FMO DATABASE

FMODB ID: 2JNRR

Calculation Name: 1GO3-F-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1GO3

Chain ID: F

ChEMBL ID:

UniProt ID: Q57840

Base Structure: X-ray

Registration Date: 2023-06-22

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	107
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-799464.678468
FMO2-HF: Nuclear repulsion	756456.968646
FMO2-HF: Total energy	-43007.709822
FMO2-MP2: Total energy	-43133.78767

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(F:1:MET)

Summations of interaction energy for fragment #1(F:1:MET)

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.
-3.73	-1.646	7.431	-3.276	-6.24	-0.037

Interaction energy analysis for fragmet #1(F:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.016 / q_NPA : -0.015

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	F	3	GLY	0	0.033	0.025	3.587	-0.908	1.403	0.031	-0.999	-1.343	-0.001
4	F	4	LYS	1	0.942	0.954	2.306	-3.304	-3.935	5.807	-2.020	-3.157	-0.030
5	F	5	LYS	1	0.981	0.970	2.695	1.047	1.303	1.591	-0.262	-1.585	-0.006
6	F	6	ILE	0	0.038	0.046	3.960	-0.004	0.144	0.002	0.005	-0.155	0.000
7	F	7	LEU	0	-0.054	-0.043	6.703	0.349	0.349	0.000	0.000	0.000	0.000
8	F	8	GLY	0	0.021	0.009	9.846	0.193	0.193	0.000	0.000	0.000	0.000
9	F	9	GLU	-1	-1.006	-0.993	11.656	-0.752	-0.752	0.000	0.000	0.000	0.000
10	F	10	ARG	1	0.878	0.937	13.634	0.478	0.478	0.000	0.000	0.000	0.000
11	F	11	TYR	0	-0.015	-0.005	16.603	-0.001	-0.001	0.000	0.000	0.000	0.000
12	F	12	VAL	0	-0.048	-0.026	18.753	0.007	0.007	0.000	0.000	0.000	0.000
13	F	13	THR	0	0.074	0.037	21.075	0.006	0.006	0.000	0.000	0.000	0.000
14	F	14	VAL	0	-0.003	-0.016	23.624	-0.026	-0.026	0.000	0.000	0.000	0.000
15	F	15	SER	0	0.000	-0.015	24.839	-0.007	-0.007	0.000	0.000	0.000	0.000
16	F	16	GLU	-1	-0.766	-0.885	22.596	-0.352	-0.352	0.000	0.000	0.000	0.000
17	F	17	ALA	0	-0.029	-0.010	21.027	-0.022	-0.022	0.000	0.000	0.000	0.000
18	F	18	ALA	0	0.018	0.005	22.482	-0.014	-0.014	0.000	0.000	0.000	0.000
19	F	19	GLU	-1	-0.819	-0.901	25.099	-0.269	-0.269	0.000	0.000	0.000	0.000
20	F	20	ILE	0	-0.035	-0.022	19.553	-0.016	-0.016	0.000	0.000	0.000	0.000
21	F	21	MET	0	-0.023	-0.022	19.327	-0.044	-0.044	0.000	0.000	0.000	0.000
22	F	22	TYR	0	0.021	0.025	22.286	0.006	0.006	0.000	0.000	0.000	0.000
23	F	23	ASN	0	0.036	0.000	23.920	0.026	0.026	0.000	0.000	0.000	0.000
24	F	24	ARG	1	0.860	0.938	17.987	0.396	0.396	0.000	0.000	0.000	0.000
25	F	25	ALA	0	-0.007	-0.007	22.236	-0.001	-0.001	0.000	0.000	0.000	0.000
26	F	26	GLN	0	-0.048	-0.011	24.628	0.027	0.027	0.000	0.000	0.000	0.000
27	F	27	ILE	0	-0.060	-0.023	20.626	0.000	0.000	0.000	0.000	0.000	0.000
28	F	28	GLY	0	-0.033	-0.022	23.207	-0.008	-0.008	0.000	0.000	0.000	0.000
29	F	29	GLU	-1	-0.960	-0.966	23.979	-0.135	-0.135	0.000	0.000	0.000	0.000
30	F	30	LEU	0	-0.058	-0.020	20.748	-0.026	-0.026	0.000	0.000	0.000	0.000
31	F	31	SER	0	0.043	0.016	17.508	0.026	0.026	0.000	0.000	0.000	0.000
32	F	32	TYR	0	0.073	0.017	20.447	-0.006	-0.006	0.000	0.000	0.000	0.000
33	F	33	GLU	-1	-0.904	-0.962	16.234	0.037	0.037	0.000	0.000	0.000	0.000
34	F	34	GLN	0	-0.010	0.003	16.552	0.011	0.011	0.000	0.000	0.000	0.000
35	F	35	GLY	0	0.034	0.022	19.505	-0.012	-0.012	0.000	0.000	0.000	0.000
36	F	36	CYS	0	-0.030	-0.016	21.690	0.010	0.010	0.000	0.000	0.000	0.000
37	F	37	ALA	0	0.002	0.006	19.396	0.003	0.003	0.000	0.000	0.000	0.000
38	F	38	LEU	0	-0.008	0.002	21.527	-0.004	-0.004	0.000	0.000	0.000	0.000
39	F	39	ASP	-1	-0.847	-0.922	24.105	-0.078	-0.078	0.000	0.000	0.000	0.000
40	F	40	TYR	0	0.003	-0.003	23.418	0.002	0.002	0.000	0.000	0.000	0.000
41	F	41	LEU	0	-0.023	-0.027	20.945	0.001	0.001	0.000	0.000	0.000	0.000
42	F	42	GLN	0	-0.015	-0.020	25.403	-0.010	-0.010	0.000	0.000	0.000	0.000
43	F	43	LYS	1	0.801	0.904	28.739	0.077	0.077	0.000	0.000	0.000	0.000
44	F	44	PHE	0	-0.061	-0.032	27.437	0.012	0.012	0.000	0.000	0.000	0.000
45	F	45	ALA	0	-0.002	0.031	28.303	-0.003	-0.003	0.000	0.000	0.000	0.000
46	F	46	LYS	1	0.872	0.936	29.681	0.091	0.091	0.000	0.000	0.000	0.000
47	F	47	LEU	0	0.018	0.018	32.011	0.005	0.005	0.000	0.000	0.000	0.000
48	F	48	ASP	-1	-0.809	-0.885	31.643	-0.164	-0.164	0.000	0.000	0.000	0.000
49	F	49	LYS	1	0.830	0.892	25.640	0.278	0.278	0.000	0.000	0.000	0.000
50	F	50	GLU	-1	-0.958	-0.981	29.400	-0.170	-0.170	0.000	0.000	0.000	0.000
51	F	51	GLU	-1	-0.785	-0.895	31.615	-0.135	-0.135	0.000	0.000	0.000	0.000
52	F	52	ALA	0	0.014	0.007	28.690	0.002	0.002	0.000	0.000	0.000	0.000
53	F	53	LYS	1	0.825	0.901	24.406	0.300	0.300	0.000	0.000	0.000	0.000
54	F	54	LYS	1	0.865	0.944	28.610	0.139	0.139	0.000	0.000	0.000	0.000
55	F	55	LEU	0	0.032	0.022	31.547	0.005	0.005	0.000	0.000	0.000	0.000
56	F	56	VAL	0	-0.015	-0.032	25.531	0.004	0.004	0.000	0.000	0.000	0.000
57	F	57	GLU	-1	-0.952	-0.973	28.634	-0.201	-0.201	0.000	0.000	0.000	0.000
58	F	58	GLU	-1	-0.801	-0.863	30.035	-0.108	-0.108	0.000	0.000	0.000	0.000
59	F	59	LEU	0	-0.001	-0.008	30.323	0.008	0.008	0.000	0.000	0.000	0.000
60	F	60	ILE	0	-0.024	-0.014	25.618	0.004	0.004	0.000	0.000	0.000	0.000
61	F	61	SER	0	-0.089	-0.046	29.612	0.003	0.003	0.000	0.000	0.000	0.000
62	F	62	LEU	0	-0.081	-0.024	32.709	0.007	0.007	0.000	0.000	0.000	0.000
63	F	63	GLY	0	-0.041	-0.015	30.818	0.009	0.009	0.000	0.000	0.000	0.000
64	F	64	ILE	0	-0.055	-0.013	28.367	0.004	0.004	0.000	0.000	0.000	0.000
65	F	65	ASP	-1	-0.834	-0.885	24.332	-0.140	-0.140	0.000	0.000	0.000	0.000
66	F	66	GLU	-1	-0.759	-0.899	19.527	-0.345	-0.345	0.000	0.000	0.000	0.000
67	F	67	LYS	1	0.915	0.962	18.748	0.144	0.144	0.000	0.000	0.000	0.000
68	F	68	THR	0	-0.033	-0.059	22.558	0.013	0.013	0.000	0.000	0.000	0.000
69	F	69	ALA	0	0.029	0.028	26.208	0.008	0.008	0.000	0.000	0.000	0.000
70	F	70	VAL	0	-0.010	-0.003	22.441	0.003	0.003	0.000	0.000	0.000	0.000
71	F	71	LYS	1	0.933	0.973	23.451	0.117	0.117	0.000	0.000	0.000	0.000
72	F	72	ILE	0	0.018	0.001	26.622	0.011	0.011	0.000	0.000	0.000	0.000
73	F	73	ALA	0	0.020	0.012	28.101	0.008	0.008	0.000	0.000	0.000	0.000
74	F	74	ASP	-1	-0.876	-0.935	25.093	-0.175	-0.175	0.000	0.000	0.000	0.000
75	F	75	ILE	0	-0.107	-0.065	28.748	0.009	0.009	0.000	0.000	0.000	0.000
76	F	76	LEU	0	-0.016	-0.004	31.359	0.006	0.006	0.000	0.000	0.000	0.000
77	F	77	PRO	0	-0.060	-0.028	33.282	0.006	0.006	0.000	0.000	0.000	0.000
78	F	78	GLU	-1	-0.919	-0.970	36.157	-0.055	-0.055	0.000	0.000	0.000	0.000
79	F	79	ASP	-1	-0.878	-0.939	39.476	-0.034	-0.034	0.000	0.000	0.000	0.000
80	F	80	LEU	0	0.023	-0.014	39.100	-0.001	-0.001	0.000	0.000	0.000	0.000
81	F	81	ASP	-1	-0.900	-0.946	38.595	-0.018	-0.018	0.000	0.000	0.000	0.000
82	F	82	ASP	-1	-0.790	-0.877	35.823	-0.042	-0.042	0.000	0.000	0.000	0.000
83	F	83	LEU	0	-0.040	-0.027	34.397	-0.003	-0.003	0.000	0.000	0.000	0.000
84	F	84	ARG	1	0.876	0.938	33.993	0.020	0.020	0.000	0.000	0.000	0.000
85	F	85	ALA	0	-0.052	-0.010	32.955	0.005	0.005	0.000	0.000	0.000	0.000
86	F	86	ILE	0	-0.046	-0.018	28.933	0.001	0.001	0.000	0.000	0.000	0.000
87	F	87	TYR	0	-0.042	-0.028	29.360	-0.003	-0.003	0.000	0.000	0.000	0.000
88	F	88	TYR	0	0.058	0.020	28.119	0.012	0.012	0.000	0.000	0.000	0.000
89	F	89	LYS	1	0.822	0.902	29.777	-0.029	-0.029	0.000	0.000	0.000	0.000
90	F	90	ARG	1	0.859	0.941	27.205	0.066	0.066	0.000	0.000	0.000	0.000
91	F	91	GLU	-1	-0.890	-0.926	32.175	-0.014	-0.014	0.000	0.000	0.000	0.000
92	F	92	LEU	0	-0.027	-0.023	34.512	-0.006	-0.006	0.000	0.000	0.000	0.000
93	F	93	PRO	0	-0.001	0.003	33.670	0.002	0.002	0.000	0.000	0.000	0.000
94	F	94	GLU	-1	-0.895	-0.947	36.172	-0.034	-0.034	0.000	0.000	0.000	0.000
95	F	95	ASN	0	-0.041	-0.025	35.185	0.004	0.004	0.000	0.000	0.000	0.000
96	F	96	ALA	0	0.002	0.000	37.704	-0.004	-0.004	0.000	0.000	0.000	0.000
97	F	97	GLU	-1	-0.864	-0.961	38.748	-0.047	-0.047	0.000	0.000	0.000	0.000
98	F	98	GLU	-1	-0.899	-0.951	38.714	-0.081	-0.081	0.000	0.000	0.000	0.000
99	F	99	ILE	0	-0.022	-0.010	33.873	-0.005	-0.005	0.000	0.000	0.000	0.000
100	F	100	LEU	0	0.001	0.003	37.236	-0.005	-0.005	0.000	0.000	0.000	0.000
101	F	101	GLU	-1	-0.833	-0.868	39.350	-0.061	-0.061	0.000	0.000	0.000	0.000
102	F	102	ILE	0	-0.013	-0.021	35.910	-0.003	-0.003	0.000	0.000	0.000	0.000
103	F	103	VAL	0	0.014	0.021	34.704	-0.006	-0.006	0.000	0.000	0.000	0.000
104	F	104	ARG	1	0.739	0.841	37.210	0.057	0.057	0.000	0.000	0.000	0.000
105	F	105	LYS	1	0.850	0.879	38.748	0.101	0.101	0.000	0.000	0.000	0.000
106	F	106	TYR	0	-0.105	-0.032	34.668	-0.010	-0.010	0.000	0.000	0.000	0.000
107	F	107	ILE	0	-0.042	0.005	38.499	0.005	0.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(F:1:MET)