FMO DATABASE

FMODB ID: KGM43

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1351816.885622
FMO2-HF: Nuclear repulsion	1295748.746046
FMO2-HF: Total energy	-56068.139576
FMO2-MP2: Total energy	-56232.094306

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.
-181.617	-180.079	17.123	-8.422	-10.24	0.093

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 : -0.864 / q_NPA : -0.949

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	-0.057	-0.029	1.827	-26.292	-29.277	14.064	-5.509	-5.569	0.057
4	A	12	ALA	0	0.007	0.021	2.241	-15.308	-14.085	2.882	-1.051	-3.055	0.019
5	A	13	THR	0	0.028	0.013	3.977	-11.737	-11.265	0.021	-0.216	-0.278	0.001
6	A	14	SER	0	0.030	0.012	6.967	1.097	1.097	0.000	0.000	0.000	0.000
7	A	15	VAL	0	0.061	0.025	10.059	0.218	0.218	0.000	0.000	0.000	0.000
8	A	16	GLY	0	0.029	0.017	6.420	-0.787	-0.787	0.000	0.000	0.000	0.000
9	A	17	HIS	0	0.010	-0.004	6.938	-3.003	-3.003	0.000	0.000	0.000	0.000
10	A	18	LEU	0	-0.012	-0.008	7.707	-1.678	-1.678	0.000	0.000	0.000	0.000
11	A	19	ILE	0	0.029	0.019	9.199	-1.785	-1.785	0.000	0.000	0.000	0.000
12	A	20	GLU	-1	-0.959	-0.976	6.685	44.860	44.860	0.000	0.000	0.000	0.000
13	A	21	LYS	1	0.937	0.955	8.817	-28.124	-28.124	0.000	0.000	0.000	0.000
14	A	22	ALA	0	-0.001	0.008	11.821	-1.723	-1.723	0.000	0.000	0.000	0.000
15	A	23	THR	0	-0.035	-0.010	11.886	-0.803	-0.803	0.000	0.000	0.000	0.000
16	A	24	PHE	0	-0.027	-0.015	10.749	0.146	0.146	0.000	0.000	0.000	0.000
17	A	25	ALA	0	0.016	-0.002	13.606	-1.598	-1.598	0.000	0.000	0.000	0.000
18	A	26	GLY	0	-0.081	-0.025	15.964	-1.131	-1.131	0.000	0.000	0.000	0.000
19	A	27	VAL	0	0.016	0.020	16.686	-1.116	-1.116	0.000	0.000	0.000	0.000
20	A	28	GLN	0	0.000	0.003	19.412	0.138	0.138	0.000	0.000	0.000	0.000
21	A	29	THR	0	0.028	-0.021	21.879	-0.655	-0.655	0.000	0.000	0.000	0.000
22	A	30	GLU	-1	-0.850	-0.927	20.701	14.798	14.798	0.000	0.000	0.000	0.000
23	A	31	ASP	-1	-0.864	-0.922	19.326	14.521	14.521	0.000	0.000	0.000	0.000
24	A	32	TRP	0	0.035	-0.022	20.489	0.682	0.682	0.000	0.000	0.000	0.000
25	A	33	GLY	0	0.012	0.025	22.668	-0.090	-0.090	0.000	0.000	0.000	0.000
26	A	34	GLN	0	0.015	0.006	15.495	-0.310	-0.310	0.000	0.000	0.000	0.000
27	A	35	PHE	0	-0.025	-0.031	16.671	0.784	0.784	0.000	0.000	0.000	0.000
28	A	36	MET	0	0.023	0.025	18.832	0.418	0.418	0.000	0.000	0.000	0.000
29	A	37	HIS	0	0.056	0.033	16.884	-0.245	-0.245	0.000	0.000	0.000	0.000
30	A	38	ILE	0	-0.059	-0.037	13.513	0.756	0.756	0.000	0.000	0.000	0.000
31	A	39	CYS	0	-0.024	-0.017	16.519	0.553	0.553	0.000	0.000	0.000	0.000
32	A	40	ASP	-1	-0.849	-0.920	18.862	13.801	13.801	0.000	0.000	0.000	0.000
33	A	41	ILE	0	-0.066	-0.037	14.394	0.056	0.056	0.000	0.000	0.000	0.000
34	A	42	ILE	0	-0.106	-0.056	13.937	0.516	0.516	0.000	0.000	0.000	0.000
35	A	43	ASN	0	0.003	-0.027	16.874	0.073	0.073	0.000	0.000	0.000	0.000
36	A	44	THR	0	-0.068	-0.003	19.050	-0.363	-0.363	0.000	0.000	0.000	0.000
37	A	45	THR	0	-0.054	-0.029	13.933	-0.121	-0.121	0.000	0.000	0.000	0.000
38	A	46	GLN	0	0.015	-0.007	16.300	0.312	0.312	0.000	0.000	0.000	0.000
39	A	47	ASP	-1	-0.868	-0.935	11.891	20.026	20.026	0.000	0.000	0.000	0.000
40	A	48	GLY	0	0.002	0.017	12.454	1.618	1.618	0.000	0.000	0.000	0.000
41	A	49	PRO	0	0.044	0.006	13.253	1.531	1.531	0.000	0.000	0.000	0.000
42	A	50	LYS	1	0.963	0.976	10.828	-21.298	-21.298	0.000	0.000	0.000	0.000
43	A	51	ASP	-1	-0.895	-0.960	8.770	29.472	29.472	0.000	0.000	0.000	0.000
44	A	52	ALA	0	0.013	0.021	8.894	3.494	3.494	0.000	0.000	0.000	0.000
45	A	53	VAL	0	-0.001	-0.005	10.496	1.805	1.805	0.000	0.000	0.000	0.000
46	A	54	LYS	1	0.900	0.954	6.689	-29.520	-29.520	0.000	0.000	0.000	0.000
47	A	55	ALA	0	0.024	0.017	6.633	3.617	3.617	0.000	0.000	0.000	0.000
48	A	56	LEU	0	0.031	0.006	7.533	-0.048	-0.048	0.000	0.000	0.000	0.000
49	A	57	LYS	1	0.899	0.961	9.664	-25.512	-25.512	0.000	0.000	0.000	0.000
50	A	58	LYS	1	0.867	0.947	2.980	-88.720	-85.892	0.156	-1.646	-1.338	0.016
51	A	59	ARG	1	0.881	0.967	8.844	-31.067	-31.067	0.000	0.000	0.000	0.000
52	A	60	ILE	0	0.021	0.017	10.506	-2.155	-2.155	0.000	0.000	0.000	0.000
53	A	61	SER	0	-0.021	-0.034	11.621	-2.268	-2.268	0.000	0.000	0.000	0.000
54	A	62	LYS	1	0.844	0.924	13.066	-22.206	-22.206	0.000	0.000	0.000	0.000
55	A	63	ASN	0	0.036	0.013	13.652	-1.277	-1.277	0.000	0.000	0.000	0.000
56	A	64	TYR	0	0.006	-0.012	15.723	-1.410	-1.410	0.000	0.000	0.000	0.000
57	A	65	ASN	0	0.000	0.013	16.799	-2.045	-2.045	0.000	0.000	0.000	0.000
58	A	66	HIS	0	0.076	0.021	18.623	0.595	0.595	0.000	0.000	0.000	0.000
59	A	67	LYS	1	0.963	0.988	19.623	-13.337	-13.337	0.000	0.000	0.000	0.000
60	A	68	GLU	-1	-0.821	-0.872	13.962	24.237	24.237	0.000	0.000	0.000	0.000
61	A	69	ILE	0	0.006	0.017	16.331	0.628	0.628	0.000	0.000	0.000	0.000
62	A	70	GLN	0	-0.015	-0.012	17.941	-0.037	-0.037	0.000	0.000	0.000	0.000
63	A	71	LEU	0	0.027	0.015	17.240	-0.258	-0.258	0.000	0.000	0.000	0.000
64	A	72	THR	0	0.002	-0.028	13.890	0.697	0.697	0.000	0.000	0.000	0.000
65	A	73	LEU	0	-0.060	-0.025	16.273	-0.178	-0.178	0.000	0.000	0.000	0.000
66	A	74	SER	0	-0.024	-0.018	19.343	-0.607	-0.607	0.000	0.000	0.000	0.000
67	A	75	LEU	0	0.003	0.030	13.823	-0.247	-0.247	0.000	0.000	0.000	0.000
68	A	76	ILE	0	-0.049	-0.033	16.064	0.016	0.016	0.000	0.000	0.000	0.000
69	A	77	ASP	-1	-0.944	-0.986	18.373	12.585	12.585	0.000	0.000	0.000	0.000
70	A	78	MET	0	0.010	0.019	20.248	-0.603	-0.603	0.000	0.000	0.000	0.000
71	A	79	CYS	0	0.006	-0.014	17.355	-0.103	-0.103	0.000	0.000	0.000	0.000
72	A	80	VAL	0	-0.097	-0.056	19.960	-0.323	-0.323	0.000	0.000	0.000	0.000
73	A	81	GLN	0	-0.058	-0.025	22.299	-0.828	-0.828	0.000	0.000	0.000	0.000
74	A	82	ASN	0	0.005	0.018	22.547	-0.708	-0.708	0.000	0.000	0.000	0.000
75	A	83	CYS	0	-0.042	0.000	18.835	0.081	0.081	0.000	0.000	0.000	0.000
76	A	84	GLY	0	0.054	0.045	22.493	-0.279	-0.279	0.000	0.000	0.000	0.000
77	A	85	PRO	0	0.103	0.027	23.011	0.608	0.608	0.000	0.000	0.000	0.000
78	A	86	SER	0	-0.020	-0.005	19.722	0.290	0.290	0.000	0.000	0.000	0.000
79	A	87	PHE	0	0.024	0.018	15.260	1.004	1.004	0.000	0.000	0.000	0.000
80	A	88	GLN	0	0.029	0.010	19.256	0.306	0.306	0.000	0.000	0.000	0.000
81	A	89	SER	0	0.009	-0.010	21.201	-0.280	-0.280	0.000	0.000	0.000	0.000
82	A	90	LEU	0	-0.092	-0.049	14.831	0.098	0.098	0.000	0.000	0.000	0.000
83	A	91	ILE	0	0.005	0.014	16.187	0.733	0.733	0.000	0.000	0.000	0.000
84	A	92	VAL	0	-0.018	-0.006	18.505	-0.125	-0.125	0.000	0.000	0.000	0.000
85	A	93	LYS	1	0.962	1.012	17.651	-15.701	-15.701	0.000	0.000	0.000	0.000
86	A	94	LYS	1	0.961	0.963	19.237	-12.352	-12.352	0.000	0.000	0.000	0.000
87	A	95	GLU	-1	-0.969	-1.007	15.481	18.164	18.164	0.000	0.000	0.000	0.000
88	A	96	PHE	0	-0.032	-0.002	13.439	1.278	1.278	0.000	0.000	0.000	0.000
89	A	97	VAL	0	0.066	0.011	16.586	0.080	0.080	0.000	0.000	0.000	0.000
90	A	98	LYS	1	0.950	0.981	19.927	-12.983	-12.983	0.000	0.000	0.000	0.000
91	A	99	GLU	-1	-0.969	-0.978	16.369	15.179	15.179	0.000	0.000	0.000	0.000
92	A	100	ASN	0	-0.058	-0.047	13.006	1.101	1.101	0.000	0.000	0.000	0.000
93	A	101	LEU	0	0.025	0.027	16.767	-0.226	-0.226	0.000	0.000	0.000	0.000
94	A	102	VAL	0	0.031	0.010	19.393	-0.363	-0.363	0.000	0.000	0.000	0.000
95	A	103	LYS	1	0.929	0.973	18.936	-15.552	-15.552	0.000	0.000	0.000	0.000
96	A	104	LEU	0	0.008	0.001	17.916	-0.444	-0.444	0.000	0.000	0.000	0.000
97	A	105	LEU	0	-0.006	0.010	21.438	-0.342	-0.342	0.000	0.000	0.000	0.000
98	A	106	ASN	0	-0.072	-0.024	23.752	-0.598	-0.598	0.000	0.000	0.000	0.000
99	A	107	PRO	0	0.110	0.028	25.500	0.292	0.292	0.000	0.000	0.000	0.000
100	A	108	ARG	1	0.916	0.983	21.843	-14.176	-14.176	0.000	0.000	0.000	0.000
101	A	109	TYR	0	-0.033	-0.023	18.533	0.135	0.135	0.000	0.000	0.000	0.000
102	A	110	ASN	0	-0.044	-0.026	23.223	-0.111	-0.111	0.000	0.000	0.000	0.000
103	A	111	LEU	0	0.027	0.035	22.256	-0.118	-0.118	0.000	0.000	0.000	0.000
104	A	112	PRO	0	0.015	0.005	25.174	-0.426	-0.426	0.000	0.000	0.000	0.000
105	A	113	LEU	0	0.077	0.008	27.772	0.279	0.279	0.000	0.000	0.000	0.000
106	A	114	ASP	-1	-0.931	-0.934	28.344	10.780	10.780	0.000	0.000	0.000	0.000
107	A	115	ILE	0	0.019	-0.014	22.434	0.123	0.123	0.000	0.000	0.000	0.000
108	A	116	GLN	0	-0.028	-0.004	25.249	0.559	0.559	0.000	0.000	0.000	0.000
109	A	117	ASN	0	0.045	-0.001	27.138	0.065	0.065	0.000	0.000	0.000	0.000
110	A	118	ARG	1	0.894	0.959	22.526	-13.789	-13.789	0.000	0.000	0.000	0.000
111	A	119	ILE	0	0.012	0.012	21.595	0.217	0.217	0.000	0.000	0.000	0.000
112	A	120	LEU	0	-0.005	-0.008	24.882	0.021	0.021	0.000	0.000	0.000	0.000
113	A	121	ASN	0	0.027	0.006	28.195	-0.346	-0.346	0.000	0.000	0.000	0.000
114	A	122	PHE	0	-0.006	0.017	21.220	-0.129	-0.129	0.000	0.000	0.000	0.000
115	A	123	ILE	0	-0.018	0.016	23.473	-0.131	-0.131	0.000	0.000	0.000	0.000
116	A	124	LYS	1	0.962	0.974	26.662	-9.522	-9.522	0.000	0.000	0.000	0.000
117	A	125	THR	0	-0.014	-0.018	28.112	-0.426	-0.426	0.000	0.000	0.000	0.000
118	A	126	TRP	0	0.016	-0.015	20.275	0.104	0.104	0.000	0.000	0.000	0.000
119	A	127	SER	0	-0.043	-0.023	27.284	-0.151	-0.151	0.000	0.000	0.000	0.000
120	A	128	GLN	0	-0.074	-0.025	29.630	-0.381	-0.381	0.000	0.000	0.000	0.000
121	A	129	GLY	0	-0.019	0.014	29.800	-0.280	-0.280	0.000	0.000	0.000	0.000
122	A	130	PHE	0	-0.011	-0.020	25.006	0.137	0.137	0.000	0.000	0.000	0.000
123	A	131	PRO	0	0.005	0.007	29.585	-0.203	-0.203	0.000	0.000	0.000	0.000
124	A	132	GLY	0	0.024	0.004	29.917	0.288	0.288	0.000	0.000	0.000	0.000
125	A	133	GLY	0	-0.028	-0.027	28.056	-0.063	-0.063	0.000	0.000	0.000	0.000
126	A	134	VAL	0	-0.021	-0.006	25.243	-0.034	-0.034	0.000	0.000	0.000	0.000
127	A	135	ASP	-1	-0.812	-0.880	25.867	10.805	10.805	0.000	0.000	0.000	0.000
128	A	136	VAL	0	0.003	-0.012	25.742	0.473	0.473	0.000	0.000	0.000	0.000
129	A	137	SER	0	0.015	-0.009	27.436	-0.248	-0.248	0.000	0.000	0.000	0.000
130	A	138	GLU	-1	-0.861	-0.929	22.616	13.524	13.524	0.000	0.000	0.000	0.000
131	A	139	VAL	0	-0.005	-0.006	24.238	-0.087	-0.087	0.000	0.000	0.000	0.000
132	A	140	LYS	1	0.945	0.978	25.731	-9.702	-9.702	0.000	0.000	0.000	0.000
133	A	141	GLU	-1	-0.908	-0.958	28.733	9.518	9.518	0.000	0.000	0.000	0.000
134	A	142	VAL	0	-0.073	-0.030	24.037	0.002	0.002	0.000	0.000	0.000	0.000
135	A	143	TYR	0	0.026	-0.006	27.237	-0.135	-0.135	0.000	0.000	0.000	0.000
136	A	144	LEU	0	0.023	0.008	29.552	-0.274	-0.274	0.000	0.000	0.000	0.000
137	A	145	ASP	-1	-0.923	-0.956	29.461	10.164	10.164	0.000	0.000	0.000	0.000
138	A	146	LEU	0	-0.096	-0.058	26.715	-0.110	-0.110	0.000	0.000	0.000	0.000
139	A	147	VAL	0	-0.051	-0.006	30.925	-0.170	-0.170	0.000	0.000	0.000	0.000
140	A	148	LYS	1	0.911	0.967	34.408	-9.329	-9.329	0.000	0.000	0.000	0.000
141	A	149	LYS	1	0.947	0.987	28.882	-10.865	-10.865	0.000	0.000	0.000	0.000

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