FMO DATABASE

FMODB ID: NNG8Q

Calculation Name: 2FRG-P-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2FRG

Chain ID: P

ChEMBL ID:

UniProt ID: Q86YW5

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:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	104
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-768258.903551
FMO2-HF: Nuclear repulsion	727170.730004
FMO2-HF: Total energy	-41088.173547
FMO2-MP2: Total energy	-41205.254145

3D Structure Molmil

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(P:20:GLY)

Summations of interaction energy for fragment #1(P:20: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.
-1.34	1.258	-0.015	-1.453	-1.129	0.006

Interaction energy analysis for fragmet #1(P:20:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.038 / q_NPA : 0.018

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	P	22	LEU	0	-0.027	-0.012	3.670	-0.857	1.758	-0.014	-1.428	-1.173	0.006
4	P	23	PRO	0	-0.050	-0.006	4.307	-1.278	-1.295	-0.001	-0.025	0.044	0.000
5	P	24	GLU	-1	-0.796	-0.900	6.809	-0.228	-0.228	0.000	0.000	0.000	0.000
6	P	25	VAL	0	-0.045	-0.022	8.279	-0.011	-0.011	0.000	0.000	0.000	0.000
7	P	26	LEU	0	-0.015	0.000	11.238	0.136	0.136	0.000	0.000	0.000	0.000
8	P	27	GLN	0	0.019	-0.004	14.640	-0.010	-0.010	0.000	0.000	0.000	0.000
9	P	28	ALA	0	0.014	0.013	18.156	0.034	0.034	0.000	0.000	0.000	0.000
10	P	29	PRO	0	0.016	0.030	21.166	-0.013	-0.013	0.000	0.000	0.000	0.000
11	P	30	VAL	0	0.072	0.034	24.785	-0.003	-0.003	0.000	0.000	0.000	0.000
12	P	31	GLY	0	-0.031	-0.014	26.860	0.014	0.014	0.000	0.000	0.000	0.000
13	P	32	SER	0	-0.067	-0.041	23.445	0.009	0.009	0.000	0.000	0.000	0.000
14	P	33	SER	0	0.014	0.001	23.115	-0.012	-0.012	0.000	0.000	0.000	0.000
15	P	34	ILE	0	-0.018	-0.003	16.666	0.012	0.012	0.000	0.000	0.000	0.000
16	P	35	LEU	0	-0.008	-0.006	18.266	0.001	0.001	0.000	0.000	0.000	0.000
17	P	36	VAL	0	0.031	0.016	12.239	0.005	0.005	0.000	0.000	0.000	0.000
18	P	37	GLN	0	0.000	0.009	13.101	0.015	0.015	0.000	0.000	0.000	0.000
19	P	38	CYS	0	-0.090	-0.012	11.292	0.086	0.086	0.000	0.000	0.000	0.000
20	P	39	HIS	0	0.063	0.022	9.959	0.090	0.090	0.000	0.000	0.000	0.000
21	P	40	TYR	0	-0.068	-0.060	11.723	-0.055	-0.055	0.000	0.000	0.000	0.000
22	P	41	ARG	1	0.942	0.962	12.305	0.033	0.033	0.000	0.000	0.000	0.000
23	P	42	LEU	0	0.061	0.029	15.702	-0.041	-0.041	0.000	0.000	0.000	0.000
24	P	43	GLN	0	-0.031	-0.027	18.375	-0.018	-0.018	0.000	0.000	0.000	0.000
25	P	44	ASP	-1	-0.901	-0.948	16.502	-0.047	-0.047	0.000	0.000	0.000	0.000
26	P	45	VAL	0	-0.005	-0.006	19.717	-0.023	-0.023	0.000	0.000	0.000	0.000
27	P	46	LYS	1	0.913	0.940	21.820	-0.007	-0.007	0.000	0.000	0.000	0.000
28	P	47	ALA	0	-0.007	0.025	20.167	-0.007	-0.007	0.000	0.000	0.000	0.000
29	P	48	GLN	0	-0.004	0.000	21.667	0.018	0.018	0.000	0.000	0.000	0.000
30	P	49	LYS	1	0.800	0.894	17.003	0.054	0.054	0.000	0.000	0.000	0.000
31	P	50	VAL	0	0.003	-0.009	17.509	0.022	0.022	0.000	0.000	0.000	0.000
32	P	51	TRP	0	0.047	0.035	13.846	-0.057	-0.057	0.000	0.000	0.000	0.000
33	P	52	CYS	0	-0.102	-0.053	15.761	0.020	0.020	0.000	0.000	0.000	0.000
34	P	53	ARG	1	0.898	0.936	16.690	0.298	0.298	0.000	0.000	0.000	0.000
35	P	54	PHE	0	-0.038	-0.025	11.929	0.002	0.002	0.000	0.000	0.000	0.000
36	P	55	LEU	0	-0.027	-0.011	17.306	0.031	0.031	0.000	0.000	0.000	0.000
37	P	56	PRO	0	-0.017	-0.029	20.015	-0.028	-0.028	0.000	0.000	0.000	0.000
38	P	57	GLU	-1	-0.925	-0.949	21.701	-0.317	-0.317	0.000	0.000	0.000	0.000
39	P	58	GLY	0	0.032	0.022	18.618	-0.007	-0.007	0.000	0.000	0.000	0.000
40	P	60	GLN	0	0.041	0.026	17.830	0.023	0.023	0.000	0.000	0.000	0.000
41	P	61	PRO	0	-0.016	-0.023	20.579	-0.010	-0.010	0.000	0.000	0.000	0.000
42	P	62	LEU	0	-0.058	-0.019	20.512	0.023	0.023	0.000	0.000	0.000	0.000
43	P	63	VAL	0	0.000	-0.003	21.930	0.025	0.025	0.000	0.000	0.000	0.000
44	P	64	SER	0	-0.020	-0.002	21.592	-0.024	-0.024	0.000	0.000	0.000	0.000
45	P	65	SER	0	0.012	0.008	21.025	0.008	0.008	0.000	0.000	0.000	0.000
46	P	66	ALA	0	0.005	-0.008	23.106	0.004	0.004	0.000	0.000	0.000	0.000
47	P	67	VAL	0	-0.015	-0.007	24.008	0.001	0.001	0.000	0.000	0.000	0.000
48	P	68	ASP	-1	-0.934	-0.977	25.253	-0.003	-0.003	0.000	0.000	0.000	0.000
49	P	69	ARG	1	0.837	0.933	26.510	0.032	0.032	0.000	0.000	0.000	0.000
50	P	70	ARG	1	0.823	0.892	25.416	0.074	0.074	0.000	0.000	0.000	0.000
51	P	71	ALA	0	0.005	0.003	24.343	0.003	0.003	0.000	0.000	0.000	0.000
52	P	72	PRO	0	-0.009	-0.015	24.679	-0.014	-0.014	0.000	0.000	0.000	0.000
53	P	73	ALA	0	0.033	0.025	23.286	-0.006	-0.006	0.000	0.000	0.000	0.000
54	P	74	GLY	0	-0.023	-0.016	25.371	0.000	0.000	0.000	0.000	0.000	0.000
55	P	75	ARG	1	0.938	0.947	27.564	0.146	0.146	0.000	0.000	0.000	0.000
56	P	76	ARG	1	0.772	0.857	24.937	0.190	0.190	0.000	0.000	0.000	0.000
57	P	77	THR	0	0.052	0.048	20.679	-0.004	-0.004	0.000	0.000	0.000	0.000
58	P	78	PHE	0	-0.009	-0.006	22.299	0.012	0.012	0.000	0.000	0.000	0.000
59	P	79	LEU	0	0.011	0.012	17.902	-0.011	-0.011	0.000	0.000	0.000	0.000
60	P	80	THR	0	0.048	0.013	20.769	0.010	0.010	0.000	0.000	0.000	0.000
61	P	81	ASP	-1	-0.765	-0.839	20.425	-0.031	-0.031	0.000	0.000	0.000	0.000
62	P	82	LEU	0	0.021	-0.001	20.633	0.004	0.004	0.000	0.000	0.000	0.000
63	P	83	GLY	0	0.010	0.017	21.849	0.010	0.010	0.000	0.000	0.000	0.000
64	P	84	GLY	0	-0.042	-0.039	21.038	0.010	0.010	0.000	0.000	0.000	0.000
65	P	85	GLY	0	0.007	0.001	17.197	0.035	0.035	0.000	0.000	0.000	0.000
66	P	86	LEU	0	-0.005	0.016	15.811	0.005	0.005	0.000	0.000	0.000	0.000
67	P	87	LEU	0	-0.016	-0.017	15.281	-0.020	-0.020	0.000	0.000	0.000	0.000
68	P	88	GLN	0	0.000	0.005	15.915	0.003	0.003	0.000	0.000	0.000	0.000
69	P	89	VAL	0	0.014	0.000	15.483	-0.014	-0.014	0.000	0.000	0.000	0.000
70	P	90	GLU	-1	-0.804	-0.868	18.219	-0.061	-0.061	0.000	0.000	0.000	0.000
71	P	91	MET	0	-0.022	-0.002	18.790	-0.030	-0.030	0.000	0.000	0.000	0.000
72	P	92	VAL	0	0.003	-0.006	21.598	0.011	0.011	0.000	0.000	0.000	0.000
73	P	93	THR	0	-0.060	-0.039	24.851	-0.005	-0.005	0.000	0.000	0.000	0.000
74	P	94	LEU	0	0.006	0.003	20.514	-0.004	-0.004	0.000	0.000	0.000	0.000
75	P	95	GLN	0	-0.001	-0.010	24.877	0.027	0.027	0.000	0.000	0.000	0.000
76	P	96	GLU	-1	-0.887	-0.949	24.825	-0.193	-0.193	0.000	0.000	0.000	0.000
77	P	97	GLU	-1	-0.845	-0.924	24.581	-0.204	-0.204	0.000	0.000	0.000	0.000
78	P	98	ASP	-1	-0.787	-0.840	21.611	-0.237	-0.237	0.000	0.000	0.000	0.000
79	P	99	ALA	0	0.016	0.029	19.918	-0.037	-0.037	0.000	0.000	0.000	0.000
80	P	100	GLY	0	0.009	0.003	18.171	0.017	0.017	0.000	0.000	0.000	0.000
81	P	101	GLU	-1	-0.845	-0.909	10.942	-1.432	-1.432	0.000	0.000	0.000	0.000
82	P	102	TYR	0	-0.046	-0.043	13.611	0.074	0.074	0.000	0.000	0.000	0.000
83	P	103	GLY	0	0.025	0.003	12.020	-0.188	-0.188	0.000	0.000	0.000	0.000
84	P	105	MET	0	0.024	0.007	12.115	-0.125	-0.125	0.000	0.000	0.000	0.000
85	P	106	VAL	0	-0.015	-0.010	13.828	0.078	0.078	0.000	0.000	0.000	0.000
86	P	107	ASP	-1	-0.851	-0.925	16.134	-0.259	-0.259	0.000	0.000	0.000	0.000
87	P	108	GLY	0	0.053	0.018	19.067	0.027	0.027	0.000	0.000	0.000	0.000
88	P	109	ALA	0	-0.006	-0.015	21.097	-0.012	-0.012	0.000	0.000	0.000	0.000
89	P	110	ARG	1	0.896	0.944	19.332	0.021	0.021	0.000	0.000	0.000	0.000
90	P	111	GLY	0	0.029	0.034	19.165	-0.005	-0.005	0.000	0.000	0.000	0.000
91	P	112	PRO	0	0.000	0.009	16.750	0.010	0.010	0.000	0.000	0.000	0.000
92	P	113	GLN	0	-0.006	0.000	11.591	0.002	0.002	0.000	0.000	0.000	0.000
93	P	114	ILE	0	0.011	0.004	8.456	0.064	0.064	0.000	0.000	0.000	0.000
94	P	115	LEU	0	-0.080	-0.040	8.887	-0.107	-0.107	0.000	0.000	0.000	0.000
95	P	116	HIS	0	-0.021	-0.028	6.999	-0.286	-0.286	0.000	0.000	0.000	0.000
96	P	117	ARG	1	0.868	0.927	6.167	3.049	3.049	0.000	0.000	0.000	0.000
97	P	118	VAL	0	0.014	0.009	8.418	-0.099	-0.099	0.000	0.000	0.000	0.000
98	P	119	SER	0	0.003	0.005	11.040	0.105	0.105	0.000	0.000	0.000	0.000
99	P	120	LEU	0	-0.006	-0.007	12.792	0.056	0.056	0.000	0.000	0.000	0.000
100	P	121	ASN	0	-0.048	-0.026	14.765	0.016	0.016	0.000	0.000	0.000	0.000
101	P	122	ILE	0	0.027	0.006	18.422	0.027	0.027	0.000	0.000	0.000	0.000
102	P	123	LEU	0	-0.044	-0.023	21.359	0.003	0.003	0.000	0.000	0.000	0.000
103	P	124	PRO	0	0.016	0.010	23.849	0.006	0.006	0.000	0.000	0.000	0.000
104	P	125	PRO	0	-0.004	0.001	27.276	0.009	0.009	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(P:20:GLY)