FMO DATABASE

FMODB ID: 85NVY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-589022.174487
FMO2-HF: Nuclear repulsion	553930.725012
FMO2-HF: Total energy	-35091.449476
FMO2-MP2: Total energy	-35192.519819

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.
-1.584	0.334	1.278	-1.302	-1.894	0.004

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 : 0.061 / q_NPA : 0.024

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	D	135	GLY	0	0.035	0.023	3.866	0.410	1.136	-0.003	-0.305	-0.418	0.000
4	D	136	SER	0	-0.014	-0.014	2.393	-1.635	-0.923	1.280	-0.846	-1.146	0.004
5	D	137	SER	0	0.051	0.026	3.398	-0.030	0.450	0.001	-0.151	-0.330	0.000
6	D	138	SER	0	-0.034	-0.031	5.401	0.645	0.645	0.000	0.000	0.000	0.000
7	D	139	LYS	1	0.905	0.962	7.480	-0.282	-0.282	0.000	0.000	0.000	0.000
8	D	140	ALA	0	0.034	0.028	7.577	0.069	0.069	0.000	0.000	0.000	0.000
9	D	141	ILE	0	0.029	0.013	9.232	0.074	0.074	0.000	0.000	0.000	0.000
10	D	142	SER	0	-0.015	0.002	11.442	0.076	0.076	0.000	0.000	0.000	0.000
11	D	143	ASP	-1	-0.908	-0.956	11.998	0.095	0.095	0.000	0.000	0.000	0.000
12	D	144	ILE	0	-0.011	-0.001	12.445	0.018	0.018	0.000	0.000	0.000	0.000
13	D	145	SER	0	-0.046	-0.028	15.414	0.016	0.016	0.000	0.000	0.000	0.000
14	D	146	PHE	0	0.023	0.019	17.145	0.024	0.024	0.000	0.000	0.000	0.000
15	D	147	GLN	0	0.005	-0.006	18.253	0.024	0.024	0.000	0.000	0.000	0.000
16	D	148	VAL	0	0.015	-0.003	18.605	0.011	0.011	0.000	0.000	0.000	0.000
17	D	149	GLU	-1	-0.948	-0.972	21.141	-0.074	-0.074	0.000	0.000	0.000	0.000
18	D	150	ARG	1	0.878	0.948	22.452	0.038	0.038	0.000	0.000	0.000	0.000
19	D	151	LEU	0	-0.037	-0.015	21.854	0.007	0.007	0.000	0.000	0.000	0.000
20	D	152	ALA	0	0.016	0.009	25.355	0.004	0.004	0.000	0.000	0.000	0.000
21	D	153	GLY	0	0.000	0.009	27.267	0.005	0.005	0.000	0.000	0.000	0.000
22	D	154	GLN	0	-0.014	-0.003	28.788	0.008	0.008	0.000	0.000	0.000	0.000
23	D	155	LEU	0	0.018	0.002	29.145	0.003	0.003	0.000	0.000	0.000	0.000
24	D	156	SER	0	0.000	0.007	31.255	0.003	0.003	0.000	0.000	0.000	0.000
25	D	157	ALA	0	0.017	0.012	33.232	0.003	0.003	0.000	0.000	0.000	0.000
26	D	158	PHE	0	-0.011	-0.017	32.565	0.004	0.004	0.000	0.000	0.000	0.000
27	D	159	ASP	-1	-0.891	-0.948	35.045	-0.055	-0.055	0.000	0.000	0.000	0.000
28	D	160	THR	0	-0.054	-0.025	36.857	0.004	0.004	0.000	0.000	0.000	0.000
29	D	161	VAL	0	-0.022	-0.011	39.070	0.002	0.002	0.000	0.000	0.000	0.000
30	D	162	ILE	0	-0.002	0.001	37.891	0.002	0.002	0.000	0.000	0.000	0.000
31	D	163	GLY	0	-0.053	-0.024	40.796	0.001	0.001	0.000	0.000	0.000	0.000
32	D	164	LYS	1	0.856	0.919	42.406	0.036	0.036	0.000	0.000	0.000	0.000
33	D	165	GLY	0	-0.014	0.003	45.200	0.002	0.002	0.000	0.000	0.000	0.000
34	D	166	GLY	0	0.003	0.020	44.686	0.001	0.001	0.000	0.000	0.000	0.000
35	D	167	LYS	1	0.900	0.947	43.358	0.032	0.032	0.000	0.000	0.000	0.000
36	D	168	VAL	0	0.017	0.010	36.952	0.002	0.002	0.000	0.000	0.000	0.000
37	D	169	GLU	-1	-0.937	-0.974	38.426	-0.027	-0.027	0.000	0.000	0.000	0.000
38	D	170	GLU	-1	-0.775	-0.910	37.694	-0.051	-0.051	0.000	0.000	0.000	0.000
39	D	171	LYS	1	0.946	0.990	35.324	0.025	0.025	0.000	0.000	0.000	0.000
40	D	172	ASN	0	-0.023	-0.013	33.785	-0.002	-0.002	0.000	0.000	0.000	0.000
41	D	173	LEU	0	-0.010	0.002	32.586	-0.004	-0.004	0.000	0.000	0.000	0.000
42	D	174	GLU	-1	-0.929	-0.972	31.903	-0.058	-0.058	0.000	0.000	0.000	0.000
43	D	175	ASN	0	-0.045	-0.037	29.958	-0.001	-0.001	0.000	0.000	0.000	0.000
44	D	176	LEU	0	-0.012	0.001	27.656	-0.003	-0.003	0.000	0.000	0.000	0.000
45	D	177	MET	0	0.015	0.014	26.958	-0.012	-0.012	0.000	0.000	0.000	0.000
46	D	178	GLU	-1	-0.929	-0.964	23.990	-0.095	-0.095	0.000	0.000	0.000	0.000
47	D	179	MET	0	0.001	0.000	23.420	-0.009	-0.009	0.000	0.000	0.000	0.000
48	D	180	LEU	0	-0.023	-0.012	22.025	-0.015	-0.015	0.000	0.000	0.000	0.000
49	D	181	MET	0	0.047	0.017	21.498	-0.023	-0.023	0.000	0.000	0.000	0.000
50	D	182	ASN	0	-0.019	-0.001	18.795	-0.036	-0.036	0.000	0.000	0.000	0.000
51	D	183	GLN	0	0.016	-0.020	17.101	-0.038	-0.038	0.000	0.000	0.000	0.000
52	D	184	LEU	0	0.035	0.019	16.555	-0.039	-0.039	0.000	0.000	0.000	0.000
53	D	185	VAL	0	0.016	0.019	16.865	-0.036	-0.036	0.000	0.000	0.000	0.000
54	D	186	LYS	1	0.841	0.929	13.653	0.071	0.071	0.000	0.000	0.000	0.000
55	D	187	LEU	0	-0.038	-0.014	12.167	-0.088	-0.088	0.000	0.000	0.000	0.000
56	D	188	ASP	-1	-0.896	-0.932	11.896	-0.493	-0.493	0.000	0.000	0.000	0.000
57	D	189	ALA	0	-0.076	-0.032	11.466	-0.059	-0.059	0.000	0.000	0.000	0.000
58	D	190	ILE	0	-0.111	-0.050	6.967	-0.189	-0.189	0.000	0.000	0.000	0.000
59	D	191	SER	0	-0.032	-0.009	6.433	-0.040	-0.040	0.000	0.000	0.000	0.000
60	D	192	GLY	0	0.032	-0.015	6.430	-0.595	-0.595	0.000	0.000	0.000	0.000
61	D	193	ASP	-1	-0.964	-0.970	7.613	-0.681	-0.681	0.000	0.000	0.000	0.000
62	D	194	GLY	0	0.048	0.020	9.530	-0.042	-0.042	0.000	0.000	0.000	0.000
63	D	195	ASP	-1	-0.855	-0.955	12.262	-0.481	-0.481	0.000	0.000	0.000	0.000
64	D	196	VAL	0	0.043	0.039	7.468	0.044	0.044	0.000	0.000	0.000	0.000
65	D	197	LYS	1	0.960	0.958	10.720	0.486	0.486	0.000	0.000	0.000	0.000
66	D	198	LEU	0	-0.045	-0.021	12.826	0.083	0.083	0.000	0.000	0.000	0.000
67	D	199	LYS	1	0.932	0.953	13.447	0.393	0.393	0.000	0.000	0.000	0.000
68	D	200	LYS	1	1.004	1.014	12.326	0.670	0.670	0.000	0.000	0.000	0.000
69	D	201	LYS	1	0.979	0.996	14.433	0.310	0.310	0.000	0.000	0.000	0.000
70	D	202	MET	0	-0.023	0.003	17.525	0.033	0.033	0.000	0.000	0.000	0.000
71	D	203	GLN	0	-0.017	-0.018	16.374	0.061	0.061	0.000	0.000	0.000	0.000
72	D	204	GLU	-1	-0.848	-0.952	17.034	-0.327	-0.327	0.000	0.000	0.000	0.000
73	D	205	GLU	-1	-0.943	-0.943	19.309	-0.176	-0.176	0.000	0.000	0.000	0.000
74	D	206	ARG	1	0.883	0.945	21.705	0.174	0.174	0.000	0.000	0.000	0.000
75	D	207	LEU	0	-0.001	-0.014	18.923	0.021	0.021	0.000	0.000	0.000	0.000
76	D	208	HIS	0	0.018	0.017	21.641	0.024	0.024	0.000	0.000	0.000	0.000
77	D	209	LYS	1	0.997	1.007	25.058	0.121	0.121	0.000	0.000	0.000	0.000
78	D	210	TYR	0	-0.068	-0.051	24.214	0.011	0.011	0.000	0.000	0.000	0.000
79	D	211	VAL	0	0.029	0.015	25.133	0.011	0.011	0.000	0.000	0.000	0.000
80	D	212	GLU	-1	-0.874	-0.930	28.017	-0.117	-0.117	0.000	0.000	0.000	0.000
81	D	213	ALA	0	-0.048	-0.020	30.598	0.008	0.008	0.000	0.000	0.000	0.000
82	D	214	LEU	0	-0.015	-0.016	29.478	0.008	0.008	0.000	0.000	0.000	0.000
83	D	215	ASP	-1	-0.859	-0.938	31.701	-0.088	-0.088	0.000	0.000	0.000	0.000
84	D	216	LEU	0	-0.050	-0.035	33.965	0.006	0.006	0.000	0.000	0.000	0.000
85	D	217	LEU	0	-0.051	-0.016	34.361	0.006	0.006	0.000	0.000	0.000	0.000
86	D	218	LYS	1	0.976	0.981	33.600	0.073	0.073	0.000	0.000	0.000	0.000
87	D	219	ILE	0	-0.021	0.007	37.559	0.004	0.004	0.000	0.000	0.000	0.000
88	D	220	LYS	1	0.901	0.953	40.095	0.048	0.048	0.000	0.000	0.000	0.000
89	D	221	ASN	0	-0.028	-0.011	39.965	0.005	0.005	0.000	0.000	0.000	0.000
90	D	222	SER	0	-0.035	-0.012	40.936	0.002	0.002	0.000	0.000	0.000	0.000

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Overview

Highlights

Manual

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