FMO DATABASE

FMODB ID: 43YQN

Calculation Name: 3DA5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DA5

Chain ID: A

ChEMBL ID:

UniProt ID: D0VWU1

Base Structure: X-ray

Registration Date: 2023-03-14

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	121
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1143605.327629
FMO2-HF: Nuclear repulsion	1094041.228171
FMO2-HF: Total energy	-49564.099457
FMO2-MP2: Total energy	-49714.090938

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(A:8:LYS)

Summations of interaction energy for fragment #1(A:8:LYS)

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.
42.238	44.885	5.745	-2.793	-5.597	-0.015

Interaction energy analysis for fragmet #1(A:8:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.961 / q_NPA : 0.977

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	A	10	THR	0	0.032	0.021	3.891	-4.332	-2.478	-0.012	-0.910	-0.932	0.004
4	A	11	LEU	0	0.025	-0.004	5.941	2.898	2.898	0.000	0.000	0.000	0.000
5	A	12	TRP	0	0.012	-0.006	8.900	1.676	1.676	0.000	0.000	0.000	0.000
6	A	13	GLU	-1	-0.832	-0.903	8.011	-22.906	-22.906	0.000	0.000	0.000	0.000
7	A	14	LEU	0	-0.075	-0.038	6.422	1.299	1.299	0.000	0.000	0.000	0.000
8	A	15	VAL	0	-0.016	0.001	9.948	1.426	1.426	0.000	0.000	0.000	0.000
9	A	16	GLY	0	0.003	0.011	13.054	1.423	1.423	0.000	0.000	0.000	0.000
10	A	17	ARG	1	0.789	0.874	11.775	22.405	22.405	0.000	0.000	0.000	0.000
11	A	18	ASN	0	0.069	0.050	15.807	1.062	1.062	0.000	0.000	0.000	0.000
12	A	19	LYS	1	0.964	0.967	17.878	12.967	12.967	0.000	0.000	0.000	0.000
13	A	20	ASP	-1	-0.819	-0.879	19.678	-13.014	-13.014	0.000	0.000	0.000	0.000
14	A	21	ALA	0	0.029	0.010	17.647	-0.130	-0.130	0.000	0.000	0.000	0.000
15	A	22	LEU	0	-0.032	-0.015	13.647	-0.783	-0.783	0.000	0.000	0.000	0.000
16	A	23	ARG	1	0.767	0.857	16.714	12.667	12.667	0.000	0.000	0.000	0.000
17	A	24	ASP	-1	-0.825	-0.913	19.605	-13.714	-13.714	0.000	0.000	0.000	0.000
18	A	25	PHE	0	0.053	0.038	10.970	-0.459	-0.459	0.000	0.000	0.000	0.000
19	A	26	LEU	0	-0.010	-0.013	13.439	-0.593	-0.593	0.000	0.000	0.000	0.000
20	A	27	LYS	1	0.853	0.907	16.351	12.661	12.661	0.000	0.000	0.000	0.000
21	A	28	GLU	-1	-0.922	-0.953	17.712	-16.331	-16.331	0.000	0.000	0.000	0.000
22	A	29	HIS	1	0.844	0.912	14.115	19.557	19.557	0.000	0.000	0.000	0.000
23	A	30	ARG	1	0.866	0.943	15.856	12.735	12.735	0.000	0.000	0.000	0.000
24	A	31	GLY	0	-0.066	-0.037	17.186	0.651	0.651	0.000	0.000	0.000	0.000
25	A	32	THR	0	0.011	0.009	14.887	-0.243	-0.243	0.000	0.000	0.000	0.000
26	A	33	ILE	0	-0.039	0.003	9.976	-1.691	-1.691	0.000	0.000	0.000	0.000
27	A	34	LEU	0	-0.064	-0.033	10.320	1.742	1.742	0.000	0.000	0.000	0.000
28	A	35	LEU	0	0.038	0.012	8.339	-2.522	-2.522	0.000	0.000	0.000	0.000
29	A	36	ARG	1	0.889	0.947	3.190	48.853	49.248	0.006	-0.075	-0.326	0.000
30	A	37	ASP	-1	-0.743	-0.849	5.707	-33.681	-33.681	0.000	0.000	0.000	0.000
31	A	38	ILE	0	-0.069	-0.054	2.305	-6.641	-5.758	0.757	-0.501	-1.139	-0.007
32	A	39	ALA	0	0.052	0.032	5.599	0.328	0.328	0.000	0.000	0.000	0.000
33	A	40	SER	0	0.018	0.015	8.996	2.829	2.829	0.000	0.000	0.000	0.000
34	A	41	GLU	-1	-0.884	-0.936	9.544	-26.227	-26.227	0.000	0.000	0.000	0.000
35	A	42	HIS	0	-0.006	0.002	10.402	-3.189	-3.189	0.000	0.000	0.000	0.000
36	A	43	LYS	1	0.868	0.943	5.205	34.905	34.905	0.000	0.000	0.000	0.000
37	A	44	VAL	0	0.002	-0.005	7.649	-1.868	-1.868	0.000	0.000	0.000	0.000
38	A	45	VAL	0	-0.012	-0.010	7.548	-2.690	-2.690	0.000	0.000	0.000	0.000
39	A	46	TYR	0	0.031	0.018	9.814	3.066	3.066	0.000	0.000	0.000	0.000
40	A	47	LYS	1	0.937	0.962	12.185	15.669	15.669	0.000	0.000	0.000	0.000
41	A	48	PRO	0	0.024	0.006	13.457	0.948	0.948	0.000	0.000	0.000	0.000
42	A	49	ILE	0	-0.012	0.017	16.222	0.624	0.624	0.000	0.000	0.000	0.000
43	A	50	PHE	0	-0.037	-0.028	18.068	-0.195	-0.195	0.000	0.000	0.000	0.000
44	A	51	LYS	1	0.969	1.003	22.463	12.813	12.813	0.000	0.000	0.000	0.000
45	A	52	ARG	1	0.964	0.976	25.787	10.075	10.075	0.000	0.000	0.000	0.000
46	A	53	TYR	0	0.001	-0.004	28.350	0.119	0.119	0.000	0.000	0.000	0.000
47	A	54	ASN	0	-0.019	0.014	25.163	0.121	0.121	0.000	0.000	0.000	0.000
48	A	55	GLY	0	0.083	0.041	26.049	-0.064	-0.064	0.000	0.000	0.000	0.000
49	A	56	ASP	-1	-0.858	-0.918	23.684	-12.785	-12.785	0.000	0.000	0.000	0.000
50	A	57	PRO	0	-0.020	-0.019	19.247	0.192	0.192	0.000	0.000	0.000	0.000
51	A	58	ASP	-1	-0.852	-0.945	21.263	-12.303	-12.303	0.000	0.000	0.000	0.000
52	A	59	LEU	0	-0.049	-0.023	18.214	-0.905	-0.905	0.000	0.000	0.000	0.000
53	A	60	ILE	0	0.022	0.014	21.037	0.639	0.639	0.000	0.000	0.000	0.000
54	A	61	GLU	-1	-0.966	-1.010	21.899	-14.067	-14.067	0.000	0.000	0.000	0.000
55	A	62	ASP	-1	-0.899	-0.956	23.835	-11.673	-11.673	0.000	0.000	0.000	0.000
56	A	63	ASN	0	0.005	0.006	24.884	0.383	0.383	0.000	0.000	0.000	0.000
57	A	64	SER	0	0.074	0.026	23.163	-0.418	-0.418	0.000	0.000	0.000	0.000
58	A	65	ASN	0	0.056	0.031	23.685	-0.396	-0.396	0.000	0.000	0.000	0.000
59	A	66	ASP	-1	-0.865	-0.932	22.300	-13.154	-13.154	0.000	0.000	0.000	0.000
60	A	67	VAL	0	-0.087	-0.043	18.276	-0.836	-0.836	0.000	0.000	0.000	0.000
61	A	68	GLU	-1	-0.905	-0.958	19.179	-13.862	-13.862	0.000	0.000	0.000	0.000
62	A	69	HIS	0	-0.002	0.017	20.839	-0.209	-0.209	0.000	0.000	0.000	0.000
63	A	70	TRP	0	0.010	-0.013	16.686	-0.637	-0.637	0.000	0.000	0.000	0.000
64	A	71	TYR	0	-0.018	-0.038	14.628	-1.132	-1.132	0.000	0.000	0.000	0.000
65	A	72	ASP	-1	-0.833	-0.933	16.895	-15.982	-15.982	0.000	0.000	0.000	0.000
66	A	73	TYR	0	-0.042	-0.011	16.796	0.258	0.258	0.000	0.000	0.000	0.000
67	A	74	HIS	1	0.750	0.837	12.101	22.582	22.582	0.000	0.000	0.000	0.000
68	A	75	LEU	0	-0.012	0.010	15.641	-0.270	-0.270	0.000	0.000	0.000	0.000
69	A	76	GLU	-1	-0.804	-0.892	16.874	-13.695	-13.695	0.000	0.000	0.000	0.000
70	A	77	ARG	1	0.744	0.867	17.542	15.176	15.176	0.000	0.000	0.000	0.000
71	A	78	TYR	0	-0.035	-0.031	13.653	0.425	0.425	0.000	0.000	0.000	0.000
72	A	79	TRP	0	-0.069	-0.042	9.188	-2.166	-2.166	0.000	0.000	0.000	0.000
73	A	80	ASN	0	0.008	0.008	16.167	0.495	0.495	0.000	0.000	0.000	0.000
74	A	81	THR	0	0.020	-0.008	19.106	0.431	0.431	0.000	0.000	0.000	0.000
75	A	82	PRO	0	0.048	0.023	19.519	-0.663	-0.663	0.000	0.000	0.000	0.000
76	A	83	GLU	-1	-0.860	-0.923	17.761	-15.163	-15.163	0.000	0.000	0.000	0.000
77	A	84	LEU	0	0.041	0.029	13.979	-1.100	-1.100	0.000	0.000	0.000	0.000
78	A	85	LYS	1	1.006	1.016	14.741	14.296	14.296	0.000	0.000	0.000	0.000
79	A	86	LYS	1	0.885	0.938	14.980	17.559	17.559	0.000	0.000	0.000	0.000
80	A	87	GLU	-1	-0.976	-0.987	9.989	-27.502	-27.502	0.000	0.000	0.000	0.000
81	A	88	PHE	0	0.035	0.013	10.861	-1.804	-1.804	0.000	0.000	0.000	0.000
82	A	89	TYR	0	0.015	0.007	11.397	-1.351	-1.351	0.000	0.000	0.000	0.000
83	A	90	LYS	1	0.907	0.947	11.130	17.699	17.699	0.000	0.000	0.000	0.000
84	A	91	LYS	1	0.800	0.936	5.901	39.631	39.631	0.000	0.000	0.000	0.000
85	A	92	PHE	0	0.001	-0.012	7.516	-3.373	-3.373	0.000	0.000	0.000	0.000
86	A	93	GLY	0	-0.002	0.019	10.100	0.656	0.656	0.000	0.000	0.000	0.000
87	A	94	PRO	0	0.007	0.011	13.245	-0.339	-0.339	0.000	0.000	0.000	0.000
88	A	95	VAL	0	0.034	0.032	15.819	-0.923	-0.923	0.000	0.000	0.000	0.000
89	A	96	ASP	-1	-0.778	-0.863	16.325	-16.581	-16.581	0.000	0.000	0.000	0.000
90	A	97	LEU	0	0.048	0.011	18.062	-0.535	-0.535	0.000	0.000	0.000	0.000
91	A	98	ASN	0	-0.038	-0.019	19.976	0.990	0.990	0.000	0.000	0.000	0.000
92	A	99	GLN	0	-0.070	-0.043	14.479	-1.343	-1.343	0.000	0.000	0.000	0.000
93	A	100	PRO	0	-0.024	0.007	17.063	0.489	0.489	0.000	0.000	0.000	0.000
94	A	101	ILE	0	0.018	-0.008	17.286	-1.393	-1.393	0.000	0.000	0.000	0.000
95	A	102	ILE	0	-0.028	-0.026	13.126	0.624	0.624	0.000	0.000	0.000	0.000
96	A	103	LEU	0	0.044	0.040	16.475	-0.488	-0.488	0.000	0.000	0.000	0.000
97	A	104	ALA	0	-0.024	-0.014	14.612	-0.353	-0.353	0.000	0.000	0.000	0.000
98	A	105	LYS	1	1.011	1.004	16.618	15.172	15.172	0.000	0.000	0.000	0.000
99	A	106	PRO	0	-0.001	0.016	15.330	-1.371	-1.371	0.000	0.000	0.000	0.000
100	A	107	LEU	0	-0.009	-0.014	12.853	0.852	0.852	0.000	0.000	0.000	0.000
101	A	108	ARG	1	0.882	0.939	16.852	17.636	17.636	0.000	0.000	0.000	0.000
102	A	109	GLN	0	0.009	0.004	19.072	-0.760	-0.760	0.000	0.000	0.000	0.000
103	A	110	HIS	0	0.019	0.000	15.182	-0.516	-0.516	0.000	0.000	0.000	0.000
104	A	111	ASN	0	0.027	0.005	19.722	0.226	0.226	0.000	0.000	0.000	0.000
105	A	112	ARG	1	0.939	0.976	18.670	15.121	15.121	0.000	0.000	0.000	0.000
106	A	113	GLY	0	0.033	0.039	20.823	0.160	0.160	0.000	0.000	0.000	0.000
107	A	114	ASP	-1	-0.853	-0.949	20.280	-14.581	-14.581	0.000	0.000	0.000	0.000
108	A	115	LEU	0	-0.042	-0.032	19.816	-0.047	-0.047	0.000	0.000	0.000	0.000
109	A	116	VAL	0	-0.023	-0.001	14.450	0.160	0.160	0.000	0.000	0.000	0.000
110	A	117	HIS	0	0.041	0.026	17.298	-0.280	-0.280	0.000	0.000	0.000	0.000
111	A	118	LEU	0	-0.046	-0.024	11.152	-0.984	-0.984	0.000	0.000	0.000	0.000
112	A	119	LEU	0	0.052	0.031	13.021	0.920	0.920	0.000	0.000	0.000	0.000
113	A	120	PRO	0	0.039	0.005	11.472	-2.857	-2.857	0.000	0.000	0.000	0.000
114	A	121	GLN	0	-0.030	-0.023	9.887	-2.098	-2.098	0.000	0.000	0.000	0.000
115	A	122	PHE	0	-0.022	-0.006	8.912	-2.330	-2.330	0.000	0.000	0.000	0.000
116	A	123	VAL	0	-0.004	0.016	6.637	-4.000	-4.000	0.000	0.000	0.000	0.000
117	A	124	VAL	0	-0.018	-0.009	1.941	-7.197	-7.950	4.996	-1.298	-2.944	-0.012
118	A	125	PRO	0	0.019	0.021	5.174	1.663	1.802	-0.001	-0.005	-0.132	0.000
119	A	126	VAL	0	-0.078	-0.044	5.040	-6.643	-6.514	-0.001	-0.004	-0.124	0.000
120	A	127	TYR	0	0.025	0.005	7.099	3.574	3.574	0.000	0.000	0.000	0.000
121	A	128	ASN	0	0.026	0.015	9.991	1.048	1.048	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:8:LYS)