FMO DATABASE

FMODB ID: 43R7N

Calculation Name: 3NRY-A-Xray320

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NRY

Chain ID: A

ChEMBL ID:

UniProt ID: O43663

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	130
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1108107.640221
FMO2-HF: Nuclear repulsion	1052595.504028
FMO2-HF: Total energy	-55512.136193
FMO2-MP2: Total energy	-55673.727121

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:1:GLY )

Summations of interaction energy for fragment #1(A:1: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.
-0.511	1.826	0.304	-1.091	-1.549	0.001

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.053 / q_NPA : 0.017

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	3	ALA	0	-0.011	0.004	3.728	-0.463	0.890	0.000	-0.655	-0.697	0.001
4	A	4	ALA	0	0.071	0.026	2.501	-1.308	-0.622	0.304	-0.346	-0.645	0.000
5	A	5	LEU	0	0.012	0.008	4.025	-0.129	0.169	0.000	-0.090	-0.207	0.000
6	A	6	LYS	1	0.960	0.978	5.806	0.805	0.805	0.000	0.000	0.000	0.000
7	A	7	ASN	0	0.036	0.016	7.724	0.174	0.174	0.000	0.000	0.000	0.000
8	A	8	TYR	0	0.014	0.019	7.954	0.093	0.093	0.000	0.000	0.000	0.000
9	A	9	TYR	0	-0.008	-0.030	9.591	0.143	0.143	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.962	-0.972	11.734	-0.154	-0.154	0.000	0.000	0.000	0.000
11	A	11	VAL	0	0.062	0.039	12.873	0.047	0.047	0.000	0.000	0.000	0.000
12	A	12	HIS	0	-0.036	-0.010	13.903	0.021	0.021	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.955	0.971	15.704	0.211	0.211	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.898	-0.946	17.462	-0.064	-0.064	0.000	0.000	0.000	0.000
15	A	15	LEU	0	-0.041	-0.011	17.293	0.024	0.024	0.000	0.000	0.000	0.000
16	A	16	PHE	0	-0.022	-0.020	20.014	0.014	0.014	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.903	-0.957	21.759	-0.114	-0.114	0.000	0.000	0.000	0.000
18	A	18	GLY	0	-0.008	-0.004	23.183	0.016	0.016	0.000	0.000	0.000	0.000
19	A	19	VAL	0	-0.022	-0.010	23.870	0.011	0.011	0.000	0.000	0.000	0.000
20	A	20	GLN	0	0.012	0.001	26.058	0.017	0.017	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.946	0.993	27.753	0.063	0.063	0.000	0.000	0.000	0.000
22	A	22	TRP	0	-0.054	-0.039	28.970	0.006	0.006	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.706	-0.822	30.429	-0.076	-0.076	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.954	-0.974	32.162	-0.055	-0.055	0.000	0.000	0.000	0.000
25	A	25	THR	0	-0.066	-0.051	33.273	0.008	0.008	0.000	0.000	0.000	0.000
26	A	26	TRP	0	-0.007	-0.003	34.878	0.007	0.007	0.000	0.000	0.000	0.000
27	A	27	ARG	1	0.838	0.902	35.175	0.074	0.074	0.000	0.000	0.000	0.000
28	A	28	LEU	0	0.007	0.006	37.702	0.004	0.004	0.000	0.000	0.000	0.000
29	A	29	PHE	0	-0.026	-0.013	39.440	0.004	0.004	0.000	0.000	0.000	0.000
30	A	30	LEU	0	0.011	-0.005	39.663	0.003	0.003	0.000	0.000	0.000	0.000
31	A	31	GLU	-1	-0.861	-0.880	42.600	-0.039	-0.039	0.000	0.000	0.000	0.000
32	A	32	PHE	0	-0.014	-0.035	43.458	0.003	0.003	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.795	-0.862	44.048	-0.030	-0.030	0.000	0.000	0.000	0.000
34	A	34	ARG	1	0.864	0.905	43.700	0.045	0.045	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.938	0.969	48.700	0.031	0.031	0.000	0.000	0.000	0.000
36	A	36	ALA	0	-0.019	-0.010	49.731	0.002	0.002	0.000	0.000	0.000	0.000
37	A	37	SER	0	-0.064	-0.035	50.474	0.001	0.001	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.868	-0.927	52.351	-0.027	-0.027	0.000	0.000	0.000	0.000
39	A	39	PRO	0	-0.035	-0.011	54.456	0.002	0.002	0.000	0.000	0.000	0.000
40	A	40	ASN	0	0.026	0.008	57.643	0.002	0.002	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.848	0.913	55.433	0.024	0.024	0.000	0.000	0.000	0.000
42	A	42	PHE	0	-0.015	-0.005	58.598	0.001	0.001	0.000	0.000	0.000	0.000
43	A	43	THR	0	-0.007	0.005	61.952	0.001	0.001	0.000	0.000	0.000	0.000
44	A	44	ASN	0	-0.015	-0.002	57.351	0.000	0.000	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.942	0.974	60.069	0.023	0.023	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.074	0.037	59.543	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	47	GLY	0	0.022	0.023	58.200	0.000	0.000	0.000	0.000	0.000	0.000
48	A	48	ASN	0	0.007	-0.012	59.037	0.000	0.000	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.015	-0.010	53.665	0.001	0.001	0.000	0.000	0.000	0.000
50	A	50	LEU	0	0.008	0.026	53.537	0.000	0.000	0.000	0.000	0.000	0.000
51	A	51	LYS	1	0.884	0.946	52.047	0.017	0.017	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.881	-0.962	48.958	-0.027	-0.027	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.830	-0.920	48.071	-0.025	-0.025	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.963	0.987	47.603	0.014	0.014	0.000	0.000	0.000	0.000
55	A	55	GLN	0	0.031	0.035	42.293	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.876	0.923	43.366	0.026	0.026	0.000	0.000	0.000	0.000
57	A	57	ALA	0	0.017	-0.003	43.322	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	58	LYS	1	0.796	0.900	38.870	0.033	0.033	0.000	0.000	0.000	0.000
59	A	59	LEU	0	0.001	-0.016	38.425	0.000	0.000	0.000	0.000	0.000	0.000
60	A	60	GLN	0	0.027	0.022	38.321	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.941	0.967	38.983	0.018	0.018	0.000	0.000	0.000	0.000
62	A	62	MET	0	-0.024	-0.013	34.167	0.002	0.002	0.000	0.000	0.000	0.000
63	A	63	LEU	0	0.005	0.014	34.078	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	64	PRO	0	0.067	0.035	33.135	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	65	LYS	1	0.809	0.905	29.460	0.034	0.034	0.000	0.000	0.000	0.000
66	A	66	LEU	0	-0.045	-0.037	29.538	0.000	0.000	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.792	-0.881	28.250	-0.060	-0.060	0.000	0.000	0.000	0.000
68	A	68	GLU	-1	-0.902	-0.937	28.071	-0.040	-0.040	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.853	-0.921	25.849	-0.038	-0.038	0.000	0.000	0.000	0.000
70	A	70	LEU	0	-0.041	-0.015	22.772	-0.004	-0.004	0.000	0.000	0.000	0.000
71	A	71	LYS	1	0.927	0.957	23.197	0.050	0.050	0.000	0.000	0.000	0.000
72	A	72	ALA	0	0.021	0.023	23.275	-0.007	-0.007	0.000	0.000	0.000	0.000
73	A	73	ARG	1	0.924	0.959	19.487	0.059	0.059	0.000	0.000	0.000	0.000
74	A	74	ILE	0	-0.006	-0.009	18.466	-0.021	-0.021	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.861	-0.929	18.689	-0.089	-0.089	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.017	-0.016	16.561	-0.007	-0.007	0.000	0.000	0.000	0.000
77	A	77	TRP	0	0.004	0.007	12.562	-0.003	-0.003	0.000	0.000	0.000	0.000
78	A	78	GLU	-1	-0.866	-0.950	14.145	-0.211	-0.211	0.000	0.000	0.000	0.000
79	A	79	GLN	0	-0.058	-0.030	15.867	-0.021	-0.021	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.959	-0.961	9.472	-0.115	-0.115	0.000	0.000	0.000	0.000
81	A	81	HIS	0	-0.066	-0.037	8.780	-0.177	-0.177	0.000	0.000	0.000	0.000
82	A	82	SER	0	-0.035	-0.006	11.760	-0.030	-0.030	0.000	0.000	0.000	0.000
83	A	83	LYS	1	0.866	0.937	11.854	0.602	0.602	0.000	0.000	0.000	0.000
84	A	84	ALA	0	0.022	0.019	16.345	0.024	0.024	0.000	0.000	0.000	0.000
85	A	85	PHE	0	-0.020	-0.020	18.453	-0.023	-0.023	0.000	0.000	0.000	0.000
86	A	86	MET	0	-0.068	-0.028	20.029	0.028	0.028	0.000	0.000	0.000	0.000
87	A	87	VAL	0	-0.003	-0.012	22.445	-0.014	-0.014	0.000	0.000	0.000	0.000
88	A	88	ASN	0	-0.044	-0.027	25.036	0.005	0.005	0.000	0.000	0.000	0.000
89	A	89	GLY	0	0.009	0.011	26.270	0.008	0.008	0.000	0.000	0.000	0.000
90	A	90	GLN	0	0.005	-0.005	26.860	0.004	0.004	0.000	0.000	0.000	0.000
91	A	91	LYS	1	1.017	1.011	23.820	0.107	0.107	0.000	0.000	0.000	0.000
92	A	92	PHE	0	0.054	0.026	24.895	0.011	0.011	0.000	0.000	0.000	0.000
93	A	93	MET	0	0.027	0.006	25.714	0.007	0.007	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.939	-0.965	28.290	-0.090	-0.090	0.000	0.000	0.000	0.000
95	A	95	TYR	0	-0.040	-0.044	29.568	0.008	0.008	0.000	0.000	0.000	0.000
96	A	96	VAL	0	-0.006	-0.006	29.902	0.007	0.007	0.000	0.000	0.000	0.000
97	A	97	ALA	0	-0.014	-0.008	32.282	0.006	0.006	0.000	0.000	0.000	0.000
98	A	98	GLU	-1	-0.873	-0.933	34.266	-0.074	-0.074	0.000	0.000	0.000	0.000
99	A	99	GLN	0	0.010	0.011	34.584	0.008	0.008	0.000	0.000	0.000	0.000
100	A	100	TRP	0	-0.031	-0.036	35.385	0.007	0.007	0.000	0.000	0.000	0.000
101	A	101	GLU	-1	-0.801	-0.875	38.630	-0.037	-0.037	0.000	0.000	0.000	0.000
102	A	102	MET	0	-0.015	-0.009	38.129	0.003	0.003	0.000	0.000	0.000	0.000
103	A	103	HIS	0	-0.037	-0.022	41.132	0.002	0.002	0.000	0.000	0.000	0.000
104	A	104	ARG	1	0.782	0.872	42.744	0.039	0.039	0.000	0.000	0.000	0.000
105	A	105	LEU	0	-0.021	-0.021	43.577	0.003	0.003	0.000	0.000	0.000	0.000
106	A	106	GLU	-1	-0.887	-0.925	45.615	-0.039	-0.039	0.000	0.000	0.000	0.000
107	A	107	LYS	1	0.855	0.919	46.173	0.035	0.035	0.000	0.000	0.000	0.000
108	A	108	GLU	-1	-0.980	-0.994	48.979	-0.029	-0.029	0.000	0.000	0.000	0.000
109	A	109	ARG	1	0.995	0.993	46.912	0.040	0.040	0.000	0.000	0.000	0.000
110	A	110	ALA	0	0.046	0.035	51.611	0.001	0.001	0.000	0.000	0.000	0.000
111	A	111	LYS	1	0.872	0.927	52.442	0.027	0.027	0.000	0.000	0.000	0.000
112	A	112	GLN	0	0.015	0.007	54.462	0.000	0.000	0.000	0.000	0.000	0.000
113	A	113	GLU	-1	-0.924	-0.955	55.953	-0.028	-0.028	0.000	0.000	0.000	0.000
114	A	114	ARG	1	0.956	0.969	55.116	0.027	0.027	0.000	0.000	0.000	0.000
115	A	115	GLN	0	-0.038	-0.007	59.363	0.001	0.001	0.000	0.000	0.000	0.000
116	A	116	LEU	0	0.039	0.004	59.463	0.001	0.001	0.000	0.000	0.000	0.000
117	A	117	LYS	1	0.969	1.001	61.891	0.025	0.025	0.000	0.000	0.000	0.000
118	A	118	ASN	0	-0.004	-0.014	63.304	0.001	0.001	0.000	0.000	0.000	0.000
119	A	119	LYS	1	0.958	0.989	65.185	0.018	0.018	0.000	0.000	0.000	0.000
120	A	120	LYS	1	1.014	1.002	66.093	0.023	0.023	0.000	0.000	0.000	0.000
121	A	121	GLN	0	-0.007	0.009	67.842	0.000	0.000	0.000	0.000	0.000	0.000
122	A	122	THR	0	-0.046	-0.033	69.740	0.001	0.001	0.000	0.000	0.000	0.000
123	A	123	GLU	-1	-0.975	-0.991	70.807	-0.019	-0.019	0.000	0.000	0.000	0.000
124	A	124	THR	0	-0.016	-0.022	71.534	0.000	0.000	0.000	0.000	0.000	0.000
125	A	125	GLU	-1	-0.940	-0.962	73.658	-0.016	-0.016	0.000	0.000	0.000	0.000
126	A	126	MET	0	-0.061	-0.032	75.644	0.001	0.001	0.000	0.000	0.000	0.000
127	A	127	LEU	0	-0.060	-0.024	74.687	0.000	0.000	0.000	0.000	0.000	0.000
128	A	128	TYR	0	-0.067	-0.043	74.620	0.000	0.000	0.000	0.000	0.000	0.000
129	A	129	GLY	0	-0.005	0.025	79.038	0.000	0.000	0.000	0.000	0.000	0.000
130	A	130	SER	-1	-0.980	-0.983	80.175	-0.013	-0.013	0.000	0.000	0.000	0.000

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