
62	A	74	ARG	1	0.883	0.938	16.862	0.180	0.180	0.000	0.000	0.000	0.000
63	A	75	HIS	0	0.058	0.026	15.719	0.065	0.065	0.000	0.000	0.000	0.000
64	A	76	MET	0	-0.037	-0.018	15.268	-0.008	-0.008	0.000	0.000	0.000	0.000
65	A	77	GLU	-1	-0.935	-0.951	15.860	-0.631	-0.631	0.000	0.000	0.000	0.000
66	A	78	ILE	0	-0.030	-0.023	16.153	-0.048	-0.048	0.000	0.000	0.000	0.000
67	A	79	ASN	0	0.002	0.010	18.061	0.056	0.056	0.000	0.000	0.000	0.000
68	A	80	PHE	0	0.028	-0.007	19.604	0.006	0.006	0.000	0.000	0.000	0.000
69	A	81	SER	0	-0.047	-0.013	21.348	-0.007	-0.007	0.000	0.000	0.000	0.000
70	A	82	ARG	1	0.915	0.946	21.660	0.250	0.250	0.000	0.000	0.000	0.000
71	A	83	PRO	0	0.012	0.018	23.821	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	84	ALA	0	0.002	0.001	23.691	0.008	0.008	0.000	0.000	0.000	0.000
73	A	85	GLN	0	0.019	-0.006	25.726	0.002	0.002	0.000	0.000	0.000	0.000
74	A	86	ILE	0	0.034	0.004	28.262	0.015	0.015	0.000	0.000	0.000	0.000
75	A	87	ASP	-1	-0.895	-0.954	29.701	0.109	0.109	0.000	0.000	0.000	0.000
76	A	88	ASN	0	-0.008	0.014	25.348	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	89	LEU	0	0.023	0.015	22.384	0.009	0.009	0.000	0.000	0.000	0.000
78	A	90	LEU	0	-0.026	-0.020	19.888	-0.023	-0.023	0.000	0.000	0.000	0.000
79	A	91	THR	0	0.011	0.009	15.065	0.081	0.081	0.000	0.000	0.000	0.000
80	A	92	ILE	0	-0.044	-0.020	13.306	-0.108	-0.108	0.000	0.000	0.000	0.000
81	A	93	LYS	1	0.823	0.892	10.265	-0.162	-0.162	0.000	0.000	0.000	0.000
82	A	94	THR	0	0.041	0.017	8.064	-0.487	-0.487	0.000	0.000	0.000	0.000
83	A	95	ARG	1	0.889	0.961	2.942	3.484	5.468	0.528	-0.800	-1.712	0.008
84	A	96	ILE	0	-0.001	0.009	3.716	-1.942	-1.491	0.000	-0.157	-0.294	0.000
85	A	97	SER	0	-0.026	-0.024	1.941	-10.366	-11.409	5.345	-2.219	-2.083	-0.030
86	A	98	ARG	1	0.877	0.943	4.115	1.804	1.885	-0.001	-0.017	-0.064	0.000
87	A	99	LEU	0	0.054	0.041	7.040	0.397	0.397	0.000	0.000	0.000	0.000
88	A	100	GLN	0	0.051	-0.002	9.077	-0.089	-0.089	0.000	0.000	0.000	0.000
89	A	101	GLY	0	0.010	0.009	12.838	0.049	0.049	0.000	0.000	0.000	0.000
90	A	102	ALA	0	-0.009	0.001	14.935	0.077	0.077	0.000	0.000	0.000	0.000
91	A	103	ARG	1	0.839	0.910	14.030	0.410	0.410	0.000	0.000	0.000	0.000
92	A	104	PHE	0	-0.007	-0.013	8.447	-0.012	-0.012	0.000	0.000	0.000	0.000
93	A	105	PHE	0	0.048	0.025	8.309	0.119	0.119	0.000	0.000	0.000	0.000
94	A	106	MET	0	0.032	0.025	6.631	-0.645	-0.645	0.000	0.000	0.000	0.000
95	A	107	GLU	-1	-0.856	-0.905	6.517	-3.192	-3.192	0.000	0.000	0.000	0.000
96	A	108	GLN	0	-0.018	-0.039	7.930	0.094	0.094	0.000	0.000	0.000	0.000
97	A	109	TYR	0	-0.024	-0.025	8.893	-0.031	-0.031	0.000	0.000	0.000	0.000
98	A	110	ILE	0	0.030	0.027	13.193	0.136	0.136	0.000	0.000	0.000	0.000
99	A	111	LEU	0	0.021	0.000	14.692	-0.064	-0.064	0.000	0.000	0.000	0.000
100	A	112	HIS	0	0.005	0.009	18.560	0.075	0.075	0.000	0.000	0.000	0.000
101	A	113	GLY	0	0.040	0.020	21.374	-0.023	-0.023	0.000	0.000	0.000	0.000
102	A	114	GLU	-1	-0.930	-0.966	19.455	0.006	0.006	0.000	0.000	0.000	0.000
103	A	115	SER	0	-0.043	-0.012	20.572	-0.068	-0.068	0.000	0.000	0.000	0.000
104	A	116	MET	0	-0.004	0.006	14.364	0.026	0.026	0.000	0.000	0.000	0.000
105	A	117	LEU	0	-0.019	0.000	19.108	-0.004	-0.004	0.000	0.000	0.000	0.000
106	A	118	VAL	0	0.046	0.025	18.105	-0.021	-0.021	0.000	0.000	0.000	0.000
107	A	119	THR	0	-0.020	-0.014	14.234	-0.016	-0.016	0.000	0.000	0.000	0.000
108	A	120	ALA	0	0.010	0.000	13.288	0.040	0.040	0.000	0.000	0.000	0.000
109	A	121	LYS	1	0.880	0.954	10.419	1.343	1.343	0.000	0.000	0.000	0.000
110	A	122	VAL	0	0.003	0.001	11.124	0.161	0.161	0.000	0.000	0.000	0.000
111	A	123	GLU	-1	-0.819	-0.889	11.207	-0.710	-0.710	0.000	0.000	0.000	0.000
112	A	124	ILE	0	-0.010	-0.001	12.105	0.116	0.116	0.000	0.000	0.000	0.000
113	A	125	ALA	0	-0.010	-0.011	13.892	-0.038	-0.038	0.000	0.000	0.000	0.000
114	A	126	LEU	0	0.011	0.008	16.608	0.047	0.047	0.000	0.000	0.000	0.000
115	A	127	ILE	0	-0.032	-0.022	18.437	-0.035	-0.035	0.000	0.000	0.000	0.000
116	A	128	ASN	0	0.048	-0.010	22.223	0.016	0.016	0.000	0.000	0.000	0.000
117	A	129	GLU	-1	-0.805	-0.870	25.380	0.083	0.083	0.000	0.000	0.000	0.000
118	A	130	GLU	-1	-0.829	-0.890	28.343	0.033	0.033	0.000	0.000	0.000	0.000
119	A	131	GLY	0	-0.038	-0.017	26.042	-0.014	-0.014	0.000	0.000	0.000	0.000
120	A	132	LYS	1	0.811	0.906	25.971	-0.033	-0.033	0.000	0.000	0.000	0.000
121	A	133	PRO	0	-0.023	-0.014	21.760	0.016	0.016	0.000	0.000	0.000	0.000
122	A	134	ARG	1	0.794	0.861	21.005	-0.033	-0.033	0.000	0.000	0.000	0.000
123	A	135	ARG	1	0.918	0.955	17.826	0.117	0.117	0.000	0.000	0.000	0.000
124	A	136	LEU	0	-0.020	-0.021	12.134	0.021	0.021	0.000	0.000	0.000	0.000
125	A	137	PRO	0	0.037	0.034	15.686	-0.029	-0.029	0.000	0.000	0.000	0.000
126	A	138	LYS	1	0.937	0.982	13.722	-0.429	-0.429	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Manual

Support

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