FMO DATABASE

FMODB ID: Q176Y

Calculation Name: 2RKK-A-Xray319

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	159
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1574278.18213
FMO2-HF: Nuclear repulsion	1509871.805338
FMO2-HF: Total energy	-64406.376792
FMO2-MP2: Total energy	-64590.252444

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.
-5.21	-2.179	1.036	-1.519	-2.548	-0.003

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 : -0.020 / q_NPA : -0.015

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	0.104	0.010	3.797	-1.758	-0.388	-0.001	-0.586	-0.783	0.002
4	A	3	SER	0	-0.002	0.004	2.272	-3.869	-2.443	1.035	-0.891	-1.570	-0.005
5	A	4	ASN	0	-0.026	-0.022	3.846	0.165	0.400	0.002	-0.042	-0.195	0.000
6	A	5	ALA	0	0.066	0.035	6.241	0.141	0.141	0.000	0.000	0.000	0.000
7	A	6	ALA	0	0.015	0.025	6.789	-0.025	-0.025	0.000	0.000	0.000	0.000
8	A	7	ARG	1	0.802	0.905	7.489	0.159	0.159	0.000	0.000	0.000	0.000
9	A	8	VAL	0	0.024	0.025	9.818	0.034	0.034	0.000	0.000	0.000	0.000
10	A	9	VAL	0	0.045	0.012	11.646	-0.002	-0.002	0.000	0.000	0.000	0.000
11	A	10	ALA	0	-0.039	-0.013	12.381	-0.001	-0.001	0.000	0.000	0.000	0.000
12	A	11	THR	0	-0.028	-0.030	13.786	-0.004	-0.004	0.000	0.000	0.000	0.000
13	A	12	ALA	0	-0.028	-0.016	15.789	0.001	0.001	0.000	0.000	0.000	0.000
14	A	13	LYS	1	1.006	1.004	16.008	-0.106	-0.106	0.000	0.000	0.000	0.000
15	A	14	ASP	-1	-0.970	-0.977	18.365	0.008	0.008	0.000	0.000	0.000	0.000
16	A	15	PHE	0	-0.029	-0.046	19.393	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	16	ASP	-1	-0.869	-0.924	21.749	0.052	0.052	0.000	0.000	0.000	0.000
18	A	17	LYS	1	0.917	0.964	23.079	-0.024	-0.024	0.000	0.000	0.000	0.000
19	A	18	VAL	0	-0.070	-0.025	24.500	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	19	GLY	0	-0.003	0.002	26.442	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	20	LEU	0	-0.049	-0.038	24.888	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	21	GLY	0	0.042	0.019	25.484	0.002	0.002	0.000	0.000	0.000	0.000
23	A	22	ILE	0	0.054	0.032	24.974	0.004	0.004	0.000	0.000	0.000	0.000
24	A	23	ILE	0	-0.047	-0.030	21.703	0.004	0.004	0.000	0.000	0.000	0.000
25	A	24	GLY	0	0.074	0.026	20.372	0.005	0.005	0.000	0.000	0.000	0.000
26	A	25	TYR	0	0.008	0.034	20.257	0.009	0.009	0.000	0.000	0.000	0.000
27	A	26	TYR	0	0.008	-0.031	20.928	0.008	0.008	0.000	0.000	0.000	0.000
28	A	27	LEU	0	-0.027	-0.011	16.278	0.009	0.009	0.000	0.000	0.000	0.000
29	A	28	GLN	0	-0.023	-0.029	16.237	0.018	0.018	0.000	0.000	0.000	0.000
30	A	29	LEU	0	0.051	0.018	16.752	0.017	0.017	0.000	0.000	0.000	0.000
31	A	30	TYR	0	0.019	0.011	12.924	0.007	0.007	0.000	0.000	0.000	0.000
32	A	31	ALA	0	-0.001	-0.017	12.743	0.017	0.017	0.000	0.000	0.000	0.000
33	A	32	VAL	0	-0.023	-0.006	12.937	0.044	0.044	0.000	0.000	0.000	0.000
34	A	33	GLU	-1	-0.908	-0.965	14.581	0.121	0.121	0.000	0.000	0.000	0.000
35	A	34	LEU	0	-0.033	-0.024	9.666	0.003	0.003	0.000	0.000	0.000	0.000
36	A	35	ILE	0	-0.016	0.009	10.119	0.050	0.050	0.000	0.000	0.000	0.000
37	A	36	LEU	0	-0.085	-0.051	11.205	0.003	0.003	0.000	0.000	0.000	0.000
38	A	37	SER	0	-0.065	-0.030	10.899	-0.033	-0.033	0.000	0.000	0.000	0.000
39	A	38	GLU	-1	-0.926	-0.965	6.307	-0.086	-0.086	0.000	0.000	0.000	0.000
40	A	39	GLU	-1	-0.974	-0.992	9.951	-0.035	-0.035	0.000	0.000	0.000	0.000
41	A	40	ASP	-1	-0.934	-0.959	8.354	-0.312	-0.312	0.000	0.000	0.000	0.000
42	A	41	ARG	1	0.904	0.965	9.264	-0.078	-0.078	0.000	0.000	0.000	0.000
43	A	42	SER	0	0.053	0.018	8.796	-0.080	-0.080	0.000	0.000	0.000	0.000
44	A	43	GLN	0	-0.015	-0.031	11.227	0.027	0.027	0.000	0.000	0.000	0.000
45	A	44	GLU	-1	-0.918	-0.961	8.952	0.770	0.770	0.000	0.000	0.000	0.000
46	A	45	MET	0	0.028	0.026	8.444	-0.016	-0.016	0.000	0.000	0.000	0.000
47	A	46	THR	0	-0.032	-0.013	11.639	-0.091	-0.091	0.000	0.000	0.000	0.000
48	A	47	ALA	0	0.001	0.000	15.002	-0.040	-0.040	0.000	0.000	0.000	0.000
49	A	48	LEU	0	0.037	0.021	10.755	-0.030	-0.030	0.000	0.000	0.000	0.000
50	A	49	ALA	0	-0.004	-0.001	14.684	-0.037	-0.037	0.000	0.000	0.000	0.000
51	A	50	THR	0	-0.006	-0.001	16.249	-0.030	-0.030	0.000	0.000	0.000	0.000
52	A	51	GLU	-1	-0.917	-0.943	17.407	0.128	0.128	0.000	0.000	0.000	0.000
53	A	52	LEU	0	-0.036	-0.018	13.972	-0.018	-0.018	0.000	0.000	0.000	0.000
54	A	53	LEU	0	-0.015	-0.023	18.504	-0.016	-0.016	0.000	0.000	0.000	0.000
55	A	54	ASP	-1	-0.938	-0.940	21.346	0.067	0.067	0.000	0.000	0.000	0.000
56	A	55	THR	0	-0.004	-0.026	21.067	-0.011	-0.011	0.000	0.000	0.000	0.000
57	A	56	ILE	0	-0.056	-0.027	19.744	-0.009	-0.009	0.000	0.000	0.000	0.000
58	A	57	GLU	-1	-0.964	-0.983	23.459	0.054	0.054	0.000	0.000	0.000	0.000
59	A	58	ALA	0	-0.007	0.000	26.538	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	59	PHE	0	-0.002	-0.008	26.008	-0.006	-0.006	0.000	0.000	0.000	0.000
61	A	60	LYS	1	0.962	0.980	27.777	-0.052	-0.052	0.000	0.000	0.000	0.000
62	A	61	LYS	1	0.951	0.973	29.525	-0.045	-0.045	0.000	0.000	0.000	0.000
63	A	62	GLU	-1	-0.997	-1.004	31.475	0.030	0.030	0.000	0.000	0.000	0.000
64	A	63	ILE	0	-0.007	0.014	30.399	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	64	GLY	0	-0.106	-0.074	33.866	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	65	NME	0	0.015	0.007	35.110	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	75	ACE	0	-0.016	-0.020	39.060	0.000	0.000	0.000	0.000	0.000	0.000
68	A	76	LEU	0	0.022	0.008	35.606	0.000	0.000	0.000	0.000	0.000	0.000
69	A	77	HIS	0	0.052	0.019	36.713	0.002	0.002	0.000	0.000	0.000	0.000
70	A	78	VAL	0	-0.050	-0.017	39.090	0.000	0.000	0.000	0.000	0.000	0.000
71	A	79	MET	0	0.054	0.018	33.826	0.000	0.000	0.000	0.000	0.000	0.000
72	A	80	ASN	0	0.098	0.068	33.934	0.001	0.001	0.000	0.000	0.000	0.000
73	A	81	THR	0	0.027	0.014	33.372	0.002	0.002	0.000	0.000	0.000	0.000
74	A	82	LEU	0	-0.044	-0.019	30.423	0.001	0.001	0.000	0.000	0.000	0.000
75	A	83	ILE	0	-0.016	0.001	28.257	0.003	0.003	0.000	0.000	0.000	0.000
76	A	84	HIS	0	-0.055	-0.005	29.882	0.002	0.002	0.000	0.000	0.000	0.000
77	A	85	ASP	-1	-0.829	-0.924	32.483	0.032	0.032	0.000	0.000	0.000	0.000
78	A	86	GLN	0	0.017	-0.008	26.444	0.004	0.004	0.000	0.000	0.000	0.000
79	A	87	GLU	-1	-0.885	-0.918	28.809	0.033	0.033	0.000	0.000	0.000	0.000
80	A	88	LYS	1	0.904	0.944	30.957	-0.027	-0.027	0.000	0.000	0.000	0.000
81	A	89	ALA	0	-0.011	0.013	27.511	0.000	0.000	0.000	0.000	0.000	0.000
82	A	90	LYS	1	0.894	0.972	26.023	-0.040	-0.040	0.000	0.000	0.000	0.000
83	A	91	ILE	0	-0.004	-0.016	27.225	0.000	0.000	0.000	0.000	0.000	0.000
84	A	92	TYR	0	-0.011	0.002	28.109	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	93	MET	0	0.009	0.010	23.093	0.000	0.000	0.000	0.000	0.000	0.000
86	A	94	LEU	0	-0.018	-0.015	24.686	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	95	ASN	0	-0.033	-0.031	26.527	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	96	PHE	0	0.035	0.028	23.327	-0.002	-0.002	0.000	0.000	0.000	0.000
89	A	97	THR	0	0.028	-0.001	21.520	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	98	MET	0	-0.060	-0.013	24.412	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	99	SER	0	-0.019	-0.008	26.607	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	100	LEU	0	0.027	0.022	21.780	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	101	TYR	0	0.021	-0.019	21.735	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	102	ASN	0	-0.004	-0.029	24.486	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	103	GLU	-1	-0.973	-0.975	27.877	0.010	0.010	0.000	0.000	0.000	0.000
96	A	104	LYS	1	0.945	0.966	23.171	-0.010	-0.010	0.000	0.000	0.000	0.000
97	A	105	LEU	0	-0.055	-0.020	24.428	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	106	LYS	1	0.970	0.979	26.666	-0.015	-0.015	0.000	0.000	0.000	0.000
99	A	107	GLN	0	0.025	0.033	25.442	0.001	0.001	0.000	0.000	0.000	0.000
100	A	108	LEU	0	-0.066	-0.032	22.477	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	109	LYS	1	0.805	0.918	26.564	-0.015	-0.015	0.000	0.000	0.000	0.000
102	A	110	ASP	-1	-0.878	-0.951	30.095	0.006	0.006	0.000	0.000	0.000	0.000
103	A	111	GLY	0	-0.016	0.006	29.956	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	112	PRO	0	0.007	0.015	28.062	0.000	0.000	0.000	0.000	0.000	0.000
105	A	113	TRP	0	0.021	0.008	24.562	0.000	0.000	0.000	0.000	0.000	0.000
106	A	114	ASP	-1	-0.798	-0.900	23.965	-0.013	-0.013	0.000	0.000	0.000	0.000
107	A	115	VAL	0	0.005	-0.032	18.135	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	116	MET	0	-0.016	-0.001	19.461	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	117	LEU	0	0.056	0.037	20.828	0.001	0.001	0.000	0.000	0.000	0.000
110	A	118	LYS	1	0.991	1.000	12.823	0.103	0.103	0.000	0.000	0.000	0.000
111	A	119	ARG	1	0.946	0.958	16.033	0.017	0.017	0.000	0.000	0.000	0.000
112	A	120	SER	0	0.013	0.004	17.140	0.006	0.006	0.000	0.000	0.000	0.000
113	A	121	LEU	0	0.022	0.001	17.862	0.007	0.007	0.000	0.000	0.000	0.000
114	A	122	TRP	0	-0.036	-0.022	9.255	0.002	0.002	0.000	0.000	0.000	0.000
115	A	123	CYS	0	0.034	0.039	14.821	0.010	0.010	0.000	0.000	0.000	0.000
116	A	124	CYS	0	-0.017	0.006	16.961	0.010	0.010	0.000	0.000	0.000	0.000
117	A	125	ILE	0	-0.033	-0.021	12.730	0.016	0.016	0.000	0.000	0.000	0.000
118	A	126	ASP	-1	-0.792	-0.881	12.166	0.030	0.030	0.000	0.000	0.000	0.000
119	A	127	LEU	0	-0.007	0.005	14.892	0.011	0.011	0.000	0.000	0.000	0.000
120	A	128	PHE	0	-0.005	-0.028	18.041	0.003	0.003	0.000	0.000	0.000	0.000
121	A	129	SER	0	-0.042	-0.050	14.155	0.012	0.012	0.000	0.000	0.000	0.000
122	A	130	CYS	0	-0.026	0.010	16.117	0.007	0.007	0.000	0.000	0.000	0.000
123	A	131	ILE	0	-0.026	-0.018	17.676	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	132	LEU	0	-0.059	-0.042	17.768	-0.003	-0.003	0.000	0.000	0.000	0.000
125	A	133	HIS	0	-0.050	-0.011	14.133	0.009	0.009	0.000	0.000	0.000	0.000
126	A	134	LEU	0	0.007	0.007	17.960	-0.005	-0.005	0.000	0.000	0.000	0.000
127	A	135	TRP	0	-0.026	-0.012	20.783	-0.006	-0.006	0.000	0.000	0.000	0.000
128	A	136	LYS	1	0.985	0.993	17.910	-0.088	-0.088	0.000	0.000	0.000	0.000
129	A	137	GLU	-1	-0.830	-0.909	22.949	0.046	0.046	0.000	0.000	0.000	0.000
130	A	138	ASN	0	-0.055	-0.024	26.112	-0.002	-0.002	0.000	0.000	0.000	0.000
131	A	139	ILE	0	-0.089	-0.050	22.952	-0.003	-0.003	0.000	0.000	0.000	0.000
132	A	140	SER	0	0.030	0.026	26.842	0.000	0.000	0.000	0.000	0.000	0.000
133	A	141	GLU	-1	-0.786	-0.889	25.001	0.045	0.045	0.000	0.000	0.000	0.000
134	A	142	THR	0	0.007	-0.001	26.634	0.002	0.002	0.000	0.000	0.000	0.000
135	A	143	SER	0	-0.025	-0.017	27.371	0.002	0.002	0.000	0.000	0.000	0.000
136	A	144	THR	0	0.077	0.029	21.541	0.003	0.003	0.000	0.000	0.000	0.000
137	A	145	ASN	0	-0.019	-0.010	22.451	0.006	0.006	0.000	0.000	0.000	0.000
138	A	146	SER	0	-0.052	-0.038	23.415	0.001	0.001	0.000	0.000	0.000	0.000
139	A	147	LEU	0	0.022	0.010	21.365	0.000	0.000	0.000	0.000	0.000	0.000
140	A	148	GLN	0	0.028	0.010	18.690	-0.001	-0.001	0.000	0.000	0.000	0.000
141	A	149	LYS	1	0.893	0.949	19.213	-0.041	-0.041	0.000	0.000	0.000	0.000
142	A	150	ARG	1	0.945	0.988	21.246	-0.041	-0.041	0.000	0.000	0.000	0.000
143	A	151	ILE	0	0.040	0.035	14.926	-0.003	-0.003	0.000	0.000	0.000	0.000
144	A	152	LYS	1	0.950	0.970	15.279	-0.122	-0.122	0.000	0.000	0.000	0.000
145	A	153	TYR	0	0.044	0.010	17.921	-0.004	-0.004	0.000	0.000	0.000	0.000
146	A	154	CYS	0	-0.017	0.001	17.153	-0.008	-0.008	0.000	0.000	0.000	0.000
147	A	155	LYS	1	0.951	0.965	10.146	-0.229	-0.229	0.000	0.000	0.000	0.000
148	A	156	ILE	0	-0.047	-0.007	15.480	-0.002	-0.002	0.000	0.000	0.000	0.000
149	A	157	TYR	0	0.042	0.007	18.389	-0.007	-0.007	0.000	0.000	0.000	0.000
150	A	158	LEU	0	-0.010	0.006	13.730	-0.007	-0.007	0.000	0.000	0.000	0.000
151	A	159	SER	0	-0.054	-0.023	15.758	-0.012	-0.012	0.000	0.000	0.000	0.000
152	A	160	LYS	1	0.931	0.972	16.810	-0.022	-0.022	0.000	0.000	0.000	0.000
153	A	161	LEU	0	0.023	0.015	18.745	-0.004	-0.004	0.000	0.000	0.000	0.000
154	A	162	ALA	0	-0.060	-0.023	15.890	-0.006	-0.006	0.000	0.000	0.000	0.000
155	A	163	LYS	1	0.901	0.954	17.406	-0.020	-0.020	0.000	0.000	0.000	0.000
156	A	164	GLY	0	0.016	0.011	20.550	0.001	0.001	0.000	0.000	0.000	0.000
157	A	165	GLU	-1	-0.955	-0.993	21.987	0.009	0.009	0.000	0.000	0.000	0.000
158	A	166	ILE	0	-0.124	-0.070	24.012	0.003	0.003	0.000	0.000	0.000	0.000
159	A	167	GLY	-1	-0.875	-0.905	24.829	-0.008	-0.008	0.000	0.000	0.000	0.000

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