FMO DATABASE

FMODB ID: N1YNQ

Calculation Name: 3Q4H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3Q4H

Chain ID: A

ChEMBL ID:

UniProt ID: A0QQ43

Base Structure: X-ray

Registration Date: 2023-06-20

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	90
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-449342.47136
FMO2-HF: Nuclear repulsion	416658.97478
FMO2-HF: Total energy	-32683.49658
FMO2-MP2: Total energy	-32777.956311

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:5:ASP)

Summations of interaction energy for fragment #1(A:5:ASP)

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.
7.869	13.831	0.752	-2.944	-3.769	0.023

Interaction energy analysis for fragmet #1(A:5:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.916 / q_NPA : -0.961

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	7	HIS	0	-0.037	-0.026	2.789	-17.806	-12.992	0.710	-2.640	-2.884	0.022
4	A	8	ILE	0	0.051	0.030	3.357	-8.415	-7.477	0.043	-0.278	-0.702	0.001
5	A	9	PRO	0	0.029	0.004	5.019	-6.196	-5.986	-0.001	-0.026	-0.183	0.000
6	A	10	GLN	0	-0.016	0.000	7.493	-6.875	-6.875	0.000	0.000	0.000	0.000
7	A	11	LEU	0	0.004	0.024	8.251	-2.983	-2.983	0.000	0.000	0.000	0.000
8	A	12	ILE	0	0.060	0.028	8.741	-2.555	-2.555	0.000	0.000	0.000	0.000
9	A	13	ALA	0	-0.019	-0.002	11.484	-2.263	-2.263	0.000	0.000	0.000	0.000
10	A	14	SER	0	-0.064	-0.045	12.723	-2.304	-2.304	0.000	0.000	0.000	0.000
11	A	15	GLU	-1	-0.896	-0.949	13.805	19.311	19.311	0.000	0.000	0.000	0.000
12	A	16	ALA	0	0.042	0.030	15.511	-1.410	-1.410	0.000	0.000	0.000	0.000
13	A	17	ASN	0	-0.029	-0.025	17.390	-1.523	-1.523	0.000	0.000	0.000	0.000
14	A	18	PHE	0	-0.036	-0.019	18.693	-1.192	-1.192	0.000	0.000	0.000	0.000
15	A	19	GLY	0	0.064	0.017	19.885	-0.833	-0.833	0.000	0.000	0.000	0.000
16	A	20	ALA	0	0.005	0.004	21.603	-0.780	-0.780	0.000	0.000	0.000	0.000
17	A	21	LYS	1	0.946	0.960	22.962	-13.777	-13.777	0.000	0.000	0.000	0.000
18	A	22	ALA	0	0.014	0.023	24.595	-0.591	-0.591	0.000	0.000	0.000	0.000
19	A	23	ALA	0	0.000	-0.003	25.907	-0.554	-0.554	0.000	0.000	0.000	0.000
20	A	24	LEU	0	0.005	-0.008	27.352	-0.500	-0.500	0.000	0.000	0.000	0.000
21	A	25	MET	0	-0.004	0.020	29.295	-0.570	-0.570	0.000	0.000	0.000	0.000
22	A	26	ARG	1	0.830	0.897	27.150	-11.031	-11.031	0.000	0.000	0.000	0.000
23	A	27	SER	0	-0.009	-0.002	32.045	-0.440	-0.440	0.000	0.000	0.000	0.000
24	A	28	THR	0	-0.017	-0.021	33.184	-0.316	-0.316	0.000	0.000	0.000	0.000
25	A	29	ILE	0	-0.021	-0.013	34.503	-0.266	-0.266	0.000	0.000	0.000	0.000
26	A	30	ALA	0	0.008	0.007	36.660	-0.264	-0.264	0.000	0.000	0.000	0.000
27	A	31	GLN	0	0.001	-0.009	36.069	-0.454	-0.454	0.000	0.000	0.000	0.000
28	A	32	ALA	0	-0.025	-0.006	39.563	-0.219	-0.219	0.000	0.000	0.000	0.000
29	A	33	GLU	-1	-0.836	-0.915	41.203	6.975	6.975	0.000	0.000	0.000	0.000
30	A	34	GLN	0	-0.041	-0.020	41.408	-0.023	-0.023	0.000	0.000	0.000	0.000
31	A	35	ALA	0	-0.008	-0.007	44.207	-0.194	-0.194	0.000	0.000	0.000	0.000
32	A	36	ALA	0	0.007	0.018	45.631	-0.163	-0.163	0.000	0.000	0.000	0.000
33	A	37	MET	0	-0.020	-0.019	46.779	-0.139	-0.139	0.000	0.000	0.000	0.000
34	A	38	SER	0	-0.086	-0.040	48.507	-0.176	-0.176	0.000	0.000	0.000	0.000
35	A	39	SER	0	0.007	-0.008	50.779	-0.069	-0.069	0.000	0.000	0.000	0.000
36	A	40	GLN	0	-0.011	-0.005	52.436	-0.046	-0.046	0.000	0.000	0.000	0.000
37	A	41	ALA	0	-0.037	-0.034	54.052	-0.106	-0.106	0.000	0.000	0.000	0.000
38	A	42	PHE	0	-0.029	-0.003	54.396	-0.101	-0.101	0.000	0.000	0.000	0.000
39	A	43	HIS	0	-0.008	0.024	54.497	-0.199	-0.199	0.000	0.000	0.000	0.000
40	A	44	MET	0	0.035	0.001	59.482	-0.051	-0.051	0.000	0.000	0.000	0.000
41	A	45	GLY	0	-0.010	-0.014	61.746	0.012	0.012	0.000	0.000	0.000	0.000
42	A	46	GLU	-1	-0.909	-0.947	60.754	5.159	5.159	0.000	0.000	0.000	0.000
43	A	47	ALA	0	0.032	0.008	58.691	0.088	0.088	0.000	0.000	0.000	0.000
44	A	48	SER	0	0.035	0.028	56.920	0.131	0.131	0.000	0.000	0.000	0.000
45	A	49	ALA	0	-0.020	0.002	55.906	0.120	0.120	0.000	0.000	0.000	0.000
46	A	50	ALA	0	0.025	0.013	55.065	0.107	0.107	0.000	0.000	0.000	0.000
47	A	51	PHE	0	0.017	0.019	50.164	0.127	0.127	0.000	0.000	0.000	0.000
48	A	52	GLN	0	0.027	-0.014	51.276	0.048	0.048	0.000	0.000	0.000	0.000
49	A	53	ALA	0	-0.024	0.001	51.129	0.117	0.117	0.000	0.000	0.000	0.000
50	A	54	ALA	0	-0.019	-0.016	48.804	0.135	0.135	0.000	0.000	0.000	0.000
51	A	55	HIS	0	-0.061	-0.031	45.915	0.050	0.050	0.000	0.000	0.000	0.000
52	A	56	ALA	0	0.036	0.007	46.281	0.170	0.170	0.000	0.000	0.000	0.000
53	A	57	ARG	1	0.929	0.982	42.957	-6.983	-6.983	0.000	0.000	0.000	0.000
54	A	58	PHE	0	-0.007	-0.003	40.193	0.205	0.205	0.000	0.000	0.000	0.000
55	A	59	VAL	0	0.052	0.020	41.542	0.242	0.242	0.000	0.000	0.000	0.000
56	A	60	GLU	-1	-0.882	-0.934	41.381	7.330	7.330	0.000	0.000	0.000	0.000
57	A	61	VAL	0	-0.053	-0.044	38.158	0.204	0.204	0.000	0.000	0.000	0.000
58	A	62	SER	0	0.041	0.023	37.116	0.327	0.327	0.000	0.000	0.000	0.000
59	A	63	ALA	0	0.017	0.028	36.000	0.311	0.311	0.000	0.000	0.000	0.000
60	A	64	LYS	1	0.872	0.940	35.600	-7.395	-7.395	0.000	0.000	0.000	0.000
61	A	65	VAL	0	0.024	0.007	32.174	0.270	0.270	0.000	0.000	0.000	0.000
62	A	66	ASN	0	-0.010	-0.020	31.560	0.609	0.609	0.000	0.000	0.000	0.000
63	A	67	ALA	0	0.034	0.023	30.844	0.314	0.314	0.000	0.000	0.000	0.000
64	A	68	LEU	0	-0.027	-0.025	29.868	0.281	0.281	0.000	0.000	0.000	0.000
65	A	69	LEU	0	-0.038	-0.016	27.180	0.453	0.453	0.000	0.000	0.000	0.000
66	A	70	ASP	-1	-0.847	-0.916	25.982	10.998	10.998	0.000	0.000	0.000	0.000
67	A	71	ILE	0	-0.027	-0.005	25.156	0.393	0.393	0.000	0.000	0.000	0.000
68	A	72	ALA	0	-0.015	-0.012	23.194	0.514	0.514	0.000	0.000	0.000	0.000
69	A	73	GLN	0	0.026	0.013	21.478	1.189	1.189	0.000	0.000	0.000	0.000
70	A	74	LEU	0	-0.020	-0.014	20.333	0.709	0.709	0.000	0.000	0.000	0.000
71	A	75	ASN	0	-0.058	-0.016	19.152	0.799	0.799	0.000	0.000	0.000	0.000
72	A	76	ILE	0	-0.021	-0.007	16.896	0.673	0.673	0.000	0.000	0.000	0.000
73	A	77	GLY	0	0.010	0.008	17.928	0.167	0.167	0.000	0.000	0.000	0.000
74	A	78	ASP	-1	-0.925	-0.978	17.802	15.375	15.375	0.000	0.000	0.000	0.000
75	A	79	ALA	0	-0.028	0.001	18.392	0.562	0.562	0.000	0.000	0.000	0.000
76	A	80	ALA	0	0.014	0.022	15.720	0.490	0.490	0.000	0.000	0.000	0.000
77	A	81	SER	0	0.036	0.005	13.539	1.051	1.051	0.000	0.000	0.000	0.000
78	A	82	SER	0	-0.009	0.006	13.398	1.589	1.589	0.000	0.000	0.000	0.000
79	A	83	TYR	0	0.007	0.005	13.360	0.182	0.182	0.000	0.000	0.000	0.000
80	A	84	VAL	0	0.028	0.015	8.667	1.039	1.039	0.000	0.000	0.000	0.000
81	A	85	ALA	0	-0.027	-0.011	9.809	2.378	2.378	0.000	0.000	0.000	0.000
82	A	86	GLN	0	-0.074	-0.060	11.384	0.449	0.449	0.000	0.000	0.000	0.000
83	A	87	ASP	-1	-0.955	-0.970	10.295	24.694	24.694	0.000	0.000	0.000	0.000
84	A	88	ALA	0	0.053	0.023	7.211	1.066	1.066	0.000	0.000	0.000	0.000
85	A	89	ALA	0	-0.003	0.064	8.686	2.092	2.092	0.000	0.000	0.000	0.000
86	A	90	ALA	0	-0.013	-0.009	11.233	-0.603	-0.603	0.000	0.000	0.000	0.000
87	A	91	ALA	0	-0.008	-0.008	8.954	-1.008	-1.008	0.000	0.000	0.000	0.000
88	A	92	SER	0	-0.108	-0.111	7.646	2.160	2.160	0.000	0.000	0.000	0.000
89	A	93	THR	0	-0.080	-0.039	8.950	-0.598	-0.598	0.000	0.000	0.000	0.000
90	A	94	TYR	0	-0.046	-0.002	12.493	-1.825	-1.825	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:5:ASP)