FMO DATABASE

FMODB ID: 14RRZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1567460.486406
FMO2-HF: Nuclear repulsion	1503224.423858
FMO2-HF: Total energy	-64236.062549
FMO2-MP2: Total energy	-64419.3827

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.
-5.202	-2.16	1.034	-1.51	-2.567	-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 : -0.021 / q_NPA : -0.016

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	-1.761	-0.377	-0.005	-0.585	-0.795	0.002
4	A	3	SER	0	0.000	0.004	2.271	-3.825	-2.402	1.038	-0.883	-1.578	-0.005
5	A	4	ASN	0	-0.028	-0.024	3.846	0.177	0.412	0.001	-0.042	-0.194	0.000
6	A	5	ALA	0	0.068	0.036	6.241	0.141	0.141	0.000	0.000	0.000	0.000
7	A	6	ALA	0	0.015	0.026	6.789	-0.018	-0.018	0.000	0.000	0.000	0.000
8	A	7	ARG	1	0.797	0.903	7.487	0.186	0.186	0.000	0.000	0.000	0.000
9	A	8	VAL	0	0.020	0.023	9.817	0.035	0.035	0.000	0.000	0.000	0.000
10	A	9	VAL	0	0.045	0.013	11.645	-0.001	-0.001	0.000	0.000	0.000	0.000
11	A	10	ALA	0	-0.034	-0.012	12.380	0.001	0.001	0.000	0.000	0.000	0.000
12	A	11	THR	0	-0.031	-0.032	13.785	-0.002	-0.002	0.000	0.000	0.000	0.000
13	A	12	ALA	0	-0.028	-0.016	15.788	0.002	0.002	0.000	0.000	0.000	0.000
14	A	13	LYS	1	1.010	1.006	16.008	-0.097	-0.097	0.000	0.000	0.000	0.000
15	A	14	ASP	-1	-0.971	-0.978	18.365	0.004	0.004	0.000	0.000	0.000	0.000
16	A	15	PHE	0	-0.029	-0.046	19.393	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	16	ASP	-1	-0.870	-0.924	21.749	0.047	0.047	0.000	0.000	0.000	0.000
18	A	17	LYS	1	0.918	0.964	23.078	-0.020	-0.020	0.000	0.000	0.000	0.000
19	A	18	VAL	0	-0.071	-0.026	24.499	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	19	GLY	0	-0.002	0.002	26.441	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	20	LEU	0	-0.051	-0.038	24.887	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	21	GLY	0	0.044	0.020	25.484	0.002	0.002	0.000	0.000	0.000	0.000
23	A	22	ILE	0	0.057	0.033	24.974	0.003	0.003	0.000	0.000	0.000	0.000
24	A	23	ILE	0	-0.051	-0.032	21.703	0.004	0.004	0.000	0.000	0.000	0.000
25	A	24	GLY	0	0.073	0.024	20.372	0.004	0.004	0.000	0.000	0.000	0.000
26	A	25	TYR	0	0.007	0.035	20.257	0.008	0.008	0.000	0.000	0.000	0.000
27	A	26	TYR	0	0.009	-0.030	20.927	0.007	0.007	0.000	0.000	0.000	0.000
28	A	27	LEU	0	-0.024	-0.010	16.278	0.008	0.008	0.000	0.000	0.000	0.000
29	A	28	GLN	0	-0.032	-0.031	16.237	0.016	0.016	0.000	0.000	0.000	0.000
30	A	29	LEU	0	0.060	0.021	16.751	0.016	0.016	0.000	0.000	0.000	0.000
31	A	30	TYR	0	0.016	0.009	12.924	0.005	0.005	0.000	0.000	0.000	0.000
32	A	31	ALA	0	0.001	-0.016	12.743	0.015	0.015	0.000	0.000	0.000	0.000
33	A	32	VAL	0	-0.029	-0.008	12.937	0.040	0.040	0.000	0.000	0.000	0.000
34	A	33	GLU	-1	-0.903	-0.964	14.596	0.114	0.114	0.000	0.000	0.000	0.000
35	A	34	LEU	0	-0.035	-0.024	9.666	0.001	0.001	0.000	0.000	0.000	0.000
36	A	35	ILE	0	-0.015	0.009	10.132	0.044	0.044	0.000	0.000	0.000	0.000
37	A	36	LEU	0	-0.083	-0.050	11.218	0.004	0.004	0.000	0.000	0.000	0.000
38	A	37	SER	0	-0.066	-0.031	10.919	-0.030	-0.030	0.000	0.000	0.000	0.000
39	A	38	GLU	-1	-0.924	-0.964	6.251	-0.124	-0.124	0.000	0.000	0.000	0.000
40	A	39	GLU	-1	-0.973	-0.992	9.969	-0.038	-0.038	0.000	0.000	0.000	0.000
41	A	40	ASP	-1	-0.933	-0.959	8.361	-0.332	-0.332	0.000	0.000	0.000	0.000
42	A	41	ARG	1	0.903	0.965	9.269	-0.074	-0.074	0.000	0.000	0.000	0.000
43	A	42	SER	0	0.054	0.020	8.789	-0.078	-0.078	0.000	0.000	0.000	0.000
44	A	43	GLN	0	-0.014	-0.030	11.223	0.028	0.028	0.000	0.000	0.000	0.000
45	A	44	GLU	-1	-0.919	-0.962	8.952	0.753	0.753	0.000	0.000	0.000	0.000
46	A	45	MET	0	0.027	0.026	8.444	-0.018	-0.018	0.000	0.000	0.000	0.000
47	A	46	THR	0	-0.030	-0.013	11.638	-0.086	-0.086	0.000	0.000	0.000	0.000
48	A	47	ALA	0	0.001	-0.001	15.003	-0.038	-0.038	0.000	0.000	0.000	0.000
49	A	48	LEU	0	0.036	0.021	10.755	-0.030	-0.030	0.000	0.000	0.000	0.000
50	A	49	ALA	0	-0.002	-0.001	14.683	-0.035	-0.035	0.000	0.000	0.000	0.000
51	A	50	THR	0	-0.008	-0.002	16.248	-0.028	-0.028	0.000	0.000	0.000	0.000
52	A	51	GLU	-1	-0.917	-0.943	17.407	0.121	0.121	0.000	0.000	0.000	0.000
53	A	52	LEU	0	-0.036	-0.019	13.971	-0.017	-0.017	0.000	0.000	0.000	0.000
54	A	53	LEU	0	-0.015	-0.024	18.503	-0.014	-0.014	0.000	0.000	0.000	0.000
55	A	54	ASP	-1	-0.936	-0.940	21.345	0.063	0.063	0.000	0.000	0.000	0.000
56	A	55	THR	0	-0.005	-0.026	21.068	-0.010	-0.010	0.000	0.000	0.000	0.000
57	A	56	ILE	0	-0.058	-0.028	19.744	-0.008	-0.008	0.000	0.000	0.000	0.000
58	A	57	GLU	-1	-0.962	-0.983	23.458	0.050	0.050	0.000	0.000	0.000	0.000
59	A	58	ALA	0	-0.007	0.000	26.538	-0.006	-0.006	0.000	0.000	0.000	0.000
60	A	59	PHE	0	-0.002	-0.009	26.007	-0.005	-0.005	0.000	0.000	0.000	0.000
61	A	60	LYS	1	0.960	0.979	27.777	-0.049	-0.049	0.000	0.000	0.000	0.000
62	A	61	LYS	1	0.945	0.971	29.525	-0.042	-0.042	0.000	0.000	0.000	0.000
63	A	62	GLU	-1	-0.993	-1.002	31.473	0.028	0.028	0.000	0.000	0.000	0.000
64	A	63	ILE	0	-0.016	0.015	30.399	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	64	GLY	0	-0.081	-0.031	33.931	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	76	LEU	0	-0.004	0.007	35.602	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	77	HIS	0	0.046	-0.004	36.712	0.001	0.001	0.000	0.000	0.000	0.000
68	A	78	VAL	0	-0.024	-0.008	39.086	0.000	0.000	0.000	0.000	0.000	0.000
69	A	79	MET	0	0.046	0.015	33.825	0.000	0.000	0.000	0.000	0.000	0.000
70	A	80	ASN	0	0.093	0.065	33.934	0.001	0.001	0.000	0.000	0.000	0.000
71	A	81	THR	0	0.024	0.011	33.372	0.002	0.002	0.000	0.000	0.000	0.000
72	A	82	LEU	0	-0.037	-0.017	30.423	0.001	0.001	0.000	0.000	0.000	0.000
73	A	83	ILE	0	-0.022	-0.002	28.256	0.003	0.003	0.000	0.000	0.000	0.000
74	A	84	HIS	0	-0.043	-0.034	29.882	0.002	0.002	0.000	0.000	0.000	0.000
75	A	85	ASP	-1	-0.828	-0.921	32.483	0.030	0.030	0.000	0.000	0.000	0.000
76	A	86	GLN	0	0.017	-0.009	26.444	0.003	0.003	0.000	0.000	0.000	0.000
77	A	87	GLU	-1	-0.887	-0.919	28.809	0.032	0.032	0.000	0.000	0.000	0.000
78	A	88	LYS	1	0.905	0.945	30.957	-0.025	-0.025	0.000	0.000	0.000	0.000
79	A	89	ALA	0	-0.008	0.014	27.511	0.000	0.000	0.000	0.000	0.000	0.000
80	A	90	LYS	1	0.895	0.972	26.020	-0.039	-0.039	0.000	0.000	0.000	0.000
81	A	91	ILE	0	-0.006	-0.016	27.222	0.000	0.000	0.000	0.000	0.000	0.000
82	A	92	TYR	0	-0.012	0.002	28.109	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	93	MET	0	0.006	0.009	23.091	0.000	0.000	0.000	0.000	0.000	0.000
84	A	94	LEU	0	-0.014	-0.014	24.683	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	95	ASN	0	-0.036	-0.031	26.525	-0.002	-0.002	0.000	0.000	0.000	0.000
86	A	96	PHE	0	0.037	0.029	23.327	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	97	THR	0	0.026	-0.001	21.518	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	98	MET	0	-0.057	-0.012	24.410	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	99	SER	0	-0.020	-0.008	26.605	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	100	LEU	0	0.029	0.023	21.780	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	101	TYR	0	0.017	-0.020	21.733	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	102	ASN	0	-0.001	-0.029	24.483	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	103	GLU	-1	-0.972	-0.974	27.875	0.008	0.008	0.000	0.000	0.000	0.000
94	A	104	LYS	1	0.944	0.966	23.169	-0.008	-0.008	0.000	0.000	0.000	0.000
95	A	105	LEU	0	-0.050	-0.018	24.426	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	106	LYS	1	0.971	0.981	26.664	-0.014	-0.014	0.000	0.000	0.000	0.000
97	A	107	GLN	0	0.029	0.036	25.443	0.001	0.001	0.000	0.000	0.000	0.000
98	A	108	LEU	0	-0.069	-0.035	22.475	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	109	LYS	1	0.808	0.918	26.562	-0.015	-0.015	0.000	0.000	0.000	0.000
100	A	110	ASP	-1	-0.875	-0.950	30.093	0.005	0.005	0.000	0.000	0.000	0.000
101	A	111	GLY	0	-0.010	0.011	29.954	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	112	PRO	0	0.006	0.015	28.062	0.000	0.000	0.000	0.000	0.000	0.000
103	A	113	TRP	0	-0.010	-0.008	24.561	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	114	ASP	-1	-0.799	-0.902	23.965	-0.014	-0.014	0.000	0.000	0.000	0.000
105	A	115	VAL	0	0.011	-0.027	18.135	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	116	MET	0	-0.007	0.004	19.461	-0.004	-0.004	0.000	0.000	0.000	0.000
107	A	117	LEU	0	0.050	0.034	20.828	0.001	0.001	0.000	0.000	0.000	0.000
108	A	118	LYS	1	0.983	0.997	12.822	0.107	0.107	0.000	0.000	0.000	0.000
109	A	119	ARG	1	0.954	0.962	16.032	0.020	0.020	0.000	0.000	0.000	0.000
110	A	120	SER	0	0.017	0.005	17.140	0.005	0.005	0.000	0.000	0.000	0.000
111	A	121	LEU	0	0.017	-0.002	17.860	0.007	0.007	0.000	0.000	0.000	0.000
112	A	122	TRP	0	-0.035	-0.021	9.252	0.001	0.001	0.000	0.000	0.000	0.000
113	A	123	CYS	0	0.035	0.040	14.819	0.009	0.009	0.000	0.000	0.000	0.000
114	A	124	CYS	0	-0.013	0.007	16.961	0.010	0.010	0.000	0.000	0.000	0.000
115	A	125	ILE	0	-0.036	-0.023	12.728	0.015	0.015	0.000	0.000	0.000	0.000
116	A	126	ASP	-1	-0.788	-0.880	12.164	0.017	0.017	0.000	0.000	0.000	0.000
117	A	127	LEU	0	-0.008	0.005	14.889	0.011	0.011	0.000	0.000	0.000	0.000
118	A	128	PHE	0	-0.002	-0.027	18.038	0.003	0.003	0.000	0.000	0.000	0.000
119	A	129	SER	0	-0.044	-0.050	14.152	0.012	0.012	0.000	0.000	0.000	0.000
120	A	130	CYS	0	-0.027	0.011	16.115	0.007	0.007	0.000	0.000	0.000	0.000
121	A	131	ILE	0	-0.024	-0.018	17.676	0.000	0.000	0.000	0.000	0.000	0.000
122	A	132	LEU	0	-0.058	-0.042	17.770	-0.002	-0.002	0.000	0.000	0.000	0.000
123	A	133	HIS	0	-0.049	-0.011	14.120	0.009	0.009	0.000	0.000	0.000	0.000
124	A	134	LEU	0	0.008	0.007	17.950	-0.005	-0.005	0.000	0.000	0.000	0.000
125	A	135	TRP	0	-0.023	-0.011	20.770	-0.005	-0.005	0.000	0.000	0.000	0.000
126	A	136	LYS	1	0.981	0.992	17.894	-0.084	-0.084	0.000	0.000	0.000	0.000
127	A	137	GLU	-1	-0.829	-0.909	22.938	0.045	0.045	0.000	0.000	0.000	0.000
128	A	138	ASN	0	-0.054	-0.024	26.101	-0.002	-0.002	0.000	0.000	0.000	0.000
129	A	139	ILE	0	-0.089	-0.051	22.948	-0.003	-0.003	0.000	0.000	0.000	0.000
130	A	140	SER	0	0.033	0.029	26.837	0.000	0.000	0.000	0.000	0.000	0.000
131	A	141	GLU	-1	-0.787	-0.889	24.999	0.046	0.046	0.000	0.000	0.000	0.000
132	A	142	THR	0	0.008	-0.001	26.634	0.002	0.002	0.000	0.000	0.000	0.000
133	A	143	SER	0	-0.026	-0.017	27.373	0.002	0.002	0.000	0.000	0.000	0.000
134	A	144	THR	0	0.076	0.030	21.540	0.003	0.003	0.000	0.000	0.000	0.000
135	A	145	ASN	0	-0.017	-0.009	22.454	0.007	0.007	0.000	0.000	0.000	0.000
136	A	146	SER	0	-0.050	-0.038	23.423	0.002	0.002	0.000	0.000	0.000	0.000
137	A	147	LEU	0	0.021	0.010	21.362	0.000	0.000	0.000	0.000	0.000	0.000
138	A	148	GLN	0	0.025	0.010	18.691	-0.001	-0.001	0.000	0.000	0.000	0.000
139	A	149	LYS	1	0.898	0.950	19.210	-0.042	-0.042	0.000	0.000	0.000	0.000
140	A	150	ARG	1	0.944	0.988	21.243	-0.039	-0.039	0.000	0.000	0.000	0.000
141	A	151	ILE	0	0.039	0.035	14.923	-0.003	-0.003	0.000	0.000	0.000	0.000
142	A	152	LYS	1	0.953	0.972	15.276	-0.127	-0.127	0.000	0.000	0.000	0.000
143	A	153	TYR	0	0.044	0.009	17.918	-0.004	-0.004	0.000	0.000	0.000	0.000
144	A	154	CYS	0	-0.019	0.001	17.151	-0.008	-0.008	0.000	0.000	0.000	0.000
145	A	155	LYS	1	0.956	0.967	10.144	-0.226	-0.226	0.000	0.000	0.000	0.000
146	A	156	ILE	0	-0.043	-0.004	15.477	-0.001	-0.001	0.000	0.000	0.000	0.000
147	A	157	TYR	0	0.040	0.005	18.387	-0.007	-0.007	0.000	0.000	0.000	0.000
148	A	158	LEU	0	-0.013	0.005	13.728	-0.007	-0.007	0.000	0.000	0.000	0.000
149	A	159	SER	0	-0.045	-0.018	15.757	-0.012	-0.012	0.000	0.000	0.000	0.000
150	A	160	LYS	1	0.936	0.973	16.808	-0.023	-0.023	0.000	0.000	0.000	0.000
151	A	161	LEU	0	0.006	0.005	18.745	-0.004	-0.004	0.000	0.000	0.000	0.000
152	A	162	ALA	0	-0.049	-0.018	15.890	-0.006	-0.006	0.000	0.000	0.000	0.000
153	A	163	LYS	1	0.916	0.966	17.404	-0.024	-0.024	0.000	0.000	0.000	0.000
154	A	164	GLY	0	0.016	0.012	20.550	0.001	0.001	0.000	0.000	0.000	0.000
155	A	165	GLU	-1	-0.938	-0.983	21.986	0.011	0.011	0.000	0.000	0.000	0.000
156	A	166	ILE	0	-0.070	-0.033	24.011	0.002	0.002	0.000	0.000	0.000	0.000
157	A	167	GLY	0	0.015	0.028	24.868	-0.001	-0.001	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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