FMO DATABASE

FMODB ID: ZVZ6N

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	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	146
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1382421.687163
FMO2-HF: Nuclear repulsion	1324366.429743
FMO2-HF: Total energy	-58055.25742
FMO2-MP2: Total energy	-58223.68612

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.
-21.093	-13.865	2.434	-3.691	-5.969	0.031

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 : 0.050 / q_NPA : 0.010

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	-0.022	-0.007	2.766	-3.945	-1.086	0.896	-1.516	-2.239	0.011
4	A	5	ALA	0	0.049	0.029	2.381	-7.759	-5.032	1.535	-1.720	-2.542	0.020
5	A	6	ASN	0	0.028	0.011	3.602	-2.653	-1.629	0.006	-0.368	-0.661	0.000
6	A	7	LYS	1	0.935	0.964	5.290	-1.235	-1.103	-0.001	-0.010	-0.120	0.000
7	A	8	GLU	-1	-0.923	-0.967	6.805	2.400	2.400	0.000	0.000	0.000	0.000
8	A	9	ARG	1	0.963	0.997	3.587	1.377	1.537	0.000	-0.030	-0.130	0.000
9	A	10	CYS	0	-0.030	0.001	9.375	-0.087	-0.087	0.000	0.000	0.000	0.000
10	A	11	LEU	0	-0.026	-0.019	11.676	-0.019	-0.019	0.000	0.000	0.000	0.000
11	A	12	GLU	-1	-0.909	-0.953	10.984	0.364	0.364	0.000	0.000	0.000	0.000
12	A	13	MET	0	-0.034	-0.001	11.444	-0.045	-0.045	0.000	0.000	0.000	0.000
13	A	14	VAL	0	0.028	0.012	15.523	-0.004	-0.004	0.000	0.000	0.000	0.000
14	A	15	ALA	0	-0.037	-0.016	17.055	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	16	ALA	0	-0.031	-0.018	18.059	-0.006	-0.006	0.000	0.000	0.000	0.000
16	A	17	TRP	0	0.052	0.018	19.081	-0.004	-0.004	0.000	0.000	0.000	0.000
17	A	18	ASN	0	-0.027	-0.005	21.401	-0.022	-0.022	0.000	0.000	0.000	0.000
18	A	19	ARG	1	0.867	0.964	19.270	-0.080	-0.080	0.000	0.000	0.000	0.000
19	A	20	TRP	0	-0.051	-0.027	24.769	-0.005	-0.005	0.000	0.000	0.000	0.000
20	A	21	ASP	-1	-0.830	-0.935	21.990	-0.036	-0.036	0.000	0.000	0.000	0.000
21	A	22	VAL	0	0.070	0.023	21.647	-0.010	-0.010	0.000	0.000	0.000	0.000
22	A	23	SER	0	-0.067	-0.030	21.155	-0.027	-0.027	0.000	0.000	0.000	0.000
23	A	24	GLY	0	0.034	0.024	19.035	-0.023	-0.023	0.000	0.000	0.000	0.000
24	A	25	VAL	0	-0.041	-0.028	16.946	-0.021	-0.021	0.000	0.000	0.000	0.000
25	A	26	VAL	0	0.018	0.006	16.265	-0.054	-0.054	0.000	0.000	0.000	0.000
26	A	27	ALA	0	-0.013	0.015	16.611	-0.056	-0.056	0.000	0.000	0.000	0.000
27	A	28	HIS	0	-0.065	-0.052	11.752	-0.153	-0.153	0.000	0.000	0.000	0.000
28	A	29	TRP	0	-0.020	-0.009	12.121	-0.158	-0.158	0.000	0.000	0.000	0.000
29	A	30	ALA	0	-0.017	-0.003	13.021	0.007	0.007	0.000	0.000	0.000	0.000
30	A	31	PRO	0	-0.042	-0.029	14.499	0.062	0.062	0.000	0.000	0.000	0.000
31	A	32	ASP	-1	-0.934	-0.971	16.456	-0.629	-0.629	0.000	0.000	0.000	0.000
32	A	33	VAL	0	-0.058	-0.012	15.625	-0.029	-0.029	0.000	0.000	0.000	0.000
33	A	34	VAL	0	-0.022	-0.001	17.122	0.072	0.072	0.000	0.000	0.000	0.000
34	A	35	HIS	0	-0.032	-0.029	18.286	-0.029	-0.029	0.000	0.000	0.000	0.000
35	A	36	TYR	0	-0.040	-0.026	18.647	0.036	0.036	0.000	0.000	0.000	0.000
36	A	37	ASP	-1	-0.905	-0.963	22.405	-0.177	-0.177	0.000	0.000	0.000	0.000
37	A	38	ASP	-1	-0.940	-0.985	23.552	-0.167	-0.167	0.000	0.000	0.000	0.000
38	A	39	GLU	-1	-0.981	-0.986	25.234	-0.148	-0.148	0.000	0.000	0.000	0.000
39	A	40	ASP	-1	-0.916	-0.956	22.117	-0.335	-0.335	0.000	0.000	0.000	0.000
40	A	41	LYS	1	0.960	0.978	24.516	0.171	0.171	0.000	0.000	0.000	0.000
41	A	42	PRO	0	-0.024	-0.010	24.046	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	43	VAL	0	0.005	0.021	24.259	0.026	0.026	0.000	0.000	0.000	0.000
43	A	44	SER	0	-0.015	-0.019	24.480	-0.021	-0.021	0.000	0.000	0.000	0.000
44	A	45	ALA	0	0.084	0.022	22.821	0.009	0.009	0.000	0.000	0.000	0.000
45	A	46	GLU	-1	-0.978	-0.982	24.217	-0.140	-0.140	0.000	0.000	0.000	0.000
46	A	47	GLU	-1	-0.816	-0.900	27.609	-0.109	-0.109	0.000	0.000	0.000	0.000
47	A	48	VAL	0	0.007	0.016	21.624	0.017	0.017	0.000	0.000	0.000	0.000
48	A	49	VAL	0	0.007	-0.009	23.236	0.017	0.017	0.000	0.000	0.000	0.000
49	A	50	ARG	1	0.829	0.910	25.476	0.125	0.125	0.000	0.000	0.000	0.000
50	A	51	ARG	1	0.916	0.969	24.131	0.161	0.161	0.000	0.000	0.000	0.000
51	A	52	MET	0	-0.037	-0.019	20.462	0.008	0.008	0.000	0.000	0.000	0.000
52	A	53	ASN	0	0.010	-0.014	26.024	0.020	0.020	0.000	0.000	0.000	0.000
53	A	54	SER	0	0.013	0.028	28.669	0.013	0.013	0.000	0.000	0.000	0.000
54	A	55	ALA	0	0.025	-0.005	27.586	0.010	0.010	0.000	0.000	0.000	0.000
55	A	56	VAL	0	-0.022	-0.008	26.691	0.012	0.012	0.000	0.000	0.000	0.000
56	A	57	GLU	-1	-0.979	-0.974	29.499	-0.031	-0.031	0.000	0.000	0.000	0.000
57	A	58	ALA	0	-0.047	-0.020	32.757	0.007	0.007	0.000	0.000	0.000	0.000
58	A	59	PHE	0	-0.027	-0.029	30.229	0.007	0.007	0.000	0.000	0.000	0.000
59	A	60	PRO	0	0.034	0.030	31.030	0.003	0.003	0.000	0.000	0.000	0.000
60	A	61	ASP	-1	-0.810	-0.893	31.432	0.045	0.045	0.000	0.000	0.000	0.000
61	A	62	LEU	0	-0.042	-0.006	25.703	0.008	0.008	0.000	0.000	0.000	0.000
62	A	63	ARG	1	0.948	0.975	26.043	-0.105	-0.105	0.000	0.000	0.000	0.000
63	A	64	LEU	0	-0.025	-0.027	20.577	-0.007	-0.007	0.000	0.000	0.000	0.000
64	A	65	ASP	-1	-0.936	-0.971	22.498	0.208	0.208	0.000	0.000	0.000	0.000
65	A	66	VAL	0	0.031	0.006	16.225	-0.023	-0.023	0.000	0.000	0.000	0.000
66	A	67	ARG	1	0.877	0.932	19.686	-0.104	-0.104	0.000	0.000	0.000	0.000
67	A	68	SER	0	-0.085	-0.051	17.929	0.006	0.006	0.000	0.000	0.000	0.000
68	A	69	ILE	0	0.057	0.035	11.385	-0.018	-0.018	0.000	0.000	0.000	0.000
69	A	70	VAL	0	-0.042	-0.012	12.216	0.156	0.156	0.000	0.000	0.000	0.000
70	A	71	GLY	0	0.023	0.001	8.656	-0.112	-0.112	0.000	0.000	0.000	0.000
71	A	72	GLU	-1	-0.945	-0.972	8.114	0.010	0.010	0.000	0.000	0.000	0.000
72	A	73	GLY	0	0.002	0.012	6.273	-0.148	-0.148	0.000	0.000	0.000	0.000
73	A	74	ASP	-1	-0.870	-0.947	5.265	-2.666	-2.666	0.000	0.000	0.000	0.000
74	A	75	ARG	1	0.887	0.951	7.009	0.904	0.904	0.000	0.000	0.000	0.000
75	A	76	VAL	0	-0.034	-0.030	8.351	0.116	0.116	0.000	0.000	0.000	0.000
76	A	77	MET	0	0.008	0.025	11.037	0.022	0.022	0.000	0.000	0.000	0.000
77	A	78	LEU	0	-0.020	-0.021	13.176	0.135	0.135	0.000	0.000	0.000	0.000
78	A	79	ARG	1	0.952	0.989	16.812	-0.131	-0.131	0.000	0.000	0.000	0.000
79	A	80	ILE	0	0.025	0.007	18.020	0.053	0.053	0.000	0.000	0.000	0.000
80	A	81	THR	0	-0.050	-0.009	21.914	-0.016	-0.016	0.000	0.000	0.000	0.000
81	A	82	CYS	0	0.024	0.037	24.986	0.011	0.011	0.000	0.000	0.000	0.000
82	A	83	SER	0	-0.083	-0.057	27.012	0.003	0.003	0.000	0.000	0.000	0.000
83	A	84	ALA	0	0.063	0.031	29.919	0.003	0.003	0.000	0.000	0.000	0.000
84	A	85	THR	0	-0.032	-0.030	32.409	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	86	HIS	0	-0.024	-0.001	35.397	0.000	0.000	0.000	0.000	0.000	0.000
86	A	87	GLN	0	-0.039	-0.034	36.650	0.003	0.003	0.000	0.000	0.000	0.000
87	A	88	GLY	0	0.034	0.033	36.874	0.000	0.000	0.000	0.000	0.000	0.000
88	A	89	VAL	0	-0.023	-0.025	37.504	0.000	0.000	0.000	0.000	0.000	0.000
89	A	90	PHE	0	-0.002	0.004	30.316	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	91	MET	0	-0.008	0.002	31.737	0.000	0.000	0.000	0.000	0.000	0.000
91	A	92	GLY	0	0.006	0.008	35.581	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	93	ILE	0	-0.094	-0.046	36.932	0.005	0.005	0.000	0.000	0.000	0.000
93	A	94	ALA	0	0.025	0.004	39.429	0.002	0.002	0.000	0.000	0.000	0.000
94	A	95	PRO	0	0.002	0.013	39.889	0.000	0.000	0.000	0.000	0.000	0.000
95	A	96	THR	0	0.023	-0.002	39.906	0.003	0.003	0.000	0.000	0.000	0.000
96	A	97	GLY	0	-0.022	-0.001	40.769	0.002	0.002	0.000	0.000	0.000	0.000
97	A	98	ARG	1	0.906	0.954	39.963	-0.006	-0.006	0.000	0.000	0.000	0.000
98	A	99	LYN	0	0.017	0.018	33.013	0.001	0.001	0.000	0.000	0.000	0.000
99	A	100	VAL	0	-0.009	-0.009	33.037	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	101	ARG	1	0.919	0.945	31.365	-0.041	-0.041	0.000	0.000	0.000	0.000
101	A	102	TRP	0	0.015	0.005	26.370	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	103	THR	0	-0.075	-0.046	25.095	0.020	0.020	0.000	0.000	0.000	0.000
103	A	104	TYR	0	-0.082	-0.102	19.959	-0.011	-0.011	0.000	0.000	0.000	0.000
104	A	105	LEU	0	-0.037	-0.031	20.738	0.034	0.034	0.000	0.000	0.000	0.000
105	A	106	GLU	-1	-0.818	-0.908	16.267	-0.208	-0.208	0.000	0.000	0.000	0.000
106	A	107	GLU	-1	-0.846	-0.923	14.657	-0.461	-0.461	0.000	0.000	0.000	0.000
107	A	108	LEU	0	-0.011	-0.008	11.435	-0.026	-0.026	0.000	0.000	0.000	0.000
108	A	109	ARG	1	0.874	0.938	10.375	1.056	1.056	0.000	0.000	0.000	0.000
109	A	110	PHE	0	-0.030	-0.030	6.171	0.180	0.180	0.000	0.000	0.000	0.000
110	A	111	SER	0	0.010	0.004	7.764	-0.306	-0.306	0.000	0.000	0.000	0.000
111	A	112	GLU	-1	-0.888	-0.950	4.030	-6.300	-6.048	-0.001	-0.046	-0.206	0.000
112	A	113	ALA	0	-0.055	-0.029	5.026	-0.875	-0.801	-0.001	-0.001	-0.071	0.000
113	A	114	GLY	0	-0.041	-0.021	5.304	0.331	0.331	0.000	0.000	0.000	0.000
114	A	115	LYS	1	0.883	0.947	5.971	1.158	1.158	0.000	0.000	0.000	0.000
115	A	116	VAL	0	0.015	0.005	9.550	-0.215	-0.215	0.000	0.000	0.000	0.000
116	A	117	VAL	0	0.016	-0.005	11.006	0.106	0.106	0.000	0.000	0.000	0.000
117	A	118	GLU	-1	-0.821	-0.892	13.203	-0.601	-0.601	0.000	0.000	0.000	0.000
118	A	119	HIS	1	0.848	0.896	14.142	0.263	0.263	0.000	0.000	0.000	0.000
119	A	120	TRP	0	0.020	0.010	14.816	-0.005	-0.005	0.000	0.000	0.000	0.000
120	A	121	ASP	-1	-0.776	-0.788	19.041	-0.198	-0.198	0.000	0.000	0.000	0.000
121	A	122	VAL	0	0.068	0.024	21.706	0.009	0.009	0.000	0.000	0.000	0.000
122	A	123	PHE	0	0.044	0.019	23.982	0.021	0.021	0.000	0.000	0.000	0.000
123	A	124	ASN	0	-0.011	-0.011	26.720	0.011	0.011	0.000	0.000	0.000	0.000
124	A	125	PHE	0	0.089	0.023	28.956	0.017	0.017	0.000	0.000	0.000	0.000
125	A	126	SER	0	-0.023	-0.012	32.163	0.005	0.005	0.000	0.000	0.000	0.000
126	A	127	PRO	0	-0.118	-0.071	30.449	0.004	0.004	0.000	0.000	0.000	0.000
127	A	128	LEU	0	0.079	0.055	33.720	0.005	0.005	0.000	0.000	0.000	0.000
128	A	129	PHE	0	-0.014	-0.013	35.255	0.002	0.002	0.000	0.000	0.000	0.000
129	A	130	ARG	1	0.923	0.970	33.251	-0.032	-0.032	0.000	0.000	0.000	0.000
130	A	131	ASP	-1	-0.908	-0.948	36.557	0.031	0.031	0.000	0.000	0.000	0.000
131	A	132	LEU	0	-0.069	-0.037	38.066	0.000	0.000	0.000	0.000	0.000	0.000
132	A	133	GLY	0	0.045	0.025	41.090	-0.003	-0.003	0.000	0.000	0.000	0.000
133	A	134	VAL	0	-0.055	-0.025	41.383	-0.002	-0.002	0.000	0.000	0.000	0.000
134	A	135	VAL	0	0.005	0.022	42.592	-0.002	-0.002	0.000	0.000	0.000	0.000
135	A	136	PRO	0	0.011	-0.026	42.583	-0.003	-0.003	0.000	0.000	0.000	0.000
136	A	137	ASP	-1	-0.889	-0.948	41.182	-0.017	-0.017	0.000	0.000	0.000	0.000
137	A	138	GLY	0	-0.002	0.005	38.398	-0.002	-0.002	0.000	0.000	0.000	0.000
138	A	139	LEU	0	-0.018	-0.011	37.561	-0.004	-0.004	0.000	0.000	0.000	0.000
139	A	140	LYS	1	0.959	0.978	38.030	0.025	0.025	0.000	0.000	0.000	0.000
140	A	141	LEU	0	0.019	0.010	33.601	-0.004	-0.004	0.000	0.000	0.000	0.000
141	A	142	ALA	0	-0.005	-0.008	33.379	-0.004	-0.004	0.000	0.000	0.000	0.000
142	A	143	ALA	0	0.010	0.007	33.049	-0.007	-0.007	0.000	0.000	0.000	0.000
143	A	144	ALA	0	-0.017	0.004	33.911	-0.007	-0.007	0.000	0.000	0.000	0.000
144	A	145	LEU	0	-0.079	-0.047	28.660	-0.005	-0.005	0.000	0.000	0.000	0.000
145	A	146	GLU	-1	-0.959	-0.971	28.504	-0.098	-0.098	0.000	0.000	0.000	0.000
146	A	147	HIS	0	0.005	0.025	24.096	0.011	0.011	0.000	0.000	0.000	0.000

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