FMO DATABASE

FMODB ID: 6634Z

Calculation Name: 4R1K-A-Xray322

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4R1K

Chain ID: A

ChEMBL ID:

UniProt ID: B0MNI9

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	136
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1285227.199408
FMO2-HF: Nuclear repulsion	1228332.987207
FMO2-HF: Total energy	-56894.2122
FMO2-MP2: Total energy	-57055.986256

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:0:GLY )

Summations of interaction energy for fragment #1(A:0:GLY )

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.
-173.478	-169.699	4.696	-4.986	-3.49	-0.054

Interaction energy analysis for fragmet #1(A:0:GLY )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.763 / q_NPA : 0.868

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	31	GLU	-1	-0.871	-0.943	3.743	-22.439	-20.241	-0.007	-1.126	-1.065	-0.007
4	A	32	GLY	0	0.004	0.010	5.339	-3.599	-3.599	0.000	0.000	0.000	0.000
5	A	33	ASN	0	0.020	-0.004	5.653	2.004	2.004	0.000	0.000	0.000	0.000
6	A	34	ILE	0	-0.014	-0.005	7.622	0.872	0.872	0.000	0.000	0.000	0.000
7	A	35	LYS	1	0.935	0.984	8.443	28.590	28.590	0.000	0.000	0.000	0.000
8	A	36	GLU	-1	-0.858	-0.935	2.234	-90.476	-88.895	4.703	-3.860	-2.425	-0.047
9	A	37	ASN	0	-0.032	-0.025	6.507	1.703	1.703	0.000	0.000	0.000	0.000
10	A	38	ALA	0	0.036	0.020	9.335	1.985	1.985	0.000	0.000	0.000	0.000
11	A	39	VAL	0	0.025	0.012	8.825	1.644	1.644	0.000	0.000	0.000	0.000
12	A	40	ARG	1	0.893	0.941	7.024	35.129	35.129	0.000	0.000	0.000	0.000
13	A	41	MET	0	-0.027	0.017	11.292	1.817	1.817	0.000	0.000	0.000	0.000
14	A	42	MET	0	0.034	0.029	14.166	1.423	1.423	0.000	0.000	0.000	0.000
15	A	43	GLU	-1	-0.848	-0.897	12.504	-19.057	-19.057	0.000	0.000	0.000	0.000
16	A	44	CYS	0	-0.092	-0.039	15.218	0.929	0.929	0.000	0.000	0.000	0.000
17	A	45	ILE	0	-0.001	0.014	17.591	1.115	1.115	0.000	0.000	0.000	0.000
18	A	46	VAL	0	-0.036	-0.015	17.630	0.883	0.883	0.000	0.000	0.000	0.000
19	A	47	ASN	0	-0.039	-0.028	16.983	1.046	1.046	0.000	0.000	0.000	0.000
20	A	48	LYS	1	0.893	0.965	20.792	12.858	12.858	0.000	0.000	0.000	0.000
21	A	49	ASP	-1	-0.858	-0.935	19.678	-14.675	-14.675	0.000	0.000	0.000	0.000
22	A	50	SER	0	0.044	-0.014	20.792	-0.448	-0.448	0.000	0.000	0.000	0.000
23	A	51	GLU	-1	-0.932	-0.947	22.005	-12.431	-12.431	0.000	0.000	0.000	0.000
24	A	52	LYS	1	0.888	0.940	15.920	17.409	17.409	0.000	0.000	0.000	0.000
25	A	53	LEU	0	0.023	0.012	17.726	-0.791	-0.791	0.000	0.000	0.000	0.000
26	A	54	PHE	0	-0.006	-0.010	18.997	-0.224	-0.224	0.000	0.000	0.000	0.000
27	A	55	ASP	-1	-0.955	-0.972	17.379	-17.069	-17.069	0.000	0.000	0.000	0.000
28	A	56	PHE	0	0.003	-0.001	11.891	-1.098	-1.098	0.000	0.000	0.000	0.000
29	A	57	TYR	0	-0.020	-0.009	17.286	0.096	0.096	0.000	0.000	0.000	0.000
30	A	58	ASN	0	-0.011	0.020	20.259	0.054	0.054	0.000	0.000	0.000	0.000
31	A	59	LYS	1	0.913	0.948	21.581	13.312	13.312	0.000	0.000	0.000	0.000
32	A	60	ASP	-1	-0.823	-0.897	23.369	-10.491	-10.491	0.000	0.000	0.000	0.000
33	A	61	MET	0	-0.024	-0.002	25.001	0.436	0.436	0.000	0.000	0.000	0.000
34	A	62	LYS	1	0.790	0.917	19.062	16.316	16.316	0.000	0.000	0.000	0.000
35	A	63	ASP	-1	-0.928	-0.961	25.921	-11.532	-11.532	0.000	0.000	0.000	0.000
36	A	64	ASN	0	-0.078	-0.032	28.636	0.609	0.609	0.000	0.000	0.000	0.000
37	A	65	TYR	0	-0.008	-0.009	29.250	0.480	0.480	0.000	0.000	0.000	0.000
38	A	66	LYS	1	1.002	1.012	27.465	10.412	10.412	0.000	0.000	0.000	0.000
39	A	67	ASP	-1	-0.907	-0.968	29.353	-9.809	-9.809	0.000	0.000	0.000	0.000
40	A	68	SER	0	-0.015	-0.014	31.701	0.064	0.064	0.000	0.000	0.000	0.000
41	A	69	SER	0	0.032	0.011	26.505	-0.048	-0.048	0.000	0.000	0.000	0.000
42	A	70	LEU	0	-0.027	-0.015	25.446	-0.189	-0.189	0.000	0.000	0.000	0.000
43	A	71	ASP	-1	-0.983	-0.992	28.079	-9.401	-9.401	0.000	0.000	0.000	0.000
44	A	72	GLU	-1	-0.847	-0.931	29.221	-10.278	-10.278	0.000	0.000	0.000	0.000
45	A	73	ILE	0	-0.043	-0.022	23.297	-0.192	-0.192	0.000	0.000	0.000	0.000
46	A	74	ARG	1	0.921	0.967	26.748	10.007	10.007	0.000	0.000	0.000	0.000
47	A	75	GLN	0	0.074	0.044	29.205	0.046	0.046	0.000	0.000	0.000	0.000
48	A	76	LEU	0	-0.034	-0.014	23.268	0.004	0.004	0.000	0.000	0.000	0.000
49	A	77	PHE	0	-0.049	-0.050	22.343	-0.177	-0.177	0.000	0.000	0.000	0.000
50	A	78	GLU	-1	-0.954	-0.970	27.496	-9.220	-9.220	0.000	0.000	0.000	0.000
51	A	79	TYR	0	-0.059	-0.030	28.499	0.250	0.250	0.000	0.000	0.000	0.000
52	A	80	ILE	0	-0.040	-0.007	24.186	-0.134	-0.134	0.000	0.000	0.000	0.000
53	A	81	ASP	-1	-0.830	-0.893	28.475	-9.857	-9.857	0.000	0.000	0.000	0.000
54	A	82	GLY	0	0.033	0.015	29.752	-0.066	-0.066	0.000	0.000	0.000	0.000
55	A	83	ALA	0	-0.064	-0.047	25.515	-0.404	-0.404	0.000	0.000	0.000	0.000
56	A	84	ILE	0	0.001	-0.007	20.803	0.248	0.248	0.000	0.000	0.000	0.000
57	A	85	THR	0	-0.032	-0.004	22.542	-0.486	-0.486	0.000	0.000	0.000	0.000
58	A	86	SER	0	-0.059	-0.018	20.485	-0.486	-0.486	0.000	0.000	0.000	0.000
59	A	87	TYR	0	-0.021	-0.063	13.468	-0.126	-0.126	0.000	0.000	0.000	0.000
60	A	88	ASN	0	-0.037	-0.017	16.717	-0.283	-0.283	0.000	0.000	0.000	0.000
61	A	89	TYR	0	-0.046	-0.027	13.010	-0.897	-0.897	0.000	0.000	0.000	0.000
62	A	90	GLU	-1	-0.833	-0.904	15.696	-14.643	-14.643	0.000	0.000	0.000	0.000
63	A	91	GLY	0	-0.029	-0.036	16.233	-1.035	-1.035	0.000	0.000	0.000	0.000
64	A	92	LYS	1	0.926	0.956	15.479	17.331	17.331	0.000	0.000	0.000	0.000
65	A	93	GLY	0	0.140	0.082	16.577	0.315	0.315	0.000	0.000	0.000	0.000
66	A	94	GLY	0	-0.027	-0.029	20.220	-0.197	-0.197	0.000	0.000	0.000	0.000
67	A	95	GLY	0	-0.010	0.009	21.537	-0.327	-0.327	0.000	0.000	0.000	0.000
68	A	96	GLN	0	-0.032	-0.016	22.209	0.499	0.499	0.000	0.000	0.000	0.000
69	A	97	GLU	-1	-0.893	-0.955	18.388	-17.707	-17.707	0.000	0.000	0.000	0.000
70	A	98	ALA	0	-0.047	-0.010	21.752	0.828	0.828	0.000	0.000	0.000	0.000
71	A	99	LYS	1	0.949	0.967	19.593	14.889	14.889	0.000	0.000	0.000	0.000
72	A	100	ASN	0	-0.031	-0.025	23.092	0.742	0.742	0.000	0.000	0.000	0.000
73	A	101	ASP	-1	-0.857	-0.921	24.309	-11.527	-11.527	0.000	0.000	0.000	0.000
74	A	102	GLY	0	-0.057	-0.027	22.839	-0.219	-0.219	0.000	0.000	0.000	0.000
75	A	103	ILE	0	-0.030	-0.011	19.810	-1.039	-1.039	0.000	0.000	0.000	0.000
76	A	104	ILE	0	0.011	-0.004	15.622	0.739	0.739	0.000	0.000	0.000	0.000
77	A	105	CYS	0	-0.045	-0.018	19.276	-0.229	-0.229	0.000	0.000	0.000	0.000
78	A	106	TYR	0	0.012	0.001	20.923	0.093	0.093	0.000	0.000	0.000	0.000
79	A	107	TYR	0	0.014	0.005	15.727	-0.288	-0.288	0.000	0.000	0.000	0.000
80	A	108	SER	0	0.008	0.016	18.290	-0.586	-0.586	0.000	0.000	0.000	0.000
81	A	109	CYS	0	-0.107	-0.037	16.245	-0.572	-0.572	0.000	0.000	0.000	0.000
82	A	110	HIS	0	-0.016	-0.032	18.870	0.639	0.639	0.000	0.000	0.000	0.000
83	A	111	PRO	0	-0.037	-0.029	14.518	0.031	0.031	0.000	0.000	0.000	0.000
84	A	112	GLU	-1	-0.910	-0.947	16.571	-13.235	-13.235	0.000	0.000	0.000	0.000
85	A	113	PHE	0	-0.040	-0.027	13.023	-1.322	-1.322	0.000	0.000	0.000	0.000
86	A	114	ASP	-1	-0.727	-0.825	18.690	-12.630	-12.630	0.000	0.000	0.000	0.000
87	A	115	PHE	0	-0.068	-0.070	20.297	-0.837	-0.837	0.000	0.000	0.000	0.000
88	A	116	THR	0	0.045	0.036	22.263	0.704	0.704	0.000	0.000	0.000	0.000
89	A	117	THR	0	-0.037	-0.020	24.519	-0.445	-0.445	0.000	0.000	0.000	0.000
90	A	118	GLU	-1	-0.912	-0.962	27.043	-10.103	-10.103	0.000	0.000	0.000	0.000
91	A	119	THR	0	-0.100	-0.063	29.377	0.242	0.242	0.000	0.000	0.000	0.000
92	A	120	GLY	0	-0.038	-0.015	30.404	0.337	0.337	0.000	0.000	0.000	0.000
93	A	121	GLN	0	-0.089	-0.023	30.088	0.261	0.261	0.000	0.000	0.000	0.000
94	A	122	GLU	-1	-0.873	-0.934	25.650	-12.044	-12.044	0.000	0.000	0.000	0.000
95	A	123	TYR	0	-0.082	-0.065	24.983	0.467	0.467	0.000	0.000	0.000	0.000
96	A	124	THR	0	0.032	0.018	23.015	-0.134	-0.134	0.000	0.000	0.000	0.000
97	A	125	ILE	0	-0.072	-0.040	19.576	0.365	0.365	0.000	0.000	0.000	0.000
98	A	126	SER	0	0.031	0.018	20.460	-0.470	-0.470	0.000	0.000	0.000	0.000
99	A	127	PHE	0	-0.008	-0.019	17.457	0.489	0.489	0.000	0.000	0.000	0.000
100	A	128	SER	0	-0.025	-0.018	19.298	-0.312	-0.312	0.000	0.000	0.000	0.000
101	A	129	TYR	0	0.000	-0.021	12.365	-1.075	-1.075	0.000	0.000	0.000	0.000
102	A	130	HIS	0	-0.011	-0.009	18.420	0.227	0.227	0.000	0.000	0.000	0.000
103	A	131	TYR	0	-0.026	-0.004	9.809	-0.990	-0.990	0.000	0.000	0.000	0.000
104	A	132	ILE	0	0.018	0.012	13.943	-0.775	-0.775	0.000	0.000	0.000	0.000
105	A	133	TRP	0	-0.080	-0.063	17.231	0.928	0.928	0.000	0.000	0.000	0.000
106	A	134	ASN	0	0.059	0.019	19.553	-0.171	-0.171	0.000	0.000	0.000	0.000
107	A	135	GLU	-1	-1.010	-1.000	21.916	-10.817	-10.817	0.000	0.000	0.000	0.000
108	A	136	HIS	1	0.803	0.886	23.986	11.923	11.923	0.000	0.000	0.000	0.000
109	A	137	PRO	0	0.105	0.055	20.882	-0.306	-0.306	0.000	0.000	0.000	0.000
110	A	138	GLU	-1	-0.832	-0.900	20.913	-12.806	-12.806	0.000	0.000	0.000	0.000
111	A	139	TYR	0	-0.036	-0.040	23.156	0.358	0.358	0.000	0.000	0.000	0.000
112	A	140	GLU	-1	-0.848	-0.904	17.411	-17.633	-17.633	0.000	0.000	0.000	0.000
113	A	141	GLY	0	-0.011	-0.004	16.788	-0.309	-0.309	0.000	0.000	0.000	0.000
114	A	142	ILE	0	-0.042	-0.035	16.423	0.570	0.570	0.000	0.000	0.000	0.000
115	A	143	ASN	0	-0.011	-0.012	19.637	-0.011	-0.011	0.000	0.000	0.000	0.000
116	A	144	MET	0	-0.027	-0.008	22.804	0.755	0.755	0.000	0.000	0.000	0.000
117	A	145	ILE	0	0.031	0.016	20.769	-0.791	-0.791	0.000	0.000	0.000	0.000
118	A	146	GLN	0	0.025	0.023	23.734	1.176	1.176	0.000	0.000	0.000	0.000
119	A	147	ILE	0	0.009	0.008	24.474	-0.497	-0.497	0.000	0.000	0.000	0.000
120	A	148	CYS	0	-0.008	0.025	26.604	0.448	0.448	0.000	0.000	0.000	0.000
121	A	149	LYS	1	0.999	1.007	28.019	9.027	9.027	0.000	0.000	0.000	0.000
122	A	150	ASP	-1	-0.873	-0.932	29.469	-9.480	-9.480	0.000	0.000	0.000	0.000
123	A	151	GLY	0	0.052	0.028	28.192	0.118	0.118	0.000	0.000	0.000	0.000
124	A	152	ASN	0	-0.036	-0.030	29.082	0.189	0.189	0.000	0.000	0.000	0.000
125	A	153	TRP	0	0.009	-0.023	25.075	0.224	0.224	0.000	0.000	0.000	0.000
126	A	154	GLY	0	-0.048	-0.021	31.625	0.094	0.094	0.000	0.000	0.000	0.000
127	A	155	GLU	-1	-1.005	-0.997	34.158	-8.067	-8.067	0.000	0.000	0.000	0.000
128	A	156	LYS	1	0.842	0.931	29.821	10.048	10.048	0.000	0.000	0.000	0.000
129	A	157	LEU	0	-0.019	-0.009	29.287	0.319	0.319	0.000	0.000	0.000	0.000
130	A	158	ILE	0	-0.062	-0.048	28.549	-0.434	-0.434	0.000	0.000	0.000	0.000
131	A	159	ILE	0	0.017	0.027	24.833	0.321	0.321	0.000	0.000	0.000	0.000
132	A	160	GLY	0	0.029	0.016	26.569	-0.483	-0.483	0.000	0.000	0.000	0.000
133	A	161	ARG	1	0.925	0.966	27.186	10.855	10.855	0.000	0.000	0.000	0.000
134	A	162	ASN	0	0.003	-0.007	27.293	-0.783	-0.783	0.000	0.000	0.000	0.000
135	A	163	TYR	0	-0.085	-0.069	25.884	0.216	0.216	0.000	0.000	0.000	0.000
136	A	1	NME	0	0.017	0.017	27.220	-0.274	-0.274	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:GLY )