FMO DATABASE

FMODB ID: KR1Y3

Calculation Name: 2NRK-A-Xray316

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NRK

Chain ID: A

ChEMBL ID:

UniProt ID: Q837C3

Base Structure: X-ray

Registration Date: 2021-09-06

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	168
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1849329.252725
FMO2-HF: Nuclear repulsion	1781225.122455
FMO2-HF: Total energy	-68104.13027
FMO2-MP2: Total energy	-68306.761721

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:3:ACE )

Summations of interaction energy for fragment #1(A:3:ACE )

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.
-0.241	0.806	0.012	-0.408	-0.651	0

Interaction energy analysis for fragmet #1(A:3:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.006 / q_NPA : -0.012

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].
3	A	5	VAL	0	-0.047	-0.019	3.874	1.356	2.016	-0.005	-0.308	-0.348
4	A	6	THR	0	0.008	0.010	7.030	0.001	0.001	0.000	0.000	0.000
5	A	7	GLU	-1	-0.807	-0.918	9.522	-0.220	-0.220	0.000	0.000	0.000
6	A	8	TYR	0	0.020	0.027	12.384	0.018	0.018	0.000	0.000	0.000
7	A	9	GLN	0	0.007	-0.011	9.388	0.036	0.036	0.000	0.000	0.000
8	A	10	PRO	0	0.040	0.014	14.614	0.031	0.031	0.000	0.000	0.000
9	A	11	ALA	0	0.076	0.036	15.205	0.013	0.013	0.000	0.000	0.000
10	A	12	TRP	0	-0.066	-0.031	9.670	0.016	0.016	0.000	0.000	0.000
11	A	13	VAL	0	0.010	0.002	14.944	0.024	0.024	0.000	0.000	0.000
12	A	14	GLU	-1	-0.903	-0.942	18.395	0.088	0.088	0.000	0.000	0.000
13	A	15	GLN	0	0.020	-0.003	12.501	0.070	0.070	0.000	0.000	0.000
14	A	16	PHE	0	-0.031	-0.007	16.631	0.017	0.017	0.000	0.000	0.000
15	A	17	GLU	-1	-0.930	-0.973	17.533	0.092	0.092	0.000	0.000	0.000
16	A	18	GLU	-1	-0.958	-0.965	19.208	0.159	0.159	0.000	0.000	0.000
17	A	19	GLU	-1	-0.778	-0.877	16.614	0.277	0.277	0.000	0.000	0.000
18	A	20	ALA	0	-0.029	-0.020	19.371	-0.005	-0.005	0.000	0.000	0.000
19	A	21	GLN	0	-0.044	-0.023	21.430	-0.007	-0.007	0.000	0.000	0.000
20	A	22	ALA	0	0.045	0.029	21.261	-0.008	-0.008	0.000	0.000	0.000
21	A	23	LEU	0	-0.010	-0.013	18.568	-0.007	-0.007	0.000	0.000	0.000
22	A	24	LYS	1	0.937	0.960	22.920	-0.118	-0.118	0.000	0.000	0.000
23	A	25	GLN	0	-0.061	-0.018	26.226	-0.001	-0.001	0.000	0.000	0.000
24	A	26	ILE	0	-0.030	-0.006	23.394	-0.007	-0.007	0.000	0.000	0.000
25	A	27	LEU	0	-0.026	-0.022	23.798	-0.006	-0.006	0.000	0.000	0.000
26	A	28	LYS	1	0.920	0.969	27.890	-0.099	-0.099	0.000	0.000	0.000
27	A	29	GLU	-1	-0.858	-0.948	30.800	0.077	0.077	0.000	0.000	0.000
28	A	30	ASN	0	-0.019	0.011	29.542	-0.007	-0.007	0.000	0.000	0.000
29	A	31	CYS	0	-0.066	-0.023	26.149	0.004	0.004	0.000	0.000	0.000
30	A	32	LEU	0	0.042	0.031	28.851	-0.005	-0.005	0.000	0.000	0.000
31	A	33	LYS	1	0.888	0.940	25.861	-0.081	-0.081	0.000	0.000	0.000
32	A	34	VAL	0	0.001	0.001	21.195	0.008	0.008	0.000	0.000	0.000
33	A	35	GLU	-1	-0.894	-0.956	21.983	0.072	0.072	0.000	0.000	0.000
34	A	36	HIS	0	0.003	0.017	14.676	0.001	0.001	0.000	0.000	0.000
35	A	37	ILE	0	0.006	-0.014	16.176	-0.029	-0.029	0.000	0.000	0.000
36	A	38	GLY	0	0.065	0.037	13.771	0.023	0.023	0.000	0.000	0.000
37	A	39	SER	0	-0.026	-0.030	11.355	-0.040	-0.040	0.000	0.000	0.000
38	A	40	THR	0	0.069	0.048	10.557	-0.045	-0.045	0.000	0.000	0.000
39	A	41	SER	0	-0.018	0.013	13.299	-0.018	-0.018	0.000	0.000	0.000
40	A	42	VAL	0	0.015	-0.004	16.236	-0.012	-0.012	0.000	0.000	0.000
41	A	43	PRO	0	0.022	0.002	17.212	-0.015	-0.015	0.000	0.000	0.000
42	A	44	ASN	0	-0.007	-0.016	18.109	-0.009	-0.009	0.000	0.000	0.000
43	A	45	LEU	0	-0.055	0.010	13.937	-0.029	-0.029	0.000	0.000	0.000
44	A	46	ALA	0	0.032	0.016	12.068	0.011	0.011	0.000	0.000	0.000
45	A	47	ALA	0	-0.042	-0.057	9.631	0.022	0.022	0.000	0.000	0.000
46	A	48	LYS	1	0.951	0.996	3.293	-0.675	-0.478	0.017	-0.068	-0.146
47	A	49	PRO	0	-0.009	0.016	4.578	0.037	0.106	0.000	-0.009	-0.061
48	A	50	ILE	0	-0.053	-0.034	4.081	0.247	0.342	0.000	-0.016	-0.078
49	A	51	ILE	0	-0.013	0.006	7.897	-0.154	-0.154	0.000	0.000	0.000
50	A	52	ASP	-1	-0.861	-0.925	11.569	0.418	0.418	0.000	0.000	0.000
51	A	53	PHE	0	0.009	-0.013	13.535	-0.052	-0.052	0.000	0.000	0.000
52	A	54	LEU	0	-0.013	0.006	17.087	0.010	0.010	0.000	0.000	0.000
53	A	55	VAL	0	0.008	0.001	20.032	-0.011	-0.011	0.000	0.000	0.000
54	A	56	ILE	0	0.005	0.010	22.693	0.000	0.000	0.000	0.000	0.000
55	A	57	VAL	0	0.002	-0.005	26.095	-0.001	-0.001	0.000	0.000	0.000
56	A	58	GLU	-1	-0.912	-0.961	28.647	0.062	0.062	0.000	0.000	0.000
57	A	59	GLU	-1	-0.929	-0.977	31.527	0.068	0.068	0.000	0.000	0.000
58	A	60	ILE	0	-0.028	-0.036	24.860	0.006	0.006	0.000	0.000	0.000
59	A	61	GLU	-1	-0.914	-0.955	28.404	0.087	0.087	0.000	0.000	0.000
60	A	62	LYS	1	0.965	0.983	30.613	-0.076	-0.076	0.000	0.000	0.000
61	A	63	VAL	0	-0.067	-0.027	24.379	0.004	0.004	0.000	0.000	0.000
62	A	64	ASP	-1	-0.729	-0.819	26.681	0.136	0.136	0.000	0.000	0.000
63	A	65	LEU	0	-0.054	-0.020	27.935	0.002	0.002	0.000	0.000	0.000
64	A	66	LEU	0	-0.020	-0.009	26.602	-0.001	-0.001	0.000	0.000	0.000
65	A	67	GLN	0	-0.025	-0.002	23.497	0.004	0.004	0.000	0.000	0.000
66	A	68	TRP	0	0.036	-0.003	23.683	0.014	0.014	0.000	0.000	0.000
67	A	69	GLU	-1	-0.935	-0.964	25.229	0.132	0.132	0.000	0.000	0.000
68	A	70	PHE	0	-0.025	-0.031	20.579	0.013	0.013	0.000	0.000	0.000
69	A	71	GLU	-1	-0.888	-0.941	20.429	0.217	0.217	0.000	0.000	0.000
70	A	72	ARG	1	0.916	0.985	21.035	-0.134	-0.134	0.000	0.000	0.000
71	A	73	ILE	0	-0.074	-0.030	20.012	0.000	0.000	0.000	0.000	0.000
72	A	74	GLY	0	-0.030	-0.026	17.242	0.029	0.029	0.000	0.000	0.000
73	A	75	TYR	0	-0.091	-0.092	14.847	0.076	0.076	0.000	0.000	0.000
74	A	76	GLU	-1	-0.790	-0.873	13.826	0.432	0.432	0.000	0.000	0.000
75	A	77	TYR	0	0.014	-0.034	17.000	0.023	0.023	0.000	0.000	0.000
76	A	78	MET	0	-0.060	-0.031	15.430	-0.003	-0.003	0.000	0.000	0.000
77	A	79	GLY	0	0.047	0.032	18.912	-0.019	-0.019	0.000	0.000	0.000
78	A	80	GLU	-1	-0.825	-0.917	20.687	0.123	0.123	0.000	0.000	0.000
79	A	81	PHE	0	-0.069	-0.038	13.860	0.015	0.015	0.000	0.000	0.000
80	A	82	GLY	0	0.029	0.008	18.630	0.007	0.007	0.000	0.000	0.000
81	A	83	LEU	0	-0.060	-0.025	18.629	-0.013	-0.013	0.000	0.000	0.000
82	A	84	SER	0	0.027	0.017	22.265	0.003	0.003	0.000	0.000	0.000
83	A	85	GLY	0	0.015	-0.002	25.613	-0.002	-0.002	0.000	0.000	0.000
84	A	86	ARG	1	0.825	0.940	16.116	-0.203	-0.203	0.000	0.000	0.000
85	A	87	ARG	1	0.806	0.876	21.863	-0.131	-0.131	0.000	0.000	0.000
86	A	88	TYR	0	-0.030	-0.015	11.521	0.032	0.032	0.000	0.000	0.000
87	A	89	LEU	0	0.020	0.025	16.551	0.001	0.001	0.000	0.000	0.000
88	A	90	ARG	1	0.788	0.880	11.238	-0.421	-0.421	0.000	0.000	0.000
89	A	91	LYS	1	0.918	1.005	11.804	-0.388	-0.388	0.000	0.000	0.000
90	A	92	GLY	0	0.037	0.011	10.152	0.123	0.123	0.000	0.000	0.000
91	A	93	PRO	0	0.020	0.003	10.819	0.121	0.121	0.000	0.000	0.000
92	A	94	ILE	0	-0.002	0.004	9.937	0.033	0.033	0.000	0.000	0.000
93	A	95	LYS	1	0.994	0.988	5.757	-0.541	-0.541	0.000	0.000	0.000
94	A	96	ARG	1	0.875	0.930	5.148	-1.300	-1.300	0.000	0.000	0.000
95	A	97	THR	0	-0.055	-0.039	6.228	0.266	0.266	0.000	0.000	0.000
96	A	98	HIS	0	0.033	0.020	8.877	-0.164	-0.164	0.000	0.000	0.000
97	A	99	HIS	0	-0.014	0.006	7.968	0.217	0.217	0.000	0.000	0.000
98	A	100	VAL	0	0.026	0.019	12.438	-0.046	-0.046	0.000	0.000	0.000
99	A	101	HIS	0	-0.065	-0.041	13.507	-0.020	-0.020	0.000	0.000	0.000
100	A	102	ILE	0	0.008	0.006	18.254	-0.018	-0.018	0.000	0.000	0.000
101	A	103	TYR	0	0.001	-0.029	20.075	0.006	0.006	0.000	0.000	0.000
102	A	104	GLN	0	0.057	0.034	24.758	0.003	0.003	0.000	0.000	0.000
103	A	105	PHE	0	0.014	-0.010	28.445	-0.002	-0.002	0.000	0.000	0.000
104	A	106	ASP	-1	-0.868	-0.911	30.318	0.063	0.063	0.000	0.000	0.000
105	A	107	ASN	0	-0.017	-0.001	25.956	-0.009	-0.009	0.000	0.000	0.000
106	A	108	THR	0	0.020	-0.017	27.253	0.004	0.004	0.000	0.000	0.000
107	A	109	GLN	0	0.012	0.011	27.305	-0.002	-0.002	0.000	0.000	0.000
108	A	110	GLU	-1	-0.764	-0.852	21.234	0.105	0.105	0.000	0.000	0.000
109	A	111	ILE	0	-0.011	0.000	22.834	0.006	0.006	0.000	0.000	0.000
110	A	112	LEU	0	0.013	-0.004	23.904	0.001	0.001	0.000	0.000	0.000
111	A	113	ARG	1	0.765	0.885	17.721	-0.102	-0.102	0.000	0.000	0.000
112	A	114	HIS	0	-0.015	-0.020	17.136	-0.008	-0.008	0.000	0.000	0.000
113	A	115	LEU	0	-0.006	-0.009	20.629	-0.005	-0.005	0.000	0.000	0.000
114	A	116	ALA	0	0.013	0.011	23.081	-0.008	-0.008	0.000	0.000	0.000
115	A	117	PHE	0	0.003	-0.002	16.059	-0.011	-0.011	0.000	0.000	0.000
116	A	118	ARG	1	0.798	0.894	19.391	-0.084	-0.084	0.000	0.000	0.000
117	A	119	ASN	0	0.026	0.000	20.499	-0.006	-0.006	0.000	0.000	0.000
118	A	120	TYR	0	0.024	0.001	23.274	-0.006	-0.006	0.000	0.000	0.000
119	A	121	LEU	0	-0.026	-0.020	17.555	-0.012	-0.012	0.000	0.000	0.000
120	A	122	ARG	1	0.826	0.908	20.357	-0.059	-0.059	0.000	0.000	0.000
121	A	123	GLU	-1	-0.904	-0.934	22.934	0.000	0.000	0.000	0.000	0.000
122	A	124	ASN	0	-0.103	-0.041	24.480	-0.008	-0.008	0.000	0.000	0.000
123	A	125	PRO	0	0.097	0.044	22.706	-0.008	-0.008	0.000	0.000	0.000
124	A	126	ALA	0	0.018	0.010	22.395	-0.013	-0.013	0.000	0.000	0.000
125	A	127	ILE	0	0.046	0.023	21.250	-0.014	-0.014	0.000	0.000	0.000
126	A	128	ALA	0	0.026	0.010	18.743	-0.013	-0.013	0.000	0.000	0.000
127	A	129	THR	0	-0.002	-0.011	17.915	-0.025	-0.025	0.000	0.000	0.000
128	A	130	THR	0	-0.033	-0.005	18.632	-0.027	-0.027	0.000	0.000	0.000
129	A	131	TYR	0	0.033	0.008	13.459	-0.032	-0.032	0.000	0.000	0.000
130	A	132	GLY	0	0.015	-0.008	13.882	-0.035	-0.035	0.000	0.000	0.000
131	A	133	THR	0	-0.041	-0.020	13.911	-0.075	-0.075	0.000	0.000	0.000
132	A	134	LEU	0	0.013	0.017	14.775	-0.040	-0.040	0.000	0.000	0.000
133	A	135	LYS	1	0.833	0.922	10.018	0.094	0.094	0.000	0.000	0.000
134	A	136	LYS	1	0.873	0.931	10.687	0.165	0.165	0.000	0.000	0.000
135	A	137	GLN	0	0.012	-0.008	12.178	-0.059	-0.059	0.000	0.000	0.000
136	A	138	LEU	0	-0.010	-0.001	11.463	-0.022	-0.022	0.000	0.000	0.000
137	A	139	ALA	0	-0.016	-0.001	7.990	-0.045	-0.045	0.000	0.000	0.000
138	A	140	GLN	0	-0.069	-0.027	9.472	-0.014	-0.014	0.000	0.000	0.000
139	A	141	ALA	0	-0.025	-0.005	12.274	0.081	0.081	0.000	0.000	0.000
140	A	142	HIS	0	-0.053	-0.032	10.248	0.065	0.065	0.000	0.000	0.000
141	A	143	PRO	0	-0.005	0.002	7.564	-0.180	-0.180	0.000	0.000	0.000
142	A	144	ASP	-1	-0.854	-0.925	6.566	-0.755	-0.755	0.000	0.000	0.000
143	A	145	SER	0	-0.063	-0.031	7.998	0.144	0.144	0.000	0.000	0.000
144	A	146	ILE	0	0.025	-0.011	4.603	-0.080	-0.054	0.000	-0.007	-0.018
145	A	147	ASP	-1	-0.879	-0.932	7.558	0.141	0.141	0.000	0.000	0.000
146	A	148	LYS	1	0.968	0.973	11.252	0.179	0.179	0.000	0.000	0.000
147	A	149	TYR	0	-0.007	0.017	7.742	0.059	0.059	0.000	0.000	0.000
148	A	150	MET	0	-0.056	-0.054	8.702	0.037	0.037	0.000	0.000	0.000
149	A	151	ASP	-1	-0.905	-0.933	11.117	-0.054	-0.054	0.000	0.000	0.000
150	A	152	GLY	0	0.071	0.036	13.749	0.004	0.004	0.000	0.000	0.000
151	A	153	LYS	1	0.848	0.923	10.121	0.038	0.038	0.000	0.000	0.000
152	A	154	ASP	-1	-0.902	-0.939	14.828	0.030	0.030	0.000	0.000	0.000
153	A	155	ALA	0	0.043	0.015	17.011	0.012	0.012	0.000	0.000	0.000
154	A	156	PHE	0	-0.033	-0.017	17.310	0.004	0.004	0.000	0.000	0.000
155	A	157	ILE	0	0.029	0.005	13.788	0.007	0.007	0.000	0.000	0.000
156	A	158	LYS	1	0.954	0.985	18.439	-0.022	-0.022	0.000	0.000	0.000
157	A	159	LYS	1	0.905	0.967	21.583	0.050	0.050	0.000	0.000	0.000
158	A	160	ILE	0	-0.001	-0.012	20.483	0.004	0.004	0.000	0.000	0.000
159	A	161	GLU	-1	-0.824	-0.915	19.258	0.056	0.056	0.000	0.000	0.000
160	A	162	LYS	1	0.924	0.968	22.832	0.007	0.007	0.000	0.000	0.000
161	A	163	GLU	-1	-0.943	-0.966	25.741	-0.028	-0.028	0.000	0.000	0.000
162	A	164	ALA	0	0.004	0.001	23.844	0.001	0.001	0.000	0.000	0.000
163	A	165	LEU	0	0.005	0.001	25.947	0.002	0.002	0.000	0.000	0.000
164	A	166	LYS	1	0.873	0.932	27.965	0.003	0.003	0.000	0.000	0.000
165	A	167	LYS	1	0.897	0.947	28.679	0.005	0.005	0.000	0.000	0.000
166	A	168	TYR	0	-0.057	-0.028	27.868	0.002	0.002	0.000	0.000	0.000
167	A	169	TRP	0	-0.053	-0.030	30.211	0.003	0.003	0.000	0.000	0.000
168	A	170	GLU	-2	-1.816	-1.876	33.501	0.008	0.008	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:ACE )