FMO DATABASE

FMODB ID: 669YZ

Calculation Name: 3NRY-A-Xray372

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: 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	OptHSide
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	130
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1109646.068271
FMO2-HF: Nuclear repulsion	1054132.557207
FMO2-HF: Total energy	-55513.511064
FMO2-MP2: Total energy	-55675.153973

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.
-0.695	1.661	0.321	-1.114	-1.563	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 : 0.049 / q_NPA : 0.016

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	-0.010	0.004	3.736	-0.502	0.870	-0.004	-0.664	-0.704	0.001
4	A	4	ALA	0	0.067	0.024	2.504	-1.362	-0.666	0.326	-0.362	-0.660	0.000
5	A	5	LEU	0	0.015	0.012	4.085	-0.176	0.112	-0.001	-0.088	-0.199	0.000
6	A	6	LYS	1	0.963	0.977	5.842	0.717	0.717	0.000	0.000	0.000	0.000
7	A	7	ASN	0	0.011	0.010	7.778	0.147	0.147	0.000	0.000	0.000	0.000
8	A	8	TYR	0	0.034	0.027	7.996	0.065	0.065	0.000	0.000	0.000	0.000
9	A	9	TYR	0	0.008	-0.019	9.627	0.129	0.129	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.877	-0.922	11.775	-0.128	-0.128	0.000	0.000	0.000	0.000
11	A	11	VAL	0	0.045	0.027	12.950	0.043	0.043	0.000	0.000	0.000	0.000
12	A	12	HIS	0	-0.028	-0.001	13.937	0.009	0.009	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.829	0.898	15.738	0.206	0.206	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.843	-0.897	17.499	-0.039	-0.039	0.000	0.000	0.000	0.000
15	A	15	LEU	0	-0.033	-0.009	17.588	0.021	0.021	0.000	0.000	0.000	0.000
16	A	16	PHE	0	-0.016	-0.022	20.050	0.011	0.011	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.882	-0.947	21.366	-0.111	-0.111	0.000	0.000	0.000	0.000
18	A	18	GLY	0	-0.002	-0.001	23.224	0.014	0.014	0.000	0.000	0.000	0.000
19	A	19	VAL	0	-0.021	-0.010	24.073	0.009	0.009	0.000	0.000	0.000	0.000
20	A	20	GLN	0	0.003	-0.002	26.185	0.016	0.016	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.800	0.896	27.792	0.058	0.058	0.000	0.000	0.000	0.000
22	A	22	TRP	0	-0.045	-0.037	29.007	0.005	0.005	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.711	-0.826	30.463	-0.069	-0.069	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.839	-0.896	32.197	-0.046	-0.046	0.000	0.000	0.000	0.000
25	A	25	THR	0	-0.031	-0.034	33.309	0.007	0.007	0.000	0.000	0.000	0.000
26	A	26	TRP	0	0.001	0.000	34.915	0.007	0.007	0.000	0.000	0.000	0.000
27	A	27	ARG	1	0.812	0.888	35.106	0.068	0.068	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.003	0.002	37.682	0.004	0.004	0.000	0.000	0.000	0.000
29	A	29	PHE	0	-0.033	-0.017	39.478	0.004	0.004	0.000	0.000	0.000	0.000
30	A	30	LEU	0	0.021	0.001	39.686	0.003	0.003	0.000	0.000	0.000	0.000
31	A	31	GLU	-1	-0.855	-0.881	42.633	-0.036	-0.036	0.000	0.000	0.000	0.000
32	A	32	PHE	0	-0.025	-0.034	43.368	0.003	0.003	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.775	-0.852	43.874	-0.027	-0.027	0.000	0.000	0.000	0.000
34	A	34	ARG	1	0.867	0.905	43.578	0.041	0.041	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.855	0.908	48.500	0.028	0.028	0.000	0.000	0.000	0.000
36	A	36	ALA	0	-0.010	-0.004	49.719	0.001	0.001	0.000	0.000	0.000	0.000
37	A	37	SER	0	-0.069	-0.044	50.553	0.001	0.001	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.824	-0.894	52.383	-0.024	-0.024	0.000	0.000	0.000	0.000
39	A	39	PRO	0	-0.026	-0.011	54.488	0.001	0.001	0.000	0.000	0.000	0.000
40	A	40	ASN	0	-0.014	-0.024	57.010	0.002	0.002	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.880	0.937	55.383	0.022	0.022	0.000	0.000	0.000	0.000
42	A	42	PHE	0	-0.029	-0.009	58.633	0.001	0.001	0.000	0.000	0.000	0.000
43	A	43	THR	0	0.008	0.011	61.987	0.001	0.001	0.000	0.000	0.000	0.000
44	A	44	ASN	0	0.024	0.027	57.465	0.000	0.000	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.904	0.951	61.315	0.018	0.018	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.039	0.024	57.878	0.000	0.000	0.000	0.000	0.000	0.000
47	A	47	GLY	0	0.013	-0.006	56.949	0.000	0.000	0.000	0.000	0.000	0.000
48	A	48	ASN	0	0.007	-0.004	57.984	0.000	0.000	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.008	0.017	53.930	0.001	0.001	0.000	0.000	0.000	0.000
50	A	50	LEU	0	0.001	0.009	53.574	0.000	0.000	0.000	0.000	0.000	0.000
51	A	51	LYS	1	0.901	0.947	52.143	0.013	0.013	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.797	-0.899	49.000	-0.024	-0.024	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.787	-0.886	48.114	-0.022	-0.022	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.956	0.981	47.647	0.011	0.011	0.000	0.000	0.000	0.000
55	A	55	GLN	0	0.019	0.024	42.518	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.839	0.900	43.410	0.023	0.023	0.000	0.000	0.000	0.000
57	A	57	ALA	0	0.010	-0.009	43.364	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	58	LYS	1	0.817	0.914	39.160	0.029	0.029	0.000	0.000	0.000	0.000
59	A	59	LEU	0	0.005	-0.010	38.481	0.000	0.000	0.000	0.000	0.000	0.000
60	A	60	GLN	0	0.043	0.033	38.362	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.929	0.963	38.904	0.014	0.014	0.000	0.000	0.000	0.000
62	A	62	MET	0	-0.023	-0.012	34.415	0.002	0.002	0.000	0.000	0.000	0.000
63	A	63	LEU	0	0.017	0.021	33.888	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	64	PRO	0	0.068	0.031	33.175	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	65	LYS	1	0.804	0.900	29.743	0.024	0.024	0.000	0.000	0.000	0.000
66	A	66	LEU	0	-0.026	-0.020	29.536	0.000	0.000	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.799	-0.884	28.291	-0.052	-0.052	0.000	0.000	0.000	0.000
68	A	68	GLU	-1	-0.902	-0.947	28.107	-0.033	-0.033	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.856	-0.919	25.852	-0.027	-0.027	0.000	0.000	0.000	0.000
70	A	70	LEU	0	-0.023	-0.010	22.712	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	71	LYS	1	0.848	0.903	23.232	0.038	0.038	0.000	0.000	0.000	0.000
72	A	72	ALA	0	0.012	0.012	23.311	-0.006	-0.006	0.000	0.000	0.000	0.000
73	A	73	ARG	1	0.856	0.912	19.493	0.046	0.046	0.000	0.000	0.000	0.000
74	A	74	ILE	0	0.004	-0.006	18.500	-0.017	-0.017	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.802	-0.878	18.714	-0.074	-0.074	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.005	-0.010	16.691	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	77	TRP	0	0.005	0.009	12.660	-0.004	-0.004	0.000	0.000	0.000	0.000
78	A	78	GLU	-1	-0.853	-0.932	14.164	-0.193	-0.193	0.000	0.000	0.000	0.000
79	A	79	GLN	0	-0.059	-0.033	15.874	-0.017	-0.017	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.941	-0.959	9.814	-0.067	-0.067	0.000	0.000	0.000	0.000
81	A	81	HIS	0	-0.083	-0.049	8.779	-0.170	-0.170	0.000	0.000	0.000	0.000
82	A	82	SER	0	-0.046	-0.011	11.764	-0.035	-0.035	0.000	0.000	0.000	0.000
83	A	83	LYS	1	0.859	0.936	11.096	0.622	0.622	0.000	0.000	0.000	0.000
84	A	84	ALA	0	0.022	0.019	16.342	0.022	0.022	0.000	0.000	0.000	0.000
85	A	85	PHE	0	-0.032	-0.030	18.432	-0.022	-0.022	0.000	0.000	0.000	0.000
86	A	86	MET	0	-0.058	-0.025	20.042	0.026	0.026	0.000	0.000	0.000	0.000
87	A	87	VAL	0	-0.001	-0.011	22.417	-0.013	-0.013	0.000	0.000	0.000	0.000
88	A	88	ASN	0	-0.047	-0.029	25.050	0.003	0.003	0.000	0.000	0.000	0.000
89	A	89	GLY	0	0.013	0.012	26.272	0.008	0.008	0.000	0.000	0.000	0.000
90	A	90	GLN	0	-0.011	-0.015	26.826	0.004	0.004	0.000	0.000	0.000	0.000
91	A	91	LYS	1	0.959	0.976	23.939	0.094	0.094	0.000	0.000	0.000	0.000
92	A	92	PHE	0	0.050	0.024	24.907	0.010	0.010	0.000	0.000	0.000	0.000
93	A	93	MET	0	0.041	0.012	25.727	0.006	0.006	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.874	-0.925	28.276	-0.084	-0.084	0.000	0.000	0.000	0.000
95	A	95	TYR	0	-0.039	-0.038	29.583	0.006	0.006	0.000	0.000	0.000	0.000
96	A	96	VAL	0	-0.015	-0.009	29.871	0.006	0.006	0.000	0.000	0.000	0.000
97	A	97	ALA	0	-0.019	-0.010	32.306	0.006	0.006	0.000	0.000	0.000	0.000
98	A	98	GLU	-1	-0.865	-0.930	34.284	-0.067	-0.067	0.000	0.000	0.000	0.000
99	A	99	GLN	0	0.028	0.025	34.598	0.006	0.006	0.000	0.000	0.000	0.000
100	A	100	TRP	0	-0.020	-0.033	35.404	0.006	0.006	0.000	0.000	0.000	0.000
101	A	101	GLU	-1	-0.777	-0.858	38.654	-0.033	-0.033	0.000	0.000	0.000	0.000
102	A	102	MET	0	-0.018	-0.010	37.972	0.003	0.003	0.000	0.000	0.000	0.000
103	A	103	HIS	0	-0.055	-0.031	41.159	0.002	0.002	0.000	0.000	0.000	0.000
104	A	104	ARG	1	0.742	0.838	42.769	0.035	0.035	0.000	0.000	0.000	0.000
105	A	105	LEU	0	-0.032	-0.019	43.520	0.002	0.002	0.000	0.000	0.000	0.000
106	A	106	GLU	-1	-0.892	-0.939	45.636	-0.035	-0.035	0.000	0.000	0.000	0.000
107	A	107	LYS	1	0.820	0.895	46.489	0.031	0.031	0.000	0.000	0.000	0.000
108	A	108	GLU	-1	-0.937	-0.973	48.874	-0.026	-0.026	0.000	0.000	0.000	0.000
109	A	109	ARG	1	1.001	1.001	46.546	0.037	0.037	0.000	0.000	0.000	0.000
110	A	110	ALA	0	0.026	0.022	51.634	0.001	0.001	0.000	0.000	0.000	0.000
111	A	111	LYS	1	0.871	0.933	52.060	0.025	0.025	0.000	0.000	0.000	0.000
112	A	112	GLN	0	0.011	0.007	54.262	0.000	0.000	0.000	0.000	0.000	0.000
113	A	113	GLU	-1	-0.832	-0.901	55.985	-0.024	-0.024	0.000	0.000	0.000	0.000
114	A	114	ARG	1	0.989	0.984	54.889	0.025	0.025	0.000	0.000	0.000	0.000
115	A	115	GLN	0	-0.034	-0.004	59.386	0.001	0.001	0.000	0.000	0.000	0.000
116	A	116	LEU	0	0.044	0.008	59.473	0.001	0.001	0.000	0.000	0.000	0.000
117	A	117	LYS	1	0.844	0.931	60.457	0.024	0.024	0.000	0.000	0.000	0.000
118	A	118	ASN	0	0.004	-0.010	63.716	0.000	0.000	0.000	0.000	0.000	0.000
119	A	119	LYS	1	0.942	0.980	65.204	0.017	0.017	0.000	0.000	0.000	0.000
120	A	120	LYS	1	0.998	0.992	66.304	0.021	0.021	0.000	0.000	0.000	0.000
121	A	121	GLN	0	0.006	0.016	67.860	0.000	0.000	0.000	0.000	0.000	0.000
122	A	122	THR	0	-0.045	-0.029	69.760	0.001	0.001	0.000	0.000	0.000	0.000
123	A	123	GLU	-1	-0.934	-0.964	70.676	-0.017	-0.017	0.000	0.000	0.000	0.000
124	A	124	THR	0	0.001	-0.027	71.766	0.000	0.000	0.000	0.000	0.000	0.000
125	A	125	GLU	-1	-0.969	-0.979	73.674	-0.015	-0.015	0.000	0.000	0.000	0.000
126	A	126	MET	0	-0.065	-0.034	75.670	0.001	0.001	0.000	0.000	0.000	0.000
127	A	127	LEU	0	-0.070	-0.020	74.471	0.000	0.000	0.000	0.000	0.000	0.000
128	A	128	TYR	0	-0.042	-0.031	74.446	0.000	0.000	0.000	0.000	0.000	0.000
129	A	129	GLY	0	0.029	0.048	79.034	0.000	0.000	0.000	0.000	0.000	0.000
130	A	130	SER	0	-0.048	-0.024	80.193	0.000	0.000	0.000	0.000	0.000	0.000

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