FMO DATABASE

FMODB ID: 82LLY

Calculation Name: 2RKK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2RKK

Chain ID: A

ChEMBL ID:

UniProt ID: Q06263

Base Structure: X-ray

Registration Date: 2023-06-20

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	157
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1570490.060914
FMO2-HF: Nuclear repulsion	1506251.977049
FMO2-HF: Total energy	-64238.083865
FMO2-MP2: Total energy	-64421.136893

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:1:SER)

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

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.
-4.799	-5.392	6.926	-2.902	-3.429	-0.017

Interaction energy analysis for fragmet #1(A:1:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / q_NPA : -0.012

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	2	ALA	0	0.107	0.035	3.880	-2.200	-0.870	0.003	-0.561	-0.771	0.002
4	A	3	SER	0	-0.022	-0.013	1.968	-4.442	-6.661	6.923	-2.265	-2.439	-0.019
5	A	4	ASN	0	-0.024	0.001	4.044	0.301	0.597	0.000	-0.076	-0.219	0.000
6	A	5	ALA	0	0.077	0.032	6.283	0.139	0.139	0.000	0.000	0.000	0.000
7	A	6	ALA	0	0.022	0.013	7.300	-0.010	-0.010	0.000	0.000	0.000	0.000
8	A	7	ARG	1	0.757	0.844	7.715	0.075	0.075	0.000	0.000	0.000	0.000
9	A	8	VAL	0	0.016	0.029	10.161	0.037	0.037	0.000	0.000	0.000	0.000
10	A	9	VAL	0	0.051	0.024	11.929	-0.002	-0.002	0.000	0.000	0.000	0.000
11	A	10	ALA	0	-0.019	-0.005	12.679	-0.001	-0.001	0.000	0.000	0.000	0.000
12	A	11	THR	0	-0.072	-0.057	13.805	-0.001	-0.001	0.000	0.000	0.000	0.000
13	A	12	ALA	0	-0.024	-0.008	16.017	0.003	0.003	0.000	0.000	0.000	0.000
14	A	13	LYS	1	0.951	0.967	16.408	-0.079	-0.079	0.000	0.000	0.000	0.000
15	A	14	ASP	-1	-0.841	-0.901	18.499	-0.019	-0.019	0.000	0.000	0.000	0.000
16	A	15	PHE	0	-0.020	-0.028	20.212	0.001	0.001	0.000	0.000	0.000	0.000
17	A	16	ASP	-1	-0.817	-0.909	21.738	0.055	0.055	0.000	0.000	0.000	0.000
18	A	17	LYS	1	0.822	0.910	22.570	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	18	VAL	0	-0.068	-0.032	24.641	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	19	GLY	0	0.041	0.026	26.818	0.000	0.000	0.000	0.000	0.000	0.000
21	A	20	LEU	0	-0.049	-0.022	24.892	0.002	0.002	0.000	0.000	0.000	0.000
22	A	21	GLY	0	0.049	0.020	25.226	0.005	0.005	0.000	0.000	0.000	0.000
23	A	22	ILE	0	0.020	0.010	24.935	0.006	0.006	0.000	0.000	0.000	0.000
24	A	23	ILE	0	-0.023	-0.018	21.555	0.008	0.008	0.000	0.000	0.000	0.000
25	A	24	GLY	0	0.048	0.035	20.447	0.009	0.009	0.000	0.000	0.000	0.000
26	A	25	TYR	0	0.035	0.023	20.176	0.011	0.011	0.000	0.000	0.000	0.000
27	A	26	TYR	0	-0.009	-0.023	21.203	0.011	0.011	0.000	0.000	0.000	0.000
28	A	27	LEU	0	-0.009	-0.018	16.504	0.017	0.017	0.000	0.000	0.000	0.000
29	A	28	GLN	0	-0.049	-0.041	16.415	0.022	0.022	0.000	0.000	0.000	0.000
30	A	29	LEU	0	0.033	0.019	17.219	0.019	0.019	0.000	0.000	0.000	0.000
31	A	30	TYR	0	0.012	-0.005	12.393	0.040	0.040	0.000	0.000	0.000	0.000
32	A	31	ALA	0	-0.006	-0.003	13.051	0.038	0.038	0.000	0.000	0.000	0.000
33	A	32	VAL	0	0.003	0.003	13.336	0.051	0.051	0.000	0.000	0.000	0.000
34	A	33	GLU	-1	-0.872	-0.932	15.045	0.213	0.213	0.000	0.000	0.000	0.000
35	A	34	LEU	0	-0.024	-0.011	9.308	0.028	0.028	0.000	0.000	0.000	0.000
36	A	35	ILE	0	-0.010	-0.012	10.354	0.078	0.078	0.000	0.000	0.000	0.000
37	A	36	LEU	0	-0.074	-0.042	11.433	0.014	0.014	0.000	0.000	0.000	0.000
38	A	37	SER	0	-0.079	-0.039	10.981	-0.018	-0.018	0.000	0.000	0.000	0.000
39	A	38	GLU	-1	-0.913	-0.959	5.536	0.871	0.871	0.000	0.000	0.000	0.000
40	A	39	GLU	-1	-0.926	-0.971	9.884	0.057	0.057	0.000	0.000	0.000	0.000
41	A	40	ASP	-1	-0.954	-0.970	8.466	-0.024	-0.024	0.000	0.000	0.000	0.000
42	A	41	ARG	1	0.885	0.956	9.414	-0.162	-0.162	0.000	0.000	0.000	0.000
43	A	42	SER	0	0.054	0.026	9.322	-0.105	-0.105	0.000	0.000	0.000	0.000
44	A	43	GLN	0	0.017	-0.010	11.136	-0.027	-0.027	0.000	0.000	0.000	0.000
45	A	44	GLU	-1	-0.912	-0.954	8.699	0.722	0.722	0.000	0.000	0.000	0.000
46	A	45	MET	0	0.011	0.010	8.211	-0.042	-0.042	0.000	0.000	0.000	0.000
47	A	46	THR	0	-0.026	-0.013	11.639	-0.072	-0.072	0.000	0.000	0.000	0.000
48	A	47	ALA	0	-0.002	0.001	15.054	-0.037	-0.037	0.000	0.000	0.000	0.000
49	A	48	LEU	0	0.022	0.010	10.973	-0.027	-0.027	0.000	0.000	0.000	0.000
50	A	49	ALA	0	0.016	-0.004	14.786	-0.027	-0.027	0.000	0.000	0.000	0.000
51	A	50	THR	0	-0.026	-0.014	16.169	-0.027	-0.027	0.000	0.000	0.000	0.000
52	A	51	GLU	-1	-0.882	-0.929	17.323	0.097	0.097	0.000	0.000	0.000	0.000
53	A	52	LEU	0	-0.019	-0.006	14.189	-0.016	-0.016	0.000	0.000	0.000	0.000
54	A	53	LEU	0	-0.005	-0.008	18.793	-0.012	-0.012	0.000	0.000	0.000	0.000
55	A	54	ASP	-1	-0.940	-0.951	21.509	0.067	0.067	0.000	0.000	0.000	0.000
56	A	55	THR	0	0.004	-0.010	21.345	-0.012	-0.012	0.000	0.000	0.000	0.000
57	A	56	ILE	0	-0.054	-0.024	19.606	-0.008	-0.008	0.000	0.000	0.000	0.000
58	A	57	GLU	-1	-0.876	-0.925	23.841	0.062	0.062	0.000	0.000	0.000	0.000
59	A	58	ALA	0	-0.002	-0.002	26.742	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	59	PHE	0	-0.018	-0.014	26.100	-0.006	-0.006	0.000	0.000	0.000	0.000
61	A	60	LYS	1	0.873	0.918	27.836	-0.076	-0.076	0.000	0.000	0.000	0.000
62	A	61	LYS	1	0.855	0.911	29.604	-0.059	-0.059	0.000	0.000	0.000	0.000
63	A	62	GLU	-1	-0.905	-0.936	31.845	0.034	0.034	0.000	0.000	0.000	0.000
64	A	63	ILE	0	-0.090	-0.028	30.594	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	64	GLY	0	-0.054	-0.032	34.062	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	76	LEU	0	0.030	0.006	35.453	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	77	HIS	0	0.062	0.013	37.024	0.003	0.003	0.000	0.000	0.000	0.000
68	A	78	VAL	0	-0.005	0.003	38.655	0.001	0.001	0.000	0.000	0.000	0.000
69	A	79	MET	0	-0.013	-0.012	33.876	0.001	0.001	0.000	0.000	0.000	0.000
70	A	80	ASN	0	0.053	0.035	33.895	0.002	0.002	0.000	0.000	0.000	0.000
71	A	81	THR	0	-0.008	0.000	33.672	0.004	0.004	0.000	0.000	0.000	0.000
72	A	82	LEU	0	0.020	0.012	30.491	0.003	0.003	0.000	0.000	0.000	0.000
73	A	83	ILE	0	0.032	0.028	28.673	0.006	0.006	0.000	0.000	0.000	0.000
74	A	84	HIS	0	-0.016	0.003	29.850	0.005	0.005	0.000	0.000	0.000	0.000
75	A	85	ASP	-1	-0.841	-0.919	31.703	0.057	0.057	0.000	0.000	0.000	0.000
76	A	86	GLN	0	0.055	0.011	26.524	0.007	0.007	0.000	0.000	0.000	0.000
77	A	87	GLU	-1	-0.776	-0.848	28.844	0.068	0.068	0.000	0.000	0.000	0.000
78	A	88	LYS	1	0.878	0.922	30.961	-0.045	-0.045	0.000	0.000	0.000	0.000
79	A	89	ALA	0	0.003	0.019	27.334	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	90	LYS	1	0.802	0.896	25.904	-0.073	-0.073	0.000	0.000	0.000	0.000
81	A	91	ILE	0	-0.031	-0.024	27.332	0.000	0.000	0.000	0.000	0.000	0.000
82	A	92	TYR	0	0.007	0.009	27.835	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	93	MET	0	0.025	0.022	22.964	-0.004	-0.004	0.000	0.000	0.000	0.000
84	A	94	LEU	0	0.007	0.015	25.141	0.000	0.000	0.000	0.000	0.000	0.000
85	A	95	ASN	0	-0.044	-0.037	26.264	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	96	PHE	0	0.040	0.036	23.593	-0.004	-0.004	0.000	0.000	0.000	0.000
87	A	97	THR	0	0.001	-0.024	21.354	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	98	MET	0	-0.050	-0.025	24.284	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	99	SER	0	-0.028	-0.014	26.605	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	100	LEU	0	0.010	0.013	21.782	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	101	TYR	0	0.022	-0.011	21.855	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	102	ASN	0	0.010	-0.015	24.451	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	103	GLU	-1	-0.894	-0.914	27.716	0.010	0.010	0.000	0.000	0.000	0.000
94	A	104	LYS	1	0.884	0.900	23.286	-0.011	-0.011	0.000	0.000	0.000	0.000
95	A	105	LEU	0	-0.051	-0.020	24.624	-0.003	-0.003	0.000	0.000	0.000	0.000
96	A	106	LYS	1	0.936	0.984	26.487	-0.021	-0.021	0.000	0.000	0.000	0.000
97	A	107	GLN	0	0.071	0.051	25.747	0.001	0.001	0.000	0.000	0.000	0.000
98	A	108	LEU	0	-0.034	-0.032	21.918	-0.002	-0.002	0.000	0.000	0.000	0.000
99	A	109	LYS	1	0.738	0.883	26.038	-0.023	-0.023	0.000	0.000	0.000	0.000
100	A	110	ASP	-1	-0.872	-0.944	29.728	0.007	0.007	0.000	0.000	0.000	0.000
101	A	111	GLY	0	0.014	0.027	29.852	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	112	PRO	0	-0.015	0.000	28.017	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	113	TRP	0	0.025	-0.001	24.611	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	114	ASP	-1	-0.801	-0.894	23.780	-0.030	-0.030	0.000	0.000	0.000	0.000
105	A	115	VAL	0	0.011	-0.024	18.331	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	116	MET	0	0.037	0.021	19.330	-0.007	-0.007	0.000	0.000	0.000	0.000
107	A	117	LEU	0	0.007	0.030	20.990	0.006	0.006	0.000	0.000	0.000	0.000
108	A	118	LYS	1	0.965	0.974	13.268	0.153	0.153	0.000	0.000	0.000	0.000
109	A	119	ARG	1	0.833	0.901	16.288	0.040	0.040	0.000	0.000	0.000	0.000
110	A	120	SER	0	0.002	-0.015	17.147	0.012	0.012	0.000	0.000	0.000	0.000
111	A	121	LEU	0	0.031	0.013	17.861	0.014	0.014	0.000	0.000	0.000	0.000
112	A	122	TRP	0	0.013	-0.011	8.863	0.027	0.027	0.000	0.000	0.000	0.000
113	A	123	CYS	0	0.025	0.029	14.810	0.020	0.020	0.000	0.000	0.000	0.000
114	A	124	CYS	0	-0.032	-0.009	17.155	0.014	0.014	0.000	0.000	0.000	0.000
115	A	125	ILE	0	-0.052	-0.027	12.369	0.026	0.026	0.000	0.000	0.000	0.000
116	A	126	ASP	-1	-0.765	-0.851	12.022	0.134	0.134	0.000	0.000	0.000	0.000
117	A	127	LEU	0	0.027	0.019	14.790	0.015	0.015	0.000	0.000	0.000	0.000
118	A	128	PHE	0	-0.002	-0.019	18.358	0.001	0.001	0.000	0.000	0.000	0.000
119	A	129	SER	0	-0.045	-0.038	14.084	0.021	0.021	0.000	0.000	0.000	0.000
120	A	130	CYS	0	-0.050	0.005	16.108	0.007	0.007	0.000	0.000	0.000	0.000
121	A	131	ILE	0	-0.025	-0.017	17.729	-0.002	-0.002	0.000	0.000	0.000	0.000
122	A	132	LEU	0	-0.055	-0.039	17.637	-0.005	-0.005	0.000	0.000	0.000	0.000
123	A	133	HIS	0	-0.063	-0.042	13.968	0.031	0.031	0.000	0.000	0.000	0.000
124	A	134	LEU	0	0.012	0.010	17.671	-0.008	-0.008	0.000	0.000	0.000	0.000
125	A	135	TRP	0	-0.037	-0.029	20.741	-0.009	-0.009	0.000	0.000	0.000	0.000
126	A	136	LYS	1	0.916	0.964	18.405	-0.169	-0.169	0.000	0.000	0.000	0.000
127	A	137	GLU	-1	-0.877	-0.938	22.404	0.113	0.113	0.000	0.000	0.000	0.000
128	A	138	ASN	0	-0.058	-0.027	25.654	-0.007	-0.007	0.000	0.000	0.000	0.000
129	A	139	ILE	0	-0.019	-0.003	23.005	-0.006	-0.006	0.000	0.000	0.000	0.000
130	A	140	SER	0	0.026	0.019	26.658	0.002	0.002	0.000	0.000	0.000	0.000
131	A	141	GLU	-1	-0.748	-0.873	24.563	0.104	0.104	0.000	0.000	0.000	0.000
132	A	142	THR	0	0.025	0.004	26.125	0.006	0.006	0.000	0.000	0.000	0.000
133	A	143	SER	0	-0.011	0.005	26.131	-0.002	-0.002	0.000	0.000	0.000	0.000
134	A	144	THR	0	0.041	0.018	21.418	0.006	0.006	0.000	0.000	0.000	0.000
135	A	145	ASN	0	0.005	-0.012	22.011	0.012	0.012	0.000	0.000	0.000	0.000
136	A	146	SER	0	-0.018	-0.020	22.844	0.003	0.003	0.000	0.000	0.000	0.000
137	A	147	LEU	0	-0.005	-0.001	20.942	-0.003	-0.003	0.000	0.000	0.000	0.000
138	A	148	GLN	0	0.061	0.033	18.058	0.000	0.000	0.000	0.000	0.000	0.000
139	A	149	LYS	1	0.794	0.898	18.991	-0.105	-0.105	0.000	0.000	0.000	0.000
140	A	150	ARG	1	0.973	1.005	21.098	-0.078	-0.078	0.000	0.000	0.000	0.000
141	A	151	ILE	0	0.044	0.031	14.833	-0.008	-0.008	0.000	0.000	0.000	0.000
142	A	152	LYS	1	0.940	0.970	16.219	-0.156	-0.156	0.000	0.000	0.000	0.000
143	A	153	TYR	0	0.038	0.011	17.812	-0.009	-0.009	0.000	0.000	0.000	0.000
144	A	154	CYS	0	-0.025	-0.011	17.071	-0.015	-0.015	0.000	0.000	0.000	0.000
145	A	155	LYS	1	0.951	0.980	10.490	-0.354	-0.354	0.000	0.000	0.000	0.000
146	A	156	ILE	0	-0.046	-0.013	15.405	-0.012	-0.012	0.000	0.000	0.000	0.000
147	A	157	TYR	0	0.059	0.015	18.347	-0.015	-0.015	0.000	0.000	0.000	0.000
148	A	158	LEU	0	-0.012	0.005	14.156	-0.015	-0.015	0.000	0.000	0.000	0.000
149	A	159	SER	0	-0.034	-0.009	15.655	-0.024	-0.024	0.000	0.000	0.000	0.000
150	A	160	LYS	1	0.852	0.911	16.576	-0.031	-0.031	0.000	0.000	0.000	0.000
151	A	161	LEU	0	0.003	-0.003	18.761	-0.008	-0.008	0.000	0.000	0.000	0.000
152	A	162	ALA	0	-0.060	-0.029	15.627	-0.010	-0.010	0.000	0.000	0.000	0.000
153	A	163	LYS	1	0.842	0.925	17.604	-0.020	-0.020	0.000	0.000	0.000	0.000
154	A	164	GLY	0	0.049	0.029	20.468	0.001	0.001	0.000	0.000	0.000	0.000
155	A	165	GLU	-1	-0.828	-0.896	21.544	0.012	0.012	0.000	0.000	0.000	0.000
156	A	166	ILE	0	-0.032	-0.011	23.931	0.005	0.005	0.000	0.000	0.000	0.000
157	A	167	GLY	0	-0.038	-0.007	25.573	-0.002	-0.002	0.000	0.000	0.000	0.000

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