FMO DATABASE

FMODB ID: 17JQZ

Calculation Name: 2DUD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2DUD

Chain ID: A

ChEMBL ID:

UniProt ID: Q04837

Base Structure: X-ray

Registration Date: 2023-06-21

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	100
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-736569.246737
FMO2-HF: Nuclear repulsion	696222.400982
FMO2-HF: Total energy	-40346.845754
FMO2-MP2: Total energy	-40466.216877

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:12:ARG)

Summations of interaction energy for fragment #1(A:12:ARG)

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.
73.842	77.607	-0.035	-2.106	-1.624	0.007

Interaction energy analysis for fragmet #1(A:12:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.013 / q_NPA : 1.009

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

Sort

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	14	LEU	0	0.025	0.038	3.734	-6.361	-2.596	-0.035	-2.106	-1.624	0.007
4	A	15	ASN	0	-0.042	-0.030	6.668	4.258	4.258	0.000	0.000	0.000	0.000
5	A	16	ARG	1	0.907	0.947	9.670	25.224	25.224	0.000	0.000	0.000	0.000
6	A	17	VAL	0	-0.008	0.011	11.474	1.049	1.049	0.000	0.000	0.000	0.000
7	A	18	HIS	0	-0.045	-0.023	13.535	-1.024	-1.024	0.000	0.000	0.000	0.000
8	A	19	LEU	0	0.032	0.019	17.614	0.402	0.402	0.000	0.000	0.000	0.000
9	A	20	LEU	0	0.000	-0.008	21.137	-0.133	-0.133	0.000	0.000	0.000	0.000
10	A	21	GLY	0	-0.007	0.007	24.068	0.233	0.233	0.000	0.000	0.000	0.000
11	A	22	ARG	1	0.866	0.930	27.342	9.330	9.330	0.000	0.000	0.000	0.000
12	A	23	VAL	0	0.024	0.011	27.557	-0.135	-0.135	0.000	0.000	0.000	0.000
13	A	24	GLY	0	0.035	0.012	30.042	0.287	0.287	0.000	0.000	0.000	0.000
14	A	25	GLN	0	-0.017	-0.020	31.798	0.548	0.548	0.000	0.000	0.000	0.000
15	A	26	ASP	-1	-0.817	-0.887	31.689	-9.112	-9.112	0.000	0.000	0.000	0.000
16	A	27	PRO	0	0.000	0.013	28.576	-0.015	-0.015	0.000	0.000	0.000	0.000
17	A	28	VAL	0	0.004	0.005	29.149	0.264	0.264	0.000	0.000	0.000	0.000
18	A	29	LEU	0	0.054	0.022	26.875	-0.453	-0.453	0.000	0.000	0.000	0.000
19	A	30	ARG	1	0.927	0.957	25.942	11.380	11.380	0.000	0.000	0.000	0.000
20	A	31	GLN	0	-0.022	-0.014	26.791	-0.691	-0.691	0.000	0.000	0.000	0.000
21	A	32	VAL	0	0.067	0.031	29.241	0.001	0.001	0.000	0.000	0.000	0.000
22	A	33	GLU	-1	-0.836	-0.916	30.493	-9.420	-9.420	0.000	0.000	0.000	0.000
23	A	34	GLY	0	0.010	0.019	29.165	-0.064	-0.064	0.000	0.000	0.000	0.000
24	A	35	LYS	1	0.808	0.900	25.246	11.227	11.227	0.000	0.000	0.000	0.000
25	A	36	ASN	0	-0.011	-0.016	21.737	0.396	0.396	0.000	0.000	0.000	0.000
26	A	37	PRO	0	0.015	0.024	23.334	-0.447	-0.447	0.000	0.000	0.000	0.000
27	A	38	VAL	0	-0.019	0.007	21.363	-0.598	-0.598	0.000	0.000	0.000	0.000
28	A	39	THR	0	0.030	0.003	23.237	0.653	0.653	0.000	0.000	0.000	0.000
29	A	40	ILE	0	-0.051	-0.036	23.551	-0.668	-0.668	0.000	0.000	0.000	0.000
30	A	41	PHE	0	0.002	0.007	23.443	0.541	0.541	0.000	0.000	0.000	0.000
31	A	42	SER	0	0.004	-0.001	26.000	-0.339	-0.339	0.000	0.000	0.000	0.000
32	A	43	LEU	0	0.045	0.006	23.411	0.206	0.206	0.000	0.000	0.000	0.000
33	A	44	ALA	0	-0.018	0.001	27.010	-0.165	-0.165	0.000	0.000	0.000	0.000
34	A	45	THR	0	-0.004	0.006	25.045	-0.021	-0.021	0.000	0.000	0.000	0.000
35	A	46	ASN	0	0.016	-0.007	27.989	0.419	0.419	0.000	0.000	0.000	0.000
36	A	47	GLU	-1	-0.887	-0.942	28.341	-11.456	-11.456	0.000	0.000	0.000	0.000
37	A	48	MET	0	-0.029	-0.040	31.036	0.345	0.345	0.000	0.000	0.000	0.000
38	A	49	TRP	0	0.039	0.032	33.934	-0.115	-0.115	0.000	0.000	0.000	0.000
39	A	62	VAL	0	0.034	0.021	39.162	0.022	0.022	0.000	0.000	0.000	0.000
40	A	63	SER	0	-0.064	-0.026	38.323	0.101	0.101	0.000	0.000	0.000	0.000
41	A	64	GLN	0	-0.010	-0.039	35.597	-0.013	-0.013	0.000	0.000	0.000	0.000
42	A	65	LYS	1	0.940	0.981	29.526	10.652	10.652	0.000	0.000	0.000	0.000
43	A	66	THR	0	-0.044	-0.012	31.430	-0.195	-0.195	0.000	0.000	0.000	0.000
44	A	67	THR	0	0.047	0.042	25.970	0.171	0.171	0.000	0.000	0.000	0.000
45	A	68	TRP	0	0.026	0.003	28.243	-0.205	-0.205	0.000	0.000	0.000	0.000
46	A	69	HIS	0	-0.058	-0.018	22.733	0.007	0.007	0.000	0.000	0.000	0.000
47	A	70	ARG	1	1.011	1.023	23.382	11.862	11.862	0.000	0.000	0.000	0.000
48	A	71	ILE	0	-0.001	0.002	20.730	-0.799	-0.799	0.000	0.000	0.000	0.000
49	A	72	SER	0	0.003	-0.012	20.372	0.503	0.503	0.000	0.000	0.000	0.000
50	A	73	VAL	0	-0.026	-0.014	18.965	-0.969	-0.969	0.000	0.000	0.000	0.000
51	A	74	PHE	0	0.030	0.004	16.888	0.435	0.435	0.000	0.000	0.000	0.000
52	A	75	ARG	1	0.911	0.939	14.560	18.513	18.513	0.000	0.000	0.000	0.000
53	A	76	PRO	0	0.056	0.011	17.676	0.459	0.459	0.000	0.000	0.000	0.000
54	A	77	GLY	0	0.088	0.055	20.267	0.478	0.478	0.000	0.000	0.000	0.000
55	A	78	LEU	0	-0.050	-0.026	17.624	0.503	0.503	0.000	0.000	0.000	0.000
56	A	79	ARG	1	0.879	0.946	21.100	13.146	13.146	0.000	0.000	0.000	0.000
57	A	80	ASP	-1	-0.796	-0.878	22.770	-11.321	-11.321	0.000	0.000	0.000	0.000
58	A	81	VAL	0	0.046	0.033	23.893	0.507	0.507	0.000	0.000	0.000	0.000
59	A	82	ALA	0	-0.080	-0.038	23.671	0.341	0.341	0.000	0.000	0.000	0.000
60	A	83	TYR	0	0.046	0.002	25.703	0.262	0.262	0.000	0.000	0.000	0.000
61	A	84	GLN	0	-0.041	-0.025	28.302	0.361	0.361	0.000	0.000	0.000	0.000
62	A	85	TYR	0	0.000	-0.004	28.190	0.353	0.353	0.000	0.000	0.000	0.000
63	A	86	VAL	0	-0.078	-0.013	25.623	0.223	0.223	0.000	0.000	0.000	0.000
64	A	87	LYS	1	0.915	0.960	29.017	9.591	9.591	0.000	0.000	0.000	0.000
65	A	88	LYS	1	0.774	0.876	32.343	8.223	8.223	0.000	0.000	0.000	0.000
66	A	89	GLY	0	0.046	0.020	33.503	0.179	0.179	0.000	0.000	0.000	0.000
67	A	90	SER	0	0.016	0.031	29.915	0.068	0.068	0.000	0.000	0.000	0.000
68	A	91	ARG	1	0.891	0.945	28.561	10.233	10.233	0.000	0.000	0.000	0.000
69	A	92	ILE	0	-0.013	-0.004	23.540	0.025	0.025	0.000	0.000	0.000	0.000
70	A	93	TYR	0	0.087	0.022	16.703	0.395	0.395	0.000	0.000	0.000	0.000
71	A	94	LEU	0	-0.088	-0.045	18.490	0.062	0.062	0.000	0.000	0.000	0.000
72	A	95	GLU	-1	-0.697	-0.838	13.310	-21.273	-21.273	0.000	0.000	0.000	0.000
73	A	96	GLY	0	0.015	-0.001	13.349	0.245	0.245	0.000	0.000	0.000	0.000
74	A	97	LYS	1	0.788	0.905	10.591	21.138	21.138	0.000	0.000	0.000	0.000
75	A	98	ILE	0	0.011	-0.010	12.864	1.644	1.644	0.000	0.000	0.000	0.000
76	A	99	ASP	-1	-0.831	-0.897	14.283	-20.168	-20.168	0.000	0.000	0.000	0.000
77	A	100	TYR	0	0.033	-0.005	15.470	1.092	1.092	0.000	0.000	0.000	0.000
78	A	101	GLY	0	-0.013	-0.014	18.905	-0.058	-0.058	0.000	0.000	0.000	0.000
79	A	102	GLU	-1	-0.908	-0.947	20.650	-12.901	-12.901	0.000	0.000	0.000	0.000
80	A	103	TYR	0	-0.105	-0.049	22.280	0.027	0.027	0.000	0.000	0.000	0.000
81	A	104	MET	0	0.071	0.045	25.951	0.130	0.130	0.000	0.000	0.000	0.000
82	A	105	ASP	-1	-0.749	-0.858	28.916	-9.116	-9.116	0.000	0.000	0.000	0.000
83	A	106	LYS	1	0.898	0.956	32.517	8.266	8.266	0.000	0.000	0.000	0.000
84	A	107	ASN	0	0.020	-0.012	31.483	0.142	0.142	0.000	0.000	0.000	0.000
85	A	108	ASN	0	-0.088	-0.065	29.917	-0.197	-0.197	0.000	0.000	0.000	0.000
86	A	109	VAL	0	0.068	0.060	24.649	0.085	0.085	0.000	0.000	0.000	0.000
87	A	110	ARG	1	0.914	0.947	26.438	9.660	9.660	0.000	0.000	0.000	0.000
88	A	111	ARG	1	0.954	0.951	19.839	13.258	13.258	0.000	0.000	0.000	0.000
89	A	112	GLN	0	-0.023	0.012	23.432	0.357	0.357	0.000	0.000	0.000	0.000
90	A	113	ALA	0	-0.076	-0.026	21.278	-0.569	-0.569	0.000	0.000	0.000	0.000
91	A	114	THR	0	0.011	-0.004	18.882	0.826	0.826	0.000	0.000	0.000	0.000
92	A	115	THR	0	0.002	0.002	17.308	-0.790	-0.790	0.000	0.000	0.000	0.000
93	A	116	ILE	0	-0.046	-0.018	14.892	0.636	0.636	0.000	0.000	0.000	0.000
94	A	117	ILE	0	-0.022	-0.018	14.529	-1.787	-1.787	0.000	0.000	0.000	0.000
95	A	118	ALA	0	-0.065	-0.025	12.141	0.107	0.107	0.000	0.000	0.000	0.000
96	A	119	ASP	-1	-0.828	-0.911	14.076	-16.690	-16.690	0.000	0.000	0.000	0.000
97	A	120	ASN	0	0.024	0.000	16.939	-0.445	-0.445	0.000	0.000	0.000	0.000
98	A	121	ILE	0	0.042	0.022	19.626	0.224	0.224	0.000	0.000	0.000	0.000
99	A	122	ILE	0	-0.010	-0.009	22.879	0.115	0.115	0.000	0.000	0.000	0.000
100	A	123	PHE	0	0.030	0.013	24.899	0.165	0.165	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:12:ARG)