FMO DATABASE

FMODB ID: 431MN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1059249.68226
FMO2-HF: Nuclear repulsion	1009952.876686
FMO2-HF: Total energy	-49296.805574
FMO2-MP2: Total energy	-49441.653038

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.
-148.816	-164.264	51.388	-20.729	-15.211	0.178

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 : -0.768 / q_NPA : -0.860

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	-0.015	-0.022	1.851	-28.226	-27.110	12.080	-6.723	-6.473	0.060
4	B	10	THR	0	-0.046	-0.068	1.585	-50.443	-68.670	39.250	-13.617	-7.406	0.113
5	B	11	GLN	0	-0.044	-0.017	3.553	-20.989	-19.979	0.055	-0.262	-0.803	0.005
6	B	12	LEU	0	-0.030	-0.016	5.751	-7.365	-7.365	0.000	0.000	0.000	0.000
7	B	13	SER	0	-0.058	-0.023	6.811	-4.972	-4.972	0.000	0.000	0.000	0.000
8	B	14	LEU	0	-0.027	-0.003	6.783	-4.596	-4.596	0.000	0.000	0.000	0.000
9	B	15	PRO	0	0.020	0.016	9.224	0.419	0.419	0.000	0.000	0.000	0.000
10	B	16	PRO	0	0.000	-0.018	11.925	0.730	0.730	0.000	0.000	0.000	0.000
11	B	17	GLY	0	0.000	0.006	12.255	-2.005	-2.005	0.000	0.000	0.000	0.000
12	B	18	PHE	0	-0.030	-0.007	11.510	-0.865	-0.865	0.000	0.000	0.000	0.000
13	B	19	ARG	1	0.810	0.857	10.160	-23.877	-23.877	0.000	0.000	0.000	0.000
14	B	20	PHE	0	-0.005	0.003	9.545	-1.407	-1.407	0.000	0.000	0.000	0.000
15	B	21	TYR	0	-0.024	-0.014	11.462	-0.692	-0.692	0.000	0.000	0.000	0.000
16	B	22	PRO	0	-0.001	0.024	14.090	-1.009	-1.009	0.000	0.000	0.000	0.000
17	B	23	THR	0	0.003	-0.039	17.019	-0.715	-0.715	0.000	0.000	0.000	0.000
18	B	24	ASP	-1	-0.766	-0.846	20.291	13.924	13.924	0.000	0.000	0.000	0.000
19	B	25	GLU	-1	-0.741	-0.878	22.523	12.639	12.639	0.000	0.000	0.000	0.000
20	B	26	GLU	-1	-0.822	-0.880	18.633	16.808	16.808	0.000	0.000	0.000	0.000
21	B	27	LEU	0	-0.023	-0.004	16.240	0.380	0.380	0.000	0.000	0.000	0.000
22	B	28	MET	0	-0.064	0.015	19.670	-0.282	-0.282	0.000	0.000	0.000	0.000
23	B	29	VAL	0	0.032	0.023	22.820	0.014	0.014	0.000	0.000	0.000	0.000
24	B	30	GLN	0	0.020	0.001	18.285	0.136	0.136	0.000	0.000	0.000	0.000
25	B	31	TYR	0	-0.029	-0.016	13.168	1.370	1.370	0.000	0.000	0.000	0.000
26	B	32	LEU	0	-0.006	-0.003	18.353	-0.096	-0.096	0.000	0.000	0.000	0.000
27	B	33	CYS	0	-0.075	-0.047	21.236	-0.512	-0.512	0.000	0.000	0.000	0.000
28	B	34	ARG	1	0.864	0.933	17.699	-18.023	-18.023	0.000	0.000	0.000	0.000
29	B	35	LYN	0	0.018	0.017	18.239	0.023	0.023	0.000	0.000	0.000	0.000
30	B	36	ALA	0	-0.035	-0.005	20.422	-0.246	-0.246	0.000	0.000	0.000	0.000
31	B	37	ALA	0	0.005	-0.006	23.817	-0.061	-0.061	0.000	0.000	0.000	0.000
32	B	38	GLY	0	-0.013	0.009	20.458	0.011	0.011	0.000	0.000	0.000	0.000
33	B	39	TYR	0	-0.026	-0.027	18.408	0.933	0.933	0.000	0.000	0.000	0.000
34	B	40	ASP	-1	-0.848	-0.918	16.455	17.545	17.545	0.000	0.000	0.000	0.000
35	B	41	PHE	0	-0.028	-0.013	13.142	0.026	0.026	0.000	0.000	0.000	0.000
36	B	42	SER	0	-0.033	-0.031	12.728	1.276	1.276	0.000	0.000	0.000	0.000
37	B	43	LEU	0	0.017	0.017	7.880	1.138	1.138	0.000	0.000	0.000	0.000
38	B	44	GLN	0	0.012	0.013	9.314	-0.134	-0.134	0.000	0.000	0.000	0.000
39	B	45	LEU	0	-0.008	-0.005	6.287	2.051	2.051	0.000	0.000	0.000	0.000
40	B	46	ILE	0	-0.050	-0.022	8.086	1.293	1.293	0.000	0.000	0.000	0.000
41	B	47	ALA	0	0.063	0.027	10.406	-0.900	-0.900	0.000	0.000	0.000	0.000
42	B	48	GLU	-1	-0.919	-0.953	12.252	15.758	15.758	0.000	0.000	0.000	0.000
43	B	49	ILE	0	-0.024	-0.013	14.557	0.324	0.324	0.000	0.000	0.000	0.000
44	B	50	ASP	-1	-0.774	-0.864	16.903	12.156	12.156	0.000	0.000	0.000	0.000
45	B	51	LEU	0	0.010	-0.012	17.276	-0.232	-0.232	0.000	0.000	0.000	0.000
46	B	52	TYR	0	-0.014	-0.018	19.877	-0.209	-0.209	0.000	0.000	0.000	0.000
47	B	53	LYS	1	0.865	0.945	21.437	-13.414	-13.414	0.000	0.000	0.000	0.000
48	B	54	PHE	0	0.005	0.000	18.285	0.080	0.080	0.000	0.000	0.000	0.000
49	B	55	ASP	-1	-0.771	-0.840	21.536	12.073	12.073	0.000	0.000	0.000	0.000
50	B	56	PRO	0	-0.015	-0.027	20.156	0.774	0.774	0.000	0.000	0.000	0.000
51	B	57	TRP	0	0.018	0.003	18.420	1.010	1.010	0.000	0.000	0.000	0.000
52	B	58	VAL	0	-0.015	-0.003	17.093	0.685	0.685	0.000	0.000	0.000	0.000
53	B	59	LEU	0	0.015	0.023	15.136	1.126	1.126	0.000	0.000	0.000	0.000
54	B	60	PRO	0	0.013	0.005	12.636	1.415	1.415	0.000	0.000	0.000	0.000
55	B	61	ASN	0	-0.043	-0.011	10.653	2.819	2.819	0.000	0.000	0.000	0.000
56	B	62	LYS	1	0.856	0.908	9.787	-24.012	-24.012	0.000	0.000	0.000	0.000
57	B	63	ALA	0	0.030	0.044	9.403	-0.710	-0.710	0.000	0.000	0.000	0.000
58	B	64	LEU	0	-0.014	-0.006	4.944	0.671	0.671	0.000	0.000	0.000	0.000
59	B	65	PHE	0	-0.007	0.003	3.822	10.357	11.002	0.004	-0.127	-0.522	0.000
60	B	66	GLY	0	0.050	0.019	5.618	-6.522	-6.514	-0.001	0.000	-0.007	0.000
61	B	67	GLU	-1	-0.842	-0.873	8.392	28.329	28.329	0.000	0.000	0.000	0.000
62	B	68	LYS	1	0.927	0.943	10.605	-22.120	-22.120	0.000	0.000	0.000	0.000
63	B	69	GLU	-1	-0.843	-0.896	12.750	18.529	18.529	0.000	0.000	0.000	0.000
64	B	70	TRP	0	-0.030	-0.005	10.045	0.196	0.196	0.000	0.000	0.000	0.000
65	B	71	TYR	0	0.002	-0.026	11.699	-2.472	-2.472	0.000	0.000	0.000	0.000
66	B	72	PHE	0	-0.022	-0.012	12.239	1.445	1.445	0.000	0.000	0.000	0.000
67	B	73	PHE	0	0.057	0.028	14.716	-0.993	-0.993	0.000	0.000	0.000	0.000
68	B	74	SER	0	0.022	0.009	17.066	-0.209	-0.209	0.000	0.000	0.000	0.000
69	B	87	ASN	0	-0.017	-0.026	31.686	0.192	0.192	0.000	0.000	0.000	0.000
70	B	88	ARG	1	0.850	0.919	24.475	-12.027	-12.027	0.000	0.000	0.000	0.000
71	B	89	VAL	0	0.046	0.011	27.709	0.194	0.194	0.000	0.000	0.000	0.000
72	B	90	ALA	0	-0.012	-0.014	24.533	0.334	0.334	0.000	0.000	0.000	0.000
73	B	91	GLY	0	0.024	0.021	24.775	0.076	0.076	0.000	0.000	0.000	0.000
74	B	92	SER	0	-0.060	-0.062	25.528	-0.540	-0.540	0.000	0.000	0.000	0.000
75	B	93	GLY	0	0.011	0.006	27.499	-0.429	-0.429	0.000	0.000	0.000	0.000
76	B	94	TYR	0	0.007	0.002	28.460	-0.073	-0.073	0.000	0.000	0.000	0.000
77	B	95	TRP	0	0.038	0.044	21.449	0.034	0.034	0.000	0.000	0.000	0.000
78	B	96	LYS	1	0.895	0.929	27.957	-9.831	-9.831	0.000	0.000	0.000	0.000
79	B	97	ALA	0	0.066	0.040	29.989	0.208	0.208	0.000	0.000	0.000	0.000
80	B	98	THR	0	-0.070	-0.049	30.277	-0.579	-0.579	0.000	0.000	0.000	0.000
81	B	99	GLY	0	0.038	0.029	30.282	0.380	0.380	0.000	0.000	0.000	0.000
82	B	100	THR	0	-0.056	-0.038	31.763	-0.433	-0.433	0.000	0.000	0.000	0.000
83	B	101	ASP	-1	-0.804	-0.891	30.186	10.718	10.718	0.000	0.000	0.000	0.000
84	B	102	LYS	1	0.760	0.873	26.371	-12.205	-12.205	0.000	0.000	0.000	0.000
85	B	103	ILE	0	0.011	-0.010	29.626	0.283	0.283	0.000	0.000	0.000	0.000
86	B	104	ILE	0	-0.026	-0.006	25.524	-0.078	-0.078	0.000	0.000	0.000	0.000
87	B	105	SER	0	-0.017	-0.024	28.888	-0.373	-0.373	0.000	0.000	0.000	0.000
88	B	106	THR	0	0.042	0.019	27.448	0.428	0.428	0.000	0.000	0.000	0.000
89	B	107	GLU	-1	-0.881	-0.926	29.452	10.330	10.330	0.000	0.000	0.000	0.000
90	B	108	GLY	0	0.008	0.017	32.230	-0.343	-0.343	0.000	0.000	0.000	0.000
91	B	109	GLN	0	-0.099	-0.062	33.100	-0.404	-0.404	0.000	0.000	0.000	0.000
92	B	110	ARG	1	0.935	0.966	31.830	-8.357	-8.357	0.000	0.000	0.000	0.000
93	B	111	VAL	0	0.028	-0.008	27.810	-0.077	-0.077	0.000	0.000	0.000	0.000
94	B	112	GLY	0	0.052	0.014	26.112	-0.128	-0.128	0.000	0.000	0.000	0.000
95	B	113	ILE	0	-0.020	-0.009	26.363	0.236	0.236	0.000	0.000	0.000	0.000
96	B	114	LYS	1	0.883	0.922	23.213	-12.851	-12.851	0.000	0.000	0.000	0.000
97	B	115	LYS	1	0.809	0.911	25.886	-11.448	-11.448	0.000	0.000	0.000	0.000
98	B	116	ALA	0	-0.008	0.000	25.486	0.634	0.634	0.000	0.000	0.000	0.000
99	B	117	LEU	0	-0.011	-0.003	25.219	-0.600	-0.600	0.000	0.000	0.000	0.000
100	B	118	VAL	0	-0.015	-0.001	25.687	0.481	0.481	0.000	0.000	0.000	0.000
101	B	119	PHE	0	-0.026	-0.032	25.201	-0.680	-0.680	0.000	0.000	0.000	0.000
102	B	129	LYS	1	0.944	0.978	30.680	-10.214	-10.214	0.000	0.000	0.000	0.000
103	B	130	THR	0	-0.024	-0.020	26.500	0.235	0.235	0.000	0.000	0.000	0.000
104	B	131	ASN	0	0.016	-0.005	24.199	-0.111	-0.111	0.000	0.000	0.000	0.000
105	B	132	TRP	0	0.034	0.034	17.866	0.628	0.628	0.000	0.000	0.000	0.000
106	B	133	ILE	0	-0.020	-0.019	22.071	-0.671	-0.671	0.000	0.000	0.000	0.000
107	B	134	MET	0	0.019	0.026	21.022	1.056	1.056	0.000	0.000	0.000	0.000
108	B	135	HIS	0	-0.068	-0.034	20.821	-0.300	-0.300	0.000	0.000	0.000	0.000
109	B	136	GLU	-1	-0.800	-0.901	21.022	12.528	12.528	0.000	0.000	0.000	0.000
110	B	137	TYR	0	0.006	-0.036	20.108	-0.075	-0.075	0.000	0.000	0.000	0.000
111	B	154	TRP	0	-0.041	-0.024	19.523	-0.050	-0.050	0.000	0.000	0.000	0.000
112	B	155	VAL	0	0.027	0.017	22.262	-0.204	-0.204	0.000	0.000	0.000	0.000
113	B	156	LEU	0	0.015	0.017	16.485	0.701	0.701	0.000	0.000	0.000	0.000
114	B	157	CYS	0	-0.073	-0.039	17.976	-1.054	-1.054	0.000	0.000	0.000	0.000
115	B	158	ARG	1	0.860	0.930	15.970	-16.382	-16.382	0.000	0.000	0.000	0.000
116	B	159	ILE	0	0.008	-0.004	16.235	-1.386	-1.386	0.000	0.000	0.000	0.000
117	B	160	TYR	0	0.051	0.011	16.145	0.968	0.968	0.000	0.000	0.000	0.000
118	B	161	LYS	1	0.918	0.977	18.116	-15.282	-15.282	0.000	0.000	0.000	0.000
119	B	162	LYS	1	0.875	0.943	20.418	-13.343	-13.343	0.000	0.000	0.000	0.000
120	B	163	GLN	0	0.067	0.026	23.405	0.913	0.913	0.000	0.000	0.000	0.000

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