FMO DATABASE

FMODB ID: Q129Y

Calculation Name: 4DUL-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4DUL

Chain ID: B

ChEMBL ID:

UniProt ID: Q9C932

Base Structure: X-ray

Registration Date: 2023-06-20

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	120
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1057374.633195
FMO2-HF: Nuclear repulsion	1008080.356668
FMO2-HF: Total energy	-49294.276527
FMO2-MP2: Total energy	-49439.345299

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(B:7:ASP)

Summations of interaction energy for fragment #1(B:7:ASP)

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.
-100.861	-89.772	4.71	-7.093	-8.704	0.064

Interaction energy analysis for fragmet #1(B:7:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.895 / q_NPA : -0.972

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	B	9	LEU	0	0.009	-0.003	2.407	-24.329	-17.790	1.343	-3.887	-3.994	0.040
4	B	10	THR	0	0.000	0.004	2.059	-25.434	-22.038	3.355	-2.955	-3.797	0.023
5	B	11	GLN	0	-0.016	-0.005	4.656	-10.270	-9.948	0.000	-0.062	-0.259	0.000
6	B	12	LEU	0	-0.036	-0.008	6.828	-4.982	-4.982	0.000	0.000	0.000	0.000
7	B	13	SER	0	-0.042	-0.022	8.602	-3.698	-3.698	0.000	0.000	0.000	0.000
8	B	14	LEU	0	-0.018	0.000	7.780	-3.123	-3.123	0.000	0.000	0.000	0.000
9	B	15	PRO	0	0.004	0.015	10.354	0.543	0.543	0.000	0.000	0.000	0.000
10	B	16	PRO	0	0.047	-0.007	12.342	1.014	1.014	0.000	0.000	0.000	0.000
11	B	17	GLY	0	-0.023	-0.005	12.673	-1.537	-1.537	0.000	0.000	0.000	0.000
12	B	18	PHE	0	-0.024	0.007	12.222	-1.382	-1.382	0.000	0.000	0.000	0.000
13	B	19	ARG	1	0.880	0.906	10.778	-23.346	-23.346	0.000	0.000	0.000	0.000
14	B	20	PHE	0	0.008	0.004	10.137	-0.885	-0.885	0.000	0.000	0.000	0.000
15	B	21	TYR	0	-0.038	-0.014	12.070	-0.559	-0.559	0.000	0.000	0.000	0.000
16	B	22	PRO	0	-0.001	0.019	14.245	-1.101	-1.101	0.000	0.000	0.000	0.000
17	B	23	THR	0	0.013	-0.020	17.103	-0.639	-0.639	0.000	0.000	0.000	0.000
18	B	24	ASP	-1	-0.873	-0.965	20.901	13.812	13.812	0.000	0.000	0.000	0.000
19	B	25	GLU	-1	-0.868	-0.942	22.806	12.418	12.418	0.000	0.000	0.000	0.000
20	B	26	GLU	-1	-0.815	-0.893	19.071	16.461	16.461	0.000	0.000	0.000	0.000
21	B	27	LEU	0	-0.047	-0.021	16.632	0.344	0.344	0.000	0.000	0.000	0.000
22	B	28	MET	0	-0.066	0.058	19.731	0.115	0.115	0.000	0.000	0.000	0.000
23	B	29	VAL	0	0.021	-0.001	23.078	-0.060	-0.060	0.000	0.000	0.000	0.000
24	B	30	GLN	0	0.011	0.003	18.886	0.210	0.210	0.000	0.000	0.000	0.000
25	B	31	TYR	0	-0.018	-0.008	13.145	0.474	0.474	0.000	0.000	0.000	0.000
26	B	32	LEU	0	-0.007	-0.003	18.660	-0.140	-0.140	0.000	0.000	0.000	0.000
27	B	33	CYS	0	-0.069	-0.026	21.401	-0.494	-0.494	0.000	0.000	0.000	0.000
28	B	34	ARG	1	0.897	0.970	18.470	-17.136	-17.136	0.000	0.000	0.000	0.000
29	B	35	LYN	0	0.070	0.086	18.423	0.069	0.069	0.000	0.000	0.000	0.000
30	B	36	ALA	0	-0.051	-0.012	20.702	-0.178	-0.178	0.000	0.000	0.000	0.000
31	B	37	ALA	0	-0.009	-0.012	23.453	-0.200	-0.200	0.000	0.000	0.000	0.000
32	B	38	GLY	0	-0.004	-0.045	20.341	0.011	0.011	0.000	0.000	0.000	0.000
33	B	39	TYR	0	-0.064	-0.038	18.204	0.819	0.819	0.000	0.000	0.000	0.000
34	B	40	ASP	-1	-0.865	-0.938	16.026	17.766	17.766	0.000	0.000	0.000	0.000
35	B	41	PHE	0	-0.035	-0.010	13.317	-0.363	-0.363	0.000	0.000	0.000	0.000
36	B	42	SER	0	-0.058	-0.033	13.253	0.892	0.892	0.000	0.000	0.000	0.000
37	B	43	LEU	0	0.022	0.006	8.248	0.662	0.662	0.000	0.000	0.000	0.000
38	B	44	GLN	0	-0.003	0.011	9.502	-0.546	-0.546	0.000	0.000	0.000	0.000
39	B	45	LEU	0	0.028	0.003	7.183	1.512	1.512	0.000	0.000	0.000	0.000
40	B	46	ILE	0	-0.052	-0.018	8.529	2.011	2.011	0.000	0.000	0.000	0.000
41	B	47	ALA	0	0.061	0.030	10.456	-1.204	-1.204	0.000	0.000	0.000	0.000
42	B	48	GLU	-1	-0.918	-0.959	12.263	15.947	15.947	0.000	0.000	0.000	0.000
43	B	49	ILE	0	-0.031	-0.026	14.409	0.599	0.599	0.000	0.000	0.000	0.000
44	B	50	ASP	-1	-0.829	-0.902	16.886	12.653	12.653	0.000	0.000	0.000	0.000
45	B	51	LEU	0	0.002	-0.017	17.658	-0.259	-0.259	0.000	0.000	0.000	0.000
46	B	52	TYR	0	-0.047	-0.043	20.292	-0.270	-0.270	0.000	0.000	0.000	0.000
47	B	53	LYS	1	0.860	0.948	21.167	-14.119	-14.119	0.000	0.000	0.000	0.000
48	B	54	PHE	0	-0.011	-0.014	18.098	0.176	0.176	0.000	0.000	0.000	0.000
49	B	55	ASP	-1	-0.731	-0.826	21.740	12.139	12.139	0.000	0.000	0.000	0.000
50	B	56	PRO	0	-0.037	-0.041	20.382	0.865	0.865	0.000	0.000	0.000	0.000
51	B	57	TRP	0	0.002	-0.009	18.526	1.016	1.016	0.000	0.000	0.000	0.000
52	B	58	VAL	0	0.012	0.012	16.769	0.552	0.552	0.000	0.000	0.000	0.000
53	B	59	LEU	0	-0.013	0.006	14.913	1.214	1.214	0.000	0.000	0.000	0.000
54	B	60	PRO	0	0.006	0.010	12.090	1.449	1.449	0.000	0.000	0.000	0.000
55	B	61	ASN	0	-0.011	-0.007	10.311	3.229	3.229	0.000	0.000	0.000	0.000
56	B	62	LYS	1	0.908	0.945	9.625	-22.591	-22.591	0.000	0.000	0.000	0.000
57	B	63	ALA	0	-0.016	0.018	9.321	-0.622	-0.622	0.000	0.000	0.000	0.000
58	B	64	LEU	0	-0.044	-0.008	5.293	1.673	1.673	0.000	0.000	0.000	0.000
59	B	65	PHE	0	0.025	0.010	3.669	11.066	11.905	0.013	-0.188	-0.664	0.001
60	B	66	GLY	0	0.038	0.020	5.169	-8.455	-8.462	-0.001	-0.001	0.010	0.000
61	B	67	GLU	-1	-0.911	-0.926	7.935	31.249	31.249	0.000	0.000	0.000	0.000
62	B	68	LYS	1	0.935	0.939	10.209	-22.313	-22.313	0.000	0.000	0.000	0.000
63	B	69	GLU	-1	-0.906	-0.948	12.274	19.649	19.649	0.000	0.000	0.000	0.000
64	B	70	TRP	0	-0.031	-0.023	9.556	-0.226	-0.226	0.000	0.000	0.000	0.000
65	B	71	TYR	0	0.038	0.025	11.714	-3.008	-3.008	0.000	0.000	0.000	0.000
66	B	72	PHE	0	-0.013	-0.012	12.111	1.374	1.374	0.000	0.000	0.000	0.000
67	B	73	PHE	0	0.082	0.039	15.218	-1.253	-1.253	0.000	0.000	0.000	0.000
68	B	74	SER	0	-0.002	-0.006	17.426	-0.233	-0.233	0.000	0.000	0.000	0.000
69	B	87	ASN	0	-0.002	-0.023	31.950	0.139	0.139	0.000	0.000	0.000	0.000
70	B	88	ARG	1	0.926	0.993	25.356	-12.234	-12.234	0.000	0.000	0.000	0.000
71	B	89	VAL	0	0.104	0.056	27.812	0.237	0.237	0.000	0.000	0.000	0.000
72	B	90	ALA	0	-0.041	-0.042	24.218	0.397	0.397	0.000	0.000	0.000	0.000
73	B	91	GLY	0	0.026	0.053	25.008	-0.015	-0.015	0.000	0.000	0.000	0.000
74	B	92	SER	0	-0.060	-0.072	25.843	-0.488	-0.488	0.000	0.000	0.000	0.000
75	B	93	GLY	0	-0.035	-0.035	27.835	-0.441	-0.441	0.000	0.000	0.000	0.000
76	B	94	TYR	0	-0.084	-0.041	28.707	-0.077	-0.077	0.000	0.000	0.000	0.000
77	B	95	TRP	0	0.032	0.009	21.717	0.105	0.105	0.000	0.000	0.000	0.000
78	B	96	LYS	1	0.896	0.936	28.183	-10.023	-10.023	0.000	0.000	0.000	0.000
79	B	97	ALA	0	0.050	0.028	29.734	0.269	0.269	0.000	0.000	0.000	0.000
80	B	98	THR	0	-0.054	-0.047	30.310	-0.578	-0.578	0.000	0.000	0.000	0.000
81	B	99	GLY	0	0.024	0.033	30.615	0.340	0.340	0.000	0.000	0.000	0.000
82	B	100	THR	0	-0.027	-0.036	32.081	-0.373	-0.373	0.000	0.000	0.000	0.000
83	B	101	ASP	-1	-0.815	-0.851	29.791	11.062	11.062	0.000	0.000	0.000	0.000
84	B	102	LYS	1	0.838	0.943	26.557	-12.221	-12.221	0.000	0.000	0.000	0.000
85	B	103	ILE	0	0.005	-0.009	29.983	0.323	0.323	0.000	0.000	0.000	0.000
86	B	104	ILE	0	0.036	0.024	26.015	-0.007	-0.007	0.000	0.000	0.000	0.000
87	B	105	SER	0	-0.046	-0.041	29.380	-0.316	-0.316	0.000	0.000	0.000	0.000
88	B	106	THR	0	0.027	0.009	27.671	0.389	0.389	0.000	0.000	0.000	0.000
89	B	107	GLU	-1	-0.873	-0.936	29.707	9.975	9.975	0.000	0.000	0.000	0.000
90	B	108	GLY	0	-0.026	0.000	32.260	-0.312	-0.312	0.000	0.000	0.000	0.000
91	B	109	GLN	0	-0.056	-0.035	33.356	-0.173	-0.173	0.000	0.000	0.000	0.000
92	B	110	ARG	1	0.942	0.962	32.138	-8.329	-8.329	0.000	0.000	0.000	0.000
93	B	111	VAL	0	0.003	-0.022	27.783	-0.039	-0.039	0.000	0.000	0.000	0.000
94	B	112	GLY	0	0.125	0.025	27.362	0.115	0.115	0.000	0.000	0.000	0.000
95	B	113	ILE	0	-0.037	-0.018	27.264	-0.190	-0.190	0.000	0.000	0.000	0.000
96	B	114	LYS	1	0.906	0.928	23.624	-12.744	-12.744	0.000	0.000	0.000	0.000
97	B	115	LYS	1	0.887	0.930	25.820	-11.457	-11.457	0.000	0.000	0.000	0.000
98	B	116	ALA	0	-0.009	0.008	25.554	0.692	0.692	0.000	0.000	0.000	0.000
99	B	117	LEU	0	-0.007	-0.001	25.433	-0.631	-0.631	0.000	0.000	0.000	0.000
100	B	118	VAL	0	-0.022	-0.004	25.738	0.395	0.395	0.000	0.000	0.000	0.000
101	B	119	PHE	0	0.020	0.020	25.070	-0.387	-0.387	0.000	0.000	0.000	0.000
102	B	129	LYS	1	1.001	1.005	30.638	-10.261	-10.261	0.000	0.000	0.000	0.000
103	B	130	THR	0	-0.023	-0.015	25.708	0.237	0.237	0.000	0.000	0.000	0.000
104	B	131	ASN	0	-0.024	-0.012	23.741	-0.261	-0.261	0.000	0.000	0.000	0.000
105	B	132	TRP	0	0.079	0.029	17.605	0.621	0.621	0.000	0.000	0.000	0.000
106	B	133	ILE	0	-0.004	0.001	21.781	-0.720	-0.720	0.000	0.000	0.000	0.000
107	B	134	MET	0	0.041	0.021	20.772	0.982	0.982	0.000	0.000	0.000	0.000
108	B	135	HIS	0	-0.098	-0.031	20.467	-0.212	-0.212	0.000	0.000	0.000	0.000
109	B	136	GLU	-1	-0.830	-0.930	21.043	13.030	13.030	0.000	0.000	0.000	0.000
110	B	137	TYR	0	0.014	0.003	20.735	-0.302	-0.302	0.000	0.000	0.000	0.000
111	B	154	TRP	0	-0.032	-0.015	20.122	-0.075	-0.075	0.000	0.000	0.000	0.000
112	B	155	VAL	0	0.026	0.021	22.236	-0.209	-0.209	0.000	0.000	0.000	0.000
113	B	156	LEU	0	0.023	0.010	15.942	0.738	0.738	0.000	0.000	0.000	0.000
114	B	157	CYS	0	-0.035	-0.034	18.191	-0.935	-0.935	0.000	0.000	0.000	0.000
115	B	158	ARG	1	0.884	0.948	16.339	-16.167	-16.167	0.000	0.000	0.000	0.000
116	B	159	ILE	0	-0.029	-0.012	16.067	-1.430	-1.430	0.000	0.000	0.000	0.000
117	B	160	TYR	0	0.033	0.008	15.897	1.025	1.025	0.000	0.000	0.000	0.000
118	B	161	LYS	1	0.961	0.997	17.773	-16.357	-16.357	0.000	0.000	0.000	0.000
119	B	162	LYS	1	0.910	0.950	19.996	-13.372	-13.372	0.000	0.000	0.000	0.000
120	B	163	GLN	0	-0.006	0.002	22.968	0.376	0.376	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:7:ASP)