FMO DATABASE

FMODB ID: GN111

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	OptHSide
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	-1567330.638783
FMO2-HF: Nuclear repulsion	1503093.31876
FMO2-HF: Total energy	-64237.320022
FMO2-MP2: Total energy	-64420.504446

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.
0.909	1.355	4.924	-2.083	-3.288	-0.012

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 : -0.027 / q_NPA : -0.021

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	0.098	0.014	3.797	-2.413	-0.968	-0.009	-0.612	-0.824	0.002
4	A	3	SER	0	-0.007	0.006	2.069	-4.814	-6.086	4.932	-1.417	-2.244	-0.014
5	A	4	ASN	0	-0.019	-0.003	3.816	0.151	0.424	0.001	-0.054	-0.220	0.000
6	A	5	ALA	0	0.084	0.039	6.216	0.203	0.203	0.000	0.000	0.000	0.000
7	A	6	ALA	0	0.027	0.027	6.842	0.010	0.010	0.000	0.000	0.000	0.000
8	A	7	ARG	1	0.711	0.813	7.560	0.915	0.915	0.000	0.000	0.000	0.000
9	A	8	VAL	0	0.022	0.024	9.796	0.086	0.086	0.000	0.000	0.000	0.000
10	A	9	VAL	0	0.046	0.015	11.611	0.025	0.025	0.000	0.000	0.000	0.000
11	A	10	ALA	0	-0.030	-0.008	12.349	0.022	0.022	0.000	0.000	0.000	0.000
12	A	11	THR	0	-0.050	-0.043	13.769	0.012	0.012	0.000	0.000	0.000	0.000
13	A	12	ALA	0	-0.033	-0.013	15.759	0.020	0.020	0.000	0.000	0.000	0.000
14	A	13	LYS	1	0.936	0.957	16.304	-0.030	-0.030	0.000	0.000	0.000	0.000
15	A	14	ASP	-1	-0.911	-0.948	18.351	-0.166	-0.166	0.000	0.000	0.000	0.000
16	A	15	PHE	0	-0.035	-0.042	19.925	0.006	0.006	0.000	0.000	0.000	0.000
17	A	16	ASP	-1	-0.845	-0.915	21.807	0.002	0.002	0.000	0.000	0.000	0.000
18	A	17	LYS	1	0.915	0.963	22.965	0.093	0.093	0.000	0.000	0.000	0.000
19	A	18	VAL	0	-0.069	-0.031	24.661	0.000	0.000	0.000	0.000	0.000	0.000
20	A	19	GLY	0	-0.002	0.008	26.405	0.002	0.002	0.000	0.000	0.000	0.000
21	A	20	LEU	0	-0.045	-0.036	24.981	0.002	0.002	0.000	0.000	0.000	0.000
22	A	21	GLY	0	0.044	0.019	25.451	0.002	0.002	0.000	0.000	0.000	0.000
23	A	22	ILE	0	0.047	0.027	24.938	0.007	0.007	0.000	0.000	0.000	0.000
24	A	23	ILE	0	-0.041	-0.026	21.622	0.008	0.008	0.000	0.000	0.000	0.000
25	A	24	GLY	0	0.063	0.025	20.337	0.003	0.003	0.000	0.000	0.000	0.000
26	A	25	TYR	0	0.020	0.025	20.220	0.014	0.014	0.000	0.000	0.000	0.000
27	A	26	TYR	0	0.000	-0.023	20.887	0.020	0.020	0.000	0.000	0.000	0.000
28	A	27	LEU	0	-0.006	-0.007	16.503	0.014	0.014	0.000	0.000	0.000	0.000
29	A	28	GLN	0	-0.032	-0.017	16.199	0.026	0.026	0.000	0.000	0.000	0.000
30	A	29	LEU	0	0.047	0.021	16.708	0.037	0.037	0.000	0.000	0.000	0.000
31	A	30	TYR	0	0.031	0.006	12.424	0.051	0.051	0.000	0.000	0.000	0.000
32	A	31	ALA	0	0.002	-0.010	12.551	0.050	0.050	0.000	0.000	0.000	0.000
33	A	32	VAL	0	-0.013	-0.006	12.891	0.095	0.095	0.000	0.000	0.000	0.000
34	A	33	GLU	-1	-0.899	-0.952	14.733	0.320	0.320	0.000	0.000	0.000	0.000
35	A	34	LEU	0	-0.022	-0.017	9.780	0.045	0.045	0.000	0.000	0.000	0.000
36	A	35	ILE	0	-0.014	-0.003	10.156	0.196	0.196	0.000	0.000	0.000	0.000
37	A	36	LEU	0	-0.083	-0.048	11.360	0.118	0.118	0.000	0.000	0.000	0.000
38	A	37	SER	0	-0.058	-0.020	11.150	-0.013	-0.013	0.000	0.000	0.000	0.000
39	A	38	GLU	-1	-0.917	-0.962	5.917	2.892	2.892	0.000	0.000	0.000	0.000
40	A	39	GLU	-1	-0.964	-0.995	10.081	0.602	0.602	0.000	0.000	0.000	0.000
41	A	40	ASP	-1	-0.949	-0.959	8.459	1.158	1.158	0.000	0.000	0.000	0.000
42	A	41	ARG	1	0.897	0.960	9.385	-0.483	-0.483	0.000	0.000	0.000	0.000
43	A	42	SER	0	0.059	0.022	8.797	-0.133	-0.133	0.000	0.000	0.000	0.000
44	A	43	GLN	0	-0.012	-0.030	11.356	-0.032	-0.032	0.000	0.000	0.000	0.000
45	A	44	GLU	-1	-0.915	-0.961	8.604	0.873	0.873	0.000	0.000	0.000	0.000
46	A	45	MET	0	0.023	0.025	8.293	-0.091	-0.091	0.000	0.000	0.000	0.000
47	A	46	THR	0	-0.026	-0.007	11.591	-0.111	-0.111	0.000	0.000	0.000	0.000
48	A	47	ALA	0	0.006	0.005	15.141	-0.066	-0.066	0.000	0.000	0.000	0.000
49	A	48	LEU	0	0.035	0.019	10.804	-0.060	-0.060	0.000	0.000	0.000	0.000
50	A	49	ALA	0	0.009	0.003	14.636	-0.057	-0.057	0.000	0.000	0.000	0.000
51	A	50	THR	0	-0.012	-0.009	16.199	-0.045	-0.045	0.000	0.000	0.000	0.000
52	A	51	GLU	-1	-0.851	-0.903	17.273	0.099	0.099	0.000	0.000	0.000	0.000
53	A	52	LEU	0	-0.025	-0.024	13.889	-0.035	-0.035	0.000	0.000	0.000	0.000
54	A	53	LEU	0	-0.012	-0.022	18.456	-0.025	-0.025	0.000	0.000	0.000	0.000
55	A	54	ASP	-1	-0.947	-0.946	21.297	0.099	0.099	0.000	0.000	0.000	0.000
56	A	55	THR	0	0.002	-0.008	21.228	-0.023	-0.023	0.000	0.000	0.000	0.000
57	A	56	ILE	0	-0.063	-0.036	19.201	-0.014	-0.014	0.000	0.000	0.000	0.000
58	A	57	GLU	-1	-0.960	-0.981	23.413	0.103	0.103	0.000	0.000	0.000	0.000
59	A	58	ALA	0	0.000	0.003	26.485	-0.011	-0.011	0.000	0.000	0.000	0.000
60	A	59	PHE	0	-0.008	-0.010	25.970	-0.011	-0.011	0.000	0.000	0.000	0.000
61	A	60	LYS	1	0.919	0.959	27.733	-0.088	-0.088	0.000	0.000	0.000	0.000
62	A	61	LYS	1	0.947	0.974	29.481	-0.078	-0.078	0.000	0.000	0.000	0.000
63	A	62	GLU	-1	-0.976	-0.988	31.430	0.026	0.026	0.000	0.000	0.000	0.000
64	A	63	ILE	0	-0.024	-0.003	30.568	-0.006	-0.006	0.000	0.000	0.000	0.000
65	A	64	GLY	0	-0.090	-0.032	33.773	-0.003	-0.003	0.000	0.000	0.000	0.000
66	A	76	LEU	0	0.008	0.002	35.430	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	77	HIS	0	0.055	0.013	36.673	0.003	0.003	0.000	0.000	0.000	0.000
68	A	78	VAL	0	-0.028	-0.013	39.079	0.001	0.001	0.000	0.000	0.000	0.000
69	A	79	MET	0	0.010	-0.004	33.811	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	80	ASN	0	0.111	0.067	33.892	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	81	THR	0	0.016	0.014	33.333	0.004	0.004	0.000	0.000	0.000	0.000
72	A	82	LEU	0	-0.010	-0.005	30.464	0.003	0.003	0.000	0.000	0.000	0.000
73	A	83	ILE	0	-0.002	0.000	28.080	0.002	0.002	0.000	0.000	0.000	0.000
74	A	84	HIS	0	-0.037	-0.021	29.841	0.007	0.007	0.000	0.000	0.000	0.000
75	A	85	ASP	-1	-0.823	-0.906	32.445	0.048	0.048	0.000	0.000	0.000	0.000
76	A	86	GLN	0	0.026	-0.001	26.394	0.000	0.000	0.000	0.000	0.000	0.000
77	A	87	GLU	-1	-0.763	-0.838	28.809	0.034	0.034	0.000	0.000	0.000	0.000
78	A	88	LYS	1	0.905	0.925	30.957	-0.036	-0.036	0.000	0.000	0.000	0.000
79	A	89	ALA	0	-0.012	0.011	27.483	-0.008	-0.008	0.000	0.000	0.000	0.000
80	A	90	LYS	1	0.823	0.908	26.143	-0.046	-0.046	0.000	0.000	0.000	0.000
81	A	91	ILE	0	-0.018	-0.013	27.208	-0.012	-0.012	0.000	0.000	0.000	0.000
82	A	92	TYR	0	-0.014	0.000	27.997	-0.010	-0.010	0.000	0.000	0.000	0.000
83	A	93	MET	0	0.023	0.021	23.104	-0.016	-0.016	0.000	0.000	0.000	0.000
84	A	94	LEU	0	-0.011	-0.004	24.963	-0.017	-0.017	0.000	0.000	0.000	0.000
85	A	95	ASN	0	-0.035	-0.034	26.508	-0.015	-0.015	0.000	0.000	0.000	0.000
86	A	96	PHE	0	0.038	0.033	23.559	-0.008	-0.008	0.000	0.000	0.000	0.000
87	A	97	THR	0	0.011	-0.015	21.573	-0.014	-0.014	0.000	0.000	0.000	0.000
88	A	98	MET	0	-0.047	-0.010	24.382	-0.020	-0.020	0.000	0.000	0.000	0.000
89	A	99	SER	0	-0.030	-0.017	26.584	-0.007	-0.007	0.000	0.000	0.000	0.000
90	A	100	LEU	0	0.013	0.017	21.957	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	101	TYR	0	0.028	-0.012	21.966	-0.005	-0.005	0.000	0.000	0.000	0.000
92	A	102	ASN	0	0.011	-0.022	24.458	-0.012	-0.012	0.000	0.000	0.000	0.000
93	A	103	GLU	-1	-0.906	-0.923	27.680	-0.133	-0.133	0.000	0.000	0.000	0.000
94	A	104	LYS	1	0.866	0.895	23.278	0.151	0.151	0.000	0.000	0.000	0.000
95	A	105	LEU	0	-0.049	-0.009	24.495	-0.012	-0.012	0.000	0.000	0.000	0.000
96	A	106	LYS	1	0.973	0.988	26.642	0.088	0.088	0.000	0.000	0.000	0.000
97	A	107	GLN	0	0.051	0.044	25.671	0.004	0.004	0.000	0.000	0.000	0.000
98	A	108	LEU	0	-0.058	-0.033	22.246	-0.006	-0.006	0.000	0.000	0.000	0.000
99	A	109	LYS	1	0.767	0.898	26.537	0.146	0.146	0.000	0.000	0.000	0.000
100	A	110	ASP	-1	-0.869	-0.947	30.071	-0.114	-0.114	0.000	0.000	0.000	0.000
101	A	111	GLY	0	-0.001	0.015	29.920	0.000	0.000	0.000	0.000	0.000	0.000
102	A	112	PRO	0	0.015	0.021	28.190	-0.004	-0.004	0.000	0.000	0.000	0.000
103	A	113	TRP	0	-0.001	-0.012	24.547	-0.015	-0.015	0.000	0.000	0.000	0.000
104	A	114	ASP	-1	-0.803	-0.897	23.984	-0.226	-0.226	0.000	0.000	0.000	0.000
105	A	115	VAL	0	0.011	-0.029	18.128	-0.021	-0.021	0.000	0.000	0.000	0.000
106	A	116	MET	0	0.031	0.022	19.473	-0.032	-0.032	0.000	0.000	0.000	0.000
107	A	117	LEU	0	0.026	0.041	20.834	-0.010	-0.010	0.000	0.000	0.000	0.000
108	A	118	LYS	1	0.990	0.993	12.976	0.634	0.634	0.000	0.000	0.000	0.000
109	A	119	ARG	1	0.892	0.933	16.196	0.227	0.227	0.000	0.000	0.000	0.000
110	A	120	SER	0	0.006	-0.017	17.140	0.007	0.007	0.000	0.000	0.000	0.000
111	A	121	LEU	0	0.019	0.002	17.879	0.015	0.015	0.000	0.000	0.000	0.000
112	A	122	TRP	0	-0.014	-0.020	9.014	-0.052	-0.052	0.000	0.000	0.000	0.000
113	A	123	CYS	0	0.033	0.037	14.783	0.017	0.017	0.000	0.000	0.000	0.000
114	A	124	CYS	0	-0.026	-0.003	16.952	0.041	0.041	0.000	0.000	0.000	0.000
115	A	125	ILE	0	-0.042	-0.020	12.562	0.018	0.018	0.000	0.000	0.000	0.000
116	A	126	ASP	-1	-0.756	-0.839	12.086	-0.385	-0.385	0.000	0.000	0.000	0.000
117	A	127	LEU	0	0.008	0.009	14.862	0.052	0.052	0.000	0.000	0.000	0.000
118	A	128	PHE	0	-0.013	-0.025	18.220	0.031	0.031	0.000	0.000	0.000	0.000
119	A	129	SER	0	-0.043	-0.044	14.113	0.026	0.026	0.000	0.000	0.000	0.000
120	A	130	CYS	0	-0.059	0.008	16.109	0.049	0.049	0.000	0.000	0.000	0.000
121	A	131	ILE	0	-0.021	-0.020	17.676	0.028	0.028	0.000	0.000	0.000	0.000
122	A	132	LEU	0	-0.059	-0.038	18.143	0.011	0.011	0.000	0.000	0.000	0.000
123	A	133	HIS	0	-0.051	-0.019	14.456	0.059	0.059	0.000	0.000	0.000	0.000
124	A	134	LEU	0	-0.006	-0.002	18.078	0.017	0.017	0.000	0.000	0.000	0.000
125	A	135	TRP	0	-0.046	-0.032	20.873	-0.004	-0.004	0.000	0.000	0.000	0.000
126	A	136	LYS	1	0.984	1.000	18.884	-0.224	-0.224	0.000	0.000	0.000	0.000
127	A	137	GLU	-1	-0.842	-0.920	23.063	0.135	0.135	0.000	0.000	0.000	0.000
128	A	138	ASN	0	-0.089	-0.046	26.224	-0.011	-0.011	0.000	0.000	0.000	0.000
129	A	139	ILE	0	-0.060	-0.028	23.331	-0.016	-0.016	0.000	0.000	0.000	0.000
130	A	140	SER	0	0.032	0.025	26.933	0.005	0.005	0.000	0.000	0.000	0.000
131	A	141	GLU	-1	-0.785	-0.894	25.074	0.051	0.051	0.000	0.000	0.000	0.000
132	A	142	THR	0	0.012	-0.006	26.670	-0.005	-0.005	0.000	0.000	0.000	0.000
133	A	143	SER	0	-0.012	-0.017	26.608	-0.013	-0.013	0.000	0.000	0.000	0.000
134	A	144	THR	0	0.042	0.018	21.580	-0.013	-0.013	0.000	0.000	0.000	0.000
135	A	145	ASN	0	0.008	0.004	22.465	-0.024	-0.024	0.000	0.000	0.000	0.000
136	A	146	SER	0	-0.055	-0.031	23.265	-0.018	-0.018	0.000	0.000	0.000	0.000
137	A	147	LEU	0	0.013	0.001	21.399	-0.022	-0.022	0.000	0.000	0.000	0.000
138	A	148	GLN	0	0.040	0.020	18.401	-0.036	-0.036	0.000	0.000	0.000	0.000
139	A	149	LYS	1	0.875	0.940	18.996	0.011	0.011	0.000	0.000	0.000	0.000
140	A	150	ARG	1	0.955	1.001	21.252	0.040	0.040	0.000	0.000	0.000	0.000
141	A	151	ILE	0	0.048	0.040	15.021	-0.037	-0.037	0.000	0.000	0.000	0.000
142	A	152	LYS	1	0.940	0.968	15.366	0.195	0.195	0.000	0.000	0.000	0.000
143	A	153	TYR	0	0.040	0.008	17.899	-0.036	-0.036	0.000	0.000	0.000	0.000
144	A	154	CYS	0	-0.031	-0.012	17.138	-0.011	-0.011	0.000	0.000	0.000	0.000
145	A	155	LYS	1	0.952	0.971	10.074	0.498	0.498	0.000	0.000	0.000	0.000
146	A	156	ILE	0	-0.050	-0.010	15.475	-0.041	-0.041	0.000	0.000	0.000	0.000
147	A	157	TYR	0	0.054	0.011	18.389	-0.015	-0.015	0.000	0.000	0.000	0.000
148	A	158	LEU	0	-0.011	0.011	14.193	-0.007	-0.007	0.000	0.000	0.000	0.000
149	A	159	SER	0	-0.043	-0.016	15.756	-0.017	-0.017	0.000	0.000	0.000	0.000
150	A	160	LYS	1	0.845	0.909	16.801	0.228	0.228	0.000	0.000	0.000	0.000
151	A	161	LEU	0	0.006	0.007	18.814	0.018	0.018	0.000	0.000	0.000	0.000
152	A	162	ALA	0	-0.051	-0.017	15.866	0.005	0.005	0.000	0.000	0.000	0.000
153	A	163	LYS	1	0.904	0.959	17.479	0.388	0.388	0.000	0.000	0.000	0.000
154	A	164	GLY	0	0.021	0.012	20.537	0.027	0.027	0.000	0.000	0.000	0.000
155	A	165	GLU	-1	-0.863	-0.929	21.802	-0.254	-0.254	0.000	0.000	0.000	0.000
156	A	166	ILE	0	-0.028	-0.004	24.022	0.016	0.016	0.000	0.000	0.000	0.000
157	A	167	GLY	0	-0.032	0.000	24.803	0.020	0.020	0.000	0.000	0.000	0.000

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