FMO DATABASE

FMODB ID: QV7LY

Calculation Name: 2DYN-A-Xray372

Preferred Name: Dynamin-1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2DYN

Chain ID: A

ChEMBL ID: CHEMBL4958

UniProt ID: Q05193

Base Structure: X-ray

Registration Date: 2023-09-20

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	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	111
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-968098.285326
FMO2-HF: Nuclear repulsion	921968.481629
FMO2-HF: Total energy	-46129.803697
FMO2-MP2: Total energy	-46264.510199

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:10:ILE)

Summations of interaction energy for fragment #1(A:10:ILE)

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.
-19.536	-18.818	15.404	-8.028	-8.096	-0.074

Interaction energy analysis for fragmet #1(A:10:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.002 / q_NPA : -0.008

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	12	VAL	0	-0.012	-0.022	3.724	-2.020	-0.612	-0.002	-0.578	-0.829	0.003
4	A	13	ILE	0	-0.053	-0.013	6.248	0.510	0.510	0.000	0.000	0.000	0.000
5	A	14	ARG	1	0.855	0.920	8.468	0.146	0.146	0.000	0.000	0.000	0.000
6	A	15	LYS	1	0.823	0.897	10.117	0.396	0.396	0.000	0.000	0.000	0.000
7	A	16	GLY	0	0.027	0.009	13.527	0.079	0.079	0.000	0.000	0.000	0.000
8	A	17	TRP	0	-0.040	-0.016	17.140	-0.054	-0.054	0.000	0.000	0.000	0.000
9	A	18	LEU	0	0.028	0.016	17.167	0.013	0.013	0.000	0.000	0.000	0.000
10	A	19	THR	0	0.001	-0.012	20.921	-0.010	-0.010	0.000	0.000	0.000	0.000
11	A	20	ILE	0	-0.037	-0.006	20.201	-0.005	-0.005	0.000	0.000	0.000	0.000
12	A	21	ASN	0	-0.037	-0.018	23.485	0.015	0.015	0.000	0.000	0.000	0.000
13	A	22	ASN	0	-0.045	-0.034	25.047	-0.004	-0.004	0.000	0.000	0.000	0.000
14	A	23	ILE	0	-0.049	-0.015	23.375	-0.007	-0.007	0.000	0.000	0.000	0.000
15	A	24	GLY	0	0.059	0.018	27.335	0.014	0.014	0.000	0.000	0.000	0.000
16	A	25	ILE	0	0.057	0.005	30.727	-0.006	-0.006	0.000	0.000	0.000	0.000
17	A	26	MET	0	-0.035	-0.009	32.867	0.001	0.001	0.000	0.000	0.000	0.000
18	A	27	LYS	1	0.890	0.950	25.920	0.210	0.210	0.000	0.000	0.000	0.000
19	A	28	GLY	0	0.002	0.003	29.686	-0.008	-0.008	0.000	0.000	0.000	0.000
20	A	29	GLY	0	0.003	-0.001	30.147	0.012	0.012	0.000	0.000	0.000	0.000
21	A	30	SER	0	-0.068	-0.028	27.330	-0.010	-0.010	0.000	0.000	0.000	0.000
22	A	31	LYS	1	0.848	0.908	23.675	0.216	0.216	0.000	0.000	0.000	0.000
23	A	32	GLU	-1	-0.775	-0.844	23.568	-0.150	-0.150	0.000	0.000	0.000	0.000
24	A	33	TYR	0	-0.056	-0.039	19.682	-0.010	-0.010	0.000	0.000	0.000	0.000
25	A	34	TRP	0	0.017	0.030	14.543	0.027	0.027	0.000	0.000	0.000	0.000
26	A	35	PHE	0	0.045	-0.005	14.557	-0.060	-0.060	0.000	0.000	0.000	0.000
27	A	36	VAL	0	-0.021	-0.015	8.777	0.048	0.048	0.000	0.000	0.000	0.000
28	A	37	LEU	0	0.001	0.008	8.396	-0.095	-0.095	0.000	0.000	0.000	0.000
29	A	38	THR	0	0.000	-0.024	3.141	0.971	1.539	0.014	-0.198	-0.384	0.000
30	A	39	ALA	0	0.019	0.001	2.681	-0.480	0.351	0.241	-0.390	-0.683	0.002
31	A	40	GLU	-1	-0.800	-0.876	2.019	-19.914	-22.052	15.152	-6.861	-6.153	-0.079
32	A	41	ASN	0	0.000	-0.013	5.144	1.133	1.182	-0.001	-0.001	-0.047	0.000
33	A	42	LEU	0	0.025	0.037	7.446	0.020	0.020	0.000	0.000	0.000	0.000
34	A	43	SER	0	-0.024	-0.027	9.926	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	44	TRP	0	0.039	0.026	12.102	0.054	0.054	0.000	0.000	0.000	0.000
36	A	45	TYR	0	-0.021	-0.025	11.636	-0.056	-0.056	0.000	0.000	0.000	0.000
37	A	46	LYS	1	0.736	0.846	17.553	0.241	0.241	0.000	0.000	0.000	0.000
38	A	47	ASP	-1	-0.785	-0.907	19.881	-0.199	-0.199	0.000	0.000	0.000	0.000
39	A	48	ASP	-1	-0.855	-0.936	17.516	-0.216	-0.216	0.000	0.000	0.000	0.000
40	A	49	GLU	-1	-0.809	-0.883	17.367	-0.183	-0.183	0.000	0.000	0.000	0.000
41	A	50	GLU	-1	-0.820	-0.877	12.325	-0.594	-0.594	0.000	0.000	0.000	0.000
42	A	51	LYS	1	0.838	0.901	15.942	0.154	0.154	0.000	0.000	0.000	0.000
43	A	52	GLU	-1	-0.816	-0.887	18.550	-0.236	-0.236	0.000	0.000	0.000	0.000
44	A	53	LYS	1	0.920	0.969	10.464	1.052	1.052	0.000	0.000	0.000	0.000
45	A	54	LYS	1	0.770	0.872	16.562	0.318	0.318	0.000	0.000	0.000	0.000
46	A	55	TYR	0	-0.014	-0.019	16.654	0.049	0.049	0.000	0.000	0.000	0.000
47	A	56	MET	0	-0.016	-0.010	9.839	-0.093	-0.093	0.000	0.000	0.000	0.000
48	A	57	LEU	0	-0.042	-0.003	12.201	0.092	0.092	0.000	0.000	0.000	0.000
49	A	58	SER	0	0.009	-0.014	9.439	-0.099	-0.099	0.000	0.000	0.000	0.000
50	A	59	VAL	0	-0.007	-0.020	7.884	0.154	0.154	0.000	0.000	0.000	0.000
51	A	60	ASP	-1	-0.838	-0.887	10.467	-0.727	-0.727	0.000	0.000	0.000	0.000
52	A	61	ASN	0	-0.085	-0.065	12.329	-0.013	-0.013	0.000	0.000	0.000	0.000
53	A	62	LEU	0	-0.036	0.005	12.938	0.036	0.036	0.000	0.000	0.000	0.000
54	A	63	LYS	1	0.840	0.903	15.461	0.127	0.127	0.000	0.000	0.000	0.000
55	A	64	LEU	0	0.014	0.015	17.287	-0.023	-0.023	0.000	0.000	0.000	0.000
56	A	65	ARG	1	0.802	0.887	19.425	0.152	0.152	0.000	0.000	0.000	0.000
57	A	66	ASP	-1	-0.788	-0.898	23.189	-0.067	-0.067	0.000	0.000	0.000	0.000
58	A	67	VAL	0	-0.041	-0.028	25.586	-0.006	-0.006	0.000	0.000	0.000	0.000
59	A	68	GLU	-1	-0.892	-0.943	28.168	-0.047	-0.047	0.000	0.000	0.000	0.000
60	A	69	LYS	1	0.855	0.948	31.848	0.040	0.040	0.000	0.000	0.000	0.000
61	A	70	GLY	0	0.005	-0.001	33.117	0.005	0.005	0.000	0.000	0.000	0.000
62	A	71	PHE	0	0.008	-0.016	35.505	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	72	MET	0	-0.015	-0.014	37.131	0.002	0.002	0.000	0.000	0.000	0.000
64	A	73	SER	0	-0.002	0.003	31.950	-0.004	-0.004	0.000	0.000	0.000	0.000
65	A	74	SER	0	0.002	0.020	32.328	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	75	LYS	1	0.828	0.904	27.133	0.108	0.108	0.000	0.000	0.000	0.000
67	A	76	HIS	0	-0.014	-0.006	27.206	0.008	0.008	0.000	0.000	0.000	0.000
68	A	77	ILE	0	-0.006	-0.010	25.432	-0.011	-0.011	0.000	0.000	0.000	0.000
69	A	78	PHE	0	0.030	0.018	17.974	0.010	0.010	0.000	0.000	0.000	0.000
70	A	79	ALA	0	0.001	-0.005	21.712	-0.014	-0.014	0.000	0.000	0.000	0.000
71	A	80	LEU	0	0.001	0.010	15.178	0.006	0.006	0.000	0.000	0.000	0.000
72	A	81	PHE	0	0.004	-0.019	18.976	-0.005	-0.005	0.000	0.000	0.000	0.000
73	A	82	ASN	0	0.046	0.009	16.380	0.011	0.011	0.000	0.000	0.000	0.000
74	A	83	THR	0	-0.027	-0.040	19.219	0.018	0.018	0.000	0.000	0.000	0.000
75	A	84	GLU	-1	-0.821	-0.866	20.069	-0.166	-0.166	0.000	0.000	0.000	0.000
76	A	85	GLN	0	-0.063	-0.025	20.409	0.007	0.007	0.000	0.000	0.000	0.000
77	A	86	ARG	1	0.761	0.858	22.878	0.175	0.175	0.000	0.000	0.000	0.000
78	A	87	ASN	0	-0.029	-0.020	23.544	0.024	0.024	0.000	0.000	0.000	0.000
79	A	88	VAL	0	0.033	0.048	17.847	-0.016	-0.016	0.000	0.000	0.000	0.000
80	A	89	TYR	0	-0.002	-0.007	18.882	-0.050	-0.050	0.000	0.000	0.000	0.000
81	A	90	LYS	1	0.899	0.948	20.931	0.354	0.354	0.000	0.000	0.000	0.000
82	A	91	ASP	-1	-0.755	-0.851	23.957	-0.171	-0.171	0.000	0.000	0.000	0.000
83	A	92	TYR	0	-0.019	0.012	23.575	0.018	0.018	0.000	0.000	0.000	0.000
84	A	93	ARG	1	0.983	0.970	23.607	0.118	0.118	0.000	0.000	0.000	0.000
85	A	94	GLN	0	-0.005	-0.003	22.340	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	95	LEU	0	-0.024	0.004	17.542	0.005	0.005	0.000	0.000	0.000	0.000
87	A	96	GLU	-1	-0.783	-0.877	20.930	-0.140	-0.140	0.000	0.000	0.000	0.000
88	A	97	LEU	0	-0.044	-0.022	17.452	-0.016	-0.016	0.000	0.000	0.000	0.000
89	A	98	ALA	0	-0.002	-0.003	21.903	0.019	0.019	0.000	0.000	0.000	0.000
90	A	99	CYS	0	-0.021	0.006	22.181	-0.014	-0.014	0.000	0.000	0.000	0.000
91	A	100	GLU	-1	-0.809	-0.907	24.952	-0.073	-0.073	0.000	0.000	0.000	0.000
92	A	101	THR	0	-0.054	-0.049	27.003	0.004	0.004	0.000	0.000	0.000	0.000
93	A	102	GLN	0	-0.001	-0.006	26.332	-0.014	-0.014	0.000	0.000	0.000	0.000
94	A	103	GLU	-1	-0.817	-0.904	25.348	-0.007	-0.007	0.000	0.000	0.000	0.000
95	A	104	GLU	-1	-0.904	-0.953	22.155	-0.072	-0.072	0.000	0.000	0.000	0.000
96	A	105	VAL	0	0.027	0.010	21.241	-0.009	-0.009	0.000	0.000	0.000	0.000
97	A	106	ASP	-1	-0.781	-0.888	20.729	-0.018	-0.018	0.000	0.000	0.000	0.000
98	A	107	SER	0	-0.004	0.015	19.549	0.013	0.013	0.000	0.000	0.000	0.000
99	A	108	TRP	0	0.031	0.004	13.803	0.007	0.007	0.000	0.000	0.000	0.000
100	A	109	LYS	1	0.797	0.898	16.002	0.031	0.031	0.000	0.000	0.000	0.000
101	A	110	ALA	0	-0.011	-0.003	16.446	0.011	0.011	0.000	0.000	0.000	0.000
102	A	111	SER	0	-0.056	-0.032	12.882	0.063	0.063	0.000	0.000	0.000	0.000
103	A	112	PHE	0	0.045	0.001	11.748	0.001	0.001	0.000	0.000	0.000	0.000
104	A	113	LEU	0	-0.003	0.004	12.464	-0.002	-0.002	0.000	0.000	0.000	0.000
105	A	114	ARG	1	0.874	0.947	9.470	-0.590	-0.590	0.000	0.000	0.000	0.000
106	A	115	ALA	0	0.016	0.001	8.199	0.229	0.229	0.000	0.000	0.000	0.000
107	A	116	GLY	0	0.016	0.019	9.156	-0.131	-0.131	0.000	0.000	0.000	0.000
108	A	117	VAL	0	-0.016	0.007	11.281	-0.045	-0.045	0.000	0.000	0.000	0.000
109	A	118	TYR	0	-0.020	-0.019	13.774	0.027	0.027	0.000	0.000	0.000	0.000
110	A	119	PRO	0	0.026	0.012	17.025	-0.032	-0.032	0.000	0.000	0.000	0.000
111	A	120	GLU	-1	-0.871	-0.905	20.327	-0.091	-0.091	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:10:ILE)