FMO DATABASE

FMODB ID: R8L98

Calculation Name: 2GEX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2GEX

Chain ID: A

ChEMBL ID:

UniProt ID: Q9RN64

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

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	146
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1384258.511892
FMO2-HF: Nuclear repulsion	1326202.476155
FMO2-HF: Total energy	-58056.035737
FMO2-MP2: Total energy	-58224.472864

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:2:SER)

Summations of interaction energy for fragment #1(A:2:SER)

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.
-19.466	-12.829	2.721	-3.587	-5.77	0.029

Interaction energy analysis for fragmet #1(A:2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.037 / q_NPA : 0.007

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	4	THR	0	-0.054	-0.018	2.796	-3.309	-0.560	0.706	-1.388	-2.067	0.008
4	A	5	ALA	0	0.070	0.042	2.320	-7.864	-5.351	2.010	-1.837	-2.686	0.021
5	A	6	ASN	0	0.042	0.027	3.829	-2.268	-1.314	0.006	-0.311	-0.648	0.000
6	A	7	LYS	1	0.961	0.982	5.485	-1.443	-1.443	0.000	0.000	0.000	0.000
7	A	8	GLU	-1	-0.909	-0.961	6.131	2.995	2.995	0.000	0.000	0.000	0.000
8	A	9	ARG	1	0.963	0.989	3.558	0.882	1.070	0.001	-0.040	-0.149	0.000
9	A	10	CYS	0	-0.051	-0.012	9.448	-0.162	-0.162	0.000	0.000	0.000	0.000
10	A	11	LEU	0	-0.034	-0.026	11.678	-0.053	-0.053	0.000	0.000	0.000	0.000
11	A	12	GLU	-1	-0.886	-0.942	11.305	0.425	0.425	0.000	0.000	0.000	0.000
12	A	13	MET	0	-0.028	0.000	11.732	-0.072	-0.072	0.000	0.000	0.000	0.000
13	A	14	VAL	0	0.029	0.010	15.715	-0.020	-0.020	0.000	0.000	0.000	0.000
14	A	15	ALA	0	-0.026	-0.008	17.104	-0.015	-0.015	0.000	0.000	0.000	0.000
15	A	16	ALA	0	-0.020	-0.013	18.267	-0.014	-0.014	0.000	0.000	0.000	0.000
16	A	17	TRP	0	0.052	0.016	19.173	-0.015	-0.015	0.000	0.000	0.000	0.000
17	A	18	ASN	0	-0.074	-0.034	20.952	-0.022	-0.022	0.000	0.000	0.000	0.000
18	A	19	ARG	1	0.844	0.938	19.083	-0.136	-0.136	0.000	0.000	0.000	0.000
19	A	20	TRP	0	-0.057	-0.039	24.942	-0.009	-0.009	0.000	0.000	0.000	0.000
20	A	21	ASP	-1	-0.799	-0.893	22.000	0.020	0.020	0.000	0.000	0.000	0.000
21	A	22	VAL	0	0.067	0.021	21.814	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	23	SER	0	-0.030	-0.013	21.290	-0.023	-0.023	0.000	0.000	0.000	0.000
23	A	24	GLY	0	0.001	0.004	19.187	-0.019	-0.019	0.000	0.000	0.000	0.000
24	A	25	VAL	0	-0.042	-0.026	17.136	-0.007	-0.007	0.000	0.000	0.000	0.000
25	A	26	VAL	0	0.022	0.007	16.392	-0.043	-0.043	0.000	0.000	0.000	0.000
26	A	27	ALA	0	0.001	0.022	16.709	-0.055	-0.055	0.000	0.000	0.000	0.000
27	A	28	HIS	0	-0.012	-0.006	11.755	-0.136	-0.136	0.000	0.000	0.000	0.000
28	A	29	TRP	0	-0.012	-0.006	12.193	-0.143	-0.143	0.000	0.000	0.000	0.000
29	A	30	ALA	0	-0.010	0.005	12.920	0.015	0.015	0.000	0.000	0.000	0.000
30	A	31	PRO	0	-0.038	-0.026	14.484	0.057	0.057	0.000	0.000	0.000	0.000
31	A	32	ASP	-1	-0.929	-0.969	16.392	-0.566	-0.566	0.000	0.000	0.000	0.000
32	A	33	VAL	0	-0.057	-0.013	15.493	-0.029	-0.029	0.000	0.000	0.000	0.000
33	A	34	VAL	0	-0.022	0.001	17.099	0.064	0.064	0.000	0.000	0.000	0.000
34	A	35	HIS	0	-0.031	-0.031	18.281	-0.026	-0.026	0.000	0.000	0.000	0.000
35	A	36	TYR	0	-0.058	-0.055	18.250	0.030	0.030	0.000	0.000	0.000	0.000
36	A	37	ASP	-1	-0.887	-0.967	22.416	-0.147	-0.147	0.000	0.000	0.000	0.000
37	A	38	ASP	-1	-0.946	-0.981	23.579	-0.139	-0.139	0.000	0.000	0.000	0.000
38	A	39	GLU	-1	-0.987	-0.991	25.258	-0.128	-0.128	0.000	0.000	0.000	0.000
39	A	40	ASP	-1	-0.901	-0.934	22.056	-0.292	-0.292	0.000	0.000	0.000	0.000
40	A	41	LYS	1	0.981	0.987	24.499	0.148	0.148	0.000	0.000	0.000	0.000
41	A	42	PRO	0	-0.044	-0.019	24.044	0.001	0.001	0.000	0.000	0.000	0.000
42	A	43	VAL	0	0.003	0.022	24.262	0.022	0.022	0.000	0.000	0.000	0.000
43	A	44	SER	0	-0.006	-0.012	24.489	-0.018	-0.018	0.000	0.000	0.000	0.000
44	A	45	ALA	0	0.073	0.014	22.826	0.009	0.009	0.000	0.000	0.000	0.000
45	A	46	GLU	-1	-0.978	-0.981	24.246	-0.116	-0.116	0.000	0.000	0.000	0.000
46	A	47	GLU	-1	-0.781	-0.860	27.651	-0.083	-0.083	0.000	0.000	0.000	0.000
47	A	48	VAL	0	-0.006	0.004	21.745	0.016	0.016	0.000	0.000	0.000	0.000
48	A	49	VAL	0	0.001	-0.007	23.405	0.017	0.017	0.000	0.000	0.000	0.000
49	A	50	ARG	1	0.810	0.881	25.565	0.099	0.099	0.000	0.000	0.000	0.000
50	A	51	ARG	1	0.877	0.940	24.457	0.123	0.123	0.000	0.000	0.000	0.000
51	A	52	MET	0	-0.034	-0.018	20.537	0.007	0.007	0.000	0.000	0.000	0.000
52	A	53	ASN	0	-0.006	-0.020	26.160	0.019	0.019	0.000	0.000	0.000	0.000
53	A	54	SER	0	0.021	0.030	28.801	0.011	0.011	0.000	0.000	0.000	0.000
54	A	55	ALA	0	0.015	-0.008	27.753	0.009	0.009	0.000	0.000	0.000	0.000
55	A	56	VAL	0	-0.011	-0.008	26.760	0.011	0.011	0.000	0.000	0.000	0.000
56	A	57	GLU	-1	-0.968	-0.966	29.666	-0.011	-0.011	0.000	0.000	0.000	0.000
57	A	58	ALA	0	-0.043	-0.017	32.903	0.005	0.005	0.000	0.000	0.000	0.000
58	A	59	PHE	0	-0.039	-0.035	30.423	0.005	0.005	0.000	0.000	0.000	0.000
59	A	60	PRO	0	0.039	0.028	31.220	0.005	0.005	0.000	0.000	0.000	0.000
60	A	61	ASP	-1	-0.802	-0.867	31.601	0.065	0.065	0.000	0.000	0.000	0.000
61	A	62	LEU	0	-0.050	-0.011	26.216	0.008	0.008	0.000	0.000	0.000	0.000
62	A	63	ARG	1	0.893	0.940	25.675	-0.133	-0.133	0.000	0.000	0.000	0.000
63	A	64	LEU	0	-0.026	-0.023	21.003	-0.009	-0.009	0.000	0.000	0.000	0.000
64	A	65	ASP	-1	-0.869	-0.930	22.446	0.227	0.227	0.000	0.000	0.000	0.000
65	A	66	VAL	0	0.039	0.003	16.179	-0.023	-0.023	0.000	0.000	0.000	0.000
66	A	67	ARG	1	0.862	0.934	19.656	-0.134	-0.134	0.000	0.000	0.000	0.000
67	A	68	SER	0	-0.022	-0.026	17.958	0.008	0.008	0.000	0.000	0.000	0.000
68	A	69	ILE	0	0.007	0.014	11.508	-0.025	-0.025	0.000	0.000	0.000	0.000
69	A	70	VAL	0	-0.030	-0.005	12.216	0.139	0.139	0.000	0.000	0.000	0.000
70	A	71	GLY	0	0.028	0.006	8.662	-0.093	-0.093	0.000	0.000	0.000	0.000
71	A	72	GLU	-1	-0.948	-0.975	8.175	-0.064	-0.064	0.000	0.000	0.000	0.000
72	A	73	GLY	0	0.005	0.011	6.286	-0.124	-0.124	0.000	0.000	0.000	0.000
73	A	74	ASP	-1	-0.845	-0.922	5.281	-2.487	-2.487	0.000	0.000	0.000	0.000
74	A	75	ARG	1	0.874	0.926	7.020	0.851	0.851	0.000	0.000	0.000	0.000
75	A	76	VAL	0	-0.045	-0.037	8.411	0.124	0.124	0.000	0.000	0.000	0.000
76	A	77	MET	0	0.023	0.034	11.055	0.015	0.015	0.000	0.000	0.000	0.000
77	A	78	LEU	0	-0.033	-0.025	13.389	0.132	0.132	0.000	0.000	0.000	0.000
78	A	79	ARG	1	0.921	0.963	16.871	-0.173	-0.173	0.000	0.000	0.000	0.000
79	A	80	ILE	0	0.034	0.010	18.027	0.052	0.052	0.000	0.000	0.000	0.000
80	A	81	THR	0	-0.030	0.002	22.058	-0.019	-0.019	0.000	0.000	0.000	0.000
81	A	82	CYS	0	0.020	0.039	25.121	0.015	0.015	0.000	0.000	0.000	0.000
82	A	83	SER	0	-0.053	-0.050	27.201	0.000	0.000	0.000	0.000	0.000	0.000
83	A	84	ALA	0	0.051	0.030	30.119	0.005	0.005	0.000	0.000	0.000	0.000
84	A	85	THR	0	-0.044	-0.048	32.605	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	86	HIS	0	-0.015	0.014	35.587	0.001	0.001	0.000	0.000	0.000	0.000
86	A	87	GLN	0	-0.030	-0.031	36.831	0.000	0.000	0.000	0.000	0.000	0.000
87	A	88	GLY	0	0.034	0.031	37.043	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	89	VAL	0	-0.036	-0.030	37.665	0.000	0.000	0.000	0.000	0.000	0.000
89	A	90	PHE	0	0.003	0.009	30.680	0.000	0.000	0.000	0.000	0.000	0.000
90	A	91	MET	0	-0.008	-0.001	31.708	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	92	GLY	0	0.010	0.010	35.685	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	93	ILE	0	-0.099	-0.047	37.099	0.003	0.003	0.000	0.000	0.000	0.000
93	A	94	ALA	0	0.033	0.009	39.572	0.003	0.003	0.000	0.000	0.000	0.000
94	A	95	PRO	0	-0.006	0.007	39.890	0.000	0.000	0.000	0.000	0.000	0.000
95	A	96	THR	0	0.005	-0.023	40.061	0.002	0.002	0.000	0.000	0.000	0.000
96	A	97	GLY	0	-0.011	0.006	40.945	0.002	0.002	0.000	0.000	0.000	0.000
97	A	98	ARG	1	0.895	0.949	40.075	-0.018	-0.018	0.000	0.000	0.000	0.000
98	A	99	LYN	0	0.039	0.031	33.911	0.000	0.000	0.000	0.000	0.000	0.000
99	A	100	VAL	0	-0.024	-0.018	33.350	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	101	ARG	1	0.841	0.892	31.542	-0.054	-0.054	0.000	0.000	0.000	0.000
101	A	102	TRP	0	0.020	0.008	26.435	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	103	THR	0	-0.060	-0.037	25.245	0.020	0.020	0.000	0.000	0.000	0.000
103	A	104	TYR	0	-0.036	-0.040	19.772	-0.005	-0.005	0.000	0.000	0.000	0.000
104	A	105	LEU	0	-0.035	-0.029	20.870	0.033	0.033	0.000	0.000	0.000	0.000
105	A	106	GLU	-1	-0.823	-0.914	16.178	-0.158	-0.158	0.000	0.000	0.000	0.000
106	A	107	GLU	-1	-0.812	-0.890	14.645	-0.422	-0.422	0.000	0.000	0.000	0.000
107	A	108	LEU	0	-0.007	-0.001	11.375	-0.019	-0.019	0.000	0.000	0.000	0.000
108	A	109	ARG	1	0.805	0.882	10.349	1.004	1.004	0.000	0.000	0.000	0.000
109	A	110	PHE	0	-0.020	-0.026	6.182	0.187	0.187	0.000	0.000	0.000	0.000
110	A	111	SER	0	0.030	0.014	7.665	-0.304	-0.304	0.000	0.000	0.000	0.000
111	A	112	GLU	-1	-0.909	-0.955	4.539	-5.523	-5.364	-0.001	-0.010	-0.148	0.000
112	A	113	ALA	0	-0.055	-0.035	4.892	-0.863	-0.789	-0.001	-0.001	-0.072	0.000
113	A	114	GLY	0	-0.043	-0.030	5.310	0.340	0.340	0.000	0.000	0.000	0.000
114	A	115	LYS	1	0.780	0.883	5.979	1.006	1.006	0.000	0.000	0.000	0.000
115	A	116	VAL	0	0.006	-0.001	9.566	-0.210	-0.210	0.000	0.000	0.000	0.000
116	A	117	VAL	0	0.026	-0.003	10.990	0.096	0.096	0.000	0.000	0.000	0.000
117	A	118	GLU	-1	-0.794	-0.853	13.190	-0.573	-0.573	0.000	0.000	0.000	0.000
118	A	119	HIS	1	0.829	0.906	14.157	0.204	0.204	0.000	0.000	0.000	0.000
119	A	120	TRP	0	0.014	0.004	14.873	-0.011	-0.011	0.000	0.000	0.000	0.000
120	A	121	ASP	-1	-0.782	-0.838	19.115	-0.125	-0.125	0.000	0.000	0.000	0.000
121	A	122	VAL	0	0.049	0.008	21.787	0.003	0.003	0.000	0.000	0.000	0.000
122	A	123	PHE	0	0.044	0.022	24.084	0.023	0.023	0.000	0.000	0.000	0.000
123	A	124	ASN	0	0.000	0.019	26.832	0.007	0.007	0.000	0.000	0.000	0.000
124	A	125	PHE	0	0.092	0.023	29.079	0.017	0.017	0.000	0.000	0.000	0.000
125	A	126	SER	0	-0.031	-0.039	32.230	0.003	0.003	0.000	0.000	0.000	0.000
126	A	127	PRO	0	-0.108	-0.062	30.597	0.004	0.004	0.000	0.000	0.000	0.000
127	A	128	LEU	0	0.056	0.043	33.710	0.004	0.004	0.000	0.000	0.000	0.000
128	A	129	PHE	0	-0.006	-0.013	35.413	0.001	0.001	0.000	0.000	0.000	0.000
129	A	130	ARG	1	0.854	0.933	33.743	-0.048	-0.048	0.000	0.000	0.000	0.000
130	A	131	ASP	-1	-0.809	-0.890	37.047	0.049	0.049	0.000	0.000	0.000	0.000
131	A	132	LEU	0	-0.045	-0.016	38.462	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	133	GLY	0	0.046	0.026	41.255	-0.003	-0.003	0.000	0.000	0.000	0.000
133	A	134	VAL	0	-0.048	-0.024	41.487	-0.002	-0.002	0.000	0.000	0.000	0.000
134	A	135	VAL	0	0.007	0.026	42.731	-0.003	-0.003	0.000	0.000	0.000	0.000
135	A	136	PRO	0	0.056	-0.004	42.719	-0.002	-0.002	0.000	0.000	0.000	0.000
136	A	137	ASP	-1	-0.866	-0.928	41.408	-0.004	-0.004	0.000	0.000	0.000	0.000
137	A	138	GLY	0	0.012	0.011	38.545	-0.001	-0.001	0.000	0.000	0.000	0.000
138	A	139	LEU	0	-0.017	-0.006	37.693	-0.003	-0.003	0.000	0.000	0.000	0.000
139	A	140	LYS	1	0.865	0.924	38.144	0.008	0.008	0.000	0.000	0.000	0.000
140	A	141	LEU	0	0.007	0.002	33.612	-0.004	-0.004	0.000	0.000	0.000	0.000
141	A	142	ALA	0	0.003	-0.004	33.505	-0.003	-0.003	0.000	0.000	0.000	0.000
142	A	143	ALA	0	0.014	0.006	33.159	-0.006	-0.006	0.000	0.000	0.000	0.000
143	A	144	ALA	0	-0.023	0.003	34.019	-0.006	-0.006	0.000	0.000	0.000	0.000
144	A	145	LEU	0	-0.086	-0.047	28.926	-0.004	-0.004	0.000	0.000	0.000	0.000
145	A	146	GLU	-1	-0.952	-0.969	28.613	-0.069	-0.069	0.000	0.000	0.000	0.000
146	A	147	HIS	0	0.014	0.028	24.221	0.007	0.007	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:SER)