FMO DATABASE

FMODB ID: 5J81Z

Calculation Name: 3RRU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3RRU

Chain ID: A

ChEMBL ID:

UniProt ID: O75674

Base Structure: X-ray

Registration Date: 2023-09-23

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	141
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1356229.086331
FMO2-HF: Nuclear repulsion	1300158.822047
FMO2-HF: Total energy	-56070.264284
FMO2-MP2: Total energy	-56234.08924

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:9:ASP)

Summations of interaction energy for fragment #1(A:9:ASP)

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.
-236.269	-245.084	38.901	-16.25	-13.837	0.188

Interaction energy analysis for fragmet #1(A:9:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.754 / q_NPA : -0.870

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	11	TYR	0	-0.015	-0.011	1.806	-22.574	-24.745	12.114	-4.937	-5.006	0.050
4	A	12	ALA	0	0.009	0.012	2.711	-12.308	-10.712	0.367	-0.466	-1.497	0.003
5	A	13	THR	0	-0.014	-0.001	4.183	-8.578	-8.309	0.000	-0.046	-0.224	0.000
6	A	14	SER	0	0.031	0.001	6.642	1.127	1.127	0.000	0.000	0.000	0.000
7	A	15	VAL	0	0.031	0.026	10.312	-0.478	-0.478	0.000	0.000	0.000	0.000
8	A	16	GLY	0	0.027	0.007	6.815	-0.648	-0.648	0.000	0.000	0.000	0.000
9	A	17	HIS	0	0.042	0.025	6.509	-2.217	-2.217	0.000	0.000	0.000	0.000
10	A	18	LEU	0	0.000	0.005	7.919	-1.634	-1.634	0.000	0.000	0.000	0.000
11	A	19	ILE	0	0.024	0.017	9.228	-1.177	-1.177	0.000	0.000	0.000	0.000
12	A	20	GLU	-1	-0.892	-0.916	6.071	42.297	42.297	0.000	0.000	0.000	0.000
13	A	21	LYS	1	0.815	0.879	8.648	-32.090	-32.090	0.000	0.000	0.000	0.000
14	A	22	ALA	0	-0.009	-0.001	11.827	-1.547	-1.547	0.000	0.000	0.000	0.000
15	A	23	THR	0	-0.020	-0.024	11.153	-0.393	-0.393	0.000	0.000	0.000	0.000
16	A	24	PHE	0	-0.008	0.003	10.656	0.459	0.459	0.000	0.000	0.000	0.000
17	A	25	ALA	0	0.005	-0.017	13.031	-1.912	-1.912	0.000	0.000	0.000	0.000
18	A	26	GLY	0	-0.047	-0.002	15.572	-1.129	-1.129	0.000	0.000	0.000	0.000
19	A	27	VAL	0	-0.023	-0.002	16.382	-1.206	-1.206	0.000	0.000	0.000	0.000
20	A	28	GLN	0	0.003	-0.006	18.816	0.078	0.078	0.000	0.000	0.000	0.000
21	A	29	THR	0	-0.006	-0.026	21.515	-0.670	-0.670	0.000	0.000	0.000	0.000
22	A	30	GLU	-1	-0.816	-0.890	20.309	15.155	15.155	0.000	0.000	0.000	0.000
23	A	31	ASP	-1	-0.859	-0.908	19.165	14.402	14.402	0.000	0.000	0.000	0.000
24	A	32	TRP	0	0.049	-0.015	20.078	0.788	0.788	0.000	0.000	0.000	0.000
25	A	33	GLY	0	0.021	0.031	22.417	-0.133	-0.133	0.000	0.000	0.000	0.000
26	A	34	GLN	0	0.026	-0.006	14.954	-0.213	-0.213	0.000	0.000	0.000	0.000
27	A	35	PHE	0	-0.065	-0.037	16.977	0.746	0.746	0.000	0.000	0.000	0.000
28	A	36	MET	0	0.035	0.032	18.723	0.446	0.446	0.000	0.000	0.000	0.000
29	A	37	HIS	0	0.041	0.028	17.277	-0.395	-0.395	0.000	0.000	0.000	0.000
30	A	38	ILE	0	-0.030	-0.025	13.715	0.711	0.711	0.000	0.000	0.000	0.000
31	A	39	CYS	0	-0.049	-0.032	16.601	0.412	0.412	0.000	0.000	0.000	0.000
32	A	40	ASP	-1	-0.855	-0.922	19.145	13.457	13.457	0.000	0.000	0.000	0.000
33	A	41	ILE	0	-0.043	-0.007	14.592	0.123	0.123	0.000	0.000	0.000	0.000
34	A	42	ILE	0	-0.080	-0.056	14.514	0.566	0.566	0.000	0.000	0.000	0.000
35	A	43	ASN	0	-0.027	-0.030	17.448	0.003	0.003	0.000	0.000	0.000	0.000
36	A	44	THR	0	-0.032	-0.021	19.449	-0.505	-0.505	0.000	0.000	0.000	0.000
37	A	45	THR	0	-0.050	-0.012	13.526	0.006	0.006	0.000	0.000	0.000	0.000
38	A	46	GLN	0	0.031	0.006	16.656	0.423	0.423	0.000	0.000	0.000	0.000
39	A	47	ASP	-1	-0.751	-0.867	12.197	20.300	20.300	0.000	0.000	0.000	0.000
40	A	48	GLY	0	-0.003	0.005	13.087	1.633	1.633	0.000	0.000	0.000	0.000
41	A	49	PRO	0	0.014	0.002	13.561	1.574	1.574	0.000	0.000	0.000	0.000
42	A	50	LYS	1	0.822	0.896	11.573	-20.066	-20.066	0.000	0.000	0.000	0.000
43	A	51	ASP	-1	-0.860	-0.955	8.844	31.297	31.297	0.000	0.000	0.000	0.000
44	A	52	ALA	0	0.019	0.011	8.923	3.856	3.856	0.000	0.000	0.000	0.000
45	A	53	VAL	0	0.009	0.007	10.450	1.753	1.753	0.000	0.000	0.000	0.000
46	A	54	LYS	1	0.886	0.954	6.346	-30.575	-30.575	0.000	0.000	0.000	0.000
47	A	55	ALA	0	0.007	0.011	6.163	4.332	4.332	0.000	0.000	0.000	0.000
48	A	56	LEU	0	0.029	0.010	7.156	0.688	0.688	0.000	0.000	0.000	0.000
49	A	57	LYS	1	0.866	0.947	9.688	-25.205	-25.205	0.000	0.000	0.000	0.000
50	A	58	LYS	1	0.756	0.867	1.710	-145.492	-154.001	26.420	-10.801	-7.110	0.135
51	A	59	ARG	1	0.819	0.919	7.812	-31.424	-31.424	0.000	0.000	0.000	0.000
52	A	60	ILE	0	0.027	0.019	9.601	-2.657	-2.657	0.000	0.000	0.000	0.000
53	A	61	SER	0	-0.008	-0.014	10.348	-2.777	-2.777	0.000	0.000	0.000	0.000
54	A	62	LYS	1	0.833	0.919	10.916	-26.063	-26.063	0.000	0.000	0.000	0.000
55	A	63	ASN	0	0.001	-0.003	12.389	-1.668	-1.668	0.000	0.000	0.000	0.000
56	A	64	TYR	0	0.045	0.003	14.495	-1.623	-1.623	0.000	0.000	0.000	0.000
57	A	65	ASN	0	0.016	0.023	15.859	-1.971	-1.971	0.000	0.000	0.000	0.000
58	A	66	HIS	0	0.076	0.017	17.586	1.027	1.027	0.000	0.000	0.000	0.000
59	A	67	LYS	1	0.894	0.962	19.035	-14.388	-14.388	0.000	0.000	0.000	0.000
60	A	68	GLU	-1	-0.744	-0.854	12.324	27.282	27.282	0.000	0.000	0.000	0.000
61	A	69	ILE	0	-0.019	0.011	15.485	0.597	0.597	0.000	0.000	0.000	0.000
62	A	70	GLN	0	0.026	0.018	17.054	-0.109	-0.109	0.000	0.000	0.000	0.000
63	A	71	LEU	0	0.004	0.017	16.312	-0.272	-0.272	0.000	0.000	0.000	0.000
64	A	72	THR	0	0.007	-0.038	12.885	0.716	0.716	0.000	0.000	0.000	0.000
65	A	73	LEU	0	-0.063	-0.025	15.424	-0.104	-0.104	0.000	0.000	0.000	0.000
66	A	74	SER	0	-0.013	-0.036	18.635	-0.682	-0.682	0.000	0.000	0.000	0.000
67	A	75	LEU	0	0.013	0.030	13.474	-0.336	-0.336	0.000	0.000	0.000	0.000
68	A	76	ILE	0	-0.010	-0.016	14.968	-0.102	-0.102	0.000	0.000	0.000	0.000
69	A	77	ASP	-1	-0.840	-0.915	17.851	12.928	12.928	0.000	0.000	0.000	0.000
70	A	78	MET	0	0.005	0.023	20.014	-0.650	-0.650	0.000	0.000	0.000	0.000
71	A	79	CYS	0	0.036	0.005	16.967	-0.129	-0.129	0.000	0.000	0.000	0.000
72	A	80	VAL	0	-0.079	-0.044	19.518	-0.313	-0.313	0.000	0.000	0.000	0.000
73	A	81	GLN	0	-0.081	-0.040	22.021	-0.973	-0.973	0.000	0.000	0.000	0.000
74	A	82	ASN	0	-0.006	0.004	22.527	-0.902	-0.902	0.000	0.000	0.000	0.000
75	A	83	CYS	0	-0.018	0.016	20.212	0.359	0.359	0.000	0.000	0.000	0.000
76	A	84	GLY	0	0.055	0.039	22.477	-0.374	-0.374	0.000	0.000	0.000	0.000
77	A	85	PRO	0	0.058	0.011	22.652	0.690	0.690	0.000	0.000	0.000	0.000
78	A	86	SER	0	-0.018	0.008	19.977	0.179	0.179	0.000	0.000	0.000	0.000
79	A	87	PHE	0	0.055	0.025	15.022	0.993	0.993	0.000	0.000	0.000	0.000
80	A	88	GLN	0	0.027	0.005	18.994	0.330	0.330	0.000	0.000	0.000	0.000
81	A	89	SER	0	0.025	-0.022	21.335	-0.109	-0.109	0.000	0.000	0.000	0.000
82	A	90	LEU	0	-0.097	-0.044	14.999	0.163	0.163	0.000	0.000	0.000	0.000
83	A	91	ILE	0	-0.009	0.010	15.868	0.528	0.528	0.000	0.000	0.000	0.000
84	A	92	VAL	0	0.021	0.004	18.260	-0.040	-0.040	0.000	0.000	0.000	0.000
85	A	93	LYS	1	0.928	0.987	17.524	-16.319	-16.319	0.000	0.000	0.000	0.000
86	A	94	LYS	1	0.896	0.921	19.384	-13.037	-13.037	0.000	0.000	0.000	0.000
87	A	95	GLU	-1	-0.927	-0.991	14.384	20.833	20.833	0.000	0.000	0.000	0.000
88	A	96	PHE	0	-0.014	0.007	12.806	1.501	1.501	0.000	0.000	0.000	0.000
89	A	97	VAL	0	0.032	0.012	16.659	0.092	0.092	0.000	0.000	0.000	0.000
90	A	98	LYS	1	0.899	0.948	20.285	-14.440	-14.440	0.000	0.000	0.000	0.000
91	A	99	GLU	-1	-0.824	-0.898	16.780	16.007	16.007	0.000	0.000	0.000	0.000
92	A	100	ASN	0	-0.051	-0.036	13.458	1.462	1.462	0.000	0.000	0.000	0.000
93	A	101	LEU	0	0.050	0.026	16.393	-0.185	-0.185	0.000	0.000	0.000	0.000
94	A	102	VAL	0	0.044	0.016	18.825	-0.398	-0.398	0.000	0.000	0.000	0.000
95	A	103	LYS	1	0.762	0.887	17.962	-18.073	-18.073	0.000	0.000	0.000	0.000
96	A	104	LEU	0	0.001	-0.001	16.371	-0.333	-0.333	0.000	0.000	0.000	0.000
97	A	105	LEU	0	0.003	0.009	20.256	-0.403	-0.403	0.000	0.000	0.000	0.000
98	A	106	ASN	0	-0.053	-0.016	22.548	-0.588	-0.588	0.000	0.000	0.000	0.000
99	A	107	PRO	0	0.078	0.016	23.875	0.449	0.449	0.000	0.000	0.000	0.000
100	A	108	ARG	1	0.913	0.977	20.226	-15.378	-15.378	0.000	0.000	0.000	0.000
101	A	109	TYR	0	-0.003	-0.006	17.373	0.090	0.090	0.000	0.000	0.000	0.000
102	A	110	ASN	0	-0.075	-0.039	21.759	-0.104	-0.104	0.000	0.000	0.000	0.000
103	A	111	LEU	0	0.034	0.042	20.473	-0.264	-0.264	0.000	0.000	0.000	0.000
104	A	112	PRO	0	0.035	0.022	24.055	-0.431	-0.431	0.000	0.000	0.000	0.000
105	A	113	LEU	0	0.057	0.017	26.636	0.325	0.325	0.000	0.000	0.000	0.000
106	A	114	ASP	-1	-0.844	-0.915	27.399	11.123	11.123	0.000	0.000	0.000	0.000
107	A	115	ILE	0	0.002	-0.006	21.577	0.198	0.198	0.000	0.000	0.000	0.000
108	A	116	GLN	0	-0.043	-0.026	24.384	0.083	0.083	0.000	0.000	0.000	0.000
109	A	117	ASN	0	0.006	-0.014	26.211	-0.110	-0.110	0.000	0.000	0.000	0.000
110	A	118	ARG	1	0.829	0.915	22.260	-14.341	-14.341	0.000	0.000	0.000	0.000
111	A	119	ILE	0	-0.006	0.004	20.052	0.186	0.186	0.000	0.000	0.000	0.000
112	A	120	LEU	0	0.005	-0.005	23.884	-0.029	-0.029	0.000	0.000	0.000	0.000
113	A	121	ASN	0	-0.005	-0.023	27.407	-0.470	-0.470	0.000	0.000	0.000	0.000
114	A	122	PHE	0	-0.031	0.010	20.235	-0.135	-0.135	0.000	0.000	0.000	0.000
115	A	123	ILE	0	-0.009	0.006	22.483	-0.119	-0.119	0.000	0.000	0.000	0.000
116	A	124	LYS	1	0.957	0.982	25.846	-9.973	-9.973	0.000	0.000	0.000	0.000
117	A	125	THR	0	-0.014	-0.028	27.294	-0.419	-0.419	0.000	0.000	0.000	0.000
118	A	126	TRP	0	0.016	-0.007	19.334	0.100	0.100	0.000	0.000	0.000	0.000
119	A	127	SER	0	-0.028	-0.021	26.861	-0.250	-0.250	0.000	0.000	0.000	0.000
120	A	128	GLN	0	-0.034	0.002	29.570	-0.359	-0.359	0.000	0.000	0.000	0.000
121	A	129	GLY	0	-0.013	0.013	29.698	-0.313	-0.313	0.000	0.000	0.000	0.000
122	A	130	PHE	0	0.003	-0.012	25.037	0.183	0.183	0.000	0.000	0.000	0.000
123	A	131	PRO	0	0.007	0.007	29.727	-0.184	-0.184	0.000	0.000	0.000	0.000
124	A	132	GLY	0	0.012	-0.006	29.494	0.162	0.162	0.000	0.000	0.000	0.000
125	A	133	GLY	0	-0.016	-0.005	29.265	-0.140	-0.140	0.000	0.000	0.000	0.000
126	A	134	VAL	0	-0.038	-0.007	24.467	0.175	0.175	0.000	0.000	0.000	0.000
127	A	135	ASP	-1	-0.805	-0.873	26.437	11.027	11.027	0.000	0.000	0.000	0.000
128	A	136	VAL	0	0.001	0.000	25.547	0.613	0.613	0.000	0.000	0.000	0.000
129	A	137	SER	0	-0.013	-0.043	27.173	-0.101	-0.101	0.000	0.000	0.000	0.000
130	A	138	GLU	-1	-0.848	-0.907	22.247	14.168	14.168	0.000	0.000	0.000	0.000
131	A	139	VAL	0	0.014	0.005	24.077	-0.020	-0.020	0.000	0.000	0.000	0.000
132	A	140	LYS	1	0.899	0.960	25.786	-10.188	-10.188	0.000	0.000	0.000	0.000
133	A	141	GLU	-1	-0.812	-0.905	29.191	9.794	9.794	0.000	0.000	0.000	0.000
134	A	142	VAL	0	-0.050	-0.032	24.122	-0.019	-0.019	0.000	0.000	0.000	0.000
135	A	143	TYR	0	0.022	0.002	27.428	-0.096	-0.096	0.000	0.000	0.000	0.000
136	A	144	LEU	0	0.015	0.015	29.476	-0.233	-0.233	0.000	0.000	0.000	0.000
137	A	145	ASP	-1	-0.841	-0.916	29.612	10.430	10.430	0.000	0.000	0.000	0.000
138	A	146	LEU	0	-0.036	-0.028	26.200	0.038	0.038	0.000	0.000	0.000	0.000
139	A	147	VAL	0	-0.033	-0.003	30.755	-0.149	-0.149	0.000	0.000	0.000	0.000
140	A	148	LYS	1	0.761	0.874	33.073	-10.166	-10.166	0.000	0.000	0.000	0.000
141	A	149	LYS	1	0.836	0.928	29.027	-11.154	-11.154	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:9:ASP)