FMO DATABASE

FMODB ID: Q1MGY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-660211.383443
FMO2-HF: Nuclear repulsion	624479.813749
FMO2-HF: Total energy	-35731.569694
FMO2-MP2: Total energy	-35838.337388

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.
0.377	2.391	0.078	-0.788	-1.303	0.002

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 : 0.040 / q_NPA : 0.009

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	0.077	0.038	3.820	0.155	1.200	-0.001	-0.451	-0.593	0.000
4	A	7	HIS	0	0.007	0.008	3.120	-0.269	0.505	0.080	-0.294	-0.560	0.002
5	A	8	LEU	0	0.002	-0.007	4.411	-0.254	-0.059	-0.001	-0.043	-0.150	0.000
6	A	9	GLU	-1	-0.761	-0.873	5.975	-0.363	-0.363	0.000	0.000	0.000	0.000
7	A	10	ALA	0	0.033	0.024	8.256	0.125	0.125	0.000	0.000	0.000	0.000
8	A	11	GLN	0	-0.026	-0.013	7.519	0.148	0.148	0.000	0.000	0.000	0.000
9	A	12	LEU	0	0.006	-0.006	9.929	0.036	0.036	0.000	0.000	0.000	0.000
10	A	13	LYS	1	0.848	0.929	12.118	0.073	0.073	0.000	0.000	0.000	0.000
11	A	14	ARG	1	0.932	0.976	13.596	-0.018	-0.018	0.000	0.000	0.000	0.000
12	A	15	ALA	0	0.003	-0.003	14.402	0.009	0.009	0.000	0.000	0.000	0.000
13	A	16	LEU	0	0.029	0.008	15.993	0.012	0.012	0.000	0.000	0.000	0.000
14	A	17	ALA	0	-0.015	-0.004	17.847	0.015	0.015	0.000	0.000	0.000	0.000
15	A	18	GLU	-1	-0.840	-0.914	18.979	-0.036	-0.036	0.000	0.000	0.000	0.000
16	A	19	GLU	-1	-0.865	-0.935	19.352	-0.121	-0.121	0.000	0.000	0.000	0.000
17	A	20	ILE	0	-0.044	-0.033	21.364	0.003	0.003	0.000	0.000	0.000	0.000
18	A	21	GLN	0	-0.020	-0.004	23.759	0.008	0.008	0.000	0.000	0.000	0.000
19	A	22	ALA	0	-0.007	0.012	25.039	0.006	0.006	0.000	0.000	0.000	0.000
20	A	23	LEU	0	-0.118	-0.052	25.788	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	24	GLU	-1	-0.847	-0.935	28.505	-0.041	-0.041	0.000	0.000	0.000	0.000
22	A	25	ASP	-1	-0.874	-0.900	31.137	-0.058	-0.058	0.000	0.000	0.000	0.000
23	A	26	PRO	0	0.089	0.037	32.259	0.000	0.000	0.000	0.000	0.000	0.000
24	A	27	ARG	1	0.731	0.838	32.750	0.064	0.064	0.000	0.000	0.000	0.000
25	A	28	LEU	0	-0.030	-0.020	27.305	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	29	PHE	0	0.026	0.022	29.445	0.002	0.002	0.000	0.000	0.000	0.000
27	A	30	LEU	0	-0.041	-0.033	29.877	0.001	0.001	0.000	0.000	0.000	0.000
28	A	31	LEU	0	-0.045	0.005	24.432	0.002	0.002	0.000	0.000	0.000	0.000
29	A	32	THR	0	-0.018	-0.007	23.739	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	33	VAL	0	0.013	0.000	17.988	-0.009	-0.009	0.000	0.000	0.000	0.000
31	A	34	GLU	-1	-0.793	-0.889	19.670	-0.027	-0.027	0.000	0.000	0.000	0.000
32	A	35	ALA	0	-0.004	0.002	15.326	0.021	0.021	0.000	0.000	0.000	0.000
33	A	36	VAL	0	-0.018	-0.007	11.840	-0.014	-0.014	0.000	0.000	0.000	0.000
34	A	37	ARG	1	0.902	0.961	11.616	0.227	0.227	0.000	0.000	0.000	0.000
35	A	38	LEU	0	-0.064	-0.025	7.797	0.006	0.006	0.000	0.000	0.000	0.000
36	A	39	SER	0	-0.012	-0.023	10.968	-0.009	-0.009	0.000	0.000	0.000	0.000
37	A	40	LYS	1	0.958	0.953	10.119	0.085	0.085	0.000	0.000	0.000	0.000
38	A	41	ASP	-1	-0.776	-0.848	9.449	-0.528	-0.528	0.000	0.000	0.000	0.000
39	A	42	GLY	0	-0.023	-0.012	10.491	-0.040	-0.040	0.000	0.000	0.000	0.000
40	A	43	SER	0	-0.042	-0.045	11.019	0.034	0.034	0.000	0.000	0.000	0.000
41	A	44	VAL	0	-0.025	-0.020	14.387	0.040	0.040	0.000	0.000	0.000	0.000
42	A	45	LEU	0	-0.020	-0.002	11.930	-0.076	-0.076	0.000	0.000	0.000	0.000
43	A	46	SER	0	-0.009	-0.011	14.828	0.038	0.038	0.000	0.000	0.000	0.000
44	A	47	VAL	0	-0.026	-0.027	15.882	-0.020	-0.020	0.000	0.000	0.000	0.000
45	A	48	TYR	0	0.010	0.016	16.283	0.001	0.001	0.000	0.000	0.000	0.000
46	A	49	VAL	0	-0.005	-0.010	20.213	0.007	0.007	0.000	0.000	0.000	0.000
47	A	50	GLU	-1	-0.876	-0.928	23.046	-0.007	-0.007	0.000	0.000	0.000	0.000
48	A	51	ALA	0	-0.008	-0.004	26.033	0.000	0.000	0.000	0.000	0.000	0.000
49	A	52	PHE	0	0.064	0.039	29.140	0.005	0.005	0.000	0.000	0.000	0.000
50	A	53	ARG	1	0.911	0.938	32.179	0.019	0.019	0.000	0.000	0.000	0.000
51	A	54	GLU	-1	-0.817	-0.913	33.381	-0.048	-0.048	0.000	0.000	0.000	0.000
52	A	55	GLU	-1	-0.753	-0.864	28.923	-0.049	-0.049	0.000	0.000	0.000	0.000
53	A	56	GLU	-1	-0.813	-0.893	30.347	-0.055	-0.055	0.000	0.000	0.000	0.000
54	A	57	GLY	0	-0.021	-0.010	31.744	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	58	ALA	0	0.023	0.017	28.951	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	59	LEU	0	0.013	0.006	25.548	-0.009	-0.009	0.000	0.000	0.000	0.000
57	A	60	ARG	1	0.794	0.891	27.911	0.045	0.045	0.000	0.000	0.000	0.000
58	A	61	ALA	0	-0.029	-0.013	30.045	-0.005	-0.005	0.000	0.000	0.000	0.000
59	A	62	LEU	0	0.028	0.018	23.664	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	63	SER	0	0.000	-0.021	25.854	-0.014	-0.014	0.000	0.000	0.000	0.000
61	A	64	ARG	1	0.892	0.954	26.867	0.066	0.066	0.000	0.000	0.000	0.000
62	A	65	ALA	0	-0.056	-0.020	26.523	0.000	0.000	0.000	0.000	0.000	0.000
63	A	66	GLU	-1	-0.691	-0.814	21.781	-0.216	-0.216	0.000	0.000	0.000	0.000
64	A	67	ARG	1	0.982	0.975	22.969	0.123	0.123	0.000	0.000	0.000	0.000
65	A	68	ARG	1	0.945	0.971	23.916	0.086	0.086	0.000	0.000	0.000	0.000
66	A	69	LEU	0	0.060	0.036	21.114	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	70	VAL	0	0.009	0.009	18.302	-0.014	-0.014	0.000	0.000	0.000	0.000
68	A	71	ALA	0	-0.054	-0.028	19.276	-0.019	-0.019	0.000	0.000	0.000	0.000
69	A	72	ALA	0	-0.028	-0.018	21.030	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	73	LEU	0	0.044	0.021	15.159	-0.005	-0.005	0.000	0.000	0.000	0.000
71	A	74	ALA	0	-0.042	-0.026	16.192	-0.025	-0.025	0.000	0.000	0.000	0.000
72	A	75	ARG	1	0.901	0.963	17.660	0.139	0.139	0.000	0.000	0.000	0.000
73	A	76	ARG	1	0.778	0.867	15.779	0.138	0.138	0.000	0.000	0.000	0.000
74	A	77	VAL	0	-0.004	0.016	10.517	-0.015	-0.015	0.000	0.000	0.000	0.000
75	A	78	ARG	1	0.948	0.974	10.922	0.320	0.320	0.000	0.000	0.000	0.000
76	A	79	MET	0	0.029	0.017	9.819	-0.151	-0.151	0.000	0.000	0.000	0.000
77	A	80	ARG	1	0.907	0.959	12.182	0.422	0.422	0.000	0.000	0.000	0.000
78	A	81	ARG	1	0.989	0.986	14.360	0.346	0.346	0.000	0.000	0.000	0.000
79	A	82	LEU	0	0.006	0.012	13.494	-0.066	-0.066	0.000	0.000	0.000	0.000
80	A	83	PRO	0	0.014	0.030	12.867	0.035	0.035	0.000	0.000	0.000	0.000
81	A	84	ARG	1	0.773	0.852	15.333	0.277	0.277	0.000	0.000	0.000	0.000
82	A	85	LEU	0	-0.011	-0.018	17.067	-0.030	-0.030	0.000	0.000	0.000	0.000
83	A	86	GLU	-1	-0.848	-0.889	19.009	-0.169	-0.169	0.000	0.000	0.000	0.000
84	A	87	PHE	0	-0.021	-0.021	20.075	-0.011	-0.011	0.000	0.000	0.000	0.000
85	A	88	LEU	0	0.010	0.008	20.302	0.012	0.012	0.000	0.000	0.000	0.000
86	A	89	PRO	0	0.035	0.021	23.211	0.001	0.001	0.000	0.000	0.000	0.000
87	A	90	TRP	0	0.074	0.012	22.447	-0.005	-0.005	0.000	0.000	0.000	0.000
88	A	91	ARG	1	0.834	0.895	22.680	0.045	0.045	0.000	0.000	0.000	0.000
89	A	92	ALA	0	-0.057	-0.031	22.792	0.004	0.004	0.000	0.000	0.000	0.000
90	A	93	SER	0	-0.055	-0.037	17.985	-0.013	-0.013	0.000	0.000	0.000	0.000
91	A	94	PRO	0	-0.041	-0.015	15.102	0.014	0.014	0.000	0.000	0.000	0.000

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