FMO DATABASE

FMODB ID: K38L3

Calculation Name: 2DYJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2DYJ

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SJV1

Base Structure: X-ray

Registration Date: 2023-03-13

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	91
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-661835.67089
FMO2-HF: Nuclear repulsion	626103.891075
FMO2-HF: Total energy	-35731.779815
FMO2-MP2: Total energy	-35838.5247

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:4:GLY)

Summations of interaction energy for fragment #1(A:4:GLY)

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.
0.818	2.847	0.322	-0.876	-1.476	0

Interaction energy analysis for fragmet #1(A:4:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.051 / q_NPA : 0.015

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	6	ALA	0	0.104	0.048	3.876	-0.565	0.415	-0.003	-0.439	-0.538	0.001
4	A	7	HIS	0	-0.001	0.013	2.487	-0.837	-0.035	0.326	-0.364	-0.765	-0.001
5	A	8	LEU	0	-0.005	-0.017	4.193	0.457	0.704	-0.001	-0.073	-0.173	0.000
6	A	9	GLU	-1	-0.766	-0.882	6.147	0.125	0.125	0.000	0.000	0.000	0.000
7	A	10	ALA	0	0.024	0.018	7.612	0.195	0.195	0.000	0.000	0.000	0.000
8	A	11	GLN	0	-0.021	-0.015	7.572	0.187	0.187	0.000	0.000	0.000	0.000
9	A	12	LEU	0	-0.015	-0.012	9.789	0.138	0.138	0.000	0.000	0.000	0.000
10	A	13	LYS	1	0.860	0.921	11.823	0.203	0.203	0.000	0.000	0.000	0.000
11	A	14	ARG	1	0.850	0.919	12.975	0.242	0.242	0.000	0.000	0.000	0.000
12	A	15	ALA	0	0.008	0.001	14.031	0.038	0.038	0.000	0.000	0.000	0.000
13	A	16	LEU	0	0.020	0.005	15.697	0.039	0.039	0.000	0.000	0.000	0.000
14	A	17	ALA	0	0.005	0.003	17.432	0.030	0.030	0.000	0.000	0.000	0.000
15	A	18	GLU	-1	-0.793	-0.873	18.438	-0.197	-0.197	0.000	0.000	0.000	0.000
16	A	19	GLU	-1	-0.863	-0.938	19.277	-0.203	-0.203	0.000	0.000	0.000	0.000
17	A	20	ILE	0	-0.046	-0.030	20.952	0.015	0.015	0.000	0.000	0.000	0.000
18	A	21	GLN	0	-0.017	-0.013	23.297	0.019	0.019	0.000	0.000	0.000	0.000
19	A	22	ALA	0	-0.015	0.015	25.102	0.008	0.008	0.000	0.000	0.000	0.000
20	A	23	LEU	0	-0.100	-0.049	25.850	0.002	0.002	0.000	0.000	0.000	0.000
21	A	24	GLU	-1	-0.858	-0.933	28.701	-0.074	-0.074	0.000	0.000	0.000	0.000
22	A	25	ASP	-1	-0.860	-0.894	31.167	-0.066	-0.066	0.000	0.000	0.000	0.000
23	A	26	PRO	0	0.072	0.026	32.079	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	27	ARG	1	0.738	0.840	32.640	0.069	0.069	0.000	0.000	0.000	0.000
25	A	28	LEU	0	-0.010	-0.011	27.235	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	29	PHE	0	0.017	0.018	29.140	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	30	LEU	0	-0.035	-0.026	29.354	0.004	0.004	0.000	0.000	0.000	0.000
28	A	31	LEU	0	-0.047	-0.003	24.168	0.004	0.004	0.000	0.000	0.000	0.000
29	A	32	THR	0	-0.041	-0.036	23.153	-0.010	-0.010	0.000	0.000	0.000	0.000
30	A	33	VAL	0	0.027	0.000	17.861	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	34	GLU	-1	-0.766	-0.870	18.810	-0.040	-0.040	0.000	0.000	0.000	0.000
32	A	35	ALA	0	-0.001	0.012	15.836	0.007	0.007	0.000	0.000	0.000	0.000
33	A	36	VAL	0	-0.026	-0.018	11.870	-0.025	-0.025	0.000	0.000	0.000	0.000
34	A	37	ARG	1	0.881	0.947	12.149	0.121	0.121	0.000	0.000	0.000	0.000
35	A	38	LEU	0	-0.051	-0.014	8.104	-0.015	-0.015	0.000	0.000	0.000	0.000
36	A	39	SER	0	-0.014	-0.034	11.441	0.050	0.050	0.000	0.000	0.000	0.000
37	A	40	LYS	1	0.941	0.942	10.594	-0.094	-0.094	0.000	0.000	0.000	0.000
38	A	41	ASP	-1	-0.788	-0.844	10.204	-0.236	-0.236	0.000	0.000	0.000	0.000
39	A	42	GLY	0	0.004	0.008	10.865	-0.049	-0.049	0.000	0.000	0.000	0.000
40	A	43	SER	0	-0.022	-0.034	11.372	-0.007	-0.007	0.000	0.000	0.000	0.000
41	A	44	VAL	0	-0.042	-0.023	14.598	0.018	0.018	0.000	0.000	0.000	0.000
42	A	45	LEU	0	-0.020	-0.012	12.014	-0.061	-0.061	0.000	0.000	0.000	0.000
43	A	46	SER	0	-0.008	-0.009	14.976	0.025	0.025	0.000	0.000	0.000	0.000
44	A	47	VAL	0	-0.038	-0.029	15.959	-0.034	-0.034	0.000	0.000	0.000	0.000
45	A	48	TYR	0	0.002	0.020	16.490	0.010	0.010	0.000	0.000	0.000	0.000
46	A	49	VAL	0	-0.020	-0.019	20.263	-0.006	-0.006	0.000	0.000	0.000	0.000
47	A	50	GLU	-1	-0.870	-0.905	23.028	-0.026	-0.026	0.000	0.000	0.000	0.000
48	A	51	ALA	0	0.014	0.008	25.859	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	52	PHE	0	0.067	0.039	29.029	0.007	0.007	0.000	0.000	0.000	0.000
50	A	53	ARG	1	0.888	0.930	31.831	0.035	0.035	0.000	0.000	0.000	0.000
51	A	54	GLU	-1	-0.780	-0.881	33.083	-0.047	-0.047	0.000	0.000	0.000	0.000
52	A	55	GLU	-1	-0.744	-0.855	28.963	-0.040	-0.040	0.000	0.000	0.000	0.000
53	A	56	GLU	-1	-0.813	-0.886	30.162	-0.044	-0.044	0.000	0.000	0.000	0.000
54	A	57	GLY	0	-0.020	-0.005	31.552	-0.005	-0.005	0.000	0.000	0.000	0.000
55	A	58	ALA	0	0.017	0.011	29.036	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	59	LEU	0	0.005	0.006	25.407	-0.010	-0.010	0.000	0.000	0.000	0.000
57	A	60	ARG	1	0.773	0.858	27.941	0.039	0.039	0.000	0.000	0.000	0.000
58	A	61	ALA	0	-0.047	-0.020	29.989	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	62	LEU	0	0.031	0.014	23.583	-0.006	-0.006	0.000	0.000	0.000	0.000
60	A	63	SER	0	0.000	-0.015	25.825	-0.012	-0.012	0.000	0.000	0.000	0.000
61	A	64	ARG	1	0.899	0.961	26.957	0.068	0.068	0.000	0.000	0.000	0.000
62	A	65	ALA	0	-0.004	-0.009	26.416	0.002	0.002	0.000	0.000	0.000	0.000
63	A	66	GLU	-1	-0.709	-0.817	21.504	-0.193	-0.193	0.000	0.000	0.000	0.000
64	A	67	ARG	1	0.980	0.978	22.665	0.101	0.101	0.000	0.000	0.000	0.000
65	A	68	ARG	1	0.897	0.956	23.750	0.098	0.098	0.000	0.000	0.000	0.000
66	A	69	LEU	0	0.062	0.038	21.060	-0.010	-0.010	0.000	0.000	0.000	0.000
67	A	70	VAL	0	0.004	0.001	17.947	-0.024	-0.024	0.000	0.000	0.000	0.000
68	A	71	ALA	0	-0.036	-0.026	19.117	-0.023	-0.023	0.000	0.000	0.000	0.000
69	A	72	ALA	0	-0.033	-0.013	21.110	0.000	0.000	0.000	0.000	0.000	0.000
70	A	73	LEU	0	0.042	0.013	15.035	-0.020	-0.020	0.000	0.000	0.000	0.000
71	A	74	ALA	0	-0.034	-0.025	16.285	-0.038	-0.038	0.000	0.000	0.000	0.000
72	A	75	ARG	1	0.900	0.967	17.831	0.192	0.192	0.000	0.000	0.000	0.000
73	A	76	ARG	1	0.779	0.875	16.215	0.289	0.289	0.000	0.000	0.000	0.000
74	A	77	VAL	0	0.009	0.013	10.825	-0.058	-0.058	0.000	0.000	0.000	0.000
75	A	78	ARG	1	0.954	0.981	11.221	0.397	0.397	0.000	0.000	0.000	0.000
76	A	79	MET	0	0.010	0.023	9.435	-0.103	-0.103	0.000	0.000	0.000	0.000
77	A	80	ARG	1	0.936	0.953	11.767	0.344	0.344	0.000	0.000	0.000	0.000
78	A	81	ARG	1	0.956	0.977	13.655	0.268	0.268	0.000	0.000	0.000	0.000
79	A	82	LEU	0	0.017	0.022	13.261	-0.053	-0.053	0.000	0.000	0.000	0.000
80	A	83	PRO	0	0.004	0.016	12.630	0.046	0.046	0.000	0.000	0.000	0.000
81	A	84	ARG	1	0.787	0.857	15.178	0.225	0.225	0.000	0.000	0.000	0.000
82	A	85	LEU	0	-0.019	-0.014	17.165	-0.019	-0.019	0.000	0.000	0.000	0.000
83	A	86	GLU	-1	-0.819	-0.884	18.897	-0.096	-0.096	0.000	0.000	0.000	0.000
84	A	87	PHE	0	-0.005	-0.014	20.261	-0.006	-0.006	0.000	0.000	0.000	0.000
85	A	88	LEU	0	0.012	0.010	20.403	0.014	0.014	0.000	0.000	0.000	0.000
86	A	89	PRO	0	0.024	0.018	23.239	-0.005	-0.005	0.000	0.000	0.000	0.000
87	A	90	TRP	0	0.063	0.001	22.446	0.004	0.004	0.000	0.000	0.000	0.000
88	A	91	ARG	1	0.805	0.883	22.838	0.032	0.032	0.000	0.000	0.000	0.000
89	A	92	ALA	0	-0.025	-0.008	23.148	0.008	0.008	0.000	0.000	0.000	0.000
90	A	93	SER	0	-0.049	-0.038	18.296	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	94	PRO	0	-0.051	-0.020	15.190	0.023	0.023	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:GLY)