FMO DATABASE

FMODB ID: 9GV82

Calculation Name: 3R3P-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3R3P

Chain ID: A

ChEMBL ID:

UniProt ID: A7KV39

Base Structure: X-ray

Registration Date: 2023-06-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	97
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-760908.007745
FMO2-HF: Nuclear repulsion	721357.703102
FMO2-HF: Total energy	-39550.304644
FMO2-MP2: Total energy	-39668.42973

3D Structure Molmil

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:167:THR)

Summations of interaction energy for fragment #1(A:167:THR)

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.
-13.933	-10.628	9.647	-4.724	-8.227	0.03

Interaction energy analysis for fragmet #1(A:167:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.048 / q_NPA : 0.013

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	169	PRO	0	0.059	0.005	3.414	-0.254	1.514	0.010	-0.922	-0.856	0.000
4	A	170	GLU	-1	-0.849	-0.912	6.153	-0.286	-0.286	0.000	0.000	0.000	0.000
5	A	171	ARG	1	0.778	0.879	2.039	-11.975	-12.784	8.890	-2.841	-5.241	0.029
6	A	172	ARG	1	0.954	0.972	2.975	-4.490	-2.322	0.749	-0.953	-1.964	0.001
7	A	173	VAL	0	0.026	0.021	5.047	-0.044	-0.002	-0.001	-0.002	-0.038	0.000
8	A	174	LYS	1	0.797	0.868	7.358	-0.563	-0.563	0.000	0.000	0.000	0.000
9	A	175	GLU	-1	-0.827	-0.904	4.610	2.281	2.417	-0.001	-0.006	-0.128	0.000
10	A	176	ILE	0	0.001	0.002	8.406	-0.062	-0.062	0.000	0.000	0.000	0.000
11	A	177	LEU	0	-0.032	-0.024	10.723	-0.072	-0.072	0.000	0.000	0.000	0.000
12	A	178	ASP	-1	-0.766	-0.841	11.085	0.534	0.534	0.000	0.000	0.000	0.000
13	A	179	GLU	-1	-0.896	-0.938	11.729	0.645	0.645	0.000	0.000	0.000	0.000
14	A	180	MET	0	-0.103	-0.043	14.297	-0.038	-0.038	0.000	0.000	0.000	0.000
15	A	181	ASP	-1	-0.927	-0.949	16.666	0.204	0.204	0.000	0.000	0.000	0.000
16	A	182	ILE	0	-0.057	-0.012	16.456	-0.036	-0.036	0.000	0.000	0.000	0.000
17	A	183	VAL	0	0.012	-0.004	16.380	0.014	0.014	0.000	0.000	0.000	0.000
18	A	184	TYR	0	-0.030	-0.035	12.727	-0.029	-0.029	0.000	0.000	0.000	0.000
19	A	185	PHE	0	-0.069	-0.031	17.304	0.002	0.002	0.000	0.000	0.000	0.000
20	A	186	THR	0	0.024	-0.002	11.489	0.007	0.007	0.000	0.000	0.000	0.000
21	A	187	HIS	0	-0.097	-0.062	10.400	0.069	0.069	0.000	0.000	0.000	0.000
22	A	188	HIS	0	0.027	0.036	15.545	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	189	VAL	0	-0.005	-0.008	19.196	-0.017	-0.017	0.000	0.000	0.000	0.000
24	A	190	VAL	0	0.008	0.003	22.171	0.015	0.015	0.000	0.000	0.000	0.000
25	A	191	GLU	-1	-0.811	-0.880	24.734	-0.019	-0.019	0.000	0.000	0.000	0.000
26	A	192	GLY	0	0.001	0.006	26.554	0.000	0.000	0.000	0.000	0.000	0.000
27	A	193	TRP	0	-0.088	-0.059	22.866	-0.021	-0.021	0.000	0.000	0.000	0.000
28	A	194	ASN	0	0.029	0.015	18.064	0.018	0.018	0.000	0.000	0.000	0.000
29	A	195	VAL	0	-0.042	-0.022	17.615	-0.008	-0.008	0.000	0.000	0.000	0.000
30	A	196	ALA	0	0.018	0.018	12.044	0.004	0.004	0.000	0.000	0.000	0.000
31	A	197	PHE	0	0.041	0.013	9.111	0.021	0.021	0.000	0.000	0.000	0.000
32	A	198	TYR	0	-0.008	0.014	15.120	0.008	0.008	0.000	0.000	0.000	0.000
33	A	199	LEU	0	0.047	0.011	16.337	0.014	0.014	0.000	0.000	0.000	0.000
34	A	200	GLY	0	0.031	0.028	20.088	0.006	0.006	0.000	0.000	0.000	0.000
35	A	201	LYS	1	0.941	0.952	23.799	-0.065	-0.065	0.000	0.000	0.000	0.000
36	A	202	LYS	1	0.896	0.963	25.633	-0.016	-0.016	0.000	0.000	0.000	0.000
37	A	203	LEU	0	0.023	0.016	22.108	-0.007	-0.007	0.000	0.000	0.000	0.000
38	A	204	ALA	0	-0.023	-0.018	18.901	0.000	0.000	0.000	0.000	0.000	0.000
39	A	205	ILE	0	0.021	0.019	13.432	0.007	0.007	0.000	0.000	0.000	0.000
40	A	206	GLU	-1	-0.833	-0.904	14.911	-0.153	-0.153	0.000	0.000	0.000	0.000
41	A	207	VAL	0	-0.001	0.002	9.343	0.037	0.037	0.000	0.000	0.000	0.000
42	A	208	ASN	0	0.001	0.004	12.509	-0.082	-0.082	0.000	0.000	0.000	0.000
43	A	209	GLY	0	0.117	0.060	12.833	-0.018	-0.018	0.000	0.000	0.000	0.000
44	A	210	VAL	0	-0.005	0.019	14.673	-0.025	-0.025	0.000	0.000	0.000	0.000
45	A	211	TYR	0	-0.099	-0.064	15.503	0.002	0.002	0.000	0.000	0.000	0.000
46	A	212	TRP	0	0.083	0.055	10.471	-0.041	-0.041	0.000	0.000	0.000	0.000
47	A	213	ALA	0	0.020	0.005	11.665	0.052	0.052	0.000	0.000	0.000	0.000
48	A	214	SER	0	0.012	0.006	12.106	0.059	0.059	0.000	0.000	0.000	0.000
49	A	215	LYS	1	0.809	0.910	14.404	0.300	0.300	0.000	0.000	0.000	0.000
50	A	216	GLN	0	0.011	-0.001	15.950	0.064	0.064	0.000	0.000	0.000	0.000
51	A	217	LYS	1	0.940	0.970	19.527	0.212	0.212	0.000	0.000	0.000	0.000
52	A	218	ASN	0	0.022	0.003	21.058	0.025	0.025	0.000	0.000	0.000	0.000
53	A	219	VAL	0	0.112	0.053	23.934	0.006	0.006	0.000	0.000	0.000	0.000
54	A	220	ASN	0	-0.004	0.000	25.293	0.008	0.008	0.000	0.000	0.000	0.000
55	A	221	LYS	1	0.920	0.971	24.253	0.116	0.116	0.000	0.000	0.000	0.000
56	A	222	ASP	-1	-0.861	-0.931	21.229	-0.152	-0.152	0.000	0.000	0.000	0.000
57	A	223	LYS	1	0.958	0.972	23.526	0.056	0.056	0.000	0.000	0.000	0.000
58	A	224	ARG	1	0.820	0.882	26.424	0.070	0.070	0.000	0.000	0.000	0.000
59	A	225	LYS	1	0.902	0.951	18.790	0.135	0.135	0.000	0.000	0.000	0.000
60	A	226	LEU	0	0.029	0.016	21.087	0.011	0.011	0.000	0.000	0.000	0.000
61	A	227	SER	0	-0.066	-0.036	25.020	0.010	0.010	0.000	0.000	0.000	0.000
62	A	228	GLU	-1	-0.766	-0.860	28.151	-0.047	-0.047	0.000	0.000	0.000	0.000
63	A	229	LEU	0	0.018	0.017	22.890	0.007	0.007	0.000	0.000	0.000	0.000
64	A	230	HIS	0	0.033	0.018	27.058	0.009	0.009	0.000	0.000	0.000	0.000
65	A	231	SER	0	-0.057	-0.030	28.583	0.005	0.005	0.000	0.000	0.000	0.000
66	A	232	LYS	1	0.836	0.911	29.751	0.026	0.026	0.000	0.000	0.000	0.000
67	A	233	GLY	0	-0.016	-0.016	30.536	0.003	0.003	0.000	0.000	0.000	0.000
68	A	234	TYR	0	-0.080	-0.064	24.615	0.008	0.008	0.000	0.000	0.000	0.000
69	A	235	ARG	1	0.823	0.922	24.549	-0.028	-0.028	0.000	0.000	0.000	0.000
70	A	236	VAL	0	0.025	-0.001	19.502	0.005	0.005	0.000	0.000	0.000	0.000
71	A	237	LEU	0	0.021	0.033	16.565	-0.007	-0.007	0.000	0.000	0.000	0.000
72	A	238	THR	0	-0.031	-0.026	16.457	-0.013	-0.013	0.000	0.000	0.000	0.000
73	A	239	ILE	0	-0.016	0.002	11.649	0.024	0.024	0.000	0.000	0.000	0.000
74	A	240	GLU	-1	-0.879	-0.956	13.196	-0.173	-0.173	0.000	0.000	0.000	0.000
75	A	241	ASP	-1	-0.891	-0.981	9.558	-0.247	-0.247	0.000	0.000	0.000	0.000
76	A	242	ASP	-1	-0.886	-0.948	9.957	0.250	0.250	0.000	0.000	0.000	0.000
77	A	243	GLU	-1	-0.817	-0.894	12.533	0.225	0.225	0.000	0.000	0.000	0.000
78	A	244	LEU	0	-0.088	-0.037	6.499	0.111	0.111	0.000	0.000	0.000	0.000
79	A	245	ASN	0	-0.095	-0.043	9.386	0.290	0.290	0.000	0.000	0.000	0.000
80	A	246	ASP	-1	-0.792	-0.879	11.400	0.289	0.289	0.000	0.000	0.000	0.000
81	A	247	ILE	0	0.016	-0.006	9.058	-0.044	-0.044	0.000	0.000	0.000	0.000
82	A	248	ASP	-1	-0.914	-0.946	12.119	0.265	0.265	0.000	0.000	0.000	0.000
83	A	249	LYS	1	0.837	0.904	15.721	-0.299	-0.299	0.000	0.000	0.000	0.000
84	A	250	VAL	0	0.030	0.027	11.055	-0.035	-0.035	0.000	0.000	0.000	0.000
85	A	251	LYS	1	0.881	0.924	11.795	-0.697	-0.697	0.000	0.000	0.000	0.000
86	A	252	GLN	0	0.058	0.039	15.077	-0.065	-0.065	0.000	0.000	0.000	0.000
87	A	253	GLN	0	-0.092	-0.071	16.851	-0.026	-0.026	0.000	0.000	0.000	0.000
88	A	254	ILE	0	0.043	0.011	12.741	-0.034	-0.034	0.000	0.000	0.000	0.000
89	A	255	GLN	0	-0.012	0.004	17.209	-0.011	-0.011	0.000	0.000	0.000	0.000
90	A	256	LYS	1	0.888	0.927	19.803	-0.169	-0.169	0.000	0.000	0.000	0.000
91	A	257	PHE	0	-0.024	0.013	18.925	-0.017	-0.017	0.000	0.000	0.000	0.000
92	A	258	TRP	0	0.080	0.035	19.796	-0.011	-0.011	0.000	0.000	0.000	0.000
93	A	259	VAL	0	0.016	0.003	21.844	-0.011	-0.011	0.000	0.000	0.000	0.000
94	A	260	THR	0	-0.066	-0.060	24.870	-0.012	-0.012	0.000	0.000	0.000	0.000
95	A	261	HIS	0	-0.080	-0.040	24.706	-0.021	-0.021	0.000	0.000	0.000	0.000
96	A	262	ILE	0	-0.051	-0.016	23.823	-0.009	-0.009	0.000	0.000	0.000	0.000
97	A	263	SER	0	-0.049	-0.007	26.503	-0.007	-0.007	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:167:THR)