FMO DATABASE

FMODB ID: R5G58

Calculation Name: 3OFE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3OFE

Chain ID: A

ChEMBL ID:

UniProt ID: Q8T9B6

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:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
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	81
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-584574.369677
FMO2-HF: Nuclear repulsion	551031.961003
FMO2-HF: Total energy	-33542.408674
FMO2-MP2: Total energy	-33639.810838

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:92:ARG)

Summations of interaction energy for fragment #1(A:92: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.
-152.311	-144.543	12.152	-9.503	-10.415	-0.106

Interaction energy analysis for fragmet #1(A:92:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.879 / q_NPA : 0.915

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	94	LEU	0	0.027	0.022	3.812	1.430	2.892	-0.025	-0.613	-0.823	0.002
4	A	95	MET	0	-0.039	-0.010	6.700	0.939	0.939	0.000	0.000	0.000	0.000
5	A	96	THR	0	-0.019	-0.006	10.205	0.472	0.472	0.000	0.000	0.000	0.000
6	A	97	PHE	0	0.012	-0.010	13.139	0.560	0.560	0.000	0.000	0.000	0.000
7	A	98	VAL	0	0.046	0.024	16.424	-0.059	-0.059	0.000	0.000	0.000	0.000
8	A	99	SER	0	0.013	0.002	19.077	0.616	0.616	0.000	0.000	0.000	0.000
9	A	100	VAL	0	-0.009	0.004	22.814	-0.115	-0.115	0.000	0.000	0.000	0.000
10	A	101	THR	0	-0.033	-0.013	25.822	0.351	0.351	0.000	0.000	0.000	0.000
11	A	102	GLY	0	0.012	0.002	29.100	0.076	0.076	0.000	0.000	0.000	0.000
12	A	103	ASN	0	-0.037	-0.030	31.920	-0.180	-0.180	0.000	0.000	0.000	0.000
13	A	104	PRO	0	0.002	0.017	28.592	0.262	0.262	0.000	0.000	0.000	0.000
14	A	105	THR	0	0.047	0.026	31.348	-0.046	-0.046	0.000	0.000	0.000	0.000
15	A	106	ARG	1	0.924	0.949	25.169	10.711	10.711	0.000	0.000	0.000	0.000
16	A	107	GLU	-1	-0.898	-0.946	27.350	-10.676	-10.676	0.000	0.000	0.000	0.000
17	A	108	GLU	-1	-0.899	-0.950	28.556	-9.642	-9.642	0.000	0.000	0.000	0.000
18	A	109	SER	0	0.025	-0.022	25.145	-0.333	-0.333	0.000	0.000	0.000	0.000
19	A	110	ASP	-1	-0.844	-0.885	23.509	-13.264	-13.264	0.000	0.000	0.000	0.000
20	A	111	THR	0	-0.011	-0.006	23.696	-0.533	-0.533	0.000	0.000	0.000	0.000
21	A	112	ILE	0	-0.024	-0.015	24.456	-0.312	-0.312	0.000	0.000	0.000	0.000
22	A	113	THR	0	-0.009	-0.012	20.117	-0.656	-0.656	0.000	0.000	0.000	0.000
23	A	114	LYS	1	0.984	0.991	19.915	11.792	11.792	0.000	0.000	0.000	0.000
24	A	115	LEU	0	0.011	0.025	20.664	-0.548	-0.548	0.000	0.000	0.000	0.000
25	A	116	TRP	0	0.020	0.001	19.255	-0.698	-0.698	0.000	0.000	0.000	0.000
26	A	117	GLN	0	0.016	0.007	14.958	0.215	0.215	0.000	0.000	0.000	0.000
27	A	118	THR	0	-0.051	-0.031	16.464	-0.987	-0.987	0.000	0.000	0.000	0.000
28	A	119	SER	0	-0.040	-0.012	17.988	-0.381	-0.381	0.000	0.000	0.000	0.000
29	A	120	LEU	0	0.020	0.020	13.402	-0.402	-0.402	0.000	0.000	0.000	0.000
30	A	121	TRP	0	0.007	0.010	12.844	-1.932	-1.932	0.000	0.000	0.000	0.000
31	A	122	ASN	0	-0.062	-0.040	14.400	-0.842	-0.842	0.000	0.000	0.000	0.000
32	A	123	ASN	0	-0.076	-0.035	14.500	0.908	0.908	0.000	0.000	0.000	0.000
33	A	124	HIS	0	-0.030	-0.015	10.405	-1.978	-1.978	0.000	0.000	0.000	0.000
34	A	125	ILE	0	0.007	0.015	9.040	-3.500	-3.500	0.000	0.000	0.000	0.000
35	A	126	GLN	0	-0.019	-0.008	9.140	1.093	1.093	0.000	0.000	0.000	0.000
36	A	127	ALA	0	0.006	-0.004	8.906	-2.990	-2.990	0.000	0.000	0.000	0.000
37	A	128	GLU	-1	-0.889	-0.929	10.301	-20.959	-20.959	0.000	0.000	0.000	0.000
38	A	129	ARG	1	0.802	0.883	12.882	14.256	14.256	0.000	0.000	0.000	0.000
39	A	130	TYR	0	-0.035	-0.033	12.500	1.178	1.178	0.000	0.000	0.000	0.000
40	A	131	MET	0	-0.006	0.018	17.819	-0.338	-0.338	0.000	0.000	0.000	0.000
41	A	132	VAL	0	-0.054	-0.030	18.750	0.256	0.256	0.000	0.000	0.000	0.000
42	A	133	ASP	-1	-0.810	-0.892	21.822	-11.461	-11.461	0.000	0.000	0.000	0.000
43	A	134	ASP	-1	-0.839	-0.922	25.109	-10.245	-10.245	0.000	0.000	0.000	0.000
44	A	135	ASN	0	-0.029	0.003	26.397	-0.199	-0.199	0.000	0.000	0.000	0.000
45	A	136	ARG	1	0.851	0.925	20.574	12.697	12.697	0.000	0.000	0.000	0.000
46	A	137	ALA	0	0.037	0.006	19.026	0.212	0.212	0.000	0.000	0.000	0.000
47	A	138	ILE	0	-0.021	-0.010	13.576	-0.285	-0.285	0.000	0.000	0.000	0.000
48	A	139	PHE	0	-0.004	-0.001	13.036	0.351	0.351	0.000	0.000	0.000	0.000
49	A	140	LEU	0	-0.009	-0.002	8.041	-0.851	-0.851	0.000	0.000	0.000	0.000
50	A	141	PHE	0	0.032	0.009	7.316	-0.075	-0.075	0.000	0.000	0.000	0.000
51	A	142	LYS	1	0.918	0.953	5.533	24.363	24.363	0.000	0.000	0.000	0.000
52	A	143	ASP	-1	-0.780	-0.877	1.979	-136.178	-132.622	11.990	-7.879	-7.666	-0.107
53	A	144	GLY	0	0.032	-0.005	3.262	6.104	7.206	0.009	-0.429	-0.682	0.000
54	A	145	THR	0	-0.104	-0.061	2.735	11.341	12.989	0.178	-0.582	-1.244	-0.001
55	A	146	GLN	0	0.055	0.015	5.036	4.708	4.708	0.000	0.000	0.000	0.000
56	A	147	ALA	0	-0.026	0.004	7.259	4.403	4.403	0.000	0.000	0.000	0.000
57	A	148	TRP	0	-0.016	-0.028	7.766	2.462	2.462	0.000	0.000	0.000	0.000
58	A	149	ASP	-1	-0.826	-0.898	10.522	-24.678	-24.678	0.000	0.000	0.000	0.000
59	A	150	ALA	0	-0.034	-0.023	11.480	1.877	1.877	0.000	0.000	0.000	0.000
60	A	151	LYS	1	0.807	0.894	13.185	20.041	20.041	0.000	0.000	0.000	0.000
61	A	152	ASP	-1	-0.826	-0.903	15.389	-17.377	-17.377	0.000	0.000	0.000	0.000
62	A	153	PHE	0	0.010	0.012	16.358	1.046	1.046	0.000	0.000	0.000	0.000
63	A	154	LEU	0	-0.031	-0.032	15.634	1.005	1.005	0.000	0.000	0.000	0.000
64	A	155	ILE	0	-0.029	-0.033	19.167	0.719	0.719	0.000	0.000	0.000	0.000
65	A	156	GLU	-1	-0.926	-0.948	21.436	-12.296	-12.296	0.000	0.000	0.000	0.000
66	A	157	GLN	0	-0.116	-0.038	21.425	0.930	0.930	0.000	0.000	0.000	0.000
67	A	158	GLU	-1	-0.896	-0.950	24.271	-10.117	-10.117	0.000	0.000	0.000	0.000
68	A	159	ARG	1	0.860	0.905	26.928	10.135	10.135	0.000	0.000	0.000	0.000
69	A	160	CYS	0	0.008	0.033	21.583	-0.153	-0.153	0.000	0.000	0.000	0.000
70	A	161	LYS	1	0.920	0.943	24.530	11.003	11.003	0.000	0.000	0.000	0.000
71	A	162	GLY	0	0.055	0.027	22.301	0.307	0.307	0.000	0.000	0.000	0.000
72	A	163	VAL	0	-0.026	-0.008	15.655	-0.280	-0.280	0.000	0.000	0.000	0.000
73	A	164	THR	0	-0.021	-0.003	16.504	0.343	0.343	0.000	0.000	0.000	0.000
74	A	165	ILE	0	0.019	-0.004	11.411	-0.856	-0.856	0.000	0.000	0.000	0.000
75	A	166	GLU	-1	-0.911	-0.952	10.542	-21.405	-21.405	0.000	0.000	0.000	0.000
76	A	167	ASN	0	-0.041	-0.040	13.424	0.888	0.888	0.000	0.000	0.000	0.000
77	A	168	LYS	1	0.899	0.975	14.515	19.580	19.580	0.000	0.000	0.000	0.000
78	A	169	GLU	-1	-0.930	-0.972	17.724	-13.740	-13.740	0.000	0.000	0.000	0.000
79	A	170	TYR	0	-0.035	-0.026	15.984	-0.206	-0.206	0.000	0.000	0.000	0.000
80	A	171	PRO	0	-0.007	-0.011	20.895	-0.183	-0.183	0.000	0.000	0.000	0.000
81	A	172	GLY	0	0.031	0.031	23.856	0.015	0.015	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:92:ARG)