FMO DATABASE

FMODB ID: JL299

Calculation Name: 4HWD-D-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: 4HWD

Chain ID: D

ChEMBL ID:
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UniProt ID: Q0WPX7

Base Structure: X-ray

Registration Date: 2023-06-22

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	90
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-590250.133093
FMO2-HF: Nuclear repulsion	555157.459444
FMO2-HF: Total energy	-35092.673649
FMO2-MP2: Total energy	-35193.661087

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(D:133:GLY)

Summations of interaction energy for fragment #1(D:133:GLY)

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.
-0.895	1.031	0.677	-1.062	-1.542	0

Interaction energy analysis for fragmet #1(D:133:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.052 / q_NPA : 0.019

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].
3	D	135	GLY	0	0.026	0.020	3.899	0.243	1.083	-0.003	-0.374	-0.463
4	D	136	SER	0	0.024	0.006	2.314	-0.520	0.279	0.681	-0.590	-0.890
5	D	137	SER	0	-0.016	-0.019	3.896	-0.670	-0.383	-0.001	-0.098	-0.189
6	D	138	SER	0	0.022	-0.004	5.666	0.559	0.559	0.000	0.000	0.000
7	D	139	LYS	1	0.786	0.885	7.445	0.256	0.256	0.000	0.000	0.000
8	D	140	ALA	0	0.044	0.022	7.769	0.111	0.111	0.000	0.000	0.000
9	D	141	ILE	0	0.047	0.018	9.436	0.122	0.122	0.000	0.000	0.000
10	D	142	SER	0	-0.005	0.020	11.543	0.115	0.115	0.000	0.000	0.000
11	D	143	ASP	-1	-0.845	-0.898	11.667	-0.103	-0.103	0.000	0.000	0.000
12	D	144	ILE	0	0.009	0.006	12.774	0.044	0.044	0.000	0.000	0.000
13	D	145	SER	0	-0.042	-0.042	15.298	0.038	0.038	0.000	0.000	0.000
14	D	146	PHE	0	0.033	0.019	17.282	0.032	0.032	0.000	0.000	0.000
15	D	147	GLN	0	0.023	0.010	18.438	0.032	0.032	0.000	0.000	0.000
16	D	148	VAL	0	0.029	0.011	19.047	0.017	0.017	0.000	0.000	0.000
17	D	149	GLU	-1	-0.898	-0.948	21.323	-0.129	-0.129	0.000	0.000	0.000
18	D	150	ARG	1	0.871	0.940	21.925	0.100	0.100	0.000	0.000	0.000
19	D	151	LEU	0	-0.048	-0.018	22.484	0.011	0.011	0.000	0.000	0.000
20	D	152	ALA	0	0.024	0.013	25.521	0.007	0.007	0.000	0.000	0.000
21	D	153	GLY	0	0.012	0.017	27.474	0.008	0.008	0.000	0.000	0.000
22	D	154	GLN	0	-0.037	-0.015	29.004	0.009	0.009	0.000	0.000	0.000
23	D	155	LEU	0	0.023	0.010	28.914	0.005	0.005	0.000	0.000	0.000
24	D	156	SER	0	-0.003	0.007	31.345	0.006	0.006	0.000	0.000	0.000
25	D	157	ALA	0	0.014	0.013	33.415	0.005	0.005	0.000	0.000	0.000
26	D	158	PHE	0	-0.009	-0.021	32.466	0.004	0.004	0.000	0.000	0.000
27	D	159	ASP	-1	-0.892	-0.946	35.475	-0.064	-0.064	0.000	0.000	0.000
28	D	160	THR	0	-0.053	-0.040	37.208	0.005	0.005	0.000	0.000	0.000
29	D	161	VAL	0	-0.018	0.001	39.239	0.004	0.004	0.000	0.000	0.000
30	D	162	ILE	0	0.031	0.021	38.014	0.003	0.003	0.000	0.000	0.000
31	D	163	GLY	0	-0.003	0.008	41.124	0.002	0.002	0.000	0.000	0.000
32	D	164	LYS	1	0.834	0.902	42.579	0.049	0.049	0.000	0.000	0.000
33	D	165	GLY	0	-0.008	0.011	45.471	0.002	0.002	0.000	0.000	0.000
34	D	166	GLY	0	0.005	0.018	44.671	0.002	0.002	0.000	0.000	0.000
35	D	167	LYS	1	0.861	0.923	43.559	0.046	0.046	0.000	0.000	0.000
36	D	168	VAL	0	0.017	0.008	37.104	0.001	0.001	0.000	0.000	0.000
37	D	169	GLU	-1	-0.815	-0.881	38.920	-0.051	-0.051	0.000	0.000	0.000
38	D	170	GLU	-1	-0.731	-0.861	37.938	-0.070	-0.070	0.000	0.000	0.000
39	D	171	LYS	1	0.861	0.913	35.245	0.051	0.051	0.000	0.000	0.000
40	D	172	ASN	0	-0.011	-0.004	33.704	-0.005	-0.005	0.000	0.000	0.000
41	D	173	LEU	0	0.016	0.012	32.454	-0.005	-0.005	0.000	0.000	0.000
42	D	174	GLU	-1	-0.865	-0.926	31.750	-0.083	-0.083	0.000	0.000	0.000
43	D	175	ASN	0	-0.055	-0.036	29.822	-0.003	-0.003	0.000	0.000	0.000
44	D	176	LEU	0	0.001	0.007	27.131	-0.008	-0.008	0.000	0.000	0.000
45	D	177	MET	0	0.018	0.016	26.956	-0.016	-0.016	0.000	0.000	0.000
46	D	178	GLU	-1	-0.880	-0.914	23.875	-0.162	-0.162	0.000	0.000	0.000
47	D	179	MET	0	0.010	0.000	23.528	-0.015	-0.015	0.000	0.000	0.000
48	D	180	LEU	0	0.011	-0.002	22.132	-0.020	-0.020	0.000	0.000	0.000
49	D	181	MET	0	0.052	0.023	21.585	-0.027	-0.027	0.000	0.000	0.000
50	D	182	ASN	0	-0.082	-0.046	19.564	-0.044	-0.044	0.000	0.000	0.000
51	D	183	GLN	0	-0.064	-0.042	17.536	-0.047	-0.047	0.000	0.000	0.000
52	D	184	LEU	0	0.034	0.022	16.711	-0.047	-0.047	0.000	0.000	0.000
53	D	185	VAL	0	0.022	0.005	16.934	-0.042	-0.042	0.000	0.000	0.000
54	D	186	LYS	1	0.850	0.928	13.776	0.199	0.199	0.000	0.000	0.000
55	D	187	LEU	0	-0.029	-0.018	12.426	-0.108	-0.108	0.000	0.000	0.000
56	D	188	ASP	-1	-0.863	-0.928	12.568	-0.499	-0.499	0.000	0.000	0.000
57	D	189	ALA	0	-0.051	-0.010	11.837	-0.023	-0.023	0.000	0.000	0.000
58	D	190	ILE	0	-0.084	-0.025	7.058	-0.194	-0.194	0.000	0.000	0.000
59	D	191	SER	0	0.015	0.016	6.173	-0.063	-0.063	0.000	0.000	0.000
60	D	192	GLY	0	0.021	-0.004	6.025	-0.750	-0.750	0.000	0.000	0.000
61	D	193	ASP	-1	-0.910	-0.954	7.162	-0.464	-0.464	0.000	0.000	0.000
62	D	194	GLY	0	0.029	0.000	9.823	-0.041	-0.041	0.000	0.000	0.000
63	D	195	ASP	-1	-0.812	-0.902	12.359	-0.387	-0.387	0.000	0.000	0.000
64	D	196	VAL	0	0.003	0.027	7.258	0.018	0.018	0.000	0.000	0.000
65	D	197	LYS	1	0.992	0.992	10.449	0.458	0.458	0.000	0.000	0.000
66	D	198	LEU	0	-0.046	-0.006	12.475	0.077	0.077	0.000	0.000	0.000
67	D	199	LYS	1	0.855	0.893	13.209	0.401	0.401	0.000	0.000	0.000
68	D	200	LYS	1	0.828	0.899	12.468	0.502	0.502	0.000	0.000	0.000
69	D	201	LYS	1	0.881	0.938	14.522	0.280	0.280	0.000	0.000	0.000
70	D	202	MET	0	-0.032	-0.013	17.668	0.040	0.040	0.000	0.000	0.000
71	D	203	GLN	0	-0.003	-0.025	16.846	0.056	0.056	0.000	0.000	0.000
72	D	204	GLU	-1	-0.812	-0.904	17.517	-0.345	-0.345	0.000	0.000	0.000
73	D	205	GLU	-1	-0.834	-0.893	19.639	-0.179	-0.179	0.000	0.000	0.000
74	D	206	ARG	1	0.818	0.912	22.078	0.198	0.198	0.000	0.000	0.000
75	D	207	LEU	0	0.002	-0.008	19.124	0.019	0.019	0.000	0.000	0.000
76	D	208	HIS	0	-0.001	0.000	21.472	0.027	0.027	0.000	0.000	0.000
77	D	209	LYS	1	1.014	1.017	25.397	0.130	0.130	0.000	0.000	0.000
78	D	210	TYR	0	-0.050	-0.041	24.454	0.014	0.014	0.000	0.000	0.000
79	D	211	VAL	0	0.032	0.016	25.649	0.009	0.009	0.000	0.000	0.000
80	D	212	GLU	-1	-0.884	-0.942	28.368	-0.118	-0.118	0.000	0.000	0.000
81	D	213	ALA	0	-0.033	-0.022	31.011	0.009	0.009	0.000	0.000	0.000
82	D	214	LEU	0	-0.018	-0.009	29.526	0.009	0.009	0.000	0.000	0.000
83	D	215	ASP	-1	-0.865	-0.934	32.097	-0.101	-0.101	0.000	0.000	0.000
84	D	216	LEU	0	-0.039	-0.026	34.340	0.008	0.008	0.000	0.000	0.000
85	D	217	LEU	0	-0.048	-0.021	34.128	0.006	0.006	0.000	0.000	0.000
86	D	218	LYS	1	0.893	0.938	34.270	0.085	0.085	0.000	0.000	0.000
87	D	219	ILE	0	-0.023	0.004	37.762	0.005	0.005	0.000	0.000	0.000
88	D	220	LYS	1	0.828	0.918	40.108	0.058	0.058	0.000	0.000	0.000
89	D	221	ASN	0	-0.060	-0.044	39.980	0.007	0.007	0.000	0.000	0.000
90	D	222	SER	0	-0.055	-0.046	39.982	0.004	0.004	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:133:GLY)