FMO DATABASE

FMODB ID: 721NK

Calculation Name: 2RK0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2RK0

Chain ID: A

ChEMBL ID:

UniProt ID: A8LBF3

Base Structure: X-ray

Registration Date: 2023-09-20

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	135
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1117034.0607
FMO2-HF: Nuclear repulsion	1064808.884013
FMO2-HF: Total energy	-52225.176687
FMO2-MP2: Total energy	-52378.748826

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:2:SER)

Summations of interaction energy for fragment #1(A:2: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.
-15.008	-13.498	6.132	-4.323	-3.317	-0.036

Interaction energy analysis for fragmet #1(A:2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / q_NPA : -0.006

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	4	SER	0	-0.005	-0.009	1.917	-14.468	-13.131	6.133	-4.298	-3.171	-0.036
4	A	5	GLY	0	0.049	0.026	4.628	1.174	1.347	-0.001	-0.025	-0.146	0.000
5	A	6	VAL	0	-0.003	0.007	7.908	-0.104	-0.104	0.000	0.000	0.000	0.000
6	A	7	SER	0	-0.039	-0.009	11.271	0.124	0.124	0.000	0.000	0.000	0.000
7	A	8	HIS	0	-0.008	-0.017	12.606	0.177	0.177	0.000	0.000	0.000	0.000
8	A	9	VAL	0	0.046	0.024	15.547	-0.050	-0.050	0.000	0.000	0.000	0.000
9	A	10	SER	0	-0.073	-0.037	18.185	0.059	0.059	0.000	0.000	0.000	0.000
10	A	11	LEU	0	0.017	0.009	21.190	0.004	0.004	0.000	0.000	0.000	0.000
11	A	12	THR	0	-0.011	-0.011	23.990	0.013	0.013	0.000	0.000	0.000	0.000
12	A	13	VAL	0	-0.025	-0.002	27.214	0.002	0.002	0.000	0.000	0.000	0.000
13	A	14	ARG	1	0.849	0.910	30.365	0.156	0.156	0.000	0.000	0.000	0.000
14	A	15	ASP	-1	-0.867	-0.927	33.950	-0.179	-0.179	0.000	0.000	0.000	0.000
15	A	16	LEU	0	-0.002	-0.009	29.886	-0.011	-0.011	0.000	0.000	0.000	0.000
16	A	17	ASP	-1	-0.758	-0.843	32.438	-0.224	-0.224	0.000	0.000	0.000	0.000
17	A	18	ILE	0	-0.042	-0.030	35.104	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	19	SER	0	0.029	0.005	30.436	0.002	0.002	0.000	0.000	0.000	0.000
19	A	20	CYS	0	-0.069	-0.031	30.317	-0.020	-0.020	0.000	0.000	0.000	0.000
20	A	21	ARG	1	0.817	0.903	31.394	0.187	0.187	0.000	0.000	0.000	0.000
21	A	22	TRP	0	0.053	0.037	28.229	-0.009	-0.009	0.000	0.000	0.000	0.000
22	A	23	TYR	0	0.013	-0.034	24.593	-0.017	-0.017	0.000	0.000	0.000	0.000
23	A	24	THR	0	-0.079	-0.055	28.827	-0.015	-0.015	0.000	0.000	0.000	0.000
24	A	25	GLU	-1	-0.998	-0.998	30.777	-0.193	-0.193	0.000	0.000	0.000	0.000
25	A	26	ILE	0	-0.013	-0.006	29.726	0.006	0.006	0.000	0.000	0.000	0.000
26	A	27	LEU	0	-0.026	-0.008	24.909	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	28	ASP	-1	-0.827	-0.878	26.440	-0.315	-0.315	0.000	0.000	0.000	0.000
28	A	29	TRP	0	-0.047	-0.023	23.916	-0.006	-0.006	0.000	0.000	0.000	0.000
29	A	30	LYS	1	0.958	0.986	26.305	0.382	0.382	0.000	0.000	0.000	0.000
30	A	31	GLU	-1	-0.780	-0.863	26.379	-0.329	-0.329	0.000	0.000	0.000	0.000
31	A	32	LEU	0	-0.105	-0.061	23.222	0.012	0.012	0.000	0.000	0.000	0.000
32	A	33	VAL	0	-0.036	-0.018	25.522	0.017	0.017	0.000	0.000	0.000	0.000
33	A	34	ARG	1	0.783	0.861	27.852	0.241	0.241	0.000	0.000	0.000	0.000
34	A	35	GLY	0	-0.025	-0.017	30.075	0.010	0.010	0.000	0.000	0.000	0.000
35	A	36	ARG	1	0.724	0.827	30.806	0.212	0.212	0.000	0.000	0.000	0.000
36	A	37	GLY	0	0.016	0.002	28.922	-0.014	-0.014	0.000	0.000	0.000	0.000
37	A	38	ASP	-1	-0.904	-0.945	29.580	-0.186	-0.186	0.000	0.000	0.000	0.000
38	A	39	THR	0	-0.009	0.000	30.921	0.007	0.007	0.000	0.000	0.000	0.000
39	A	40	THR	0	-0.012	-0.002	28.566	-0.011	-0.011	0.000	0.000	0.000	0.000
40	A	41	SER	0	0.002	0.001	31.109	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	42	PHE	0	-0.054	-0.037	25.805	-0.013	-0.013	0.000	0.000	0.000	0.000
42	A	43	ALA	0	0.055	0.022	27.693	0.014	0.014	0.000	0.000	0.000	0.000
43	A	44	HIS	0	-0.045	-0.023	20.524	0.016	0.016	0.000	0.000	0.000	0.000
44	A	45	GLY	0	0.096	0.032	23.889	0.035	0.035	0.000	0.000	0.000	0.000
45	A	46	VAL	0	-0.082	-0.031	20.483	-0.054	-0.054	0.000	0.000	0.000	0.000
46	A	47	LEU	0	0.048	0.035	20.811	0.047	0.047	0.000	0.000	0.000	0.000
47	A	48	PRO	0	0.031	0.013	21.778	-0.049	-0.049	0.000	0.000	0.000	0.000
48	A	49	GLY	0	0.007	0.010	19.679	-0.016	-0.016	0.000	0.000	0.000	0.000
49	A	50	GLY	0	-0.039	-0.022	17.986	-0.077	-0.077	0.000	0.000	0.000	0.000
50	A	51	LEU	0	-0.009	0.001	15.355	-0.076	-0.076	0.000	0.000	0.000	0.000
51	A	52	SER	0	0.016	0.014	17.293	0.115	0.115	0.000	0.000	0.000	0.000
52	A	53	ILE	0	0.013	0.004	18.489	-0.049	-0.049	0.000	0.000	0.000	0.000
53	A	54	VAL	0	-0.019	-0.027	20.699	0.030	0.030	0.000	0.000	0.000	0.000
54	A	55	LEU	0	0.061	0.060	23.167	0.004	0.004	0.000	0.000	0.000	0.000
55	A	56	ARG	1	0.886	0.934	23.943	0.385	0.385	0.000	0.000	0.000	0.000
56	A	57	GLU	-1	-0.776	-0.859	27.861	-0.202	-0.202	0.000	0.000	0.000	0.000
57	A	58	HIS	0	-0.010	-0.035	27.193	-0.014	-0.014	0.000	0.000	0.000	0.000
58	A	59	ASP	-1	-0.784	-0.857	32.432	-0.180	-0.180	0.000	0.000	0.000	0.000
59	A	60	GLY	0	-0.046	-0.017	34.939	0.012	0.012	0.000	0.000	0.000	0.000
60	A	61	GLY	0	0.018	0.015	33.746	0.001	0.001	0.000	0.000	0.000	0.000
61	A	62	GLY	0	0.003	-0.007	34.405	0.006	0.006	0.000	0.000	0.000	0.000
62	A	63	THR	0	-0.057	-0.048	36.244	0.006	0.006	0.000	0.000	0.000	0.000
63	A	64	ASP	-1	-0.910	-0.923	34.051	-0.122	-0.122	0.000	0.000	0.000	0.000
64	A	65	LEU	0	-0.037	-0.030	34.117	-0.006	-0.006	0.000	0.000	0.000	0.000
65	A	66	PHE	0	-0.002	0.015	25.719	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	67	ASP	-1	-0.774	-0.854	29.981	-0.104	-0.104	0.000	0.000	0.000	0.000
67	A	68	GLU	-1	-0.750	-0.866	27.479	-0.164	-0.164	0.000	0.000	0.000	0.000
68	A	69	THR	0	-0.135	-0.087	27.711	0.010	0.010	0.000	0.000	0.000	0.000
69	A	70	ARG	1	0.803	0.894	28.575	0.127	0.127	0.000	0.000	0.000	0.000
70	A	71	PRO	0	-0.033	-0.030	24.481	-0.011	-0.011	0.000	0.000	0.000	0.000
71	A	72	GLY	0	0.009	0.003	22.645	-0.008	-0.008	0.000	0.000	0.000	0.000
72	A	73	LEU	0	-0.056	-0.017	19.851	-0.007	-0.007	0.000	0.000	0.000	0.000
73	A	74	ASP	-1	-0.852	-0.911	21.821	-0.170	-0.170	0.000	0.000	0.000	0.000
74	A	75	HIS	0	-0.036	-0.039	21.479	-0.005	-0.005	0.000	0.000	0.000	0.000
75	A	76	LEU	0	-0.053	-0.025	18.140	-0.043	-0.043	0.000	0.000	0.000	0.000
76	A	77	SER	0	-0.006	-0.021	19.705	0.012	0.012	0.000	0.000	0.000	0.000
77	A	78	PHE	0	-0.017	-0.015	19.001	-0.065	-0.065	0.000	0.000	0.000	0.000
78	A	79	SER	0	-0.030	-0.022	17.854	0.034	0.034	0.000	0.000	0.000	0.000
79	A	80	VAL	0	-0.020	-0.005	19.939	-0.024	-0.024	0.000	0.000	0.000	0.000
80	A	81	GLU	-1	-0.958	-0.977	21.733	-0.368	-0.368	0.000	0.000	0.000	0.000
81	A	82	SER	0	-0.107	-0.083	24.106	0.034	0.034	0.000	0.000	0.000	0.000
82	A	83	MET	0	0.059	0.009	27.833	-0.009	-0.009	0.000	0.000	0.000	0.000
83	A	84	THR	0	-0.007	0.002	30.553	0.000	0.000	0.000	0.000	0.000	0.000
84	A	85	ASP	-1	-0.824	-0.888	26.891	-0.279	-0.279	0.000	0.000	0.000	0.000
85	A	86	LEU	0	-0.014	-0.014	26.727	-0.004	-0.004	0.000	0.000	0.000	0.000
86	A	87	ASP	-1	-0.848	-0.929	30.255	-0.151	-0.151	0.000	0.000	0.000	0.000
87	A	88	VAL	0	-0.004	-0.012	31.754	0.007	0.007	0.000	0.000	0.000	0.000
88	A	89	LEU	0	-0.006	0.007	27.003	0.000	0.000	0.000	0.000	0.000	0.000
89	A	90	GLU	-1	-0.754	-0.865	31.699	-0.142	-0.142	0.000	0.000	0.000	0.000
90	A	91	GLU	-1	-0.905	-0.935	34.686	-0.142	-0.142	0.000	0.000	0.000	0.000
91	A	92	ARG	1	0.735	0.840	29.840	0.261	0.261	0.000	0.000	0.000	0.000
92	A	93	LEU	0	0.026	0.010	31.063	0.006	0.006	0.000	0.000	0.000	0.000
93	A	94	ALA	0	-0.005	-0.001	35.325	0.007	0.007	0.000	0.000	0.000	0.000
94	A	95	LYS	1	0.736	0.848	38.811	0.156	0.156	0.000	0.000	0.000	0.000
95	A	96	ALA	0	0.013	0.019	36.687	0.005	0.005	0.000	0.000	0.000	0.000
96	A	97	GLY	0	-0.068	-0.025	38.761	0.002	0.002	0.000	0.000	0.000	0.000
97	A	98	ALA	0	-0.026	-0.005	34.483	0.002	0.002	0.000	0.000	0.000	0.000
98	A	99	ALA	0	-0.001	-0.006	35.102	0.007	0.007	0.000	0.000	0.000	0.000
99	A	100	PHE	0	-0.030	-0.026	33.041	-0.013	-0.013	0.000	0.000	0.000	0.000
100	A	101	THR	0	-0.044	-0.013	32.690	0.013	0.013	0.000	0.000	0.000	0.000
101	A	102	PRO	0	-0.017	-0.019	33.421	-0.008	-0.008	0.000	0.000	0.000	0.000
102	A	103	THR	0	-0.021	-0.033	30.540	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	104	GLN	0	-0.035	-0.002	30.998	0.007	0.007	0.000	0.000	0.000	0.000
104	A	105	GLU	-1	-0.809	-0.874	30.417	-0.098	-0.098	0.000	0.000	0.000	0.000
105	A	106	LEU	0	-0.006	-0.005	27.397	0.012	0.012	0.000	0.000	0.000	0.000
106	A	107	PRO	0	-0.038	-0.035	28.431	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	108	PHE	0	-0.005	-0.014	23.930	0.010	0.010	0.000	0.000	0.000	0.000
108	A	109	GLY	0	0.004	-0.004	24.625	-0.015	-0.015	0.000	0.000	0.000	0.000
109	A	110	TRP	0	-0.045	-0.033	26.338	0.017	0.017	0.000	0.000	0.000	0.000
110	A	111	ILE	0	0.036	0.016	24.615	-0.018	-0.018	0.000	0.000	0.000	0.000
111	A	112	LEU	0	-0.017	0.013	27.280	0.017	0.017	0.000	0.000	0.000	0.000
112	A	113	ALA	0	0.050	0.027	27.968	-0.021	-0.021	0.000	0.000	0.000	0.000
113	A	114	PHE	0	-0.006	-0.029	26.280	0.012	0.012	0.000	0.000	0.000	0.000
114	A	115	ARG	1	0.780	0.884	29.291	0.169	0.169	0.000	0.000	0.000	0.000
115	A	116	ASP	-1	-0.734	-0.859	28.119	-0.266	-0.266	0.000	0.000	0.000	0.000
116	A	117	ALA	0	-0.035	-0.025	31.061	0.015	0.015	0.000	0.000	0.000	0.000
117	A	118	ASP	-1	-0.806	-0.887	30.364	-0.215	-0.215	0.000	0.000	0.000	0.000
118	A	119	ASN	0	-0.067	-0.038	31.897	0.007	0.007	0.000	0.000	0.000	0.000
119	A	120	ILE	0	0.016	0.009	25.135	0.006	0.006	0.000	0.000	0.000	0.000
120	A	121	ALA	0	-0.018	-0.002	26.099	0.003	0.003	0.000	0.000	0.000	0.000
121	A	122	LEU	0	-0.036	-0.018	24.051	-0.033	-0.033	0.000	0.000	0.000	0.000
122	A	123	GLU	-1	-0.851	-0.911	23.700	-0.201	-0.201	0.000	0.000	0.000	0.000
123	A	124	ALA	0	-0.022	0.006	23.732	-0.038	-0.038	0.000	0.000	0.000	0.000
124	A	125	MET	0	-0.017	0.003	20.503	0.040	0.040	0.000	0.000	0.000	0.000
125	A	126	LEU	0	0.018	0.031	22.508	-0.027	-0.027	0.000	0.000	0.000	0.000
126	A	127	GLY	0	0.025	0.008	22.578	0.023	0.023	0.000	0.000	0.000	0.000
127	A	128	ARG	1	0.784	0.869	23.469	0.092	0.092	0.000	0.000	0.000	0.000
128	A	129	GLU	-1	-0.888	-0.935	23.684	-0.045	-0.045	0.000	0.000	0.000	0.000
129	A	130	GLY	0	-0.043	-0.024	23.766	-0.021	-0.021	0.000	0.000	0.000	0.000
130	A	131	HIS	0	-0.034	-0.023	21.455	0.010	0.010	0.000	0.000	0.000	0.000
131	A	132	HIS	1	0.846	0.889	26.430	0.111	0.111	0.000	0.000	0.000	0.000
132	A	133	HIS	0	0.063	0.047	25.922	0.021	0.021	0.000	0.000	0.000	0.000
133	A	134	HIS	0	0.042	0.031	29.090	-0.003	-0.003	0.000	0.000	0.000	0.000
134	A	135	HIS	0	-0.019	-0.004	31.598	0.005	0.005	0.000	0.000	0.000	0.000
135	A	136	HIS	0	-0.038	0.003	31.517	0.014	0.014	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:SER)