FMO DATABASE

FMODB ID: G6QM1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-736949.584371
FMO2-HF: Nuclear repulsion	696600.21899
FMO2-HF: Total energy	-40349.365381
FMO2-MP2: Total energy	-40468.690643

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.
72.337	75.439	-0.001	-1.762	-1.34	0.006

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 : 1.010 / q_NPA : 1.002

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	0.006	-0.002	3.567	-9.438	-6.336	-0.001	-1.762	-1.340	0.006
4	A	15	ASN	0	-0.022	-0.017	6.382	4.570	4.570	0.000	0.000	0.000	0.000
5	A	16	ARG	1	0.862	0.926	9.190	24.522	24.522	0.000	0.000	0.000	0.000
6	A	17	VAL	0	-0.008	0.004	10.821	1.079	1.079	0.000	0.000	0.000	0.000
7	A	18	HIS	0	0.000	-0.005	13.201	-1.412	-1.412	0.000	0.000	0.000	0.000
8	A	19	LEU	0	-0.006	-0.007	16.991	0.485	0.485	0.000	0.000	0.000	0.000
9	A	20	LEU	0	-0.008	-0.011	20.521	0.054	0.054	0.000	0.000	0.000	0.000
10	A	21	GLY	0	0.013	0.021	23.969	0.228	0.228	0.000	0.000	0.000	0.000
11	A	22	ARG	1	0.868	0.926	27.078	9.410	9.410	0.000	0.000	0.000	0.000
12	A	23	VAL	0	0.012	0.010	27.546	-0.152	-0.152	0.000	0.000	0.000	0.000
13	A	24	GLY	0	0.005	0.002	29.785	0.354	0.354	0.000	0.000	0.000	0.000
14	A	25	GLN	0	0.000	0.000	31.344	0.564	0.564	0.000	0.000	0.000	0.000
15	A	26	ASP	-1	-0.795	-0.882	31.150	-9.201	-9.201	0.000	0.000	0.000	0.000
16	A	27	PRO	0	-0.023	0.002	28.056	-0.003	-0.003	0.000	0.000	0.000	0.000
17	A	28	VAL	0	0.003	-0.002	29.012	0.315	0.315	0.000	0.000	0.000	0.000
18	A	29	LEU	0	0.026	0.023	27.009	-0.482	-0.482	0.000	0.000	0.000	0.000
19	A	30	ARG	1	0.922	0.950	25.965	11.399	11.399	0.000	0.000	0.000	0.000
20	A	31	GLN	0	0.006	0.005	26.574	-0.671	-0.671	0.000	0.000	0.000	0.000
21	A	32	VAL	0	0.062	0.026	29.281	-0.027	-0.027	0.000	0.000	0.000	0.000
22	A	33	GLU	-1	-0.848	-0.923	30.695	-9.405	-9.405	0.000	0.000	0.000	0.000
23	A	34	GLY	0	0.021	0.025	29.782	-0.078	-0.078	0.000	0.000	0.000	0.000
24	A	35	LYS	1	0.812	0.895	25.309	11.351	11.351	0.000	0.000	0.000	0.000
25	A	36	ASN	0	0.021	0.007	21.730	0.392	0.392	0.000	0.000	0.000	0.000
26	A	37	PRO	0	0.031	0.027	24.358	-0.178	-0.178	0.000	0.000	0.000	0.000
27	A	38	VAL	0	-0.047	-0.010	21.431	-0.580	-0.580	0.000	0.000	0.000	0.000
28	A	39	THR	0	0.003	-0.010	23.395	0.646	0.646	0.000	0.000	0.000	0.000
29	A	40	ILE	0	-0.062	-0.039	23.517	-0.639	-0.639	0.000	0.000	0.000	0.000
30	A	41	PHE	0	0.037	0.014	23.319	0.480	0.480	0.000	0.000	0.000	0.000
31	A	42	SER	0	0.002	0.002	25.950	-0.296	-0.296	0.000	0.000	0.000	0.000
32	A	43	LEU	0	0.023	0.013	23.148	0.231	0.231	0.000	0.000	0.000	0.000
33	A	44	ALA	0	0.032	0.023	26.854	-0.134	-0.134	0.000	0.000	0.000	0.000
34	A	45	THR	0	0.011	-0.015	24.324	0.038	0.038	0.000	0.000	0.000	0.000
35	A	46	ASN	0	-0.037	-0.027	27.142	0.623	0.623	0.000	0.000	0.000	0.000
36	A	47	GLU	-1	-0.781	-0.856	28.165	-11.409	-11.409	0.000	0.000	0.000	0.000
37	A	48	MET	0	0.004	-0.015	30.615	0.369	0.369	0.000	0.000	0.000	0.000
38	A	49	TRP	0	0.029	0.027	33.485	-0.153	-0.153	0.000	0.000	0.000	0.000
39	A	62	VAL	0	0.035	0.025	38.690	0.011	0.011	0.000	0.000	0.000	0.000
40	A	63	SER	0	-0.070	-0.041	38.443	0.166	0.166	0.000	0.000	0.000	0.000
41	A	64	GLN	0	0.003	-0.009	34.865	-0.008	-0.008	0.000	0.000	0.000	0.000
42	A	65	LYS	1	0.846	0.919	28.538	10.965	10.965	0.000	0.000	0.000	0.000
43	A	66	THR	0	-0.021	-0.007	30.940	-0.188	-0.188	0.000	0.000	0.000	0.000
44	A	67	THR	0	-0.010	-0.016	25.186	0.026	0.026	0.000	0.000	0.000	0.000
45	A	68	TRP	0	0.002	0.011	27.316	-0.250	-0.250	0.000	0.000	0.000	0.000
46	A	69	HIS	0	0.019	0.022	22.000	-0.007	-0.007	0.000	0.000	0.000	0.000
47	A	70	ARG	1	0.949	0.972	23.597	11.959	11.959	0.000	0.000	0.000	0.000
48	A	71	ILE	0	-0.010	0.003	20.649	-0.735	-0.735	0.000	0.000	0.000	0.000
49	A	72	SER	0	-0.011	-0.011	19.594	0.503	0.503	0.000	0.000	0.000	0.000
50	A	73	VAL	0	-0.003	0.005	19.085	-0.930	-0.930	0.000	0.000	0.000	0.000
51	A	74	PHE	0	0.068	0.019	16.937	0.517	0.517	0.000	0.000	0.000	0.000
52	A	75	ARG	1	0.884	0.921	14.508	18.399	18.399	0.000	0.000	0.000	0.000
53	A	76	PRO	0	0.046	0.022	17.724	0.461	0.461	0.000	0.000	0.000	0.000
54	A	77	GLY	0	0.086	0.043	20.844	0.460	0.460	0.000	0.000	0.000	0.000
55	A	78	LEU	0	-0.007	0.001	17.678	0.392	0.392	0.000	0.000	0.000	0.000
56	A	79	ARG	1	0.760	0.841	21.262	12.876	12.876	0.000	0.000	0.000	0.000
57	A	80	ASP	-1	-0.740	-0.825	22.872	-11.261	-11.261	0.000	0.000	0.000	0.000
58	A	81	VAL	0	0.016	0.011	23.952	0.438	0.438	0.000	0.000	0.000	0.000
59	A	82	ALA	0	-0.012	-0.019	23.393	0.343	0.343	0.000	0.000	0.000	0.000
60	A	83	TYR	0	-0.012	-0.012	25.452	0.341	0.341	0.000	0.000	0.000	0.000
61	A	84	GLN	0	0.031	0.020	28.463	0.342	0.342	0.000	0.000	0.000	0.000
62	A	85	TYR	0	-0.022	0.004	27.977	0.399	0.399	0.000	0.000	0.000	0.000
63	A	86	VAL	0	-0.020	-0.002	25.289	0.276	0.276	0.000	0.000	0.000	0.000
64	A	87	LYS	1	0.860	0.918	28.738	9.666	9.666	0.000	0.000	0.000	0.000
65	A	88	LYS	1	0.861	0.920	31.906	8.224	8.224	0.000	0.000	0.000	0.000
66	A	89	GLY	0	0.029	0.024	33.268	0.201	0.201	0.000	0.000	0.000	0.000
67	A	90	SER	0	-0.034	-0.031	29.873	0.022	0.022	0.000	0.000	0.000	0.000
68	A	91	ARG	1	0.927	0.974	28.373	10.390	10.390	0.000	0.000	0.000	0.000
69	A	92	ILE	0	-0.010	-0.007	23.412	0.031	0.031	0.000	0.000	0.000	0.000
70	A	93	TYR	0	0.023	-0.013	16.574	0.349	0.349	0.000	0.000	0.000	0.000
71	A	94	LEU	0	-0.042	-0.020	18.186	0.123	0.123	0.000	0.000	0.000	0.000
72	A	95	GLU	-1	-0.738	-0.845	13.016	-21.554	-21.554	0.000	0.000	0.000	0.000
73	A	96	GLY	0	0.025	-0.003	13.500	0.638	0.638	0.000	0.000	0.000	0.000
74	A	97	LYS	1	0.830	0.933	10.688	20.404	20.404	0.000	0.000	0.000	0.000
75	A	98	ILE	0	0.037	0.012	12.628	1.671	1.671	0.000	0.000	0.000	0.000
76	A	99	ASP	-1	-0.814	-0.898	13.964	-19.933	-19.933	0.000	0.000	0.000	0.000
77	A	100	TYR	0	0.021	-0.019	15.478	1.171	1.171	0.000	0.000	0.000	0.000
78	A	101	GLY	0	0.028	0.022	19.170	0.680	0.680	0.000	0.000	0.000	0.000
79	A	102	GLU	-1	-0.947	-0.971	20.567	-12.755	-12.755	0.000	0.000	0.000	0.000
80	A	103	TYR	0	-0.042	-0.024	22.320	0.048	0.048	0.000	0.000	0.000	0.000
81	A	104	MET	0	0.007	0.002	25.963	0.128	0.128	0.000	0.000	0.000	0.000
82	A	105	ASP	-1	-0.759	-0.867	29.114	-9.130	-9.130	0.000	0.000	0.000	0.000
83	A	106	LYS	1	0.943	0.984	32.718	8.399	8.399	0.000	0.000	0.000	0.000
84	A	107	ASN	0	-0.028	-0.029	31.703	0.253	0.253	0.000	0.000	0.000	0.000
85	A	108	ASN	0	-0.060	-0.037	29.890	-0.078	-0.078	0.000	0.000	0.000	0.000
86	A	109	VAL	0	0.063	0.032	24.558	0.096	0.096	0.000	0.000	0.000	0.000
87	A	110	ARG	1	0.836	0.929	26.305	9.851	9.851	0.000	0.000	0.000	0.000
88	A	111	ARG	1	0.984	0.988	19.222	13.572	13.572	0.000	0.000	0.000	0.000
89	A	112	GLN	0	-0.017	-0.004	23.371	0.493	0.493	0.000	0.000	0.000	0.000
90	A	113	ALA	0	-0.009	0.004	20.991	-0.513	-0.513	0.000	0.000	0.000	0.000
91	A	114	THR	0	-0.044	-0.035	18.888	0.882	0.882	0.000	0.000	0.000	0.000
92	A	115	THR	0	0.020	0.018	16.879	-0.891	-0.891	0.000	0.000	0.000	0.000
93	A	116	ILE	0	-0.060	-0.015	14.665	0.613	0.613	0.000	0.000	0.000	0.000
94	A	117	ILE	0	-0.006	-0.006	14.585	-1.355	-1.355	0.000	0.000	0.000	0.000
95	A	118	ALA	0	-0.081	-0.046	12.267	-0.753	-0.753	0.000	0.000	0.000	0.000
96	A	119	ASP	-1	-0.809	-0.901	14.267	-17.223	-17.223	0.000	0.000	0.000	0.000
97	A	120	ASN	0	-0.025	-0.024	16.633	-0.105	-0.105	0.000	0.000	0.000	0.000
98	A	121	ILE	0	0.034	0.028	19.743	0.080	0.080	0.000	0.000	0.000	0.000
99	A	122	ILE	0	0.011	0.003	22.734	0.077	0.077	0.000	0.000	0.000	0.000
100	A	123	PHE	0	0.012	0.008	24.490	0.218	0.218	0.000	0.000	0.000	0.000

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