FMO DATABASE

FMODB ID: ZY3VN

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:

Apendix: None

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	130
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1113107.685054
FMO2-HF: Nuclear repulsion	1057593.903082
FMO2-HF: Total energy	-55513.781972
FMO2-MP2: Total energy	-55675.458758

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.
-0.778	1.542	0.087	-0.993	-1.413	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 : 0.059 / q_NPA : 0.019

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	0.007	0.006	3.863	-1.203	0.080	-0.001	-0.621	-0.660	0.002
4	A	4	ALA	0	0.057	0.027	2.863	-0.936	-0.260	0.089	-0.238	-0.527	-0.001
5	A	5	LEU	0	0.008	0.006	4.272	0.486	0.847	-0.001	-0.134	-0.226	0.000
6	A	6	LYS	1	0.963	0.974	5.963	0.695	0.695	0.000	0.000	0.000	0.000
7	A	7	ASN	0	-0.013	0.003	7.616	0.293	0.293	0.000	0.000	0.000	0.000
8	A	8	TYR	0	0.032	0.022	8.327	0.165	0.165	0.000	0.000	0.000	0.000
9	A	9	TYR	0	0.004	-0.014	9.623	0.124	0.124	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.874	-0.928	12.041	-0.130	-0.130	0.000	0.000	0.000	0.000
11	A	11	VAL	0	0.026	0.020	12.976	0.061	0.061	0.000	0.000	0.000	0.000
12	A	12	HIS	0	-0.031	-0.004	14.256	0.028	0.028	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.815	0.904	16.122	0.235	0.235	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.832	-0.902	17.646	-0.128	-0.128	0.000	0.000	0.000	0.000
15	A	15	LEU	0	-0.022	-0.010	17.806	0.028	0.028	0.000	0.000	0.000	0.000
16	A	16	PHE	0	0.004	-0.013	20.345	0.020	0.020	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.878	-0.946	20.682	-0.134	-0.134	0.000	0.000	0.000	0.000
18	A	18	GLY	0	0.003	-0.002	23.324	0.017	0.017	0.000	0.000	0.000	0.000
19	A	19	VAL	0	-0.025	-0.013	24.437	0.012	0.012	0.000	0.000	0.000	0.000
20	A	20	GLN	0	-0.003	0.000	26.357	0.020	0.020	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.805	0.887	27.953	0.077	0.077	0.000	0.000	0.000	0.000
22	A	22	TRP	0	-0.042	-0.027	29.157	0.007	0.007	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.715	-0.825	30.659	-0.083	-0.083	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.820	-0.888	32.400	-0.058	-0.058	0.000	0.000	0.000	0.000
25	A	25	THR	0	-0.017	-0.033	33.298	0.008	0.008	0.000	0.000	0.000	0.000
26	A	26	TRP	0	0.001	0.008	35.005	0.007	0.007	0.000	0.000	0.000	0.000
27	A	27	ARG	1	0.811	0.880	35.127	0.082	0.082	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.011	0.001	37.552	0.005	0.005	0.000	0.000	0.000	0.000
29	A	29	PHE	0	-0.035	-0.022	39.509	0.005	0.005	0.000	0.000	0.000	0.000
30	A	30	LEU	0	0.023	0.008	39.968	0.004	0.004	0.000	0.000	0.000	0.000
31	A	31	GLU	-1	-0.850	-0.882	42.767	-0.042	-0.042	0.000	0.000	0.000	0.000
32	A	32	PHE	0	-0.026	-0.033	43.451	0.003	0.003	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.766	-0.846	43.853	-0.041	-0.041	0.000	0.000	0.000	0.000
34	A	34	ARG	1	0.846	0.904	43.785	0.049	0.049	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.849	0.902	48.304	0.035	0.035	0.000	0.000	0.000	0.000
36	A	36	ALA	0	0.007	0.005	49.637	0.002	0.002	0.000	0.000	0.000	0.000
37	A	37	SER	0	-0.072	-0.048	51.124	0.001	0.001	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.785	-0.871	52.845	-0.029	-0.029	0.000	0.000	0.000	0.000
39	A	39	PRO	0	-0.028	-0.013	54.905	0.001	0.001	0.000	0.000	0.000	0.000
40	A	40	ASN	0	0.002	-0.007	57.610	0.002	0.002	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.862	0.931	54.981	0.031	0.031	0.000	0.000	0.000	0.000
42	A	42	PHE	0	-0.022	-0.005	58.968	0.000	0.000	0.000	0.000	0.000	0.000
43	A	43	THR	0	0.007	0.004	62.281	0.001	0.001	0.000	0.000	0.000	0.000
44	A	44	ASN	0	-0.012	0.006	57.505	0.001	0.001	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.897	0.940	61.311	0.022	0.022	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.028	0.023	57.884	0.000	0.000	0.000	0.000	0.000	0.000
47	A	47	GLY	0	0.028	0.002	57.060	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	48	ASN	0	0.002	-0.005	58.346	0.000	0.000	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.011	0.014	53.921	0.000	0.000	0.000	0.000	0.000	0.000
50	A	50	LEU	0	0.018	0.022	53.593	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	51	LYS	1	0.913	0.944	52.166	0.020	0.020	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.821	-0.899	49.070	-0.032	-0.032	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.774	-0.877	47.917	-0.036	-0.036	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.940	0.973	47.418	0.022	0.022	0.000	0.000	0.000	0.000
55	A	55	GLN	0	0.019	0.022	42.399	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.828	0.885	43.171	0.037	0.037	0.000	0.000	0.000	0.000
57	A	57	ALA	0	0.033	0.011	43.180	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	58	LYS	1	0.844	0.925	39.145	0.043	0.043	0.000	0.000	0.000	0.000
59	A	59	LEU	0	-0.016	-0.016	38.399	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	60	GLN	0	0.040	0.024	38.414	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.906	0.953	38.465	0.037	0.037	0.000	0.000	0.000	0.000
62	A	62	MET	0	-0.030	-0.013	34.346	0.001	0.001	0.000	0.000	0.000	0.000
63	A	63	LEU	0	0.014	0.024	33.979	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	64	PRO	0	0.063	0.023	33.138	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	65	LYS	1	0.779	0.890	29.303	0.064	0.064	0.000	0.000	0.000	0.000
66	A	66	LEU	0	0.002	-0.009	29.377	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.796	-0.874	28.263	-0.088	-0.088	0.000	0.000	0.000	0.000
68	A	68	GLU	-1	-0.887	-0.952	28.100	-0.098	-0.098	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.854	-0.922	25.990	-0.086	-0.086	0.000	0.000	0.000	0.000
70	A	70	LEU	0	-0.025	0.012	22.991	-0.010	-0.010	0.000	0.000	0.000	0.000
71	A	71	LYS	1	0.868	0.915	23.188	0.100	0.100	0.000	0.000	0.000	0.000
72	A	72	ALA	0	0.035	0.022	23.319	-0.013	-0.013	0.000	0.000	0.000	0.000
73	A	73	ARG	1	0.827	0.891	19.541	0.116	0.116	0.000	0.000	0.000	0.000
74	A	74	ILE	0	-0.011	-0.004	18.565	-0.033	-0.033	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.815	-0.889	19.054	-0.164	-0.164	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.010	-0.011	16.554	-0.016	-0.016	0.000	0.000	0.000	0.000
77	A	77	TRP	0	0.005	0.005	13.307	-0.025	-0.025	0.000	0.000	0.000	0.000
78	A	78	GLU	-1	-0.850	-0.936	14.678	-0.272	-0.272	0.000	0.000	0.000	0.000
79	A	79	GLN	0	-0.041	-0.024	16.322	-0.019	-0.019	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.918	-0.951	9.658	-0.633	-0.633	0.000	0.000	0.000	0.000
81	A	81	HIS	0	-0.073	-0.044	9.386	-0.255	-0.255	0.000	0.000	0.000	0.000
82	A	82	SER	0	-0.051	-0.016	12.270	0.012	0.012	0.000	0.000	0.000	0.000
83	A	83	LYS	1	0.856	0.938	11.142	0.677	0.677	0.000	0.000	0.000	0.000
84	A	84	ALA	0	0.041	0.027	17.020	0.016	0.016	0.000	0.000	0.000	0.000
85	A	85	PHE	0	-0.020	-0.029	19.053	-0.014	-0.014	0.000	0.000	0.000	0.000
86	A	86	MET	0	-0.069	-0.027	20.828	0.026	0.026	0.000	0.000	0.000	0.000
87	A	87	VAL	0	0.011	-0.006	22.419	-0.011	-0.011	0.000	0.000	0.000	0.000
88	A	88	ASN	0	-0.042	-0.026	25.157	0.004	0.004	0.000	0.000	0.000	0.000
89	A	89	GLY	0	0.027	0.024	26.517	0.008	0.008	0.000	0.000	0.000	0.000
90	A	90	GLN	0	-0.040	-0.030	27.461	0.002	0.002	0.000	0.000	0.000	0.000
91	A	91	LYS	1	0.930	0.957	23.796	0.152	0.152	0.000	0.000	0.000	0.000
92	A	92	PHE	0	0.034	0.016	25.265	0.012	0.012	0.000	0.000	0.000	0.000
93	A	93	MET	0	0.037	0.013	25.927	0.009	0.009	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.865	-0.918	28.132	-0.126	-0.126	0.000	0.000	0.000	0.000
95	A	95	TYR	0	-0.054	-0.043	29.972	0.010	0.010	0.000	0.000	0.000	0.000
96	A	96	VAL	0	-0.010	-0.004	30.063	0.008	0.008	0.000	0.000	0.000	0.000
97	A	97	ALA	0	-0.001	-0.001	32.639	0.008	0.008	0.000	0.000	0.000	0.000
98	A	98	GLU	-1	-0.847	-0.909	34.629	-0.082	-0.082	0.000	0.000	0.000	0.000
99	A	99	GLN	0	0.005	-0.004	34.828	0.009	0.009	0.000	0.000	0.000	0.000
100	A	100	TRP	0	-0.038	-0.046	35.461	0.010	0.010	0.000	0.000	0.000	0.000
101	A	101	GLU	-1	-0.767	-0.860	38.790	-0.050	-0.050	0.000	0.000	0.000	0.000
102	A	102	MET	0	-0.035	-0.018	38.504	0.005	0.005	0.000	0.000	0.000	0.000
103	A	103	HIS	0	-0.042	-0.027	41.518	0.004	0.004	0.000	0.000	0.000	0.000
104	A	104	ARG	1	0.722	0.823	43.019	0.053	0.053	0.000	0.000	0.000	0.000
105	A	105	LEU	0	-0.008	-0.006	43.951	0.003	0.003	0.000	0.000	0.000	0.000
106	A	106	GLU	-1	-0.841	-0.892	46.129	-0.044	-0.044	0.000	0.000	0.000	0.000
107	A	107	LYS	1	0.838	0.901	46.771	0.045	0.045	0.000	0.000	0.000	0.000
108	A	108	GLU	-1	-0.915	-0.949	49.026	-0.040	-0.040	0.000	0.000	0.000	0.000
109	A	109	ARG	1	0.938	0.946	46.355	0.050	0.050	0.000	0.000	0.000	0.000
110	A	110	ALA	0	-0.004	0.004	51.919	0.002	0.002	0.000	0.000	0.000	0.000
111	A	111	LYS	1	0.842	0.928	52.020	0.038	0.038	0.000	0.000	0.000	0.000
112	A	112	GLN	0	0.026	0.012	54.525	0.000	0.000	0.000	0.000	0.000	0.000
113	A	113	GLU	-1	-0.811	-0.894	56.285	-0.029	-0.029	0.000	0.000	0.000	0.000
114	A	114	ARG	1	0.989	0.990	55.067	0.033	0.033	0.000	0.000	0.000	0.000
115	A	115	GLN	0	-0.021	0.001	59.808	0.001	0.001	0.000	0.000	0.000	0.000
116	A	116	LEU	0	0.039	0.010	59.809	0.001	0.001	0.000	0.000	0.000	0.000
117	A	117	LYS	1	0.842	0.926	60.805	0.030	0.030	0.000	0.000	0.000	0.000
118	A	118	ASN	0	0.014	0.002	64.020	0.001	0.001	0.000	0.000	0.000	0.000
119	A	119	LYS	1	0.889	0.950	65.476	0.023	0.023	0.000	0.000	0.000	0.000
120	A	120	LYS	1	0.876	0.924	66.521	0.024	0.024	0.000	0.000	0.000	0.000
121	A	121	GLN	0	0.007	0.013	68.116	0.000	0.000	0.000	0.000	0.000	0.000
122	A	122	THR	0	-0.028	-0.026	70.106	0.001	0.001	0.000	0.000	0.000	0.000
123	A	123	GLU	-1	-0.817	-0.882	70.604	-0.022	-0.022	0.000	0.000	0.000	0.000
124	A	124	THR	0	0.000	-0.036	71.980	0.000	0.000	0.000	0.000	0.000	0.000
125	A	125	GLU	-1	-0.939	-0.976	73.885	-0.019	-0.019	0.000	0.000	0.000	0.000
126	A	126	MET	0	-0.061	-0.032	75.938	0.001	0.001	0.000	0.000	0.000	0.000
127	A	127	LEU	0	-0.069	-0.021	74.816	0.000	0.000	0.000	0.000	0.000	0.000
128	A	128	TYR	0	-0.050	-0.027	74.523	0.000	0.000	0.000	0.000	0.000	0.000
129	A	129	GLY	0	0.038	0.047	79.215	0.000	0.000	0.000	0.000	0.000	0.000
130	A	130	SER	0	-0.062	-0.030	80.404	0.001	0.001	0.000	0.000	0.000	0.000

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