FMO DATABASE

FMODB ID: K3413

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1058762.398603
FMO2-HF: Nuclear repulsion	1009466.747428
FMO2-HF: Total energy	-49295.651175
FMO2-MP2: Total energy	-49440.636975

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.
-139.972	-143.89	34.441	-16.919	-13.603	0.152

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 : -0.794 / q_NPA : -0.890

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	0.003	-0.008	2.032	-27.371	-22.539	5.623	-5.124	-5.331	0.052
4	B	10	THR	0	-0.035	-0.052	1.599	-47.643	-57.835	28.760	-11.433	-7.135	0.096
5	B	11	GLN	0	-0.060	-0.014	3.651	-18.912	-18.094	0.055	-0.257	-0.616	0.004
6	B	12	LEU	0	-0.031	-0.010	6.162	-6.539	-6.539	0.000	0.000	0.000	0.000
7	B	13	SER	0	-0.058	-0.026	7.505	-4.458	-4.458	0.000	0.000	0.000	0.000
8	B	14	LEU	0	-0.018	0.000	7.040	-3.897	-3.897	0.000	0.000	0.000	0.000
9	B	15	PRO	0	0.017	0.020	9.636	0.500	0.500	0.000	0.000	0.000	0.000
10	B	16	PRO	0	0.034	-0.009	11.919	0.969	0.969	0.000	0.000	0.000	0.000
11	B	17	GLY	0	-0.024	-0.010	12.563	-1.607	-1.607	0.000	0.000	0.000	0.000
12	B	18	PHE	0	-0.032	0.003	11.781	-1.485	-1.485	0.000	0.000	0.000	0.000
13	B	19	ARG	1	0.828	0.877	10.624	-23.364	-23.364	0.000	0.000	0.000	0.000
14	B	20	PHE	0	0.021	0.004	10.021	-0.751	-0.751	0.000	0.000	0.000	0.000
15	B	21	TYR	0	-0.034	-0.015	11.966	-0.681	-0.681	0.000	0.000	0.000	0.000
16	B	22	PRO	0	-0.003	0.022	14.213	-1.080	-1.080	0.000	0.000	0.000	0.000
17	B	23	THR	0	0.002	-0.042	17.027	-0.774	-0.774	0.000	0.000	0.000	0.000
18	B	24	ASP	-1	-0.792	-0.871	20.837	13.639	13.639	0.000	0.000	0.000	0.000
19	B	25	GLU	-1	-0.803	-0.926	22.788	12.439	12.439	0.000	0.000	0.000	0.000
20	B	26	GLU	-1	-0.794	-0.865	18.948	16.735	16.735	0.000	0.000	0.000	0.000
21	B	27	LEU	0	-0.041	-0.016	16.567	0.343	0.343	0.000	0.000	0.000	0.000
22	B	28	MET	0	-0.061	0.037	19.697	0.050	0.050	0.000	0.000	0.000	0.000
23	B	29	VAL	0	0.025	0.015	23.047	-0.072	-0.072	0.000	0.000	0.000	0.000
24	B	30	GLN	0	0.021	0.005	18.674	0.156	0.156	0.000	0.000	0.000	0.000
25	B	31	TYR	0	-0.028	-0.018	12.793	0.347	0.347	0.000	0.000	0.000	0.000
26	B	32	LEU	0	-0.001	-0.002	18.610	-0.114	-0.114	0.000	0.000	0.000	0.000
27	B	33	CYS	0	-0.067	-0.038	21.402	-0.481	-0.481	0.000	0.000	0.000	0.000
28	B	34	ARG	1	0.866	0.949	18.129	-17.703	-17.703	0.000	0.000	0.000	0.000
29	B	35	LYN	0	0.042	0.069	18.358	0.113	0.113	0.000	0.000	0.000	0.000
30	B	36	ALA	0	-0.056	-0.012	20.665	-0.179	-0.179	0.000	0.000	0.000	0.000
31	B	37	ALA	0	-0.011	-0.011	23.422	-0.178	-0.178	0.000	0.000	0.000	0.000
32	B	38	GLY	0	0.026	-0.035	20.300	0.036	0.036	0.000	0.000	0.000	0.000
33	B	39	TYR	0	-0.083	-0.043	18.161	0.840	0.840	0.000	0.000	0.000	0.000
34	B	40	ASP	-1	-0.831	-0.922	15.926	17.931	17.931	0.000	0.000	0.000	0.000
35	B	41	PHE	0	-0.026	0.003	13.152	-0.405	-0.405	0.000	0.000	0.000	0.000
36	B	42	SER	0	-0.053	-0.031	13.206	0.916	0.916	0.000	0.000	0.000	0.000
37	B	43	LEU	0	0.024	0.012	8.355	0.824	0.824	0.000	0.000	0.000	0.000
38	B	44	GLN	0	-0.004	0.004	9.606	-0.331	-0.331	0.000	0.000	0.000	0.000
39	B	45	LEU	0	0.020	0.003	6.789	1.348	1.348	0.000	0.000	0.000	0.000
40	B	46	ILE	0	-0.062	-0.027	8.550	1.715	1.715	0.000	0.000	0.000	0.000
41	B	47	ALA	0	0.074	0.039	10.382	-1.081	-1.081	0.000	0.000	0.000	0.000
42	B	48	GLU	-1	-0.914	-0.955	12.235	15.801	15.801	0.000	0.000	0.000	0.000
43	B	49	ILE	0	-0.035	-0.028	14.411	0.530	0.530	0.000	0.000	0.000	0.000
44	B	50	ASP	-1	-0.802	-0.893	16.868	12.312	12.312	0.000	0.000	0.000	0.000
45	B	51	LEU	0	0.007	-0.007	17.860	-0.225	-0.225	0.000	0.000	0.000	0.000
46	B	52	TYR	0	-0.021	-0.034	20.285	-0.236	-0.236	0.000	0.000	0.000	0.000
47	B	53	LYS	1	0.855	0.950	21.276	-13.719	-13.719	0.000	0.000	0.000	0.000
48	B	54	PHE	0	-0.013	-0.015	17.990	0.184	0.184	0.000	0.000	0.000	0.000
49	B	55	ASP	-1	-0.757	-0.836	21.743	11.866	11.866	0.000	0.000	0.000	0.000
50	B	56	PRO	0	-0.033	-0.036	20.662	0.755	0.755	0.000	0.000	0.000	0.000
51	B	57	TRP	0	-0.013	-0.015	18.862	0.991	0.991	0.000	0.000	0.000	0.000
52	B	58	VAL	0	0.009	0.011	16.634	0.543	0.543	0.000	0.000	0.000	0.000
53	B	59	LEU	0	-0.002	0.008	14.930	1.183	1.183	0.000	0.000	0.000	0.000
54	B	60	PRO	0	0.011	0.009	12.413	1.395	1.395	0.000	0.000	0.000	0.000
55	B	61	ASN	0	-0.016	-0.006	10.527	3.061	3.061	0.000	0.000	0.000	0.000
56	B	62	LYS	1	0.875	0.928	9.640	-23.350	-23.350	0.000	0.000	0.000	0.000
57	B	63	ALA	0	0.009	0.031	9.617	-0.375	-0.375	0.000	0.000	0.000	0.000
58	B	64	LEU	0	-0.025	-0.004	5.211	1.449	1.449	0.000	0.000	0.000	0.000
59	B	65	PHE	0	0.001	0.003	3.890	9.975	10.595	0.004	-0.105	-0.518	0.000
60	B	66	GLY	0	0.041	0.019	5.426	-7.165	-7.161	-0.001	0.000	-0.003	0.000
61	B	67	GLU	-1	-0.874	-0.894	8.128	28.984	28.984	0.000	0.000	0.000	0.000
62	B	68	LYS	1	0.947	0.944	10.394	-21.714	-21.714	0.000	0.000	0.000	0.000
63	B	69	GLU	-1	-0.857	-0.899	12.457	18.736	18.736	0.000	0.000	0.000	0.000
64	B	70	TRP	0	-0.017	-0.012	9.986	0.053	0.053	0.000	0.000	0.000	0.000
65	B	71	TYR	0	0.014	-0.028	11.898	-2.500	-2.500	0.000	0.000	0.000	0.000
66	B	72	PHE	0	-0.025	-0.013	12.342	1.376	1.376	0.000	0.000	0.000	0.000
67	B	73	PHE	0	0.086	0.043	15.275	-1.159	-1.159	0.000	0.000	0.000	0.000
68	B	74	SER	0	-0.006	-0.006	17.404	-0.173	-0.173	0.000	0.000	0.000	0.000
69	B	87	ASN	0	-0.021	-0.030	32.199	0.202	0.202	0.000	0.000	0.000	0.000
70	B	88	ARG	1	0.918	0.976	24.807	-12.127	-12.127	0.000	0.000	0.000	0.000
71	B	89	VAL	0	0.080	0.042	27.921	0.234	0.234	0.000	0.000	0.000	0.000
72	B	90	ALA	0	-0.074	-0.017	25.081	0.373	0.373	0.000	0.000	0.000	0.000
73	B	91	GLY	0	0.061	0.036	25.143	0.102	0.102	0.000	0.000	0.000	0.000
74	B	92	SER	0	-0.063	-0.060	25.985	-0.555	-0.555	0.000	0.000	0.000	0.000
75	B	93	GLY	0	0.011	-0.007	27.838	-0.429	-0.429	0.000	0.000	0.000	0.000
76	B	94	TYR	0	-0.045	-0.034	28.941	-0.012	-0.012	0.000	0.000	0.000	0.000
77	B	95	TRP	0	0.036	0.002	21.895	0.013	0.013	0.000	0.000	0.000	0.000
78	B	96	LYS	1	0.888	0.927	28.457	-9.843	-9.843	0.000	0.000	0.000	0.000
79	B	97	ALA	0	0.071	0.036	30.011	0.249	0.249	0.000	0.000	0.000	0.000
80	B	98	THR	0	-0.072	-0.049	30.426	-0.567	-0.567	0.000	0.000	0.000	0.000
81	B	99	GLY	0	0.032	0.030	30.604	0.351	0.351	0.000	0.000	0.000	0.000
82	B	100	THR	0	-0.051	-0.043	32.265	-0.384	-0.384	0.000	0.000	0.000	0.000
83	B	101	ASP	-1	-0.820	-0.904	29.825	10.752	10.752	0.000	0.000	0.000	0.000
84	B	102	LYS	1	0.831	0.926	26.895	-12.045	-12.045	0.000	0.000	0.000	0.000
85	B	103	ILE	0	0.005	-0.011	30.027	0.319	0.319	0.000	0.000	0.000	0.000
86	B	104	ILE	0	-0.029	0.002	26.001	-0.035	-0.035	0.000	0.000	0.000	0.000
87	B	105	SER	0	-0.051	-0.038	29.373	-0.302	-0.302	0.000	0.000	0.000	0.000
88	B	106	THR	0	0.027	0.005	27.610	0.420	0.420	0.000	0.000	0.000	0.000
89	B	107	GLU	-1	-0.866	-0.927	29.612	10.151	10.151	0.000	0.000	0.000	0.000
90	B	108	GLY	0	-0.016	0.002	32.130	-0.332	-0.332	0.000	0.000	0.000	0.000
91	B	109	GLN	0	-0.081	-0.051	33.245	-0.436	-0.436	0.000	0.000	0.000	0.000
92	B	110	ARG	1	0.963	0.970	32.067	-8.331	-8.331	0.000	0.000	0.000	0.000
93	B	111	VAL	0	0.071	0.048	28.015	-0.040	-0.040	0.000	0.000	0.000	0.000
94	B	112	GLY	0	-0.026	-0.060	25.949	0.047	0.047	0.000	0.000	0.000	0.000
95	B	113	ILE	0	0.039	0.018	26.628	0.086	0.086	0.000	0.000	0.000	0.000
96	B	114	LYS	1	0.842	0.877	23.483	-12.754	-12.754	0.000	0.000	0.000	0.000
97	B	115	LYS	1	0.843	0.935	25.923	-11.493	-11.493	0.000	0.000	0.000	0.000
98	B	116	ALA	0	0.004	0.019	25.706	0.621	0.621	0.000	0.000	0.000	0.000
99	B	117	LEU	0	-0.009	-0.001	25.283	-0.619	-0.619	0.000	0.000	0.000	0.000
100	B	118	VAL	0	-0.008	-0.001	25.960	0.398	0.398	0.000	0.000	0.000	0.000
101	B	119	PHE	0	0.009	0.010	25.405	-0.465	-0.465	0.000	0.000	0.000	0.000
102	B	129	LYS	1	0.961	0.987	30.917	-10.123	-10.123	0.000	0.000	0.000	0.000
103	B	130	THR	0	-0.015	-0.016	26.103	0.237	0.237	0.000	0.000	0.000	0.000
104	B	131	ASN	0	-0.008	-0.012	23.922	-0.123	-0.123	0.000	0.000	0.000	0.000
105	B	132	TRP	0	0.070	0.037	17.786	0.639	0.639	0.000	0.000	0.000	0.000
106	B	133	ILE	0	-0.006	-0.004	22.017	-0.661	-0.661	0.000	0.000	0.000	0.000
107	B	134	MET	0	0.017	0.022	21.000	1.015	1.015	0.000	0.000	0.000	0.000
108	B	135	HIS	0	-0.084	-0.044	20.750	-0.238	-0.238	0.000	0.000	0.000	0.000
109	B	136	GLU	-1	-0.813	-0.909	21.198	12.609	12.609	0.000	0.000	0.000	0.000
110	B	137	TYR	0	0.026	0.003	20.404	-0.193	-0.193	0.000	0.000	0.000	0.000
111	B	154	TRP	0	-0.041	-0.019	19.842	-0.085	-0.085	0.000	0.000	0.000	0.000
112	B	155	VAL	0	0.028	0.020	22.213	-0.201	-0.201	0.000	0.000	0.000	0.000
113	B	156	LEU	0	0.022	0.011	16.318	0.732	0.732	0.000	0.000	0.000	0.000
114	B	157	CYS	0	-0.031	-0.033	18.323	-0.917	-0.917	0.000	0.000	0.000	0.000
115	B	158	ARG	1	0.847	0.941	16.115	-16.270	-16.270	0.000	0.000	0.000	0.000
116	B	159	ILE	0	-0.006	-0.002	16.264	-1.414	-1.414	0.000	0.000	0.000	0.000
117	B	160	TYR	0	0.062	0.024	16.111	0.940	0.940	0.000	0.000	0.000	0.000
118	B	161	LYS	1	0.933	0.980	17.998	-15.327	-15.327	0.000	0.000	0.000	0.000
119	B	162	LYS	1	0.865	0.939	20.246	-13.304	-13.304	0.000	0.000	0.000	0.000
120	B	163	GLN	0	0.020	0.010	23.186	0.790	0.790	0.000	0.000	0.000	0.000

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