FMO DATABASE

FMODB ID: 2NG7R

Calculation Name: 3ON1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ON1

Chain ID: A

ChEMBL ID:

UniProt ID: Q9KA76

Base Structure: X-ray

Registration Date: 2023-09-23

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	99
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-703776.983677
FMO2-HF: Nuclear repulsion	666792.125473
FMO2-HF: Total energy	-36984.858205
FMO2-MP2: Total energy	-37094.332731

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:3:GLU)

Summations of interaction energy for fragment #1(A:3: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.
-156.473	-153.915	0.108	-1.224	-1.442	0.008

Interaction energy analysis for fragmet #1(A:3:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.944 / q_NPA : -0.979

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	5	LYS	1	1.026	0.990	3.820	-32.383	-30.831	0.006	-0.762	-0.796	0.005
4	A	6	TRP	0	0.067	0.023	6.354	-1.256	-1.256	0.000	0.000	0.000	0.000
5	A	7	LEU	0	0.004	0.009	3.497	-3.239	-2.303	0.103	-0.449	-0.591	0.003
6	A	8	SER	0	0.000	0.004	4.336	-3.586	-3.516	-0.001	-0.013	-0.055	0.000
7	A	9	LEU	0	0.009	0.000	5.772	-2.594	-2.594	0.000	0.000	0.000	0.000
8	A	10	LEU	0	0.025	0.005	8.804	-2.091	-2.091	0.000	0.000	0.000	0.000
9	A	11	GLY	0	0.075	0.041	8.631	-1.706	-1.706	0.000	0.000	0.000	0.000
10	A	12	LEU	0	-0.067	-0.035	9.941	-1.830	-1.830	0.000	0.000	0.000	0.000
11	A	13	ALA	0	0.043	0.028	12.195	-1.377	-1.377	0.000	0.000	0.000	0.000
12	A	14	ALA	0	-0.015	-0.011	13.273	-1.222	-1.222	0.000	0.000	0.000	0.000
13	A	15	ARG	1	0.925	0.973	11.374	-20.662	-20.662	0.000	0.000	0.000	0.000
14	A	16	ALA	0	-0.010	0.004	15.726	-0.850	-0.850	0.000	0.000	0.000	0.000
15	A	17	ARG	1	0.934	0.962	17.992	-12.975	-12.975	0.000	0.000	0.000	0.000
16	A	18	GLN	0	0.002	-0.003	17.796	-0.798	-0.798	0.000	0.000	0.000	0.000
17	A	19	LEU	0	-0.028	-0.001	13.774	0.128	0.128	0.000	0.000	0.000	0.000
18	A	20	LEU	0	-0.023	0.005	18.512	-0.498	-0.498	0.000	0.000	0.000	0.000
19	A	21	THR	0	-0.010	-0.015	17.187	0.657	0.657	0.000	0.000	0.000	0.000
20	A	22	GLY	0	0.010	0.004	20.210	-0.553	-0.553	0.000	0.000	0.000	0.000
21	A	23	GLU	-1	-0.812	-0.922	22.519	10.775	10.775	0.000	0.000	0.000	0.000
22	A	24	GLU	-1	-0.833	-0.930	24.378	9.499	9.499	0.000	0.000	0.000	0.000
23	A	25	GLN	0	-0.047	-0.020	24.327	-0.400	-0.400	0.000	0.000	0.000	0.000
24	A	26	VAL	0	-0.005	-0.009	21.065	-0.102	-0.102	0.000	0.000	0.000	0.000
25	A	27	VAL	0	0.043	0.022	24.466	-0.117	-0.117	0.000	0.000	0.000	0.000
26	A	28	LYS	1	0.960	0.980	27.431	-9.176	-9.176	0.000	0.000	0.000	0.000
27	A	29	ALA	0	0.016	0.003	25.624	-0.207	-0.207	0.000	0.000	0.000	0.000
28	A	30	VAL	0	-0.016	-0.005	25.153	-0.059	-0.059	0.000	0.000	0.000	0.000
29	A	31	GLN	0	-0.015	-0.012	27.624	-0.240	-0.240	0.000	0.000	0.000	0.000
30	A	32	ASN	0	-0.062	-0.024	30.574	-0.439	-0.439	0.000	0.000	0.000	0.000
31	A	33	GLY	0	0.031	0.029	29.554	-0.092	-0.092	0.000	0.000	0.000	0.000
32	A	34	GLN	0	-0.058	-0.034	26.761	0.269	0.269	0.000	0.000	0.000	0.000
33	A	35	VAL	0	-0.054	-0.030	21.966	0.443	0.443	0.000	0.000	0.000	0.000
34	A	36	THR	0	0.021	-0.006	21.556	-0.367	-0.367	0.000	0.000	0.000	0.000
35	A	37	LEU	0	-0.030	-0.012	15.966	0.217	0.217	0.000	0.000	0.000	0.000
36	A	38	VAL	0	-0.012	0.004	19.367	0.098	0.098	0.000	0.000	0.000	0.000
37	A	39	ILE	0	-0.011	0.001	12.783	0.306	0.306	0.000	0.000	0.000	0.000
38	A	40	LEU	0	-0.008	-0.015	16.302	-0.312	-0.312	0.000	0.000	0.000	0.000
39	A	41	SER	0	0.021	0.000	14.211	0.698	0.698	0.000	0.000	0.000	0.000
40	A	42	SER	0	0.036	0.009	13.609	-1.378	-1.378	0.000	0.000	0.000	0.000
41	A	43	ASP	-1	-0.798	-0.894	15.172	16.428	16.428	0.000	0.000	0.000	0.000
42	A	44	ALA	0	-0.107	-0.034	17.563	-0.730	-0.730	0.000	0.000	0.000	0.000
43	A	45	GLY	0	0.063	0.024	19.963	-0.136	-0.136	0.000	0.000	0.000	0.000
44	A	46	ILE	0	0.051	0.010	23.589	0.037	0.037	0.000	0.000	0.000	0.000
45	A	47	HIS	0	0.042	0.008	25.388	-0.054	-0.054	0.000	0.000	0.000	0.000
46	A	48	THR	0	0.003	0.011	22.417	-0.100	-0.100	0.000	0.000	0.000	0.000
47	A	49	LYS	1	0.853	0.908	19.418	-13.785	-13.785	0.000	0.000	0.000	0.000
48	A	50	LYS	1	0.948	0.980	23.729	-9.904	-9.904	0.000	0.000	0.000	0.000
49	A	51	LYS	1	0.919	0.994	27.196	-9.915	-9.915	0.000	0.000	0.000	0.000
50	A	52	LEU	0	-0.017	-0.024	22.398	-0.126	-0.126	0.000	0.000	0.000	0.000
51	A	53	LEU	0	-0.003	-0.004	22.489	0.007	0.007	0.000	0.000	0.000	0.000
52	A	54	ASP	-1	-0.869	-0.918	25.802	9.346	9.346	0.000	0.000	0.000	0.000
53	A	55	LYS	1	0.861	0.928	27.970	-9.163	-9.163	0.000	0.000	0.000	0.000
54	A	56	CYS	0	-0.040	-0.028	24.707	-0.046	-0.046	0.000	0.000	0.000	0.000
55	A	57	GLY	0	0.045	0.038	27.015	0.009	0.009	0.000	0.000	0.000	0.000
56	A	58	SER	0	-0.047	-0.023	28.951	-0.261	-0.261	0.000	0.000	0.000	0.000
57	A	59	TYR	0	-0.039	-0.022	29.136	-0.202	-0.202	0.000	0.000	0.000	0.000
58	A	60	GLN	0	-0.015	0.006	28.599	0.037	0.037	0.000	0.000	0.000	0.000
59	A	61	ILE	0	-0.039	-0.006	23.299	0.256	0.256	0.000	0.000	0.000	0.000
60	A	62	PRO	0	0.007	0.003	20.719	0.117	0.117	0.000	0.000	0.000	0.000
61	A	63	VAL	0	0.045	0.001	20.204	0.250	0.250	0.000	0.000	0.000	0.000
62	A	64	LYS	1	0.807	0.904	15.511	-15.147	-15.147	0.000	0.000	0.000	0.000
63	A	65	VAL	0	-0.003	-0.001	16.556	-0.074	-0.074	0.000	0.000	0.000	0.000
64	A	66	VAL	0	0.036	0.020	11.042	0.510	0.510	0.000	0.000	0.000	0.000
65	A	67	GLY	0	-0.004	-0.007	9.617	-0.112	-0.112	0.000	0.000	0.000	0.000
66	A	68	ASN	0	0.112	0.055	10.068	-0.863	-0.863	0.000	0.000	0.000	0.000
67	A	69	ARG	1	0.935	0.960	11.425	-13.821	-13.821	0.000	0.000	0.000	0.000
68	A	70	GLN	0	0.045	0.023	10.914	0.584	0.584	0.000	0.000	0.000	0.000
69	A	71	MET	0	-0.042	-0.015	5.510	0.074	0.074	0.000	0.000	0.000	0.000
70	A	72	LEU	0	0.007	0.003	7.883	1.261	1.261	0.000	0.000	0.000	0.000
71	A	73	GLY	0	-0.010	-0.007	10.379	-0.372	-0.372	0.000	0.000	0.000	0.000
72	A	74	ARG	1	1.022	1.015	5.306	-32.813	-32.813	0.000	0.000	0.000	0.000
73	A	75	ALA	0	-0.040	-0.007	7.211	0.059	0.059	0.000	0.000	0.000	0.000
74	A	76	ILE	0	-0.040	-0.019	8.283	-0.880	-0.880	0.000	0.000	0.000	0.000
75	A	77	GLY	0	-0.011	0.003	11.141	-1.497	-1.497	0.000	0.000	0.000	0.000
76	A	78	LYS	1	0.840	0.918	12.784	-16.386	-16.386	0.000	0.000	0.000	0.000
77	A	79	HIS	0	0.058	0.029	12.929	1.606	1.606	0.000	0.000	0.000	0.000
78	A	80	GLU	-1	-0.854	-0.928	13.182	16.844	16.844	0.000	0.000	0.000	0.000
79	A	81	ARG	1	0.842	0.916	14.212	-15.903	-15.903	0.000	0.000	0.000	0.000
80	A	82	VAL	0	0.024	0.008	14.947	0.681	0.681	0.000	0.000	0.000	0.000
81	A	83	VAL	0	0.024	0.019	17.334	0.163	0.163	0.000	0.000	0.000	0.000
82	A	84	ILE	0	0.009	0.000	13.452	-0.275	-0.275	0.000	0.000	0.000	0.000
83	A	85	GLY	0	0.024	0.019	17.585	-0.097	-0.097	0.000	0.000	0.000	0.000
84	A	86	VAL	0	-0.046	-0.031	16.212	0.188	0.188	0.000	0.000	0.000	0.000
85	A	87	LYS	1	0.974	0.976	19.025	-12.378	-12.378	0.000	0.000	0.000	0.000
86	A	88	ASP	-1	-0.806	-0.881	19.299	13.017	13.017	0.000	0.000	0.000	0.000
87	A	89	ALA	0	0.059	0.017	19.952	0.593	0.593	0.000	0.000	0.000	0.000
88	A	90	GLY	0	-0.018	-0.006	20.196	0.199	0.199	0.000	0.000	0.000	0.000
89	A	91	PHE	0	-0.002	-0.020	13.222	0.770	0.770	0.000	0.000	0.000	0.000
90	A	92	SER	0	-0.013	0.004	15.985	0.784	0.784	0.000	0.000	0.000	0.000
91	A	93	ARG	1	0.992	0.997	17.763	-12.251	-12.251	0.000	0.000	0.000	0.000
92	A	94	LYS	1	0.963	0.990	13.544	-18.063	-18.063	0.000	0.000	0.000	0.000
93	A	95	LEU	0	-0.009	-0.018	11.201	1.104	1.104	0.000	0.000	0.000	0.000
94	A	96	ALA	0	0.001	0.006	13.730	0.823	0.823	0.000	0.000	0.000	0.000
95	A	97	ALA	0	0.025	0.013	16.180	0.211	0.211	0.000	0.000	0.000	0.000
96	A	98	LEU	0	-0.049	-0.031	9.798	0.735	0.735	0.000	0.000	0.000	0.000
97	A	99	ILE	0	-0.065	-0.036	11.563	0.994	0.994	0.000	0.000	0.000	0.000
98	A	100	ASP	-1	-0.842	-0.910	13.001	15.832	15.832	0.000	0.000	0.000	0.000
99	A	101	GLU	-1	-1.030	-0.989	11.772	22.781	22.781	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:3:GLU)