FMO DATABASE

FMODB ID: ZVRZN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-964310.640313
FMO2-HF: Nuclear repulsion	918181.979697
FMO2-HF: Total energy	-46128.660616
FMO2-MP2: Total energy	-46263.201842

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.
-5.36	-2.337	0.068	-1.002	-2.089	0.002

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 : 0.045 / q_NPA : 0.018

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	-0.022	-0.022	3.579	-1.679	-0.211	0.002	-0.602	-0.869	0.003
4	A	13	ILE	0	-0.055	-0.026	6.298	0.305	0.305	0.000	0.000	0.000	0.000
5	A	14	ARG	1	0.858	0.918	8.519	-0.124	-0.124	0.000	0.000	0.000	0.000
6	A	15	LYS	1	0.855	0.928	10.332	0.199	0.199	0.000	0.000	0.000	0.000
7	A	16	GLY	0	0.004	0.004	13.679	0.043	0.043	0.000	0.000	0.000	0.000
8	A	17	TRP	0	0.019	0.018	17.181	-0.034	-0.034	0.000	0.000	0.000	0.000
9	A	18	LEU	0	0.034	0.024	17.148	0.015	0.015	0.000	0.000	0.000	0.000
10	A	19	THR	0	0.019	0.012	20.738	-0.014	-0.014	0.000	0.000	0.000	0.000
11	A	20	ILE	0	-0.040	-0.001	20.402	0.003	0.003	0.000	0.000	0.000	0.000
12	A	21	ASN	0	-0.016	-0.027	23.540	0.001	0.001	0.000	0.000	0.000	0.000
13	A	22	ASN	0	0.002	0.001	24.933	-0.001	-0.001	0.000	0.000	0.000	0.000
14	A	23	ILE	0	-0.043	-0.006	23.873	-0.008	-0.008	0.000	0.000	0.000	0.000
15	A	24	GLY	0	0.025	0.005	27.655	0.007	0.007	0.000	0.000	0.000	0.000
16	A	25	ILE	0	0.092	0.023	30.779	-0.004	-0.004	0.000	0.000	0.000	0.000
17	A	26	MET	0	-0.023	-0.007	32.945	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	27	LYS	1	0.880	0.941	25.235	0.119	0.119	0.000	0.000	0.000	0.000
19	A	28	GLY	0	-0.008	-0.008	30.280	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	29	GLY	0	0.021	0.021	30.085	0.006	0.006	0.000	0.000	0.000	0.000
21	A	30	SER	0	-0.035	-0.007	28.029	-0.008	-0.008	0.000	0.000	0.000	0.000
22	A	31	LYS	1	0.942	0.973	25.580	0.093	0.093	0.000	0.000	0.000	0.000
23	A	32	GLU	-1	-0.889	-0.934	23.379	-0.042	-0.042	0.000	0.000	0.000	0.000
24	A	33	TYR	0	-0.080	-0.055	19.620	-0.013	-0.013	0.000	0.000	0.000	0.000
25	A	34	TRP	0	0.045	0.043	14.784	0.030	0.030	0.000	0.000	0.000	0.000
26	A	35	PHE	0	0.023	-0.007	14.252	-0.047	-0.047	0.000	0.000	0.000	0.000
27	A	36	VAL	0	0.000	-0.002	8.723	0.031	0.031	0.000	0.000	0.000	0.000
28	A	37	LEU	0	0.005	0.008	8.829	-0.102	-0.102	0.000	0.000	0.000	0.000
29	A	38	THR	0	0.030	0.013	3.488	0.033	0.267	0.002	-0.044	-0.192	0.000
30	A	39	ALA	0	0.006	-0.012	3.163	-0.458	-0.008	0.029	-0.144	-0.335	0.000
31	A	40	GLU	-1	-0.912	-0.940	3.131	-3.925	-3.101	0.036	-0.212	-0.648	-0.001
32	A	41	ASN	0	-0.013	-0.017	5.211	0.463	0.510	-0.001	0.000	-0.045	0.000
33	A	42	LEU	0	0.026	0.030	7.718	0.052	0.052	0.000	0.000	0.000	0.000
34	A	43	SER	0	-0.063	-0.035	10.109	-0.020	-0.020	0.000	0.000	0.000	0.000
35	A	44	TRP	0	0.031	0.023	12.461	0.039	0.039	0.000	0.000	0.000	0.000
36	A	45	TYR	0	0.004	-0.001	10.906	-0.021	-0.021	0.000	0.000	0.000	0.000
37	A	46	LYS	1	0.855	0.927	17.469	0.136	0.136	0.000	0.000	0.000	0.000
38	A	47	ASP	-1	-0.866	-0.958	19.953	-0.115	-0.115	0.000	0.000	0.000	0.000
39	A	48	ASP	-1	-0.889	-0.960	17.729	-0.118	-0.118	0.000	0.000	0.000	0.000
40	A	49	GLU	-1	-0.943	-0.952	17.495	-0.126	-0.126	0.000	0.000	0.000	0.000
41	A	50	GLU	-1	-0.932	-0.974	12.761	-0.358	-0.358	0.000	0.000	0.000	0.000
42	A	51	LYS	1	0.967	0.991	16.056	0.129	0.129	0.000	0.000	0.000	0.000
43	A	52	GLU	-1	-0.948	-0.984	18.759	-0.155	-0.155	0.000	0.000	0.000	0.000
44	A	53	LYS	1	0.936	0.976	11.279	0.574	0.574	0.000	0.000	0.000	0.000
45	A	54	LYS	1	0.868	0.935	16.674	0.162	0.162	0.000	0.000	0.000	0.000
46	A	55	TYR	0	-0.026	-0.025	16.595	0.015	0.015	0.000	0.000	0.000	0.000
47	A	56	MET	0	0.039	0.020	10.169	-0.048	-0.048	0.000	0.000	0.000	0.000
48	A	57	LEU	0	-0.045	-0.012	12.561	0.024	0.024	0.000	0.000	0.000	0.000
49	A	58	SER	0	0.076	0.042	10.040	-0.102	-0.102	0.000	0.000	0.000	0.000
50	A	59	VAL	0	-0.019	-0.021	8.027	0.076	0.076	0.000	0.000	0.000	0.000
51	A	60	ASP	-1	-0.880	-0.929	10.663	-0.214	-0.214	0.000	0.000	0.000	0.000
52	A	61	ASN	0	-0.075	-0.041	12.456	0.015	0.015	0.000	0.000	0.000	0.000
53	A	62	LEU	0	-0.010	0.011	13.241	0.003	0.003	0.000	0.000	0.000	0.000
54	A	63	LYS	1	0.926	0.965	15.702	-0.009	-0.009	0.000	0.000	0.000	0.000
55	A	64	LEU	0	0.016	0.007	17.414	-0.017	-0.017	0.000	0.000	0.000	0.000
56	A	65	ARG	1	0.822	0.909	19.776	0.032	0.032	0.000	0.000	0.000	0.000
57	A	66	ASP	-1	-0.823	-0.910	23.496	0.033	0.033	0.000	0.000	0.000	0.000
58	A	67	VAL	0	-0.033	-0.013	25.696	-0.006	-0.006	0.000	0.000	0.000	0.000
59	A	68	GLU	-1	-0.914	-0.962	28.276	0.015	0.015	0.000	0.000	0.000	0.000
60	A	69	LYS	1	0.878	0.959	31.789	-0.017	-0.017	0.000	0.000	0.000	0.000
61	A	70	GLY	0	0.013	0.014	32.944	0.001	0.001	0.000	0.000	0.000	0.000
62	A	71	PHE	0	-0.001	-0.026	35.544	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	72	MET	0	0.011	0.004	37.032	0.001	0.001	0.000	0.000	0.000	0.000
64	A	73	SER	0	-0.035	-0.008	31.902	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	74	SER	0	0.008	0.013	32.643	0.003	0.003	0.000	0.000	0.000	0.000
66	A	75	LYS	1	0.925	0.966	27.917	0.024	0.024	0.000	0.000	0.000	0.000
67	A	76	HIS	0	-0.012	-0.006	27.262	0.000	0.000	0.000	0.000	0.000	0.000
68	A	77	ILE	0	-0.022	-0.018	25.216	-0.004	-0.004	0.000	0.000	0.000	0.000
69	A	78	PHE	0	0.050	0.037	18.000	0.008	0.008	0.000	0.000	0.000	0.000
70	A	79	ALA	0	0.005	-0.011	21.695	-0.012	-0.012	0.000	0.000	0.000	0.000
71	A	80	LEU	0	0.000	0.012	15.332	0.009	0.009	0.000	0.000	0.000	0.000
72	A	81	PHE	0	0.001	-0.032	19.212	-0.014	-0.014	0.000	0.000	0.000	0.000
73	A	82	ASN	0	0.051	0.018	17.642	0.016	0.016	0.000	0.000	0.000	0.000
74	A	83	THR	0	-0.015	-0.013	19.399	0.009	0.009	0.000	0.000	0.000	0.000
75	A	84	GLU	-1	-0.868	-0.928	20.001	-0.057	-0.057	0.000	0.000	0.000	0.000
76	A	85	GLN	0	-0.077	-0.029	20.643	0.003	0.003	0.000	0.000	0.000	0.000
77	A	86	ARG	1	0.943	0.983	22.897	0.082	0.082	0.000	0.000	0.000	0.000
78	A	87	ASN	0	-0.030	-0.025	24.035	0.014	0.014	0.000	0.000	0.000	0.000
79	A	88	VAL	0	-0.004	0.033	17.923	-0.011	-0.011	0.000	0.000	0.000	0.000
80	A	89	TYR	0	0.039	0.012	19.128	-0.029	-0.029	0.000	0.000	0.000	0.000
81	A	90	LYS	1	0.893	0.941	20.834	0.180	0.180	0.000	0.000	0.000	0.000
82	A	91	ASP	-1	-0.915	-0.968	23.949	-0.082	-0.082	0.000	0.000	0.000	0.000
83	A	92	TYR	0	-0.024	0.005	23.731	0.011	0.011	0.000	0.000	0.000	0.000
84	A	93	ARG	1	0.990	0.974	24.097	0.044	0.044	0.000	0.000	0.000	0.000
85	A	94	GLN	0	-0.001	0.005	22.567	0.003	0.003	0.000	0.000	0.000	0.000
86	A	95	LEU	0	-0.041	-0.003	17.725	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	96	GLU	-1	-0.869	-0.937	21.347	-0.028	-0.028	0.000	0.000	0.000	0.000
88	A	97	LEU	0	-0.024	-0.012	17.669	-0.012	-0.012	0.000	0.000	0.000	0.000
89	A	98	ALA	0	-0.022	-0.022	22.034	0.011	0.011	0.000	0.000	0.000	0.000
90	A	99	CYS	0	-0.024	-0.010	22.264	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	100	GLU	-1	-0.868	-0.934	25.112	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	101	THR	0	0.002	-0.003	27.118	0.001	0.001	0.000	0.000	0.000	0.000
93	A	102	GLN	0	0.048	0.021	26.485	-0.009	-0.009	0.000	0.000	0.000	0.000
94	A	103	GLU	-1	-0.874	-0.954	25.609	0.060	0.060	0.000	0.000	0.000	0.000
95	A	104	GLU	-1	-0.915	-0.960	21.889	0.032	0.032	0.000	0.000	0.000	0.000
96	A	105	VAL	0	0.026	0.006	21.204	0.005	0.005	0.000	0.000	0.000	0.000
97	A	106	ASP	-1	-0.887	-0.945	20.812	0.091	0.091	0.000	0.000	0.000	0.000
98	A	107	SER	0	-0.031	-0.006	19.493	0.024	0.024	0.000	0.000	0.000	0.000
99	A	108	TRP	0	0.017	-0.012	13.301	0.036	0.036	0.000	0.000	0.000	0.000
100	A	109	LYS	1	0.861	0.941	15.937	-0.046	-0.046	0.000	0.000	0.000	0.000
101	A	110	ALA	0	0.010	0.014	16.426	0.023	0.023	0.000	0.000	0.000	0.000
102	A	111	SER	0	-0.039	-0.025	12.688	0.052	0.052	0.000	0.000	0.000	0.000
103	A	112	PHE	0	0.053	0.004	11.752	0.057	0.057	0.000	0.000	0.000	0.000
104	A	113	LEU	0	0.013	0.020	12.368	0.022	0.022	0.000	0.000	0.000	0.000
105	A	114	ARG	1	0.856	0.947	9.033	-0.819	-0.819	0.000	0.000	0.000	0.000
106	A	115	ALA	0	0.001	-0.015	8.109	0.243	0.243	0.000	0.000	0.000	0.000
107	A	116	GLY	0	0.006	0.019	9.082	-0.085	-0.085	0.000	0.000	0.000	0.000
108	A	117	VAL	0	-0.024	-0.002	11.648	-0.060	-0.060	0.000	0.000	0.000	0.000
109	A	118	TYR	0	-0.034	-0.022	13.944	0.015	0.015	0.000	0.000	0.000	0.000
110	A	119	PRO	0	-0.006	-0.006	17.318	-0.025	-0.025	0.000	0.000	0.000	0.000
111	A	120	GLU	-1	-0.892	-0.942	20.684	0.005	0.005	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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