FMO DATABASE

FMODB ID: NN41Q

Calculation Name: 1YTF-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YTF

Chain ID: D

ChEMBL ID:

UniProt ID: P32774

Base Structure: X-ray

Registration Date: 2023-09-24

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	100
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-637533.050616
FMO2-HF: Nuclear repulsion	597940.395813
FMO2-HF: Total energy	-39592.654803
FMO2-MP2: Total energy	-39706.768339

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(D:5:GLY)

Summations of interaction energy for fragment #1(D:5: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.
-3.24	-2.044	-0.008	-0.782	-0.407	0.004

Interaction energy analysis for fragmet #1(D:5:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / q_NPA : 0.008

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	D	7	TYR	0	-0.004	-0.008	3.816	-1.487	-0.291	-0.008	-0.782	-0.407	0.004
4	D	8	GLU	-1	-0.787	-0.891	6.380	-1.742	-1.742	0.000	0.000	0.000	0.000
5	D	9	LEU	0	-0.039	-0.026	9.069	0.401	0.401	0.000	0.000	0.000	0.000
6	D	10	TYR	0	0.034	0.004	10.055	0.218	0.218	0.000	0.000	0.000	0.000
7	D	11	ARG	1	0.822	0.896	8.823	2.147	2.147	0.000	0.000	0.000	0.000
8	D	12	ARG	1	0.939	0.978	14.619	0.720	0.720	0.000	0.000	0.000	0.000
9	D	13	SER	0	-0.041	-0.021	16.536	0.110	0.110	0.000	0.000	0.000	0.000
10	D	14	THR	0	0.038	0.007	18.655	-0.011	-0.011	0.000	0.000	0.000	0.000
11	D	15	ILE	0	0.026	0.019	17.536	0.011	0.011	0.000	0.000	0.000	0.000
12	D	16	GLY	0	0.002	0.004	16.774	-0.014	-0.014	0.000	0.000	0.000	0.000
13	D	17	ASN	0	-0.008	-0.015	17.450	-0.034	-0.034	0.000	0.000	0.000	0.000
14	D	18	SER	0	0.020	0.003	20.098	0.030	0.030	0.000	0.000	0.000	0.000
15	D	19	LEU	0	-0.044	-0.006	15.563	0.024	0.024	0.000	0.000	0.000	0.000
16	D	20	VAL	0	-0.001	-0.008	16.734	0.003	0.003	0.000	0.000	0.000	0.000
17	D	21	ASP	-1	-0.860	-0.924	19.146	-0.365	-0.365	0.000	0.000	0.000	0.000
18	D	22	ALA	0	-0.047	-0.017	21.979	0.035	0.035	0.000	0.000	0.000	0.000
19	D	23	LEU	0	-0.037	-0.036	16.921	0.027	0.027	0.000	0.000	0.000	0.000
20	D	24	ASP	-1	-0.876	-0.940	20.742	-0.435	-0.435	0.000	0.000	0.000	0.000
21	D	25	THR	0	-0.058	-0.030	22.750	0.042	0.042	0.000	0.000	0.000	0.000
22	D	26	LEU	0	-0.012	-0.017	22.652	0.023	0.023	0.000	0.000	0.000	0.000
23	D	27	ILE	0	-0.044	-0.022	19.949	0.016	0.016	0.000	0.000	0.000	0.000
24	D	28	SER	0	-0.072	-0.040	24.568	0.025	0.025	0.000	0.000	0.000	0.000
25	D	29	ASP	-1	-0.981	-0.977	27.494	-0.187	-0.187	0.000	0.000	0.000	0.000
26	D	30	GLY	0	-0.032	0.002	28.398	0.018	0.018	0.000	0.000	0.000	0.000
27	D	31	ARG	1	0.940	0.953	28.072	0.173	0.173	0.000	0.000	0.000	0.000
28	D	32	ILE	0	-0.054	-0.020	22.710	0.009	0.009	0.000	0.000	0.000	0.000
29	D	33	GLU	-1	-0.905	-0.956	21.325	-0.246	-0.246	0.000	0.000	0.000	0.000
30	D	34	ALA	0	0.098	0.059	20.048	-0.042	-0.042	0.000	0.000	0.000	0.000
31	D	35	SER	0	-0.024	-0.007	16.252	0.012	0.012	0.000	0.000	0.000	0.000
32	D	36	LEU	0	-0.031	-0.027	15.151	-0.082	-0.082	0.000	0.000	0.000	0.000
33	D	37	ALA	0	0.043	0.021	15.630	-0.073	-0.073	0.000	0.000	0.000	0.000
34	D	38	MET	0	0.008	0.006	10.096	-0.025	-0.025	0.000	0.000	0.000	0.000
35	D	39	ARG	1	0.969	0.987	11.043	0.383	0.383	0.000	0.000	0.000	0.000
36	D	40	VAL	0	-0.014	-0.004	11.660	-0.133	-0.133	0.000	0.000	0.000	0.000
37	D	41	LEU	0	0.015	0.001	11.896	-0.082	-0.082	0.000	0.000	0.000	0.000
38	D	42	GLU	-1	-0.862	-0.930	7.397	-1.593	-1.593	0.000	0.000	0.000	0.000
39	D	43	THR	0	-0.080	-0.041	8.165	-0.272	-0.272	0.000	0.000	0.000	0.000
40	D	44	PHE	0	-0.037	-0.017	10.708	0.044	0.044	0.000	0.000	0.000	0.000
41	D	45	ASP	-1	-0.769	-0.870	7.327	-2.416	-2.416	0.000	0.000	0.000	0.000
42	D	46	LYS	1	0.791	0.888	7.129	0.828	0.828	0.000	0.000	0.000	0.000
43	D	47	VAL	0	0.029	0.012	8.167	0.319	0.319	0.000	0.000	0.000	0.000
44	D	48	VAL	0	-0.008	0.014	11.891	0.182	0.182	0.000	0.000	0.000	0.000
45	D	49	ALA	0	-0.002	0.001	8.478	0.164	0.164	0.000	0.000	0.000	0.000
46	D	50	GLU	-1	-0.807	-0.905	9.612	-0.441	-0.441	0.000	0.000	0.000	0.000
47	D	51	THR	0	0.006	-0.002	11.880	0.137	0.137	0.000	0.000	0.000	0.000
48	D	52	LEU	0	-0.048	-0.029	13.872	0.093	0.093	0.000	0.000	0.000	0.000
49	D	53	LYS	1	0.748	0.883	11.106	0.250	0.250	0.000	0.000	0.000	0.000
50	D	54	ASP	-1	-0.828	-0.900	14.633	-0.130	-0.130	0.000	0.000	0.000	0.000
51	D	55	ASN	0	-0.082	-0.047	17.116	0.004	0.004	0.000	0.000	0.000	0.000
52	D	56	THR	0	-0.039	-0.016	18.164	0.008	0.008	0.000	0.000	0.000	0.000
53	D	57	GLN	0	-0.017	-0.016	20.829	0.019	0.019	0.000	0.000	0.000	0.000
54	D	58	SER	0	-0.017	-0.004	23.919	0.006	0.006	0.000	0.000	0.000	0.000
55	D	59	LYS	1	0.942	1.000	23.374	0.085	0.085	0.000	0.000	0.000	0.000
56	D	60	LEU	0	0.007	-0.004	22.817	0.004	0.004	0.000	0.000	0.000	0.000
57	D	61	THR	0	-0.046	-0.032	25.672	0.014	0.014	0.000	0.000	0.000	0.000
58	D	62	VAL	0	0.039	0.025	25.246	-0.003	-0.003	0.000	0.000	0.000	0.000
59	D	63	LYS	1	0.957	0.980	28.066	0.079	0.079	0.000	0.000	0.000	0.000
60	D	64	GLY	0	0.049	0.018	31.021	-0.004	-0.004	0.000	0.000	0.000	0.000
61	D	65	ASN	0	0.003	0.022	32.178	0.011	0.011	0.000	0.000	0.000	0.000
62	D	66	LEU	0	0.000	-0.005	26.148	-0.012	-0.012	0.000	0.000	0.000	0.000
63	D	67	ASP	-1	-0.830	-0.898	29.591	-0.114	-0.114	0.000	0.000	0.000	0.000
64	D	68	THR	0	-0.036	-0.030	25.739	0.003	0.003	0.000	0.000	0.000	0.000
65	D	69	TYR	0	-0.003	-0.006	24.175	-0.013	-0.013	0.000	0.000	0.000	0.000
66	D	70	GLY	0	0.017	0.008	22.429	0.006	0.006	0.000	0.000	0.000	0.000
67	D	71	PHE	0	-0.034	-0.018	15.541	-0.019	-0.019	0.000	0.000	0.000	0.000
68	D	72	CYS	0	-0.022	-0.024	17.391	0.035	0.035	0.000	0.000	0.000	0.000
69	D	73	ASP	-1	-0.859	-0.913	13.107	-0.110	-0.110	0.000	0.000	0.000	0.000
70	D	74	ASP	-1	-0.839	-0.914	10.834	0.134	0.134	0.000	0.000	0.000	0.000
71	D	75	VAL	0	-0.034	-0.014	12.111	-0.096	-0.096	0.000	0.000	0.000	0.000
72	D	76	TRP	0	-0.008	0.005	14.319	0.043	0.043	0.000	0.000	0.000	0.000
73	D	77	THR	0	-0.054	-0.034	17.548	-0.067	-0.067	0.000	0.000	0.000	0.000
74	D	78	PHE	0	-0.005	-0.009	19.756	0.034	0.034	0.000	0.000	0.000	0.000
75	D	79	ILE	0	-0.022	-0.017	23.110	-0.029	-0.029	0.000	0.000	0.000	0.000
76	D	80	VAL	0	-0.003	0.001	25.753	0.018	0.018	0.000	0.000	0.000	0.000
77	D	81	LYS	1	0.855	0.910	28.346	0.112	0.112	0.000	0.000	0.000	0.000
78	D	82	ASN	0	-0.046	-0.026	31.882	0.003	0.003	0.000	0.000	0.000	0.000
79	D	83	CYS	0	-0.052	-0.019	30.010	0.002	0.002	0.000	0.000	0.000	0.000
80	D	84	GLN	0	0.022	0.013	32.428	0.000	0.000	0.000	0.000	0.000	0.000
81	D	85	VAL	0	-0.006	-0.026	27.511	0.000	0.000	0.000	0.000	0.000	0.000
82	D	86	THR	0	-0.030	-0.017	29.834	0.005	0.005	0.000	0.000	0.000	0.000
83	D	87	VAL	0	-0.012	-0.005	27.689	-0.005	-0.005	0.000	0.000	0.000	0.000
84	D	88	GLU	-1	-0.881	-0.941	27.826	-0.105	-0.105	0.000	0.000	0.000	0.000
85	D	104	SER	0	0.045	0.033	32.979	0.003	0.003	0.000	0.000	0.000	0.000
86	D	105	VAL	0	-0.035	-0.039	33.095	-0.003	-0.003	0.000	0.000	0.000	0.000
87	D	106	ILE	0	0.009	0.011	30.809	0.001	0.001	0.000	0.000	0.000	0.000
88	D	107	SER	0	-0.001	-0.003	33.011	0.006	0.006	0.000	0.000	0.000	0.000
89	D	108	VAL	0	-0.008	-0.007	29.140	-0.007	-0.007	0.000	0.000	0.000	0.000
90	D	109	ASP	-1	-0.881	-0.916	32.282	-0.123	-0.123	0.000	0.000	0.000	0.000
91	D	110	LYS	1	0.944	0.954	28.517	0.177	0.177	0.000	0.000	0.000	0.000
92	D	111	LEU	0	0.031	0.032	24.376	-0.012	-0.012	0.000	0.000	0.000	0.000
93	D	112	ARG	1	0.937	0.971	21.344	0.282	0.282	0.000	0.000	0.000	0.000
94	D	113	ILE	0	-0.002	-0.005	19.207	-0.022	-0.022	0.000	0.000	0.000	0.000
95	D	114	VAL	0	-0.003	-0.011	14.780	0.021	0.021	0.000	0.000	0.000	0.000
96	D	115	ALA	0	-0.013	0.000	14.531	-0.046	-0.046	0.000	0.000	0.000	0.000
97	D	116	CYS	0	0.041	0.034	9.340	-0.027	-0.027	0.000	0.000	0.000	0.000
98	D	117	ASN	0	0.034	0.017	9.927	0.018	0.018	0.000	0.000	0.000	0.000
99	D	118	SER	0	0.031	0.032	9.230	-0.039	-0.039	0.000	0.000	0.000	0.000
100	D	119	LYS	1	0.862	0.925	7.612	-0.151	-0.151	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:5:GLY)