FMO DATABASE

FMODB ID: 2N5NR

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

Total energy (hartree)

FMO2-HF: Electronic energy	-960762.054061
FMO2-HF: Nuclear repulsion	912963.356472
FMO2-HF: Total energy	-47798.697589
FMO2-MP2: Total energy	-47937.516561

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.
-15.738	-12.802	21.773	-11.38	-13.328	-0.098

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 : 0.928 / 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

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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	-0.051	0.011	3.142	-11.979	-7.080	0.085	-2.549	-2.435	0.001
4	A	5	SER	0	-0.023	-0.016	4.984	5.686	5.728	-0.001	-0.005	-0.035	0.000
5	A	6	LEU	0	0.122	0.039	7.728	-1.235	-1.235	0.000	0.000	0.000	0.000
6	A	7	THR	0	-0.052	-0.009	11.034	0.659	0.659	0.000	0.000	0.000	0.000
7	A	8	GLY	0	0.024	0.018	10.534	-2.605	-2.605	0.000	0.000	0.000	0.000
8	A	9	LYS	1	0.905	0.967	12.359	17.962	17.962	0.000	0.000	0.000	0.000
9	A	10	TRP	0	-0.056	-0.041	7.241	-3.077	-3.077	0.000	0.000	0.000	0.000
10	A	11	THR	0	-0.022	-0.022	13.299	1.854	1.854	0.000	0.000	0.000	0.000
11	A	12	ASN	0	0.042	0.008	14.128	-1.310	-1.310	0.000	0.000	0.000	0.000
12	A	13	ASP	-1	-0.890	-0.948	16.532	-15.135	-15.135	0.000	0.000	0.000	0.000
13	A	14	LEU	0	-0.032	-0.006	18.667	0.467	0.467	0.000	0.000	0.000	0.000
14	A	15	GLY	0	0.023	0.025	19.484	0.569	0.569	0.000	0.000	0.000	0.000
15	A	16	SER	0	-0.059	-0.026	20.033	0.519	0.519	0.000	0.000	0.000	0.000
16	A	17	ASN	0	-0.015	-0.024	18.066	-1.132	-1.132	0.000	0.000	0.000	0.000
17	A	18	MET	0	-0.010	0.024	14.644	1.091	1.091	0.000	0.000	0.000	0.000
18	A	19	THR	0	0.014	0.007	15.741	-1.631	-1.631	0.000	0.000	0.000	0.000
19	A	20	ILE	0	-0.011	0.003	13.876	1.086	1.086	0.000	0.000	0.000	0.000
20	A	21	GLY	0	0.051	0.021	15.423	-0.840	-0.840	0.000	0.000	0.000	0.000
21	A	22	ALA	0	-0.011	-0.005	15.275	-1.115	-1.115	0.000	0.000	0.000	0.000
22	A	23	VAL	0	-0.012	0.016	13.062	0.820	0.820	0.000	0.000	0.000	0.000
23	A	24	ASN	0	-0.008	-0.022	16.020	-0.314	-0.314	0.000	0.000	0.000	0.000
24	A	25	SER	0	0.034	-0.007	17.787	-0.345	-0.345	0.000	0.000	0.000	0.000
25	A	26	ARG	1	0.793	0.863	19.306	11.782	11.782	0.000	0.000	0.000	0.000
26	A	27	GLY	0	0.020	0.017	17.140	0.128	0.128	0.000	0.000	0.000	0.000
27	A	28	GLU	-1	-0.777	-0.831	18.183	-12.942	-12.942	0.000	0.000	0.000	0.000
28	A	29	PHE	0	0.002	-0.001	16.619	-0.560	-0.560	0.000	0.000	0.000	0.000
29	A	30	THR	0	0.019	0.003	19.467	0.390	0.390	0.000	0.000	0.000	0.000
30	A	31	GLY	0	0.050	0.008	19.528	-0.938	-0.938	0.000	0.000	0.000	0.000
31	A	32	THR	0	-0.016	0.001	20.191	0.485	0.485	0.000	0.000	0.000	0.000
32	A	33	TYR	0	0.003	-0.016	19.187	-1.104	-1.104	0.000	0.000	0.000	0.000
33	A	34	THR	0	-0.009	-0.005	21.549	0.741	0.741	0.000	0.000	0.000	0.000
34	A	35	THR	0	0.032	0.013	22.637	-0.636	-0.636	0.000	0.000	0.000	0.000
35	A	36	ALA	0	0.018	0.009	25.136	0.365	0.365	0.000	0.000	0.000	0.000
36	A	37	VAL	0	-0.022	-0.016	27.701	-0.017	-0.017	0.000	0.000	0.000	0.000
37	A	38	THR	0	-0.049	-0.040	29.287	0.204	0.204	0.000	0.000	0.000	0.000
38	A	39	ALA	0	0.025	0.032	31.992	0.334	0.334	0.000	0.000	0.000	0.000
39	A	40	THR	0	-0.005	-0.023	28.780	-0.266	-0.266	0.000	0.000	0.000	0.000
40	A	41	SER	0	-0.056	-0.019	28.102	0.101	0.101	0.000	0.000	0.000	0.000
41	A	42	ASN	0	0.068	0.022	29.092	-0.017	-0.017	0.000	0.000	0.000	0.000
42	A	43	GLU	-1	-0.841	-0.891	30.630	-9.505	-9.505	0.000	0.000	0.000	0.000
43	A	44	ILE	0	0.038	0.017	26.035	-0.309	-0.309	0.000	0.000	0.000	0.000
44	A	45	LYS	1	0.839	0.916	27.978	9.616	9.616	0.000	0.000	0.000	0.000
45	A	46	GLU	-1	-0.919	-0.956	25.460	-12.347	-12.347	0.000	0.000	0.000	0.000
46	A	47	SER	0	-0.029	-0.007	25.603	0.645	0.645	0.000	0.000	0.000	0.000
47	A	48	PRO	0	0.024	0.022	24.767	-0.585	-0.585	0.000	0.000	0.000	0.000
48	A	49	LEU	0	-0.037	-0.013	19.109	0.181	0.181	0.000	0.000	0.000	0.000
49	A	50	HIS	0	-0.010	-0.017	22.016	-0.401	-0.401	0.000	0.000	0.000	0.000
50	A	51	GLY	0	0.044	0.010	20.865	0.303	0.303	0.000	0.000	0.000	0.000
51	A	52	THR	0	-0.021	0.000	19.137	0.151	0.151	0.000	0.000	0.000	0.000
52	A	53	GLU	-1	-0.916	-0.967	12.303	-23.716	-23.716	0.000	0.000	0.000	0.000
53	A	54	ASN	0	-0.043	-0.023	16.061	0.443	0.443	0.000	0.000	0.000	0.000
54	A	55	THR	0	0.055	0.005	14.628	-1.021	-1.021	0.000	0.000	0.000	0.000
55	A	56	ILE	0	-0.013	-0.005	15.215	-0.280	-0.280	0.000	0.000	0.000	0.000
56	A	57	ASN	0	0.020	0.015	13.705	0.681	0.681	0.000	0.000	0.000	0.000
57	A	58	LYS	1	0.948	0.972	10.602	17.877	17.877	0.000	0.000	0.000	0.000
58	A	59	ARG	1	0.979	0.996	9.314	20.015	20.015	0.000	0.000	0.000	0.000
59	A	60	THR	0	0.016	-0.019	3.946	1.071	1.300	-0.001	-0.050	-0.179	0.000
60	A	61	GLN	0	0.039	0.032	6.645	-4.777	-4.777	0.000	0.000	0.000	0.000
61	A	62	PRO	0	-0.003	0.026	8.957	2.173	2.173	0.000	0.000	0.000	0.000
62	A	63	THR	0	0.053	0.018	12.091	-0.814	-0.814	0.000	0.000	0.000	0.000
63	A	64	PHE	0	0.019	0.005	12.770	-0.073	-0.073	0.000	0.000	0.000	0.000
64	A	65	GLY	0	0.035	0.017	16.669	0.235	0.235	0.000	0.000	0.000	0.000
65	A	66	PHE	0	0.000	0.001	16.806	-0.129	-0.129	0.000	0.000	0.000	0.000
66	A	67	THR	0	0.005	0.008	21.464	0.242	0.242	0.000	0.000	0.000	0.000
67	A	68	VAL	0	-0.008	-0.003	22.730	-0.199	-0.199	0.000	0.000	0.000	0.000
68	A	69	ASN	0	0.032	0.018	25.301	0.528	0.528	0.000	0.000	0.000	0.000
69	A	70	TRP	0	0.039	-0.010	24.588	-0.050	-0.050	0.000	0.000	0.000	0.000
70	A	71	LYS	1	0.857	0.907	29.803	10.233	10.233	0.000	0.000	0.000	0.000
71	A	72	PHE	0	-0.010	0.003	28.568	0.325	0.325	0.000	0.000	0.000	0.000
72	A	73	SER	0	-0.001	-0.005	32.786	0.207	0.207	0.000	0.000	0.000	0.000
73	A	74	GLU	-1	-0.847	-0.899	34.417	-8.035	-8.035	0.000	0.000	0.000	0.000
74	A	75	SER	0	-0.042	-0.021	32.285	0.014	0.014	0.000	0.000	0.000	0.000
75	A	76	THR	0	-0.018	-0.008	29.059	-0.156	-0.156	0.000	0.000	0.000	0.000
76	A	77	THR	0	-0.020	0.012	24.625	0.217	0.217	0.000	0.000	0.000	0.000
77	A	78	VAL	0	-0.007	0.011	24.453	-0.187	-0.187	0.000	0.000	0.000	0.000
78	A	79	PHE	0	0.013	-0.005	19.439	0.061	0.061	0.000	0.000	0.000	0.000
79	A	80	THR	0	-0.019	-0.015	19.220	-0.032	-0.032	0.000	0.000	0.000	0.000
80	A	81	GLY	0	0.043	0.003	16.190	0.160	0.160	0.000	0.000	0.000	0.000
81	A	82	GLN	0	-0.075	-0.027	11.769	1.229	1.229	0.000	0.000	0.000	0.000
82	A	84	PHE	0	-0.018	-0.027	8.305	-0.444	-0.444	0.000	0.000	0.000	0.000
83	A	85	ILE	0	-0.012	-0.006	2.415	-7.368	-5.646	2.340	-0.867	-3.194	-0.001
84	A	86	ASP	-1	-0.846	-0.921	5.292	-25.350	-25.350	0.000	0.000	0.000	0.000
85	A	87	ARG	1	0.990	0.975	5.871	18.119	18.119	0.000	0.000	0.000	0.000
86	A	88	ASN	0	0.015	0.008	6.840	-3.142	-3.142	0.000	0.000	0.000	0.000
87	A	89	GLY	0	0.030	0.034	2.899	-0.490	0.221	0.172	-0.346	-0.538	0.000
88	A	90	LYS	1	0.862	0.943	1.818	-13.625	-19.425	18.602	-7.141	-5.660	-0.095
89	A	91	GLU	-1	-0.792	-0.873	2.336	-53.505	-52.455	0.577	-0.411	-1.216	-0.003
90	A	92	VAL	0	-0.022	-0.022	4.584	5.150	5.233	-0.001	-0.011	-0.071	0.000
91	A	93	LEU	0	0.001	0.021	8.220	-0.257	-0.257	0.000	0.000	0.000	0.000
92	A	94	LYS	1	0.906	0.957	11.416	23.750	23.750	0.000	0.000	0.000	0.000
93	A	95	THR	0	-0.019	-0.028	14.092	0.486	0.486	0.000	0.000	0.000	0.000
94	A	96	MET	0	0.021	0.006	17.350	0.273	0.273	0.000	0.000	0.000	0.000
95	A	97	TRP	0	-0.017	-0.018	21.100	0.041	0.041	0.000	0.000	0.000	0.000
96	A	98	LEU	0	0.023	0.010	23.653	0.356	0.356	0.000	0.000	0.000	0.000
97	A	99	LEU	0	-0.025	-0.017	27.356	-0.150	-0.150	0.000	0.000	0.000	0.000
98	A	100	ARG	1	0.814	0.888	29.344	8.903	8.903	0.000	0.000	0.000	0.000
99	A	101	SER	0	0.005	-0.015	32.600	-0.072	-0.072	0.000	0.000	0.000	0.000
100	A	102	SER	0	-0.018	-0.010	35.530	0.053	0.053	0.000	0.000	0.000	0.000
101	A	103	VAL	0	0.008	-0.004	38.469	0.031	0.031	0.000	0.000	0.000	0.000
102	A	104	ASN	0	0.004	-0.007	41.706	-0.076	-0.076	0.000	0.000	0.000	0.000
103	A	105	ASP	-1	-0.814	-0.892	45.105	-6.496	-6.496	0.000	0.000	0.000	0.000
104	A	106	ILE	0	0.001	0.006	44.099	-0.163	-0.163	0.000	0.000	0.000	0.000
105	A	107	GLY	0	-0.024	-0.019	44.655	-0.120	-0.120	0.000	0.000	0.000	0.000
106	A	108	ASP	-1	-0.958	-0.988	43.321	-7.098	-7.098	0.000	0.000	0.000	0.000
107	A	109	ASP	-1	-0.885	-0.922	39.536	-8.455	-8.455	0.000	0.000	0.000	0.000
108	A	110	LYS	1	0.942	0.962	39.118	7.561	7.561	0.000	0.000	0.000	0.000
109	A	111	LYS	1	0.934	0.964	38.476	7.264	7.264	0.000	0.000	0.000	0.000
110	A	112	ALA	0	0.033	0.039	37.139	-0.103	-0.103	0.000	0.000	0.000	0.000
111	A	113	THR	0	-0.024	-0.015	31.347	-0.260	-0.260	0.000	0.000	0.000	0.000
112	A	114	ARG	1	0.939	0.986	30.564	9.432	9.432	0.000	0.000	0.000	0.000
113	A	115	VAL	0	0.026	0.006	26.480	-0.211	-0.211	0.000	0.000	0.000	0.000
114	A	116	GLY	0	0.014	0.008	24.999	0.268	0.268	0.000	0.000	0.000	0.000
115	A	117	ILE	0	-0.007	0.004	19.103	-0.369	-0.369	0.000	0.000	0.000	0.000
116	A	118	ASN	0	0.037	0.026	18.160	0.250	0.250	0.000	0.000	0.000	0.000
117	A	119	ILE	0	-0.016	0.016	12.804	-0.870	-0.870	0.000	0.000	0.000	0.000
118	A	120	PHE	0	0.031	0.011	12.750	0.566	0.566	0.000	0.000	0.000	0.000
119	A	121	THR	0	0.002	-0.007	9.182	-2.252	-2.252	0.000	0.000	0.000	0.000
120	A	122	ARG	1	0.785	0.850	5.483	40.396	40.396	0.000	0.000	0.000	0.000
121	A	123	LEU	0	-0.026	0.001	9.784	0.203	0.203	0.000	0.000	0.000	0.000

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