FMO DATABASE

FMODB ID: 2NK5R

Calculation Name: 3Q9V-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3Q9V

Chain ID: A

ChEMBL ID:

UniProt ID: Q9RRR8

Base Structure: X-ray

Registration Date: 2023-09-20

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	98
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-737647.620331
FMO2-HF: Nuclear repulsion	699152.296378
FMO2-HF: Total energy	-38495.323953
FMO2-MP2: Total energy	-38609.04838

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:124:GLU)

Summations of interaction energy for fragment #1(A:124:GLU)

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.
-39.293	-36.126	0.207	-1.6	-1.775	-0.002

Interaction energy analysis for fragmet #1(A:124:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.926 / q_NPA : -0.982

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	126	LEU	0	-0.016	-0.002	2.953	1.869	4.788	0.209	-1.567	-1.561	-0.002
4	A	127	SER	0	0.011	-0.006	5.440	-1.690	-1.690	0.000	0.000	0.000	0.000
5	A	128	MET	0	-0.060	-0.029	8.408	-0.736	-0.736	0.000	0.000	0.000	0.000
6	A	129	GLY	0	-0.001	-0.004	11.820	-1.185	-1.185	0.000	0.000	0.000	0.000
7	A	130	ASP	-1	-0.878	-0.942	13.248	17.299	17.299	0.000	0.000	0.000	0.000
8	A	131	LEU	0	-0.028	-0.012	12.850	-0.240	-0.240	0.000	0.000	0.000	0.000
9	A	132	THR	0	0.025	0.022	7.194	1.785	1.785	0.000	0.000	0.000	0.000
10	A	133	LEU	0	-0.023	-0.002	7.825	-1.460	-1.460	0.000	0.000	0.000	0.000
11	A	134	ASP	-1	-0.799	-0.920	4.593	39.114	39.228	-0.001	-0.023	-0.091	0.000
12	A	135	PRO	0	-0.024	-0.032	4.401	-2.277	-2.143	-0.001	-0.010	-0.123	0.000
13	A	136	GLN	0	-0.020	0.001	5.126	-5.450	-5.450	0.000	0.000	0.000	0.000
14	A	137	LYS	1	0.929	0.964	5.545	-35.274	-35.274	0.000	0.000	0.000	0.000
15	A	138	ARG	1	0.798	0.921	8.985	-19.716	-19.716	0.000	0.000	0.000	0.000
16	A	139	LEU	0	0.034	0.036	9.127	-1.056	-1.056	0.000	0.000	0.000	0.000
17	A	140	VAL	0	-0.013	-0.024	9.783	1.470	1.470	0.000	0.000	0.000	0.000
18	A	141	THR	0	-0.010	0.006	11.533	-1.009	-1.009	0.000	0.000	0.000	0.000
19	A	142	TYR	0	0.014	-0.011	13.537	0.573	0.573	0.000	0.000	0.000	0.000
20	A	143	LYS	1	0.900	0.949	15.743	-14.898	-14.898	0.000	0.000	0.000	0.000
21	A	144	GLY	0	-0.003	0.008	14.145	-0.484	-0.484	0.000	0.000	0.000	0.000
22	A	145	GLU	-1	-0.879	-0.920	15.206	14.716	14.716	0.000	0.000	0.000	0.000
23	A	146	GLU	-1	-0.923	-0.977	14.635	17.797	17.797	0.000	0.000	0.000	0.000
24	A	147	LEU	0	0.000	0.009	15.884	-0.963	-0.963	0.000	0.000	0.000	0.000
25	A	148	ARG	1	0.920	0.961	16.904	-13.735	-13.735	0.000	0.000	0.000	0.000
26	A	149	LEU	0	-0.011	0.009	15.605	-0.810	-0.810	0.000	0.000	0.000	0.000
27	A	150	SER	0	0.015	0.001	18.648	0.220	0.220	0.000	0.000	0.000	0.000
28	A	151	PRO	0	0.044	0.000	17.099	0.451	0.451	0.000	0.000	0.000	0.000
29	A	152	LYS	1	0.948	0.974	16.992	-11.908	-11.908	0.000	0.000	0.000	0.000
30	A	153	GLU	-1	-0.788	-0.885	18.600	12.457	12.457	0.000	0.000	0.000	0.000
31	A	154	PHE	0	0.005	0.002	9.590	0.254	0.254	0.000	0.000	0.000	0.000
32	A	155	ASP	-1	-0.835	-0.916	14.154	16.374	16.374	0.000	0.000	0.000	0.000
33	A	156	ILE	0	-0.019	-0.021	15.081	0.261	0.261	0.000	0.000	0.000	0.000
34	A	157	LEU	0	0.003	0.004	14.238	0.086	0.086	0.000	0.000	0.000	0.000
35	A	158	ALA	0	0.017	-0.002	10.641	0.654	0.654	0.000	0.000	0.000	0.000
36	A	159	LEU	0	-0.045	-0.015	11.976	0.829	0.829	0.000	0.000	0.000	0.000
37	A	160	LEU	0	-0.026	-0.033	14.565	0.100	0.100	0.000	0.000	0.000	0.000
38	A	161	ILE	0	-0.028	-0.014	10.138	-0.275	-0.275	0.000	0.000	0.000	0.000
39	A	162	ARG	1	0.935	0.982	10.983	-18.183	-18.183	0.000	0.000	0.000	0.000
40	A	163	GLN	0	0.004	0.029	12.822	0.122	0.122	0.000	0.000	0.000	0.000
41	A	164	PRO	0	0.059	0.032	13.839	-1.156	-1.156	0.000	0.000	0.000	0.000
42	A	165	GLY	0	-0.056	-0.029	16.594	-0.343	-0.343	0.000	0.000	0.000	0.000
43	A	166	ARG	1	0.822	0.891	19.143	-14.427	-14.427	0.000	0.000	0.000	0.000
44	A	167	VAL	0	-0.050	-0.031	20.984	0.094	0.094	0.000	0.000	0.000	0.000
45	A	168	TYR	0	0.058	0.033	16.835	-0.171	-0.171	0.000	0.000	0.000	0.000
46	A	169	SER	0	0.031	0.008	22.985	-0.344	-0.344	0.000	0.000	0.000	0.000
47	A	170	ARG	1	0.896	0.907	25.031	-8.856	-8.856	0.000	0.000	0.000	0.000
48	A	171	GLN	0	0.039	0.014	26.098	0.230	0.230	0.000	0.000	0.000	0.000
49	A	172	GLU	-1	-0.807	-0.877	21.687	12.526	12.526	0.000	0.000	0.000	0.000
50	A	173	ILE	0	0.003	-0.003	20.981	0.340	0.340	0.000	0.000	0.000	0.000
51	A	174	GLY	0	0.022	-0.004	22.119	0.186	0.186	0.000	0.000	0.000	0.000
52	A	175	GLN	0	-0.023	-0.007	22.893	-0.334	-0.334	0.000	0.000	0.000	0.000
53	A	176	GLU	-1	-0.934	-0.978	18.280	13.553	13.553	0.000	0.000	0.000	0.000
54	A	177	ILE	0	-0.051	-0.015	16.858	0.374	0.374	0.000	0.000	0.000	0.000
55	A	178	TRP	0	-0.020	-0.027	19.994	0.083	0.083	0.000	0.000	0.000	0.000
56	A	179	GLN	0	0.004	0.007	20.067	-0.650	-0.650	0.000	0.000	0.000	0.000
57	A	180	GLY	0	0.029	0.011	24.123	-0.324	-0.324	0.000	0.000	0.000	0.000
58	A	181	ARG	1	0.875	0.956	26.285	-10.435	-10.435	0.000	0.000	0.000	0.000
59	A	182	LEU	0	-0.054	-0.031	26.270	0.043	0.043	0.000	0.000	0.000	0.000
60	A	183	PRO	0	0.014	0.022	30.071	-0.066	-0.066	0.000	0.000	0.000	0.000
61	A	184	GLU	-1	-0.872	-0.955	33.673	7.595	7.595	0.000	0.000	0.000	0.000
62	A	185	GLY	0	0.003	0.003	35.441	-0.142	-0.142	0.000	0.000	0.000	0.000
63	A	186	SER	0	-0.061	-0.007	31.436	0.069	0.069	0.000	0.000	0.000	0.000
64	A	187	ASN	0	0.038	0.006	31.959	0.201	0.201	0.000	0.000	0.000	0.000
65	A	188	VAL	0	0.040	0.023	26.259	0.197	0.197	0.000	0.000	0.000	0.000
66	A	189	VAL	0	0.045	0.033	24.602	0.245	0.245	0.000	0.000	0.000	0.000
67	A	190	ASP	-1	-0.767	-0.845	25.921	9.726	9.726	0.000	0.000	0.000	0.000
68	A	191	VAL	0	0.013	0.011	27.981	0.121	0.121	0.000	0.000	0.000	0.000
69	A	192	HIS	0	-0.030	-0.034	23.015	0.286	0.286	0.000	0.000	0.000	0.000
70	A	193	MET	0	-0.040	-0.007	21.246	0.467	0.467	0.000	0.000	0.000	0.000
71	A	194	ALA	0	-0.030	-0.013	24.515	0.181	0.181	0.000	0.000	0.000	0.000
72	A	195	ASN	0	0.023	0.008	25.029	-0.125	-0.125	0.000	0.000	0.000	0.000
73	A	196	LEU	0	0.007	0.011	18.408	0.181	0.181	0.000	0.000	0.000	0.000
74	A	197	ARG	1	0.847	0.902	22.253	-10.533	-10.533	0.000	0.000	0.000	0.000
75	A	198	ALA	0	-0.022	-0.008	24.265	0.027	0.027	0.000	0.000	0.000	0.000
76	A	199	LYS	1	0.854	0.908	21.592	-12.228	-12.228	0.000	0.000	0.000	0.000
77	A	200	LEU	0	-0.011	-0.002	17.991	0.235	0.235	0.000	0.000	0.000	0.000
78	A	201	ARG	1	0.866	0.939	21.730	-10.070	-10.070	0.000	0.000	0.000	0.000
79	A	202	ASP	-1	-0.943	-0.957	24.401	11.233	11.233	0.000	0.000	0.000	0.000
80	A	203	LEU	0	0.006	0.021	19.021	0.025	0.025	0.000	0.000	0.000	0.000
81	A	204	ASP	-1	-0.862	-0.940	22.014	11.760	11.760	0.000	0.000	0.000	0.000
82	A	205	GLY	0	-0.011	-0.017	21.126	0.174	0.174	0.000	0.000	0.000	0.000
83	A	206	TYR	0	-0.058	-0.049	21.941	-0.305	-0.305	0.000	0.000	0.000	0.000
84	A	207	GLY	0	-0.069	-0.055	23.970	0.142	0.142	0.000	0.000	0.000	0.000
85	A	208	LEU	0	0.024	0.033	18.429	0.037	0.037	0.000	0.000	0.000	0.000
86	A	209	LEU	0	0.053	0.037	20.796	0.179	0.179	0.000	0.000	0.000	0.000
87	A	210	ARG	1	0.857	0.942	22.556	-11.916	-11.916	0.000	0.000	0.000	0.000
88	A	211	THR	0	0.052	0.030	25.279	0.304	0.304	0.000	0.000	0.000	0.000
89	A	212	VAL	0	-0.018	-0.006	26.815	-0.264	-0.264	0.000	0.000	0.000	0.000
90	A	213	ARG	1	0.951	0.977	29.441	-8.242	-8.242	0.000	0.000	0.000	0.000
91	A	214	GLY	0	0.087	0.054	32.494	0.058	0.058	0.000	0.000	0.000	0.000
92	A	215	VAL	0	-0.037	-0.029	29.046	-0.221	-0.221	0.000	0.000	0.000	0.000
93	A	216	GLY	0	0.012	-0.001	26.727	0.088	0.088	0.000	0.000	0.000	0.000
94	A	217	TYR	0	-0.079	-0.060	23.289	-0.278	-0.278	0.000	0.000	0.000	0.000
95	A	218	ALA	0	0.053	0.039	21.417	0.258	0.258	0.000	0.000	0.000	0.000
96	A	219	LEU	0	0.024	0.024	15.300	-0.463	-0.463	0.000	0.000	0.000	0.000
97	A	220	ARG	1	0.950	0.959	18.394	-13.314	-13.314	0.000	0.000	0.000	0.000
98	A	221	GLY	0	0.066	0.042	16.784	-0.386	-0.386	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:124:GLU)