FMO DATABASE

FMODB ID: R5MG8

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

Total energy (hartree)

FMO2-HF: Electronic energy	-659972.414992
FMO2-HF: Nuclear repulsion	624241.269674
FMO2-HF: Total energy	-35731.145319
FMO2-MP2: Total energy	-35837.937037

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.
1.169	3.143	0.084	-0.753	-1.305	0.001

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 : 0.049 / q_NPA : 0.011

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	0.060	0.027	3.820	0.111	1.117	-0.001	-0.428	-0.577	0.000
4	A	7	HIS	0	0.022	0.012	2.963	-0.171	0.599	0.086	-0.282	-0.575	0.001
5	A	8	LEU	0	0.010	0.002	4.266	-0.079	0.119	-0.001	-0.043	-0.153	0.000
6	A	9	GLU	-1	-0.800	-0.907	5.853	-0.233	-0.233	0.000	0.000	0.000	0.000
7	A	10	ALA	0	0.033	0.024	8.091	0.183	0.183	0.000	0.000	0.000	0.000
8	A	11	GLN	0	-0.031	-0.015	7.720	0.154	0.154	0.000	0.000	0.000	0.000
9	A	12	LEU	0	0.003	-0.005	9.985	0.076	0.076	0.000	0.000	0.000	0.000
10	A	13	LYS	1	0.943	0.992	11.996	0.156	0.156	0.000	0.000	0.000	0.000
11	A	14	ARG	1	0.939	0.970	13.441	0.054	0.054	0.000	0.000	0.000	0.000
12	A	15	ALA	0	0.010	0.001	14.267	0.020	0.020	0.000	0.000	0.000	0.000
13	A	16	LEU	0	0.034	0.007	15.864	0.022	0.022	0.000	0.000	0.000	0.000
14	A	17	ALA	0	-0.028	-0.010	17.706	0.023	0.023	0.000	0.000	0.000	0.000
15	A	18	GLU	-1	-0.860	-0.924	19.150	-0.088	-0.088	0.000	0.000	0.000	0.000
16	A	19	GLU	-1	-0.881	-0.953	19.423	-0.159	-0.159	0.000	0.000	0.000	0.000
17	A	20	ILE	0	-0.059	-0.036	21.341	0.007	0.007	0.000	0.000	0.000	0.000
18	A	21	GLN	0	-0.027	-0.012	23.624	0.010	0.010	0.000	0.000	0.000	0.000
19	A	22	ALA	0	0.008	0.022	24.913	0.008	0.008	0.000	0.000	0.000	0.000
20	A	23	LEU	0	-0.122	-0.054	25.535	0.000	0.000	0.000	0.000	0.000	0.000
21	A	24	GLU	-1	-0.839	-0.932	28.390	-0.063	-0.063	0.000	0.000	0.000	0.000
22	A	25	ASP	-1	-0.885	-0.914	31.046	-0.075	-0.075	0.000	0.000	0.000	0.000
23	A	26	PRO	0	0.091	0.034	32.130	0.000	0.000	0.000	0.000	0.000	0.000
24	A	27	ARG	1	0.723	0.846	32.618	0.082	0.082	0.000	0.000	0.000	0.000
25	A	28	LEU	0	-0.025	-0.017	27.148	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	29	PHE	0	0.031	0.024	29.301	0.000	0.000	0.000	0.000	0.000	0.000
27	A	30	LEU	0	-0.037	-0.033	29.772	0.002	0.002	0.000	0.000	0.000	0.000
28	A	31	LEU	0	-0.036	0.012	24.102	0.002	0.002	0.000	0.000	0.000	0.000
29	A	32	THR	0	0.003	0.006	23.381	-0.006	-0.006	0.000	0.000	0.000	0.000
30	A	33	VAL	0	-0.003	-0.008	17.834	-0.008	-0.008	0.000	0.000	0.000	0.000
31	A	34	GLU	-1	-0.846	-0.929	19.399	-0.041	-0.041	0.000	0.000	0.000	0.000
32	A	35	ALA	0	-0.051	-0.038	15.369	0.016	0.016	0.000	0.000	0.000	0.000
33	A	36	VAL	0	-0.014	-0.001	11.802	-0.011	-0.011	0.000	0.000	0.000	0.000
34	A	37	ARG	1	0.923	0.980	11.610	0.245	0.245	0.000	0.000	0.000	0.000
35	A	38	LEU	0	-0.048	-0.019	8.035	0.019	0.019	0.000	0.000	0.000	0.000
36	A	39	SER	0	-0.011	-0.008	10.969	0.001	0.001	0.000	0.000	0.000	0.000
37	A	40	LYS	1	0.948	0.949	10.121	0.089	0.089	0.000	0.000	0.000	0.000
38	A	41	ASP	-1	-0.791	-0.877	9.450	-0.555	-0.555	0.000	0.000	0.000	0.000
39	A	42	GLY	0	-0.030	-0.012	10.515	-0.044	-0.044	0.000	0.000	0.000	0.000
40	A	43	SER	0	-0.052	-0.046	11.021	0.027	0.027	0.000	0.000	0.000	0.000
41	A	44	VAL	0	-0.009	-0.012	14.383	0.039	0.039	0.000	0.000	0.000	0.000
42	A	45	LEU	0	-0.024	-0.004	12.015	-0.084	-0.084	0.000	0.000	0.000	0.000
43	A	46	SER	0	-0.029	-0.006	14.828	0.045	0.045	0.000	0.000	0.000	0.000
44	A	47	VAL	0	-0.017	-0.025	15.882	-0.029	-0.029	0.000	0.000	0.000	0.000
45	A	48	TYR	0	0.007	0.007	16.192	0.004	0.004	0.000	0.000	0.000	0.000
46	A	49	VAL	0	-0.008	-0.011	20.213	0.004	0.004	0.000	0.000	0.000	0.000
47	A	50	GLU	-1	-0.878	-0.936	23.046	-0.024	-0.024	0.000	0.000	0.000	0.000
48	A	51	ALA	0	-0.020	-0.011	26.033	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	52	PHE	0	0.055	0.039	29.140	0.007	0.007	0.000	0.000	0.000	0.000
50	A	53	ARG	1	0.924	0.943	32.179	0.033	0.033	0.000	0.000	0.000	0.000
51	A	54	GLU	-1	-0.909	-0.942	33.381	-0.058	-0.058	0.000	0.000	0.000	0.000
52	A	55	GLU	-1	-0.751	-0.886	28.872	-0.067	-0.067	0.000	0.000	0.000	0.000
53	A	56	GLU	-1	-0.903	-0.945	30.347	-0.068	-0.068	0.000	0.000	0.000	0.000
54	A	57	GLY	0	-0.029	-0.032	31.744	-0.007	-0.007	0.000	0.000	0.000	0.000
55	A	58	ALA	0	0.040	0.024	28.850	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	59	LEU	0	0.012	0.004	25.582	-0.011	-0.011	0.000	0.000	0.000	0.000
57	A	60	ARG	1	0.935	0.961	27.911	0.061	0.061	0.000	0.000	0.000	0.000
58	A	61	ALA	0	-0.034	-0.011	29.899	-0.005	-0.005	0.000	0.000	0.000	0.000
59	A	62	LEU	0	0.032	0.017	23.715	-0.006	-0.006	0.000	0.000	0.000	0.000
60	A	63	SER	0	0.009	-0.003	25.813	-0.016	-0.016	0.000	0.000	0.000	0.000
61	A	64	ARG	1	0.897	0.955	26.867	0.084	0.084	0.000	0.000	0.000	0.000
62	A	65	ALA	0	-0.063	-0.025	26.316	0.001	0.001	0.000	0.000	0.000	0.000
63	A	66	GLU	-1	-0.676	-0.805	21.652	-0.255	-0.255	0.000	0.000	0.000	0.000
64	A	67	ARG	1	0.980	0.971	22.905	0.145	0.145	0.000	0.000	0.000	0.000
65	A	68	ARG	1	0.942	0.972	23.865	0.109	0.109	0.000	0.000	0.000	0.000
66	A	69	LEU	0	0.069	0.040	20.972	-0.006	-0.006	0.000	0.000	0.000	0.000
67	A	70	VAL	0	0.006	0.009	18.385	-0.020	-0.020	0.000	0.000	0.000	0.000
68	A	71	ALA	0	-0.056	-0.028	19.230	-0.022	-0.022	0.000	0.000	0.000	0.000
69	A	72	ALA	0	-0.017	-0.009	20.987	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	73	LEU	0	0.040	0.017	15.188	-0.009	-0.009	0.000	0.000	0.000	0.000
71	A	74	ALA	0	-0.045	-0.027	16.142	-0.032	-0.032	0.000	0.000	0.000	0.000
72	A	75	ARG	1	0.905	0.961	17.631	0.176	0.176	0.000	0.000	0.000	0.000
73	A	76	ARG	1	0.809	0.903	15.881	0.205	0.205	0.000	0.000	0.000	0.000
74	A	77	VAL	0	-0.007	0.016	10.418	-0.028	-0.028	0.000	0.000	0.000	0.000
75	A	78	ARG	1	0.936	0.970	10.871	0.403	0.403	0.000	0.000	0.000	0.000
76	A	79	MET	0	0.033	0.012	9.876	-0.173	-0.173	0.000	0.000	0.000	0.000
77	A	80	ARG	1	0.886	0.949	12.214	0.497	0.497	0.000	0.000	0.000	0.000
78	A	81	ARG	1	1.008	0.993	14.405	0.382	0.382	0.000	0.000	0.000	0.000
79	A	82	LEU	0	0.006	0.010	13.433	-0.072	-0.072	0.000	0.000	0.000	0.000
80	A	83	PRO	0	0.004	0.026	12.791	0.046	0.046	0.000	0.000	0.000	0.000
81	A	84	ARG	1	0.773	0.859	15.336	0.316	0.316	0.000	0.000	0.000	0.000
82	A	85	LEU	0	-0.001	-0.019	16.998	-0.035	-0.035	0.000	0.000	0.000	0.000
83	A	86	GLU	-1	-0.868	-0.922	19.008	-0.187	-0.187	0.000	0.000	0.000	0.000
84	A	87	PHE	0	-0.028	-0.025	20.075	-0.014	-0.014	0.000	0.000	0.000	0.000
85	A	88	LEU	0	-0.004	0.002	20.084	0.014	0.014	0.000	0.000	0.000	0.000
86	A	89	PRO	0	0.032	0.023	23.211	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	90	TRP	0	0.052	0.005	22.448	-0.006	-0.006	0.000	0.000	0.000	0.000
88	A	91	ARG	1	0.879	0.936	22.680	0.060	0.060	0.000	0.000	0.000	0.000
89	A	92	ALA	0	-0.061	-0.030	22.767	0.005	0.005	0.000	0.000	0.000	0.000
90	A	93	SER	0	-0.037	-0.016	17.940	-0.013	-0.013	0.000	0.000	0.000	0.000
91	A	94	PRO	0	-0.036	-0.016	15.137	0.018	0.018	0.000	0.000	0.000	0.000

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Overview

Highlights

Manual

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