FMO DATABASE

FMODB ID: 14GNZ

Calculation Name: 4R1K-A-Xray372

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: 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	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. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1289194.409025
FMO2-HF: Nuclear repulsion	1232318.128425
FMO2-HF: Total energy	-56876.280601
FMO2-MP2: Total energy	-57038.059075

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.
-10.926	-11.281	8.925	-4.956	-3.614	-0.048

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 : 0 / q_Mulliken : -0.025 / q_NPA : -0.013

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	-0.835	-0.898	3.835	-0.104	2.000	-0.012	-1.170	-0.922	0.003
4	A	32	GLY	0	0.012	0.006	5.140	-0.622	-0.680	-0.001	-0.005	0.064	0.000
5	A	33	ASN	0	-0.009	-0.032	4.249	1.075	1.128	-0.001	-0.005	-0.046	0.000
6	A	34	ILE	0	-0.037	-0.010	6.622	0.457	0.457	0.000	0.000	0.000	0.000
7	A	35	LYS	1	0.850	0.916	8.638	1.263	1.263	0.000	0.000	0.000	0.000
8	A	36	GLU	-1	-0.785	-0.879	1.890	-13.434	-15.888	8.939	-3.776	-2.710	-0.051
9	A	37	ASN	0	-0.053	-0.040	6.463	0.949	0.949	0.000	0.000	0.000	0.000
10	A	38	ALA	0	0.068	0.032	9.156	0.157	0.157	0.000	0.000	0.000	0.000
11	A	39	VAL	0	0.011	0.005	9.397	0.093	0.093	0.000	0.000	0.000	0.000
12	A	40	ARG	1	0.875	0.940	7.282	-0.475	-0.475	0.000	0.000	0.000	0.000
13	A	41	MET	0	-0.025	0.011	11.648	0.011	0.011	0.000	0.000	0.000	0.000
14	A	42	MET	0	0.027	0.026	14.412	0.025	0.025	0.000	0.000	0.000	0.000
15	A	43	GLU	-1	-0.799	-0.884	13.347	0.171	0.171	0.000	0.000	0.000	0.000
16	A	44	CYS	0	-0.104	-0.036	15.379	0.038	0.038	0.000	0.000	0.000	0.000
17	A	45	ILE	0	-0.006	0.002	18.019	-0.007	-0.007	0.000	0.000	0.000	0.000
18	A	46	VAL	0	-0.033	-0.010	17.978	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	47	ASN	0	-0.100	-0.061	17.728	0.007	0.007	0.000	0.000	0.000	0.000
20	A	48	LYS	1	0.825	0.927	21.319	-0.039	-0.039	0.000	0.000	0.000	0.000
21	A	49	ASP	-1	-0.815	-0.881	19.927	0.283	0.283	0.000	0.000	0.000	0.000
22	A	50	SER	0	0.026	-0.040	21.056	0.001	0.001	0.000	0.000	0.000	0.000
23	A	51	GLU	-1	-0.904	-0.925	22.432	0.153	0.153	0.000	0.000	0.000	0.000
24	A	52	LYS	1	0.841	0.897	16.676	-0.345	-0.345	0.000	0.000	0.000	0.000
25	A	53	LEU	0	0.017	0.015	17.557	0.003	0.003	0.000	0.000	0.000	0.000
26	A	54	PHE	0	0.000	-0.008	19.033	-0.021	-0.021	0.000	0.000	0.000	0.000
27	A	55	ASP	-1	-0.874	-0.923	17.591	0.297	0.297	0.000	0.000	0.000	0.000
28	A	56	PHE	0	0.010	0.001	11.458	0.017	0.017	0.000	0.000	0.000	0.000
29	A	57	TYR	0	-0.013	-0.010	16.617	-0.056	-0.056	0.000	0.000	0.000	0.000
30	A	58	ASN	0	-0.005	0.022	19.680	0.039	0.039	0.000	0.000	0.000	0.000
31	A	59	LYS	1	0.799	0.881	20.992	-0.113	-0.113	0.000	0.000	0.000	0.000
32	A	60	ASP	-1	-0.716	-0.828	23.149	0.027	0.027	0.000	0.000	0.000	0.000
33	A	61	MET	0	-0.029	-0.005	24.045	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	62	LYS	1	0.757	0.875	18.284	-0.221	-0.221	0.000	0.000	0.000	0.000
35	A	63	ASP	-1	-0.836	-0.890	25.023	0.117	0.117	0.000	0.000	0.000	0.000
36	A	64	ASN	0	-0.098	-0.055	28.174	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	65	TYR	0	-0.025	-0.016	28.514	-0.010	-0.010	0.000	0.000	0.000	0.000
38	A	66	LYS	1	0.875	0.951	27.051	-0.104	-0.104	0.000	0.000	0.000	0.000
39	A	67	ASP	-1	-0.840	-0.915	28.524	0.086	0.086	0.000	0.000	0.000	0.000
40	A	68	SER	0	0.003	0.006	31.182	0.000	0.000	0.000	0.000	0.000	0.000
41	A	69	SER	0	0.030	0.002	25.866	-0.006	-0.006	0.000	0.000	0.000	0.000
42	A	70	LEU	0	-0.013	-0.009	25.092	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	71	ASP	-1	-0.897	-0.928	27.776	0.050	0.050	0.000	0.000	0.000	0.000
44	A	72	GLU	-1	-0.850	-0.947	28.553	0.008	0.008	0.000	0.000	0.000	0.000
45	A	73	ILE	0	-0.024	-0.003	23.010	-0.006	-0.006	0.000	0.000	0.000	0.000
46	A	74	ARG	1	0.850	0.928	26.580	-0.077	-0.077	0.000	0.000	0.000	0.000
47	A	75	GLN	0	0.002	-0.004	29.292	-0.009	-0.009	0.000	0.000	0.000	0.000
48	A	76	LEU	0	-0.020	-0.012	23.138	-0.008	-0.008	0.000	0.000	0.000	0.000
49	A	77	PHE	0	-0.020	-0.030	22.545	-0.005	-0.005	0.000	0.000	0.000	0.000
50	A	78	GLU	-1	-0.904	-0.951	27.504	0.040	0.040	0.000	0.000	0.000	0.000
51	A	79	TYR	0	-0.045	-0.025	28.982	-0.006	-0.006	0.000	0.000	0.000	0.000
52	A	80	ILE	0	-0.015	0.001	24.577	-0.007	-0.007	0.000	0.000	0.000	0.000
53	A	81	ASP	-1	-0.792	-0.859	28.885	0.000	0.000	0.000	0.000	0.000	0.000
54	A	82	GLY	0	0.042	0.024	29.993	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	83	ALA	0	-0.039	-0.034	25.683	0.003	0.003	0.000	0.000	0.000	0.000
56	A	84	ILE	0	-0.003	-0.007	21.238	-0.011	-0.011	0.000	0.000	0.000	0.000
57	A	85	THR	0	-0.040	-0.019	23.041	0.011	0.011	0.000	0.000	0.000	0.000
58	A	86	SER	0	-0.052	-0.025	20.911	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	87	TYR	0	-0.047	-0.054	14.316	-0.024	-0.024	0.000	0.000	0.000	0.000
60	A	88	ASN	0	-0.060	-0.035	17.453	0.011	0.011	0.000	0.000	0.000	0.000
61	A	89	TYR	0	-0.076	-0.064	13.237	-0.056	-0.056	0.000	0.000	0.000	0.000
62	A	90	GLU	-1	-0.817	-0.891	16.196	-0.353	-0.353	0.000	0.000	0.000	0.000
63	A	91	GLY	0	0.024	0.007	16.302	-0.074	-0.074	0.000	0.000	0.000	0.000
64	A	92	LYS	1	0.846	0.932	14.705	0.536	0.536	0.000	0.000	0.000	0.000
65	A	93	GLY	0	0.132	0.068	16.498	0.037	0.037	0.000	0.000	0.000	0.000
66	A	94	GLY	0	-0.022	-0.012	20.097	-0.026	-0.026	0.000	0.000	0.000	0.000
67	A	95	GLY	0	-0.006	-0.003	20.802	0.005	0.005	0.000	0.000	0.000	0.000
68	A	96	GLN	0	-0.035	-0.011	21.502	-0.004	-0.004	0.000	0.000	0.000	0.000
69	A	97	GLU	-1	-0.836	-0.921	17.870	-0.516	-0.516	0.000	0.000	0.000	0.000
70	A	98	ALA	0	-0.011	-0.002	21.156	0.021	0.021	0.000	0.000	0.000	0.000
71	A	99	LYS	1	0.959	0.963	18.831	0.379	0.379	0.000	0.000	0.000	0.000
72	A	100	ASN	0	-0.038	-0.012	23.058	0.023	0.023	0.000	0.000	0.000	0.000
73	A	101	ASP	-1	-0.885	-0.951	24.108	-0.144	-0.144	0.000	0.000	0.000	0.000
74	A	102	GLY	0	-0.013	0.003	22.430	0.002	0.002	0.000	0.000	0.000	0.000
75	A	103	ILE	0	-0.031	-0.009	19.278	-0.047	-0.047	0.000	0.000	0.000	0.000
76	A	104	ILE	0	0.002	-0.007	15.396	0.007	0.007	0.000	0.000	0.000	0.000
77	A	105	CYS	0	-0.050	-0.026	19.341	0.020	0.020	0.000	0.000	0.000	0.000
78	A	106	TYR	0	0.006	0.002	20.728	0.018	0.018	0.000	0.000	0.000	0.000
79	A	107	TYR	0	-0.014	-0.015	15.208	-0.066	-0.066	0.000	0.000	0.000	0.000
80	A	108	SER	0	0.001	-0.006	17.874	0.009	0.009	0.000	0.000	0.000	0.000
81	A	109	CYS	0	-0.107	-0.035	15.656	-0.052	-0.052	0.000	0.000	0.000	0.000
82	A	110	HIS	1	0.840	0.910	18.363	0.246	0.246	0.000	0.000	0.000	0.000
83	A	111	PRO	0	0.030	0.015	14.385	-0.008	-0.008	0.000	0.000	0.000	0.000
84	A	112	GLU	-1	-0.912	-0.955	16.490	-0.170	-0.170	0.000	0.000	0.000	0.000
85	A	113	PHE	0	-0.003	-0.011	13.566	-0.059	-0.059	0.000	0.000	0.000	0.000
86	A	114	ASP	-1	-0.789	-0.852	19.352	-0.153	-0.153	0.000	0.000	0.000	0.000
87	A	115	PHE	0	-0.035	-0.048	20.946	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	116	THR	0	0.055	0.025	23.001	0.008	0.008	0.000	0.000	0.000	0.000
89	A	117	THR	0	-0.035	-0.018	25.010	0.007	0.007	0.000	0.000	0.000	0.000
90	A	118	GLU	-1	-0.911	-0.959	27.411	0.033	0.033	0.000	0.000	0.000	0.000
91	A	119	THR	0	-0.088	-0.064	29.628	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	120	GLY	0	-0.042	-0.018	30.655	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	121	GLN	0	-0.073	-0.020	30.430	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	122	GLU	-1	-0.817	-0.883	26.156	-0.101	-0.101	0.000	0.000	0.000	0.000
95	A	123	TYR	0	-0.059	-0.056	25.583	0.010	0.010	0.000	0.000	0.000	0.000
96	A	124	THR	0	0.010	-0.005	23.822	-0.007	-0.007	0.000	0.000	0.000	0.000
97	A	125	ILE	0	-0.061	-0.037	20.170	0.019	0.019	0.000	0.000	0.000	0.000
98	A	126	SER	0	0.019	0.012	20.552	-0.028	-0.028	0.000	0.000	0.000	0.000
99	A	127	PHE	0	0.021	0.006	17.314	0.031	0.031	0.000	0.000	0.000	0.000
100	A	128	SER	0	-0.044	-0.044	19.636	-0.036	-0.036	0.000	0.000	0.000	0.000
101	A	129	TYR	0	0.001	-0.005	11.587	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	130	HIS	0	0.022	0.013	17.491	-0.059	-0.059	0.000	0.000	0.000	0.000
103	A	131	TYR	0	-0.010	-0.001	9.364	0.035	0.035	0.000	0.000	0.000	0.000
104	A	132	ILE	0	0.021	0.008	13.754	0.008	0.008	0.000	0.000	0.000	0.000
105	A	133	TRP	0	-0.066	-0.043	16.968	-0.015	-0.015	0.000	0.000	0.000	0.000
106	A	134	ASN	0	0.022	0.008	19.735	0.017	0.017	0.000	0.000	0.000	0.000
107	A	135	GLU	-1	-0.897	-0.941	21.814	-0.049	-0.049	0.000	0.000	0.000	0.000
108	A	136	HIS	1	0.750	0.853	23.664	0.046	0.046	0.000	0.000	0.000	0.000
109	A	137	PRO	0	0.080	0.048	20.679	-0.006	-0.006	0.000	0.000	0.000	0.000
110	A	138	GLU	-1	-0.823	-0.899	21.025	0.017	0.017	0.000	0.000	0.000	0.000
111	A	139	TYR	0	-0.070	-0.061	22.747	0.005	0.005	0.000	0.000	0.000	0.000
112	A	140	GLU	-1	-0.856	-0.916	17.150	-0.068	-0.068	0.000	0.000	0.000	0.000
113	A	141	GLY	0	0.021	0.006	16.313	0.045	0.045	0.000	0.000	0.000	0.000
114	A	142	ILE	0	-0.043	-0.041	16.429	-0.050	-0.050	0.000	0.000	0.000	0.000
115	A	143	ASN	0	-0.022	-0.010	18.889	0.005	0.005	0.000	0.000	0.000	0.000
116	A	144	MET	0	-0.032	-0.003	22.025	0.005	0.005	0.000	0.000	0.000	0.000
117	A	145	ILE	0	0.021	0.003	20.679	-0.016	-0.016	0.000	0.000	0.000	0.000
118	A	146	GLN	0	-0.003	0.002	23.328	0.015	0.015	0.000	0.000	0.000	0.000
119	A	147	ILE	0	0.044	0.016	24.299	-0.012	-0.012	0.000	0.000	0.000	0.000
120	A	148	CYS	0	-0.042	-0.003	26.469	0.006	0.006	0.000	0.000	0.000	0.000
121	A	149	LYS	1	0.885	0.942	28.168	0.024	0.024	0.000	0.000	0.000	0.000
122	A	150	ASP	-1	-0.848	-0.937	30.237	-0.066	-0.066	0.000	0.000	0.000	0.000
123	A	151	GLY	0	0.049	0.034	28.588	-0.004	-0.004	0.000	0.000	0.000	0.000
124	A	152	ASN	0	-0.061	-0.041	29.579	-0.008	-0.008	0.000	0.000	0.000	0.000
125	A	153	TRP	0	-0.035	-0.036	24.761	0.016	0.016	0.000	0.000	0.000	0.000
126	A	154	GLY	0	-0.071	-0.028	31.393	0.002	0.002	0.000	0.000	0.000	0.000
127	A	155	GLU	-1	-0.951	-0.964	34.233	-0.042	-0.042	0.000	0.000	0.000	0.000
128	A	156	LYS	1	0.870	0.944	29.740	0.089	0.089	0.000	0.000	0.000	0.000
129	A	157	LEU	0	0.002	0.019	29.260	0.006	0.006	0.000	0.000	0.000	0.000
130	A	158	ILE	0	-0.060	-0.047	27.958	-0.011	-0.011	0.000	0.000	0.000	0.000
131	A	159	ILE	0	-0.014	0.011	24.678	0.008	0.008	0.000	0.000	0.000	0.000
132	A	160	GLY	0	0.013	0.008	26.070	-0.012	-0.012	0.000	0.000	0.000	0.000
133	A	161	ARG	1	0.853	0.922	26.443	-0.004	-0.004	0.000	0.000	0.000	0.000
134	A	162	ASN	0	-0.012	-0.009	26.463	-0.018	-0.018	0.000	0.000	0.000	0.000
135	A	163	TYR	0	-0.039	-0.037	25.342	0.002	0.002	0.000	0.000	0.000	0.000

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