FMO DATABASE

FMODB ID: 94172

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1114614.924799
FMO2-HF: Nuclear repulsion	1062390.441884
FMO2-HF: Total energy	-52224.482916
FMO2-MP2: Total energy	-52377.996135

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.
-10.483	-6.481	0.876	-2.569	-2.31	-0.015

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 : 0.015 / q_NPA : 0.004

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	-0.001	-0.014	2.404	-9.920	-6.063	0.877	-2.559	-2.176	-0.015
4	A	5	GLY	0	0.035	0.027	4.994	1.015	1.160	-0.001	-0.010	-0.134	0.000
5	A	6	VAL	0	-0.004	0.002	7.996	-0.017	-0.017	0.000	0.000	0.000	0.000
6	A	7	SER	0	-0.031	-0.006	11.390	0.037	0.037	0.000	0.000	0.000	0.000
7	A	8	HIS	0	-0.018	-0.033	12.898	0.155	0.155	0.000	0.000	0.000	0.000
8	A	9	VAL	0	0.042	0.036	16.080	-0.016	-0.016	0.000	0.000	0.000	0.000
9	A	10	SER	0	-0.003	-0.004	18.403	0.032	0.032	0.000	0.000	0.000	0.000
10	A	11	LEU	0	-0.007	0.001	21.454	0.014	0.014	0.000	0.000	0.000	0.000
11	A	12	THR	0	-0.033	-0.018	24.359	0.006	0.006	0.000	0.000	0.000	0.000
12	A	13	VAL	0	-0.007	-0.004	27.547	0.003	0.003	0.000	0.000	0.000	0.000
13	A	14	ARG	1	0.905	0.949	30.646	0.136	0.136	0.000	0.000	0.000	0.000
14	A	15	ASP	-1	-0.863	-0.932	34.353	-0.160	-0.160	0.000	0.000	0.000	0.000
15	A	16	LEU	0	0.025	-0.001	30.322	-0.010	-0.010	0.000	0.000	0.000	0.000
16	A	17	ASP	-1	-0.873	-0.929	33.061	-0.200	-0.200	0.000	0.000	0.000	0.000
17	A	18	ILE	0	-0.073	-0.037	35.427	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	19	SER	0	0.074	0.033	30.340	0.001	0.001	0.000	0.000	0.000	0.000
19	A	20	CYS	0	-0.072	-0.024	30.748	-0.018	-0.018	0.000	0.000	0.000	0.000
20	A	21	ARG	1	0.941	0.980	31.825	0.166	0.166	0.000	0.000	0.000	0.000
21	A	22	TRP	0	0.051	0.049	28.567	-0.007	-0.007	0.000	0.000	0.000	0.000
22	A	23	TYR	0	-0.001	-0.050	25.524	-0.013	-0.013	0.000	0.000	0.000	0.000
23	A	24	THR	0	-0.079	-0.051	29.421	-0.014	-0.014	0.000	0.000	0.000	0.000
24	A	25	GLU	-1	-0.994	-0.993	31.202	-0.181	-0.181	0.000	0.000	0.000	0.000
25	A	26	ILE	0	-0.019	-0.006	29.817	0.003	0.003	0.000	0.000	0.000	0.000
26	A	27	LEU	0	-0.034	-0.029	25.024	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	28	ASP	-1	-0.840	-0.900	26.946	-0.298	-0.298	0.000	0.000	0.000	0.000
28	A	29	TRP	0	-0.077	-0.025	24.433	-0.008	-0.008	0.000	0.000	0.000	0.000
29	A	30	LYS	1	0.964	0.970	26.285	0.366	0.366	0.000	0.000	0.000	0.000
30	A	31	GLU	-1	-0.846	-0.915	26.481	-0.297	-0.297	0.000	0.000	0.000	0.000
31	A	32	LEU	0	-0.082	-0.057	22.777	0.012	0.012	0.000	0.000	0.000	0.000
32	A	33	VAL	0	-0.021	-0.016	25.399	0.017	0.017	0.000	0.000	0.000	0.000
33	A	34	ARG	1	0.819	0.908	27.461	0.215	0.215	0.000	0.000	0.000	0.000
34	A	35	GLY	0	-0.034	-0.024	29.618	0.010	0.010	0.000	0.000	0.000	0.000
35	A	36	ARG	1	0.759	0.851	30.433	0.183	0.183	0.000	0.000	0.000	0.000
36	A	37	GLY	0	-0.021	-0.018	28.724	-0.013	-0.013	0.000	0.000	0.000	0.000
37	A	38	ASP	-1	-0.961	-0.992	29.034	-0.150	-0.150	0.000	0.000	0.000	0.000
38	A	39	THR	0	0.010	0.014	30.532	0.005	0.005	0.000	0.000	0.000	0.000
39	A	40	THR	0	0.002	0.017	28.524	-0.011	-0.011	0.000	0.000	0.000	0.000
40	A	41	SER	0	0.044	0.033	31.099	0.002	0.002	0.000	0.000	0.000	0.000
41	A	42	PHE	0	-0.045	-0.018	26.208	-0.008	-0.008	0.000	0.000	0.000	0.000
42	A	43	ALA	0	0.083	0.035	27.667	0.013	0.013	0.000	0.000	0.000	0.000
43	A	44	HIS	0	-0.046	-0.018	20.211	0.018	0.018	0.000	0.000	0.000	0.000
44	A	45	GLY	0	0.084	0.025	24.083	0.025	0.025	0.000	0.000	0.000	0.000
45	A	46	VAL	0	-0.098	-0.042	20.450	-0.052	-0.052	0.000	0.000	0.000	0.000
46	A	47	LEU	0	0.038	0.026	20.986	0.049	0.049	0.000	0.000	0.000	0.000
47	A	48	PRO	0	0.042	0.030	22.105	-0.051	-0.051	0.000	0.000	0.000	0.000
48	A	49	GLY	0	0.021	0.007	20.220	-0.008	-0.008	0.000	0.000	0.000	0.000
49	A	50	GLY	0	-0.055	-0.032	18.083	-0.080	-0.080	0.000	0.000	0.000	0.000
50	A	51	LEU	0	0.008	0.017	15.790	-0.076	-0.076	0.000	0.000	0.000	0.000
51	A	52	SER	0	0.025	0.017	17.344	0.109	0.109	0.000	0.000	0.000	0.000
52	A	53	ILE	0	0.029	0.011	18.765	-0.037	-0.037	0.000	0.000	0.000	0.000
53	A	54	VAL	0	-0.033	-0.024	20.897	0.030	0.030	0.000	0.000	0.000	0.000
54	A	55	LEU	0	0.020	0.027	23.428	0.007	0.007	0.000	0.000	0.000	0.000
55	A	56	ARG	1	0.900	0.925	23.615	0.338	0.338	0.000	0.000	0.000	0.000
56	A	57	GLU	-1	-0.810	-0.878	28.112	-0.173	-0.173	0.000	0.000	0.000	0.000
57	A	58	HIS	0	-0.022	-0.032	27.214	-0.004	-0.004	0.000	0.000	0.000	0.000
58	A	59	ASP	-1	-0.761	-0.851	32.305	-0.155	-0.155	0.000	0.000	0.000	0.000
59	A	60	GLY	0	-0.054	-0.022	34.710	0.009	0.009	0.000	0.000	0.000	0.000
60	A	61	GLY	0	-0.001	0.002	33.928	0.003	0.003	0.000	0.000	0.000	0.000
61	A	62	GLY	0	0.013	-0.004	34.545	0.006	0.006	0.000	0.000	0.000	0.000
62	A	63	THR	0	-0.042	-0.023	36.463	0.005	0.005	0.000	0.000	0.000	0.000
63	A	64	ASP	-1	-0.946	-0.957	33.975	-0.099	-0.099	0.000	0.000	0.000	0.000
64	A	65	LEU	0	-0.039	-0.033	34.572	-0.007	-0.007	0.000	0.000	0.000	0.000
65	A	66	PHE	0	-0.012	0.002	26.275	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	67	ASP	-1	-0.825	-0.896	30.128	-0.086	-0.086	0.000	0.000	0.000	0.000
67	A	68	GLU	-1	-0.835	-0.917	27.585	-0.131	-0.131	0.000	0.000	0.000	0.000
68	A	69	THR	0	-0.141	-0.091	27.597	0.010	0.010	0.000	0.000	0.000	0.000
69	A	70	ARG	1	0.859	0.932	28.876	0.096	0.096	0.000	0.000	0.000	0.000
70	A	71	PRO	0	-0.029	-0.022	24.633	-0.009	-0.009	0.000	0.000	0.000	0.000
71	A	72	GLY	0	0.007	0.002	22.319	-0.009	-0.009	0.000	0.000	0.000	0.000
72	A	73	LEU	0	-0.063	-0.026	20.443	-0.005	-0.005	0.000	0.000	0.000	0.000
73	A	74	ASP	-1	-0.845	-0.906	22.177	-0.131	-0.131	0.000	0.000	0.000	0.000
74	A	75	HIS	0	-0.017	-0.043	22.317	-0.008	-0.008	0.000	0.000	0.000	0.000
75	A	76	LEU	0	-0.054	-0.014	18.070	-0.029	-0.029	0.000	0.000	0.000	0.000
76	A	77	SER	0	-0.001	0.006	19.613	0.008	0.008	0.000	0.000	0.000	0.000
77	A	78	PHE	0	-0.006	-0.014	18.829	-0.067	-0.067	0.000	0.000	0.000	0.000
78	A	79	SER	0	-0.029	-0.017	17.945	0.034	0.034	0.000	0.000	0.000	0.000
79	A	80	VAL	0	-0.018	-0.008	20.125	-0.023	-0.023	0.000	0.000	0.000	0.000
80	A	81	GLU	-1	-0.948	-0.977	22.211	-0.383	-0.383	0.000	0.000	0.000	0.000
81	A	82	SER	0	-0.089	-0.051	24.253	0.030	0.030	0.000	0.000	0.000	0.000
82	A	83	MET	0	0.045	0.005	27.837	-0.008	-0.008	0.000	0.000	0.000	0.000
83	A	84	THR	0	0.022	0.021	30.629	0.003	0.003	0.000	0.000	0.000	0.000
84	A	85	ASP	-1	-0.824	-0.912	26.690	-0.283	-0.283	0.000	0.000	0.000	0.000
85	A	86	LEU	0	-0.047	-0.030	27.092	-0.003	-0.003	0.000	0.000	0.000	0.000
86	A	87	ASP	-1	-0.888	-0.941	30.370	-0.150	-0.150	0.000	0.000	0.000	0.000
87	A	88	VAL	0	0.024	0.006	31.941	0.005	0.005	0.000	0.000	0.000	0.000
88	A	89	LEU	0	-0.021	-0.014	27.217	0.002	0.002	0.000	0.000	0.000	0.000
89	A	90	GLU	-1	-0.807	-0.877	31.939	-0.138	-0.138	0.000	0.000	0.000	0.000
90	A	91	GLU	-1	-0.982	-0.984	34.699	-0.147	-0.147	0.000	0.000	0.000	0.000
91	A	92	ARG	1	0.764	0.872	30.644	0.245	0.245	0.000	0.000	0.000	0.000
92	A	93	LEU	0	0.021	0.018	31.419	0.005	0.005	0.000	0.000	0.000	0.000
93	A	94	ALA	0	-0.002	0.001	35.513	0.008	0.008	0.000	0.000	0.000	0.000
94	A	95	LYS	1	0.849	0.924	39.045	0.147	0.147	0.000	0.000	0.000	0.000
95	A	96	ALA	0	0.005	0.010	36.928	0.005	0.005	0.000	0.000	0.000	0.000
96	A	97	GLY	0	-0.070	-0.021	39.035	0.003	0.003	0.000	0.000	0.000	0.000
97	A	98	ALA	0	-0.030	-0.013	34.745	0.002	0.002	0.000	0.000	0.000	0.000
98	A	99	ALA	0	0.001	-0.002	34.957	0.008	0.008	0.000	0.000	0.000	0.000
99	A	100	PHE	0	-0.014	-0.027	33.239	-0.012	-0.012	0.000	0.000	0.000	0.000
100	A	101	THR	0	-0.070	-0.014	33.070	0.012	0.012	0.000	0.000	0.000	0.000
101	A	102	PRO	0	0.006	-0.012	33.864	-0.008	-0.008	0.000	0.000	0.000	0.000
102	A	103	THR	0	0.012	-0.023	30.601	-0.005	-0.005	0.000	0.000	0.000	0.000
103	A	104	GLN	0	-0.039	-0.017	31.399	0.008	0.008	0.000	0.000	0.000	0.000
104	A	105	GLU	-1	-0.898	-0.942	30.681	-0.104	-0.104	0.000	0.000	0.000	0.000
105	A	106	LEU	0	-0.024	-0.019	27.861	0.014	0.014	0.000	0.000	0.000	0.000
106	A	107	PRO	0	-0.043	-0.038	28.461	-0.003	-0.003	0.000	0.000	0.000	0.000
107	A	108	PHE	0	-0.010	-0.026	23.865	0.005	0.005	0.000	0.000	0.000	0.000
108	A	109	GLY	0	-0.002	0.001	24.627	-0.018	-0.018	0.000	0.000	0.000	0.000
109	A	110	TRP	0	0.006	0.005	26.547	0.017	0.017	0.000	0.000	0.000	0.000
110	A	111	ILE	0	0.051	0.015	25.160	-0.019	-0.019	0.000	0.000	0.000	0.000
111	A	112	LEU	0	0.006	0.031	27.443	0.016	0.016	0.000	0.000	0.000	0.000
112	A	113	ALA	0	0.041	0.020	27.900	-0.019	-0.019	0.000	0.000	0.000	0.000
113	A	114	PHE	0	-0.012	-0.031	26.432	0.013	0.013	0.000	0.000	0.000	0.000
114	A	115	ARG	1	0.849	0.944	29.178	0.146	0.146	0.000	0.000	0.000	0.000
115	A	116	ASP	-1	-0.734	-0.845	28.733	-0.235	-0.235	0.000	0.000	0.000	0.000
116	A	117	ALA	0	-0.027	-0.023	31.009	0.014	0.014	0.000	0.000	0.000	0.000
117	A	118	ASP	-1	-0.881	-0.941	30.925	-0.179	-0.179	0.000	0.000	0.000	0.000
118	A	119	ASN	0	-0.046	-0.038	32.365	0.006	0.006	0.000	0.000	0.000	0.000
119	A	120	ILE	0	-0.012	0.005	25.712	0.005	0.005	0.000	0.000	0.000	0.000
120	A	121	ALA	0	-0.025	-0.014	26.624	-0.002	-0.002	0.000	0.000	0.000	0.000
121	A	122	LEU	0	-0.028	-0.013	23.897	-0.029	-0.029	0.000	0.000	0.000	0.000
122	A	123	GLU	-1	-0.890	-0.952	23.532	-0.184	-0.184	0.000	0.000	0.000	0.000
123	A	124	ALA	0	-0.012	0.019	23.599	-0.038	-0.038	0.000	0.000	0.000	0.000
124	A	125	MET	0	-0.016	0.001	20.810	0.038	0.038	0.000	0.000	0.000	0.000
125	A	126	LEU	0	0.015	0.026	22.754	-0.027	-0.027	0.000	0.000	0.000	0.000
126	A	127	GLY	0	0.023	0.012	22.716	0.023	0.023	0.000	0.000	0.000	0.000
127	A	128	ARG	1	0.885	0.934	23.587	0.102	0.102	0.000	0.000	0.000	0.000
128	A	129	GLU	-1	-0.951	-0.986	23.574	-0.065	-0.065	0.000	0.000	0.000	0.000
129	A	130	GLY	0	-0.011	-0.001	23.595	-0.017	-0.017	0.000	0.000	0.000	0.000
130	A	131	HIS	0	-0.009	0.013	21.664	-0.002	-0.002	0.000	0.000	0.000	0.000
131	A	132	HIS	1	0.837	0.878	26.675	0.130	0.130	0.000	0.000	0.000	0.000
132	A	133	HIS	0	0.062	0.044	25.465	0.020	0.020	0.000	0.000	0.000	0.000
133	A	134	HIS	0	0.022	0.020	30.044	-0.003	-0.003	0.000	0.000	0.000	0.000
134	A	135	HIS	0	-0.073	-0.029	32.509	0.005	0.005	0.000	0.000	0.000	0.000
135	A	136	HIS	0	0.035	0.036	32.185	0.011	0.011	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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