FMO DATABASE

FMODB ID: R8NL8

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

Total energy (hartree)

FMO2-HF: Electronic energy	-966594.319169
FMO2-HF: Nuclear repulsion	920464.85009
FMO2-HF: Total energy	-46129.469079
FMO2-MP2: Total energy	-46264.138204

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.
-14.446	-8.528	2.207	-3.65	-4.475	-0.03

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 : 0.031 / q_NPA : 0.012

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	-0.020	-0.027	3.763	-2.333	-0.756	-0.007	-0.718	-0.851	0.003
4	A	13	ILE	0	-0.052	-0.024	6.135	0.431	0.431	0.000	0.000	0.000	0.000
5	A	14	ARG	1	0.861	0.925	8.389	0.059	0.059	0.000	0.000	0.000	0.000
6	A	15	LYS	1	0.820	0.886	10.442	0.313	0.313	0.000	0.000	0.000	0.000
7	A	16	GLY	0	0.018	0.010	13.580	0.064	0.064	0.000	0.000	0.000	0.000
8	A	17	TRP	0	-0.023	-0.005	17.094	-0.050	-0.050	0.000	0.000	0.000	0.000
9	A	18	LEU	0	0.030	0.026	17.070	0.015	0.015	0.000	0.000	0.000	0.000
10	A	19	THR	0	0.016	-0.019	20.676	-0.011	-0.011	0.000	0.000	0.000	0.000
11	A	20	ILE	0	-0.044	0.000	20.149	0.001	0.001	0.000	0.000	0.000	0.000
12	A	21	ASN	0	-0.037	-0.026	23.516	0.011	0.011	0.000	0.000	0.000	0.000
13	A	22	ASN	0	-0.030	-0.014	24.954	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	23	ILE	0	-0.033	-0.005	23.709	-0.010	-0.010	0.000	0.000	0.000	0.000
15	A	24	GLY	0	0.035	0.013	27.660	0.012	0.012	0.000	0.000	0.000	0.000
16	A	25	ILE	0	0.082	0.017	30.795	-0.005	-0.005	0.000	0.000	0.000	0.000
17	A	26	MET	0	-0.030	-0.008	32.953	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	27	LYS	1	0.885	0.943	25.632	0.184	0.184	0.000	0.000	0.000	0.000
19	A	28	GLY	0	0.004	-0.001	30.255	-0.005	-0.005	0.000	0.000	0.000	0.000
20	A	29	GLY	0	0.014	0.018	30.086	0.010	0.010	0.000	0.000	0.000	0.000
21	A	30	SER	0	-0.069	-0.028	27.416	-0.008	-0.008	0.000	0.000	0.000	0.000
22	A	31	LYS	1	0.893	0.943	23.993	0.171	0.171	0.000	0.000	0.000	0.000
23	A	32	GLU	-1	-0.813	-0.874	23.107	-0.110	-0.110	0.000	0.000	0.000	0.000
24	A	33	TYR	0	-0.062	-0.048	19.625	-0.010	-0.010	0.000	0.000	0.000	0.000
25	A	34	TRP	0	0.038	0.025	14.739	0.029	0.029	0.000	0.000	0.000	0.000
26	A	35	PHE	0	0.032	-0.003	14.239	-0.060	-0.060	0.000	0.000	0.000	0.000
27	A	36	VAL	0	0.005	-0.001	8.718	0.042	0.042	0.000	0.000	0.000	0.000
28	A	37	LEU	0	-0.005	0.007	8.746	-0.131	-0.131	0.000	0.000	0.000	0.000
29	A	38	THR	0	0.027	0.008	3.540	0.217	0.449	0.002	-0.047	-0.188	0.000
30	A	39	ALA	0	0.020	-0.003	3.077	-0.276	0.209	0.039	-0.158	-0.367	0.000
31	A	40	GLU	-1	-0.884	-0.932	2.405	-13.398	-9.821	2.174	-2.727	-3.024	-0.033
32	A	41	ASN	0	-0.011	-0.022	5.283	0.851	0.898	-0.001	0.000	-0.045	0.000
33	A	42	LEU	0	0.032	0.037	7.731	0.024	0.024	0.000	0.000	0.000	0.000
34	A	43	SER	0	-0.044	-0.026	10.085	0.027	0.027	0.000	0.000	0.000	0.000
35	A	44	TRP	0	0.022	0.019	12.465	0.049	0.049	0.000	0.000	0.000	0.000
36	A	45	TYR	0	0.001	-0.006	11.629	-0.048	-0.048	0.000	0.000	0.000	0.000
37	A	46	LYS	1	0.733	0.840	17.453	0.207	0.207	0.000	0.000	0.000	0.000
38	A	47	ASP	-1	-0.811	-0.918	19.951	-0.172	-0.172	0.000	0.000	0.000	0.000
39	A	48	ASP	-1	-0.868	-0.950	17.720	-0.176	-0.176	0.000	0.000	0.000	0.000
40	A	49	GLU	-1	-0.837	-0.887	17.601	-0.159	-0.159	0.000	0.000	0.000	0.000
41	A	50	GLU	-1	-0.878	-0.915	12.478	-0.487	-0.487	0.000	0.000	0.000	0.000
42	A	51	LYS	1	0.877	0.936	16.045	0.146	0.146	0.000	0.000	0.000	0.000
43	A	52	GLU	-1	-0.832	-0.905	18.745	-0.214	-0.214	0.000	0.000	0.000	0.000
44	A	53	LYS	1	0.909	0.948	11.099	0.849	0.849	0.000	0.000	0.000	0.000
45	A	54	LYS	1	0.789	0.888	16.663	0.254	0.254	0.000	0.000	0.000	0.000
46	A	55	TYR	0	-0.007	-0.017	16.629	0.034	0.034	0.000	0.000	0.000	0.000
47	A	56	MET	0	0.036	0.034	10.020	-0.062	-0.062	0.000	0.000	0.000	0.000
48	A	57	LEU	0	-0.043	-0.007	12.609	0.048	0.048	0.000	0.000	0.000	0.000
49	A	58	SER	0	0.008	-0.015	10.122	-0.074	-0.074	0.000	0.000	0.000	0.000
50	A	59	VAL	0	-0.015	-0.023	8.045	0.124	0.124	0.000	0.000	0.000	0.000
51	A	60	ASP	-1	-0.840	-0.886	10.708	-0.573	-0.573	0.000	0.000	0.000	0.000
52	A	61	ASN	0	-0.097	-0.073	12.528	-0.014	-0.014	0.000	0.000	0.000	0.000
53	A	62	LEU	0	-0.022	0.015	13.409	0.018	0.018	0.000	0.000	0.000	0.000
54	A	63	LYS	1	0.885	0.937	15.721	0.071	0.071	0.000	0.000	0.000	0.000
55	A	64	LEU	0	-0.006	-0.004	17.393	-0.020	-0.020	0.000	0.000	0.000	0.000
56	A	65	ARG	1	0.802	0.890	19.761	0.112	0.112	0.000	0.000	0.000	0.000
57	A	66	ASP	-1	-0.799	-0.887	23.476	-0.033	-0.033	0.000	0.000	0.000	0.000
58	A	67	VAL	0	-0.027	-0.015	25.830	-0.006	-0.006	0.000	0.000	0.000	0.000
59	A	68	GLU	-1	-0.918	-0.959	28.247	-0.025	-0.025	0.000	0.000	0.000	0.000
60	A	69	LYS	1	0.847	0.933	31.753	0.019	0.019	0.000	0.000	0.000	0.000
61	A	70	GLY	0	0.012	0.015	32.897	0.004	0.004	0.000	0.000	0.000	0.000
62	A	71	PHE	0	-0.007	-0.028	35.505	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	72	MET	0	-0.001	-0.001	37.042	0.002	0.002	0.000	0.000	0.000	0.000
64	A	73	SER	0	0.004	0.011	31.842	0.000	0.000	0.000	0.000	0.000	0.000
65	A	74	SER	0	0.004	0.010	32.595	0.001	0.001	0.000	0.000	0.000	0.000
66	A	75	LYS	1	0.837	0.911	27.163	0.074	0.074	0.000	0.000	0.000	0.000
67	A	76	HIS	0	0.007	0.013	27.156	0.003	0.003	0.000	0.000	0.000	0.000
68	A	77	ILE	0	-0.010	-0.012	25.225	-0.008	-0.008	0.000	0.000	0.000	0.000
69	A	78	PHE	0	0.055	0.038	17.973	0.009	0.009	0.000	0.000	0.000	0.000
70	A	79	ALA	0	0.000	-0.012	21.671	-0.014	-0.014	0.000	0.000	0.000	0.000
71	A	80	LEU	0	0.001	0.010	15.287	0.007	0.007	0.000	0.000	0.000	0.000
72	A	81	PHE	0	0.004	-0.024	19.214	-0.009	-0.009	0.000	0.000	0.000	0.000
73	A	82	ASN	0	0.059	0.020	16.931	0.017	0.017	0.000	0.000	0.000	0.000
74	A	83	THR	0	-0.023	-0.030	19.456	0.015	0.015	0.000	0.000	0.000	0.000
75	A	84	GLU	-1	-0.828	-0.872	20.101	-0.137	-0.137	0.000	0.000	0.000	0.000
76	A	85	GLN	0	-0.076	-0.029	20.704	0.014	0.014	0.000	0.000	0.000	0.000
77	A	86	ARG	1	0.846	0.932	22.975	0.149	0.149	0.000	0.000	0.000	0.000
78	A	87	ASN	0	-0.069	-0.054	24.097	0.018	0.018	0.000	0.000	0.000	0.000
79	A	88	VAL	0	-0.001	0.030	17.934	-0.015	-0.015	0.000	0.000	0.000	0.000
80	A	89	TYR	0	0.029	0.009	19.191	-0.041	-0.041	0.000	0.000	0.000	0.000
81	A	90	LYS	1	0.906	0.948	20.889	0.294	0.294	0.000	0.000	0.000	0.000
82	A	91	ASP	-1	-0.781	-0.889	24.013	-0.144	-0.144	0.000	0.000	0.000	0.000
83	A	92	TYR	0	-0.023	0.002	23.806	0.016	0.016	0.000	0.000	0.000	0.000
84	A	93	ARG	1	0.992	0.981	24.142	0.094	0.094	0.000	0.000	0.000	0.000
85	A	94	GLN	0	-0.010	-0.013	22.602	0.000	0.000	0.000	0.000	0.000	0.000
86	A	95	LEU	0	-0.038	-0.001	17.761	0.003	0.003	0.000	0.000	0.000	0.000
87	A	96	GLU	-1	-0.817	-0.902	21.340	-0.098	-0.098	0.000	0.000	0.000	0.000
88	A	97	LEU	0	-0.032	-0.017	17.542	-0.013	-0.013	0.000	0.000	0.000	0.000
89	A	98	ALA	0	-0.003	-0.011	21.998	0.016	0.016	0.000	0.000	0.000	0.000
90	A	99	CYS	0	-0.018	-0.001	22.200	-0.009	-0.009	0.000	0.000	0.000	0.000
91	A	100	GLU	-1	-0.827	-0.913	25.038	-0.047	-0.047	0.000	0.000	0.000	0.000
92	A	101	THR	0	-0.032	-0.038	27.018	0.002	0.002	0.000	0.000	0.000	0.000
93	A	102	GLN	0	0.005	0.000	26.323	-0.014	-0.014	0.000	0.000	0.000	0.000
94	A	103	GLU	-1	-0.819	-0.914	25.518	0.018	0.018	0.000	0.000	0.000	0.000
95	A	104	GLU	-1	-0.926	-0.967	21.735	-0.033	-0.033	0.000	0.000	0.000	0.000
96	A	105	VAL	0	0.029	0.010	21.111	-0.005	-0.005	0.000	0.000	0.000	0.000
97	A	106	ASP	-1	-0.846	-0.921	20.729	0.027	0.027	0.000	0.000	0.000	0.000
98	A	107	SER	0	-0.025	0.004	19.512	0.017	0.017	0.000	0.000	0.000	0.000
99	A	108	TRP	0	0.027	-0.006	13.359	0.021	0.021	0.000	0.000	0.000	0.000
100	A	109	LYS	1	0.843	0.915	15.855	0.006	0.006	0.000	0.000	0.000	0.000
101	A	110	ALA	0	0.012	0.011	16.350	0.015	0.015	0.000	0.000	0.000	0.000
102	A	111	SER	0	-0.054	-0.032	12.659	0.055	0.055	0.000	0.000	0.000	0.000
103	A	112	PHE	0	0.045	-0.001	11.664	0.020	0.020	0.000	0.000	0.000	0.000
104	A	113	LEU	0	0.005	0.017	12.316	0.005	0.005	0.000	0.000	0.000	0.000
105	A	114	ARG	1	0.866	0.949	9.020	-0.714	-0.714	0.000	0.000	0.000	0.000
106	A	115	ALA	0	-0.001	-0.014	8.050	0.226	0.226	0.000	0.000	0.000	0.000
107	A	116	GLY	0	0.004	0.017	9.033	-0.109	-0.109	0.000	0.000	0.000	0.000
108	A	117	VAL	0	-0.020	0.002	11.619	-0.040	-0.040	0.000	0.000	0.000	0.000
109	A	118	TYR	0	-0.016	-0.009	13.931	0.028	0.028	0.000	0.000	0.000	0.000
110	A	119	PRO	0	0.019	0.005	17.298	-0.030	-0.030	0.000	0.000	0.000	0.000
111	A	120	GLU	-1	-0.859	-0.909	20.659	-0.059	-0.059	0.000	0.000	0.000	0.000

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