FMO DATABASE

FMODB ID: 76Z6K

Calculation Name: 1NQN-A-Xray372

Preferred Name: Avidin

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1NQN

Chain ID: A

ChEMBL ID: CHEMBL2189156

UniProt ID: P02701

Base Structure: X-ray

Registration Date: 2023-09-23

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	OptH
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	121
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-960285.975159
FMO2-HF: Nuclear repulsion	912487.906866
FMO2-HF: Total energy	-47798.068293
FMO2-MP2: Total energy	-47937.006908

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:2:ARG)

Summations of interaction energy for fragment #1(A:2:ARG)

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.
-12.917	-16.254	27.472	-11.553	-12.58	-0.101

Interaction energy analysis for fragmet #1(A:2:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.893 / q_NPA : 0.924

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

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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	4	CYS	0	-0.036	0.020	3.232	-10.888	-7.239	0.056	-1.790	-1.913	-0.005
4	A	5	SER	0	-0.008	-0.006	5.086	5.691	5.734	-0.001	-0.005	-0.037	0.000
5	A	6	LEU	0	0.101	0.018	7.776	-1.143	-1.143	0.000	0.000	0.000	0.000
6	A	7	THR	0	-0.046	-0.007	11.090	0.644	0.644	0.000	0.000	0.000	0.000
7	A	8	GLY	0	0.012	0.008	10.577	-2.586	-2.586	0.000	0.000	0.000	0.000
8	A	9	LYS	1	0.937	0.979	12.392	18.051	18.051	0.000	0.000	0.000	0.000
9	A	10	TRP	0	-0.049	-0.031	7.510	-3.090	-3.090	0.000	0.000	0.000	0.000
10	A	11	THR	0	-0.004	0.001	13.284	1.830	1.830	0.000	0.000	0.000	0.000
11	A	12	ASN	0	0.017	0.000	14.153	-1.389	-1.389	0.000	0.000	0.000	0.000
12	A	13	ASP	-1	-0.867	-0.932	16.575	-14.966	-14.966	0.000	0.000	0.000	0.000
13	A	14	LEU	0	-0.046	-0.017	18.722	0.452	0.452	0.000	0.000	0.000	0.000
14	A	15	GLY	0	0.019	0.019	19.467	0.572	0.572	0.000	0.000	0.000	0.000
15	A	16	SER	0	-0.081	-0.036	20.186	0.483	0.483	0.000	0.000	0.000	0.000
16	A	17	ASN	0	-0.037	-0.042	18.233	-1.348	-1.348	0.000	0.000	0.000	0.000
17	A	18	MET	0	0.016	0.034	14.918	1.124	1.124	0.000	0.000	0.000	0.000
18	A	19	THR	0	0.002	0.000	15.872	-1.579	-1.579	0.000	0.000	0.000	0.000
19	A	20	ILE	0	-0.012	0.003	14.284	1.064	1.064	0.000	0.000	0.000	0.000
20	A	21	GLY	0	0.043	0.016	15.490	-0.834	-0.834	0.000	0.000	0.000	0.000
21	A	22	ALA	0	-0.008	-0.001	15.300	-1.087	-1.087	0.000	0.000	0.000	0.000
22	A	23	VAL	0	-0.009	0.022	13.097	0.810	0.810	0.000	0.000	0.000	0.000
23	A	24	ASN	0	-0.012	-0.008	16.061	-0.291	-0.291	0.000	0.000	0.000	0.000
24	A	25	SER	0	0.047	-0.013	17.826	-0.590	-0.590	0.000	0.000	0.000	0.000
25	A	26	ARG	1	0.820	0.920	19.326	11.703	11.703	0.000	0.000	0.000	0.000
26	A	27	GLY	0	0.031	0.023	17.162	0.130	0.130	0.000	0.000	0.000	0.000
27	A	28	GLU	-1	-0.832	-0.908	18.214	-12.775	-12.775	0.000	0.000	0.000	0.000
28	A	29	PHE	0	0.006	0.001	16.833	-0.533	-0.533	0.000	0.000	0.000	0.000
29	A	30	THR	0	0.020	0.005	19.513	0.379	0.379	0.000	0.000	0.000	0.000
30	A	31	GLY	0	0.057	0.007	19.646	-0.923	-0.923	0.000	0.000	0.000	0.000
31	A	32	THR	0	-0.015	0.002	20.318	0.492	0.492	0.000	0.000	0.000	0.000
32	A	33	TYR	0	0.004	-0.014	19.874	-1.082	-1.082	0.000	0.000	0.000	0.000
33	A	34	THR	0	-0.002	-0.003	21.702	0.768	0.768	0.000	0.000	0.000	0.000
34	A	35	THR	0	0.032	0.012	22.711	-0.589	-0.589	0.000	0.000	0.000	0.000
35	A	36	ALA	0	0.013	0.015	25.156	0.342	0.342	0.000	0.000	0.000	0.000
36	A	37	VAL	0	-0.049	-0.028	27.688	-0.010	-0.010	0.000	0.000	0.000	0.000
37	A	38	THR	0	-0.046	-0.052	29.605	0.115	0.115	0.000	0.000	0.000	0.000
38	A	39	ALA	0	0.005	0.017	31.748	0.346	0.346	0.000	0.000	0.000	0.000
39	A	40	THR	0	0.005	-0.003	28.319	-0.312	-0.312	0.000	0.000	0.000	0.000
40	A	41	SER	0	-0.027	-0.014	27.920	0.103	0.103	0.000	0.000	0.000	0.000
41	A	42	ASN	0	0.035	0.024	28.973	0.011	0.011	0.000	0.000	0.000	0.000
42	A	43	GLU	-1	-0.897	-0.939	30.566	-9.487	-9.487	0.000	0.000	0.000	0.000
43	A	44	ILE	0	0.028	0.017	25.885	-0.348	-0.348	0.000	0.000	0.000	0.000
44	A	45	LYS	1	0.910	0.956	28.079	9.699	9.699	0.000	0.000	0.000	0.000
45	A	46	GLU	-1	-0.926	-0.955	25.587	-12.230	-12.230	0.000	0.000	0.000	0.000
46	A	47	SER	0	-0.035	-0.016	25.763	0.653	0.653	0.000	0.000	0.000	0.000
47	A	48	PRO	0	0.003	0.010	24.931	-0.568	-0.568	0.000	0.000	0.000	0.000
48	A	49	LEU	0	-0.024	-0.003	19.268	0.186	0.186	0.000	0.000	0.000	0.000
49	A	50	HIS	0	-0.021	-0.029	22.088	-0.427	-0.427	0.000	0.000	0.000	0.000
50	A	51	GLY	0	0.049	0.016	20.939	0.288	0.288	0.000	0.000	0.000	0.000
51	A	52	THR	0	-0.031	-0.001	19.263	0.129	0.129	0.000	0.000	0.000	0.000
52	A	53	GLU	-1	-0.904	-0.970	12.785	-22.012	-22.012	0.000	0.000	0.000	0.000
53	A	54	ASN	0	-0.047	-0.019	16.167	0.405	0.405	0.000	0.000	0.000	0.000
54	A	55	THR	0	0.068	0.017	14.768	-0.844	-0.844	0.000	0.000	0.000	0.000
55	A	56	ILE	0	0.007	0.000	15.606	-0.201	-0.201	0.000	0.000	0.000	0.000
56	A	57	ASN	0	-0.001	0.011	13.899	0.761	0.761	0.000	0.000	0.000	0.000
57	A	58	LYS	1	0.956	0.971	11.019	17.424	17.424	0.000	0.000	0.000	0.000
58	A	59	ARG	1	0.964	0.984	9.528	19.693	19.693	0.000	0.000	0.000	0.000
59	A	60	THR	0	0.012	-0.028	4.074	1.093	1.328	-0.001	-0.044	-0.191	0.000
60	A	61	GLN	0	0.019	0.028	6.535	-5.833	-5.833	0.000	0.000	0.000	0.000
61	A	62	PRO	0	0.027	0.036	8.795	2.041	2.041	0.000	0.000	0.000	0.000
62	A	63	THR	0	0.046	0.016	12.161	-0.832	-0.832	0.000	0.000	0.000	0.000
63	A	64	PHE	0	0.021	0.006	13.037	-0.087	-0.087	0.000	0.000	0.000	0.000
64	A	65	GLY	0	0.034	0.020	16.779	0.208	0.208	0.000	0.000	0.000	0.000
65	A	66	PHE	0	-0.005	0.000	17.145	-0.118	-0.118	0.000	0.000	0.000	0.000
66	A	67	THR	0	0.013	0.012	21.631	0.212	0.212	0.000	0.000	0.000	0.000
67	A	68	VAL	0	-0.020	-0.011	23.015	-0.210	-0.210	0.000	0.000	0.000	0.000
68	A	69	ASN	0	0.001	0.002	25.537	0.462	0.462	0.000	0.000	0.000	0.000
69	A	70	TRP	0	0.018	-0.033	24.712	-0.069	-0.069	0.000	0.000	0.000	0.000
70	A	71	LYS	1	0.957	0.976	30.019	9.978	9.978	0.000	0.000	0.000	0.000
71	A	72	PHE	0	-0.022	-0.009	28.802	0.380	0.380	0.000	0.000	0.000	0.000
72	A	73	SER	0	0.009	0.003	32.978	0.202	0.202	0.000	0.000	0.000	0.000
73	A	74	GLU	-1	-0.860	-0.918	34.646	-7.977	-7.977	0.000	0.000	0.000	0.000
74	A	75	SER	0	-0.055	-0.025	32.474	0.001	0.001	0.000	0.000	0.000	0.000
75	A	76	THR	0	-0.007	-0.002	29.252	-0.115	-0.115	0.000	0.000	0.000	0.000
76	A	77	THR	0	-0.026	0.009	24.817	0.233	0.233	0.000	0.000	0.000	0.000
77	A	78	VAL	0	-0.009	0.013	24.745	-0.180	-0.180	0.000	0.000	0.000	0.000
78	A	79	PHE	0	0.012	-0.004	19.685	0.040	0.040	0.000	0.000	0.000	0.000
79	A	80	THR	0	-0.025	-0.023	19.404	-0.013	-0.013	0.000	0.000	0.000	0.000
80	A	81	GLY	0	0.039	0.001	16.540	0.133	0.133	0.000	0.000	0.000	0.000
81	A	82	GLN	0	-0.068	-0.017	11.614	1.544	1.544	0.000	0.000	0.000	0.000
82	A	84	PHE	0	-0.022	-0.022	8.459	-0.371	-0.371	0.000	0.000	0.000	0.000
83	A	85	ILE	0	0.002	-0.002	2.643	-7.420	-5.029	1.234	-0.773	-2.851	0.000
84	A	86	ASP	-1	-0.876	-0.937	5.540	-26.275	-26.275	0.000	0.000	0.000	0.000
85	A	87	ARG	1	0.986	0.965	5.550	17.868	17.868	0.000	0.000	0.000	0.000
86	A	88	ASN	0	0.012	0.036	6.469	-4.001	-4.001	0.000	0.000	0.000	0.000
87	A	89	GLY	0	0.021	0.026	2.590	-0.434	-0.076	0.658	-0.281	-0.736	0.001
88	A	90	LYS	1	0.912	0.953	1.682	-10.663	-21.735	25.318	-8.362	-5.883	-0.096
89	A	91	GLU	-1	-0.793	-0.880	2.686	-50.538	-49.551	0.209	-0.292	-0.904	-0.001
90	A	92	VAL	0	-0.043	-0.028	4.707	5.056	5.128	-0.001	-0.006	-0.065	0.000
91	A	93	LEU	0	0.004	0.021	8.367	-0.203	-0.203	0.000	0.000	0.000	0.000
92	A	94	LYS	1	0.913	0.961	11.654	23.034	23.034	0.000	0.000	0.000	0.000
93	A	95	THR	0	-0.023	-0.026	14.276	0.568	0.568	0.000	0.000	0.000	0.000
94	A	96	MET	0	0.021	0.001	17.561	0.267	0.267	0.000	0.000	0.000	0.000
95	A	97	TRP	0	-0.020	-0.010	21.275	0.075	0.075	0.000	0.000	0.000	0.000
96	A	98	LEU	0	0.024	0.007	23.931	0.342	0.342	0.000	0.000	0.000	0.000
97	A	99	LEU	0	-0.028	-0.017	27.683	-0.137	-0.137	0.000	0.000	0.000	0.000
98	A	100	ARG	1	0.823	0.894	29.637	8.854	8.854	0.000	0.000	0.000	0.000
99	A	101	SER	0	-0.006	-0.016	32.907	-0.052	-0.052	0.000	0.000	0.000	0.000
100	A	102	SER	0	-0.001	0.003	35.826	0.055	0.055	0.000	0.000	0.000	0.000
101	A	103	VAL	0	0.005	-0.003	38.755	0.027	0.027	0.000	0.000	0.000	0.000
102	A	104	ASN	0	0.016	-0.006	42.004	-0.115	-0.115	0.000	0.000	0.000	0.000
103	A	105	ASP	-1	-0.831	-0.896	45.397	-6.463	-6.463	0.000	0.000	0.000	0.000
104	A	106	ILE	0	-0.012	-0.006	44.584	-0.156	-0.156	0.000	0.000	0.000	0.000
105	A	107	GLY	0	-0.014	-0.007	44.984	-0.122	-0.122	0.000	0.000	0.000	0.000
106	A	108	ASP	-1	-0.949	-0.984	43.691	-7.048	-7.048	0.000	0.000	0.000	0.000
107	A	109	ASP	-1	-0.872	-0.919	39.776	-8.423	-8.423	0.000	0.000	0.000	0.000
108	A	110	LYS	1	0.938	0.963	39.451	7.465	7.465	0.000	0.000	0.000	0.000
109	A	111	LYS	1	0.926	0.957	38.606	7.308	7.308	0.000	0.000	0.000	0.000
110	A	112	ALA	0	0.034	0.040	37.397	-0.103	-0.103	0.000	0.000	0.000	0.000
111	A	113	THR	0	-0.018	-0.011	31.669	-0.248	-0.248	0.000	0.000	0.000	0.000
112	A	114	ARG	1	0.953	0.990	30.494	9.481	9.481	0.000	0.000	0.000	0.000
113	A	115	VAL	0	0.023	0.005	26.606	-0.204	-0.204	0.000	0.000	0.000	0.000
114	A	116	GLY	0	0.019	0.004	25.157	0.257	0.257	0.000	0.000	0.000	0.000
115	A	117	ILE	0	-0.011	0.005	19.197	-0.374	-0.374	0.000	0.000	0.000	0.000
116	A	118	ASN	0	0.067	0.032	18.232	0.207	0.207	0.000	0.000	0.000	0.000
117	A	119	ILE	0	-0.028	0.011	12.927	-0.852	-0.852	0.000	0.000	0.000	0.000
118	A	120	PHE	0	0.034	0.017	12.809	0.585	0.585	0.000	0.000	0.000	0.000
119	A	121	THR	0	-0.047	-0.031	9.256	-2.412	-2.412	0.000	0.000	0.000	0.000
120	A	122	ARG	1	0.840	0.887	5.777	38.676	38.676	0.000	0.000	0.000	0.000
121	A	123	LEU	0	-0.017	0.006	9.717	0.263	0.263	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:ARG)