FMO DATABASE

FMODB ID: 6YRYZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-959875.263669
FMO2-HF: Nuclear repulsion	912076.077708
FMO2-HF: Total energy	-47799.185961
FMO2-MP2: Total energy	-47937.941008

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.
-17.391	-11.708	19.854	-10.979	-14.56	-0.11

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 : 0.921 / q_NPA : 0.960

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	4	CYS	0	-0.045	0.014	2.632	-16.340	-11.609	1.265	-2.729	-3.267	-0.015
4	A	5	SER	0	-0.031	-0.022	4.823	6.065	6.111	-0.001	-0.005	-0.040	0.000
5	A	6	LEU	0	0.107	0.043	7.549	-1.092	-1.092	0.000	0.000	0.000	0.000
6	A	7	THR	0	-0.035	-0.005	10.819	0.699	0.699	0.000	0.000	0.000	0.000
7	A	8	GLY	0	0.005	0.005	10.311	-2.792	-2.792	0.000	0.000	0.000	0.000
8	A	9	LYS	1	0.891	0.951	12.094	18.062	18.062	0.000	0.000	0.000	0.000
9	A	10	TRP	0	-0.042	-0.035	6.891	-3.177	-3.177	0.000	0.000	0.000	0.000
10	A	11	THR	0	-0.032	-0.030	13.040	1.800	1.800	0.000	0.000	0.000	0.000
11	A	12	ASN	0	0.050	0.026	14.013	-1.300	-1.300	0.000	0.000	0.000	0.000
12	A	13	ASP	-1	-0.895	-0.943	16.523	-15.120	-15.120	0.000	0.000	0.000	0.000
13	A	14	LEU	0	-0.008	0.006	18.998	0.466	0.466	0.000	0.000	0.000	0.000
14	A	15	GLY	0	0.022	0.019	19.227	0.528	0.528	0.000	0.000	0.000	0.000
15	A	16	SER	0	-0.056	-0.043	19.544	0.456	0.456	0.000	0.000	0.000	0.000
16	A	17	ASN	0	-0.014	-0.005	18.075	-1.206	-1.206	0.000	0.000	0.000	0.000
17	A	18	MET	0	-0.020	0.028	14.327	1.029	1.029	0.000	0.000	0.000	0.000
18	A	19	THR	0	0.014	-0.005	15.927	-1.420	-1.420	0.000	0.000	0.000	0.000
19	A	20	ILE	0	-0.017	-0.005	13.693	1.004	1.004	0.000	0.000	0.000	0.000
20	A	21	GLY	0	0.061	0.032	15.213	-0.894	-0.894	0.000	0.000	0.000	0.000
21	A	22	ALA	0	-0.005	-0.002	14.695	-1.181	-1.181	0.000	0.000	0.000	0.000
22	A	23	VAL	0	-0.011	0.010	12.125	0.923	0.923	0.000	0.000	0.000	0.000
23	A	24	ASN	0	0.003	-0.013	15.290	-0.246	-0.246	0.000	0.000	0.000	0.000
24	A	25	SER	0	0.004	-0.017	16.986	-0.367	-0.367	0.000	0.000	0.000	0.000
25	A	26	ARG	1	0.809	0.873	18.558	12.169	12.169	0.000	0.000	0.000	0.000
26	A	27	GLY	0	0.021	0.017	16.328	0.150	0.150	0.000	0.000	0.000	0.000
27	A	28	GLU	-1	-0.793	-0.840	17.274	-13.259	-13.259	0.000	0.000	0.000	0.000
28	A	29	PHE	0	0.013	-0.001	16.138	-0.626	-0.626	0.000	0.000	0.000	0.000
29	A	30	THR	0	0.015	0.000	18.705	0.434	0.434	0.000	0.000	0.000	0.000
30	A	31	GLY	0	0.034	0.009	19.233	-0.960	-0.960	0.000	0.000	0.000	0.000
31	A	32	THR	0	-0.062	-0.023	20.218	0.512	0.512	0.000	0.000	0.000	0.000
32	A	33	TYR	0	0.017	-0.004	18.978	-1.167	-1.167	0.000	0.000	0.000	0.000
33	A	34	THR	0	-0.006	-0.006	21.246	0.802	0.802	0.000	0.000	0.000	0.000
34	A	35	THR	0	0.008	-0.007	22.343	-0.646	-0.646	0.000	0.000	0.000	0.000
35	A	36	ALA	0	0.013	0.005	25.021	0.391	0.391	0.000	0.000	0.000	0.000
36	A	37	VAL	0	-0.064	-0.043	27.383	-0.041	-0.041	0.000	0.000	0.000	0.000
37	A	38	THR	0	-0.037	-0.028	29.254	0.197	0.197	0.000	0.000	0.000	0.000
38	A	39	ALA	0	0.029	0.043	31.713	0.310	0.310	0.000	0.000	0.000	0.000
39	A	40	THR	0	0.000	-0.027	29.151	-0.221	-0.221	0.000	0.000	0.000	0.000
40	A	41	SER	0	-0.055	-0.019	28.019	0.098	0.098	0.000	0.000	0.000	0.000
41	A	42	ASN	0	0.082	0.042	29.003	-0.105	-0.105	0.000	0.000	0.000	0.000
42	A	43	GLU	-1	-0.816	-0.884	31.233	-9.391	-9.391	0.000	0.000	0.000	0.000
43	A	44	ILE	0	0.034	0.007	25.985	-0.318	-0.318	0.000	0.000	0.000	0.000
44	A	45	LYS	1	0.849	0.928	27.909	9.580	9.580	0.000	0.000	0.000	0.000
45	A	46	GLU	-1	-0.836	-0.907	24.813	-12.808	-12.808	0.000	0.000	0.000	0.000
46	A	47	SER	0	-0.042	-0.023	25.274	0.704	0.704	0.000	0.000	0.000	0.000
47	A	48	PRO	0	0.026	0.027	24.587	-0.604	-0.604	0.000	0.000	0.000	0.000
48	A	49	LEU	0	-0.032	-0.014	18.852	0.206	0.206	0.000	0.000	0.000	0.000
49	A	50	HIS	0	-0.003	-0.011	21.757	-0.347	-0.347	0.000	0.000	0.000	0.000
50	A	51	GLY	0	0.050	0.015	20.051	0.211	0.211	0.000	0.000	0.000	0.000
51	A	52	THR	0	-0.008	0.011	18.515	0.147	0.147	0.000	0.000	0.000	0.000
52	A	53	GLU	-1	-0.856	-0.940	11.096	-25.598	-25.598	0.000	0.000	0.000	0.000
53	A	54	ASN	0	-0.031	-0.023	15.443	0.693	0.693	0.000	0.000	0.000	0.000
54	A	55	THR	0	0.050	0.012	14.469	-1.087	-1.087	0.000	0.000	0.000	0.000
55	A	56	ILE	0	-0.010	0.011	15.277	-0.314	-0.314	0.000	0.000	0.000	0.000
56	A	57	ASN	0	0.013	-0.004	13.995	0.475	0.475	0.000	0.000	0.000	0.000
57	A	58	LYS	1	0.940	0.959	10.919	17.780	17.780	0.000	0.000	0.000	0.000
58	A	59	ARG	1	0.971	1.001	9.336	19.931	19.931	0.000	0.000	0.000	0.000
59	A	60	THR	0	0.041	0.010	3.911	0.826	1.112	0.000	-0.063	-0.223	0.000
60	A	61	GLN	0	0.046	0.033	6.227	-6.390	-6.390	0.000	0.000	0.000	0.000
61	A	62	PRO	0	0.004	0.040	8.509	2.569	2.569	0.000	0.000	0.000	0.000
62	A	63	THR	0	0.052	0.011	11.687	-0.745	-0.745	0.000	0.000	0.000	0.000
63	A	64	PHE	0	0.021	0.000	12.437	-0.070	-0.070	0.000	0.000	0.000	0.000
64	A	65	GLY	0	0.022	0.016	16.330	0.370	0.370	0.000	0.000	0.000	0.000
65	A	66	PHE	0	-0.013	-0.007	16.774	-0.140	-0.140	0.000	0.000	0.000	0.000
66	A	67	THR	0	0.008	0.012	21.125	0.363	0.363	0.000	0.000	0.000	0.000
67	A	68	VAL	0	-0.018	-0.011	22.519	-0.295	-0.295	0.000	0.000	0.000	0.000
68	A	69	ASN	0	0.024	0.010	25.099	0.578	0.578	0.000	0.000	0.000	0.000
69	A	70	TRP	0	0.057	0.003	24.307	0.006	0.006	0.000	0.000	0.000	0.000
70	A	71	LYS	1	0.840	0.899	29.674	10.274	10.274	0.000	0.000	0.000	0.000
71	A	72	PHE	0	-0.005	0.011	28.245	0.313	0.313	0.000	0.000	0.000	0.000
72	A	73	SER	0	-0.009	-0.004	33.000	0.113	0.113	0.000	0.000	0.000	0.000
73	A	74	GLU	-1	-0.835	-0.886	34.424	-8.036	-8.036	0.000	0.000	0.000	0.000
74	A	75	SER	0	-0.046	-0.026	32.314	0.002	0.002	0.000	0.000	0.000	0.000
75	A	76	THR	0	-0.030	-0.012	29.003	-0.191	-0.191	0.000	0.000	0.000	0.000
76	A	77	THR	0	-0.021	0.004	24.405	0.186	0.186	0.000	0.000	0.000	0.000
77	A	78	VAL	0	-0.002	0.009	24.321	-0.172	-0.172	0.000	0.000	0.000	0.000
78	A	79	PHE	0	0.019	0.000	19.261	0.043	0.043	0.000	0.000	0.000	0.000
79	A	80	THR	0	-0.025	-0.024	18.967	0.036	0.036	0.000	0.000	0.000	0.000
80	A	81	GLY	0	0.040	0.012	16.180	0.110	0.110	0.000	0.000	0.000	0.000
81	A	82	GLN	0	-0.070	-0.035	11.647	1.371	1.371	0.000	0.000	0.000	0.000
82	A	84	PHE	0	-0.033	-0.027	8.010	-0.183	-0.183	0.000	0.000	0.000	0.000
83	A	85	ILE	0	-0.010	-0.017	2.407	-7.348	-5.771	3.016	-0.988	-3.605	-0.001
84	A	86	ASP	-1	-0.790	-0.891	5.197	-23.354	-23.269	-0.001	-0.002	-0.082	0.000
85	A	87	ARG	1	0.973	0.969	6.038	18.050	18.050	0.000	0.000	0.000	0.000
86	A	88	ASN	0	0.044	0.031	7.154	0.651	0.651	0.000	0.000	0.000	0.000
87	A	89	GLY	0	0.022	0.025	3.047	0.496	1.099	0.056	-0.270	-0.390	0.000
88	A	90	LYS	1	0.862	0.929	1.858	-13.652	-16.565	14.261	-6.158	-5.191	-0.090
89	A	91	GLU	-1	-0.787	-0.877	2.123	-59.230	-58.058	1.259	-0.747	-1.684	-0.004
90	A	92	VAL	0	-0.065	-0.039	4.406	5.773	5.869	-0.001	-0.017	-0.078	0.000
91	A	93	LEU	0	0.027	0.026	8.169	-0.540	-0.540	0.000	0.000	0.000	0.000
92	A	94	LYS	1	0.898	0.956	10.871	27.188	27.188	0.000	0.000	0.000	0.000
93	A	95	THR	0	-0.048	-0.048	13.730	0.376	0.376	0.000	0.000	0.000	0.000
94	A	96	MET	0	0.016	0.006	17.093	0.354	0.354	0.000	0.000	0.000	0.000
95	A	97	TRP	0	-0.014	-0.009	20.880	-0.047	-0.047	0.000	0.000	0.000	0.000
96	A	98	LEU	0	0.015	0.005	23.408	0.389	0.389	0.000	0.000	0.000	0.000
97	A	99	LEU	0	-0.017	-0.011	27.103	-0.172	-0.172	0.000	0.000	0.000	0.000
98	A	100	ARG	1	0.819	0.899	29.161	8.948	8.948	0.000	0.000	0.000	0.000
99	A	101	SER	0	0.019	-0.014	32.432	-0.106	-0.106	0.000	0.000	0.000	0.000
100	A	102	SER	0	-0.021	-0.025	35.313	0.050	0.050	0.000	0.000	0.000	0.000
101	A	103	VAL	0	0.001	-0.020	38.343	-0.011	-0.011	0.000	0.000	0.000	0.000
102	A	104	ASN	0	-0.023	-0.008	41.633	-0.051	-0.051	0.000	0.000	0.000	0.000
103	A	105	ASP	-1	-0.826	-0.902	44.759	-6.536	-6.536	0.000	0.000	0.000	0.000
104	A	106	ILE	0	0.011	0.003	43.728	-0.179	-0.179	0.000	0.000	0.000	0.000
105	A	107	GLY	0	-0.025	-0.015	44.334	-0.112	-0.112	0.000	0.000	0.000	0.000
106	A	108	ASP	-1	-0.851	-0.926	43.034	-7.213	-7.213	0.000	0.000	0.000	0.000
107	A	109	ASP	-1	-0.858	-0.897	39.187	-8.492	-8.492	0.000	0.000	0.000	0.000
108	A	110	LYS	1	0.929	0.958	38.829	7.646	7.646	0.000	0.000	0.000	0.000
109	A	111	LYS	1	0.867	0.917	38.532	7.192	7.192	0.000	0.000	0.000	0.000
110	A	112	ALA	0	0.006	0.029	37.329	-0.153	-0.153	0.000	0.000	0.000	0.000
111	A	113	THR	0	-0.021	-0.007	31.530	-0.259	-0.259	0.000	0.000	0.000	0.000
112	A	114	ARG	1	0.928	0.973	30.644	9.447	9.447	0.000	0.000	0.000	0.000
113	A	115	VAL	0	0.022	0.001	26.669	-0.194	-0.194	0.000	0.000	0.000	0.000
114	A	116	GLY	0	0.015	0.011	25.034	0.285	0.285	0.000	0.000	0.000	0.000
115	A	117	ILE	0	0.007	0.009	19.582	-0.350	-0.350	0.000	0.000	0.000	0.000
116	A	118	ASN	0	0.030	0.017	17.997	0.168	0.168	0.000	0.000	0.000	0.000
117	A	119	ILE	0	-0.018	0.007	12.827	-0.962	-0.962	0.000	0.000	0.000	0.000
118	A	120	PHE	0	0.028	0.022	12.522	0.529	0.529	0.000	0.000	0.000	0.000
119	A	121	THR	0	0.002	0.002	8.813	-2.251	-2.251	0.000	0.000	0.000	0.000
120	A	122	ARG	1	0.782	0.849	5.157	42.024	42.024	0.000	0.000	0.000	0.000
121	A	123	LEU	0	-0.018	-0.002	9.570	0.122	0.122	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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