FMO DATABASE

FMODB ID: QVLYY

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:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
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
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1389957.522822
FMO2-HF: Nuclear repulsion	1331901.210743
FMO2-HF: Total energy	-58056.312079
FMO2-MP2: Total energy	-58224.784784

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.
-17.242	-10.906	5.223	-4.73	-6.827	0.03

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 : 0.071 / q_NPA : 0.033

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	-0.083	-0.036	2.808	-3.942	-0.515	0.706	-1.824	-2.309	0.011
4	A	5	ALA	0	0.107	0.057	2.023	-7.676	-6.642	4.499	-2.299	-3.234	0.020
5	A	6	ASN	0	-0.011	0.019	3.588	-2.379	-1.380	0.013	-0.368	-0.644	0.000
6	A	7	LYS	1	0.988	0.999	5.274	-0.683	-0.560	-0.001	-0.010	-0.111	0.000
7	A	8	GLU	-1	-0.918	-0.964	5.366	2.037	2.037	0.000	0.000	0.000	0.000
8	A	9	ARG	1	0.962	0.979	3.557	2.840	3.134	0.007	-0.098	-0.203	0.000
9	A	10	CYS	0	-0.041	-0.004	8.970	0.070	0.070	0.000	0.000	0.000	0.000
10	A	11	LEU	0	-0.027	-0.016	11.188	0.062	0.062	0.000	0.000	0.000	0.000
11	A	12	GLU	-1	-0.905	-0.958	10.036	-0.333	-0.333	0.000	0.000	0.000	0.000
12	A	13	MET	0	-0.023	0.004	11.444	0.024	0.024	0.000	0.000	0.000	0.000
13	A	14	VAL	0	0.016	0.006	15.078	0.034	0.034	0.000	0.000	0.000	0.000
14	A	15	ALA	0	-0.013	-0.008	16.427	0.023	0.023	0.000	0.000	0.000	0.000
15	A	16	ALA	0	-0.040	-0.012	17.437	0.013	0.013	0.000	0.000	0.000	0.000
16	A	17	TRP	0	0.065	0.013	18.524	0.025	0.025	0.000	0.000	0.000	0.000
17	A	18	ASN	0	-0.083	-0.047	20.440	0.017	0.017	0.000	0.000	0.000	0.000
18	A	19	ARG	1	0.827	0.920	18.151	0.112	0.112	0.000	0.000	0.000	0.000
19	A	20	TRP	0	-0.039	-0.026	23.869	0.004	0.004	0.000	0.000	0.000	0.000
20	A	21	ASP	-1	-0.787	-0.862	21.146	-0.149	-0.149	0.000	0.000	0.000	0.000
21	A	22	VAL	0	0.069	0.019	21.123	-0.023	-0.023	0.000	0.000	0.000	0.000
22	A	23	SER	0	-0.031	-0.025	20.818	-0.027	-0.027	0.000	0.000	0.000	0.000
23	A	24	GLY	0	-0.011	-0.009	18.348	-0.032	-0.032	0.000	0.000	0.000	0.000
24	A	25	VAL	0	-0.033	-0.023	16.533	-0.040	-0.040	0.000	0.000	0.000	0.000
25	A	26	VAL	0	0.015	0.002	16.005	-0.066	-0.066	0.000	0.000	0.000	0.000
26	A	27	ALA	0	-0.016	0.005	16.210	-0.050	-0.050	0.000	0.000	0.000	0.000
27	A	28	HIS	0	0.014	0.008	11.128	-0.180	-0.180	0.000	0.000	0.000	0.000
28	A	29	TRP	0	0.009	0.004	11.921	-0.161	-0.161	0.000	0.000	0.000	0.000
29	A	30	ALA	0	-0.009	0.008	13.191	0.013	0.013	0.000	0.000	0.000	0.000
30	A	31	PRO	0	-0.054	-0.034	14.792	0.053	0.053	0.000	0.000	0.000	0.000
31	A	32	ASP	-1	-0.918	-0.970	16.476	-0.547	-0.547	0.000	0.000	0.000	0.000
32	A	33	VAL	0	-0.071	-0.018	15.738	-0.008	-0.008	0.000	0.000	0.000	0.000
33	A	34	VAL	0	-0.008	0.007	17.409	0.064	0.064	0.000	0.000	0.000	0.000
34	A	35	HIS	0	-0.015	-0.016	18.372	-0.033	-0.033	0.000	0.000	0.000	0.000
35	A	36	TYR	0	-0.053	-0.049	18.510	0.035	0.035	0.000	0.000	0.000	0.000
36	A	37	ASP	-1	-0.849	-0.918	23.018	-0.175	-0.175	0.000	0.000	0.000	0.000
37	A	38	ASP	-1	-0.959	-0.989	24.321	-0.180	-0.180	0.000	0.000	0.000	0.000
38	A	39	GLU	-1	-0.966	-0.979	25.574	-0.135	-0.135	0.000	0.000	0.000	0.000
39	A	40	ASP	-1	-0.902	-0.945	22.473	-0.279	-0.279	0.000	0.000	0.000	0.000
40	A	41	LYS	1	0.951	0.981	24.850	0.154	0.154	0.000	0.000	0.000	0.000
41	A	42	PRO	0	-0.025	-0.012	24.266	-0.006	-0.006	0.000	0.000	0.000	0.000
42	A	43	VAL	0	-0.016	0.006	24.503	0.024	0.024	0.000	0.000	0.000	0.000
43	A	44	SER	0	0.002	-0.003	24.642	-0.022	-0.022	0.000	0.000	0.000	0.000
44	A	45	ALA	0	0.072	0.013	22.689	0.004	0.004	0.000	0.000	0.000	0.000
45	A	46	GLU	-1	-0.973	-0.978	24.214	-0.157	-0.157	0.000	0.000	0.000	0.000
46	A	47	GLU	-1	-0.768	-0.848	27.658	-0.130	-0.130	0.000	0.000	0.000	0.000
47	A	48	VAL	0	-0.011	0.010	21.812	0.011	0.011	0.000	0.000	0.000	0.000
48	A	49	VAL	0	0.022	-0.001	23.154	0.010	0.010	0.000	0.000	0.000	0.000
49	A	50	ARG	1	0.791	0.865	25.381	0.140	0.140	0.000	0.000	0.000	0.000
50	A	51	ARG	1	0.827	0.894	24.812	0.190	0.190	0.000	0.000	0.000	0.000
51	A	52	MET	0	-0.036	-0.022	20.349	0.005	0.005	0.000	0.000	0.000	0.000
52	A	53	ASN	0	-0.014	-0.017	25.949	0.011	0.011	0.000	0.000	0.000	0.000
53	A	54	SER	0	0.017	-0.003	28.419	0.012	0.012	0.000	0.000	0.000	0.000
54	A	55	ALA	0	0.005	0.003	27.496	0.010	0.010	0.000	0.000	0.000	0.000
55	A	56	VAL	0	-0.032	-0.017	26.340	0.011	0.011	0.000	0.000	0.000	0.000
56	A	57	GLU	-1	-0.930	-0.946	29.281	-0.071	-0.071	0.000	0.000	0.000	0.000
57	A	58	ALA	0	-0.028	-0.010	32.567	0.009	0.009	0.000	0.000	0.000	0.000
58	A	59	PHE	0	-0.038	-0.026	29.975	0.009	0.009	0.000	0.000	0.000	0.000
59	A	60	PRO	0	0.048	0.026	30.553	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	61	ASP	-1	-0.807	-0.881	31.205	-0.023	-0.023	0.000	0.000	0.000	0.000
61	A	62	LEU	0	-0.061	-0.017	25.909	0.006	0.006	0.000	0.000	0.000	0.000
62	A	63	ARG	1	0.850	0.927	25.066	-0.015	-0.015	0.000	0.000	0.000	0.000
63	A	64	LEU	0	0.000	-0.011	20.751	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	65	ASP	-1	-0.838	-0.916	21.805	0.059	0.059	0.000	0.000	0.000	0.000
65	A	66	VAL	0	0.037	0.001	16.102	-0.012	-0.012	0.000	0.000	0.000	0.000
66	A	67	ARG	1	0.863	0.934	19.599	-0.005	-0.005	0.000	0.000	0.000	0.000
67	A	68	SER	0	-0.024	-0.014	17.749	0.020	0.020	0.000	0.000	0.000	0.000
68	A	69	ILE	0	-0.002	0.015	11.348	-0.034	-0.034	0.000	0.000	0.000	0.000
69	A	70	VAL	0	-0.038	-0.015	12.192	0.136	0.136	0.000	0.000	0.000	0.000
70	A	71	GLY	0	0.040	0.010	9.317	-0.107	-0.107	0.000	0.000	0.000	0.000
71	A	72	GLU	-1	-0.955	-0.971	8.539	0.018	0.018	0.000	0.000	0.000	0.000
72	A	73	GLY	0	0.020	0.019	6.251	-0.114	-0.114	0.000	0.000	0.000	0.000
73	A	74	ASP	-1	-0.814	-0.893	5.318	-2.254	-2.254	0.000	0.000	0.000	0.000
74	A	75	ARG	1	0.882	0.931	7.089	0.682	0.682	0.000	0.000	0.000	0.000
75	A	76	VAL	0	-0.049	-0.043	8.321	0.047	0.047	0.000	0.000	0.000	0.000
76	A	77	MET	0	0.005	0.018	10.998	0.036	0.036	0.000	0.000	0.000	0.000
77	A	78	LEU	0	-0.031	-0.022	13.176	0.101	0.101	0.000	0.000	0.000	0.000
78	A	79	ARG	1	0.930	0.964	16.744	-0.037	-0.037	0.000	0.000	0.000	0.000
79	A	80	ILE	0	0.024	0.005	17.765	0.038	0.038	0.000	0.000	0.000	0.000
80	A	81	THR	0	-0.036	0.003	21.855	-0.004	-0.004	0.000	0.000	0.000	0.000
81	A	82	CYS	0	-0.013	0.015	24.676	0.000	0.000	0.000	0.000	0.000	0.000
82	A	83	SER	0	-0.050	-0.051	26.750	0.009	0.009	0.000	0.000	0.000	0.000
83	A	84	ALA	0	0.048	0.041	29.480	0.000	0.000	0.000	0.000	0.000	0.000
84	A	85	THR	0	-0.019	-0.045	31.999	0.004	0.004	0.000	0.000	0.000	0.000
85	A	86	HIS	0	-0.010	0.027	35.354	0.000	0.000	0.000	0.000	0.000	0.000
86	A	87	GLN	0	-0.027	-0.023	36.436	0.002	0.002	0.000	0.000	0.000	0.000
87	A	88	GLY	0	0.029	0.030	36.690	0.002	0.002	0.000	0.000	0.000	0.000
88	A	89	VAL	0	-0.057	-0.042	37.595	0.001	0.001	0.000	0.000	0.000	0.000
89	A	90	PHE	0	0.013	0.014	30.540	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	91	MET	0	-0.021	-0.003	31.307	0.001	0.001	0.000	0.000	0.000	0.000
91	A	92	GLY	0	0.004	0.010	35.317	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	93	ILE	0	-0.084	-0.034	36.725	0.007	0.007	0.000	0.000	0.000	0.000
93	A	94	ALA	0	0.033	0.008	39.123	0.000	0.000	0.000	0.000	0.000	0.000
94	A	95	PRO	0	0.002	0.010	39.609	0.000	0.000	0.000	0.000	0.000	0.000
95	A	96	THR	0	0.004	-0.028	39.702	0.005	0.005	0.000	0.000	0.000	0.000
96	A	97	GLY	0	-0.020	-0.004	40.728	0.004	0.004	0.000	0.000	0.000	0.000
97	A	98	ARG	1	0.907	0.958	39.807	0.028	0.028	0.000	0.000	0.000	0.000
98	A	99	LYN	0	0.033	0.038	33.785	-0.002	-0.002	0.000	0.000	0.000	0.000
99	A	100	VAL	0	-0.024	-0.015	33.134	0.000	0.000	0.000	0.000	0.000	0.000
100	A	101	ARG	1	0.817	0.870	31.011	0.013	0.013	0.000	0.000	0.000	0.000
101	A	102	TRP	0	0.040	0.016	26.234	0.004	0.004	0.000	0.000	0.000	0.000
102	A	103	THR	0	-0.085	-0.047	24.760	0.016	0.016	0.000	0.000	0.000	0.000
103	A	104	TYR	0	-0.004	-0.010	19.390	-0.003	-0.003	0.000	0.000	0.000	0.000
104	A	105	LEU	0	-0.051	-0.036	20.977	0.027	0.027	0.000	0.000	0.000	0.000
105	A	106	GLU	-1	-0.807	-0.912	15.980	-0.375	-0.375	0.000	0.000	0.000	0.000
106	A	107	GLU	-1	-0.809	-0.889	14.848	-0.454	-0.454	0.000	0.000	0.000	0.000
107	A	108	LEU	0	-0.021	-0.010	11.554	-0.013	-0.013	0.000	0.000	0.000	0.000
108	A	109	ARG	1	0.799	0.873	10.598	0.913	0.913	0.000	0.000	0.000	0.000
109	A	110	PHE	0	-0.012	-0.010	6.640	0.079	0.079	0.000	0.000	0.000	0.000
110	A	111	SER	0	0.003	-0.001	8.311	0.015	0.015	0.000	0.000	0.000	0.000
111	A	112	GLU	-1	-0.909	-0.968	3.779	-4.868	-4.484	0.000	-0.129	-0.255	-0.001
112	A	113	ALA	0	-0.064	-0.033	4.717	-0.392	-0.317	-0.001	-0.002	-0.071	0.000
113	A	114	GLY	0	-0.040	-0.029	5.333	0.170	0.170	0.000	0.000	0.000	0.000
114	A	115	LYS	1	0.801	0.898	6.087	1.032	1.032	0.000	0.000	0.000	0.000
115	A	116	VAL	0	0.022	0.017	9.632	-0.149	-0.149	0.000	0.000	0.000	0.000
116	A	117	VAL	0	0.017	-0.008	11.166	0.130	0.130	0.000	0.000	0.000	0.000
117	A	118	GLU	-1	-0.791	-0.851	13.339	-0.509	-0.509	0.000	0.000	0.000	0.000
118	A	119	HIS	1	0.822	0.896	14.364	0.306	0.306	0.000	0.000	0.000	0.000
119	A	120	TRP	0	0.006	-0.004	15.174	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	121	ASP	-1	-0.780	-0.840	19.443	-0.235	-0.235	0.000	0.000	0.000	0.000
121	A	122	VAL	0	0.048	0.019	22.071	0.011	0.011	0.000	0.000	0.000	0.000
122	A	123	PHE	0	0.022	0.001	24.071	0.011	0.011	0.000	0.000	0.000	0.000
123	A	124	ASN	0	0.017	0.033	26.794	0.012	0.012	0.000	0.000	0.000	0.000
124	A	125	PHE	0	0.074	0.028	29.243	0.011	0.011	0.000	0.000	0.000	0.000
125	A	126	SER	0	-0.016	-0.026	32.330	0.006	0.006	0.000	0.000	0.000	0.000
126	A	127	PRO	0	-0.075	-0.050	30.591	0.005	0.005	0.000	0.000	0.000	0.000
127	A	128	LEU	0	0.046	0.055	32.885	0.005	0.005	0.000	0.000	0.000	0.000
128	A	129	PHE	0	0.031	-0.006	35.215	0.004	0.004	0.000	0.000	0.000	0.000
129	A	130	ARG	1	0.855	0.921	33.885	0.012	0.012	0.000	0.000	0.000	0.000
130	A	131	ASP	-1	-0.789	-0.868	36.442	-0.009	-0.009	0.000	0.000	0.000	0.000
131	A	132	LEU	0	-0.046	-0.022	38.176	0.002	0.002	0.000	0.000	0.000	0.000
132	A	133	GLY	0	0.009	0.008	40.831	-0.001	-0.001	0.000	0.000	0.000	0.000
133	A	134	VAL	0	-0.056	-0.033	41.344	0.000	0.000	0.000	0.000	0.000	0.000
134	A	135	VAL	0	0.008	0.024	42.515	-0.002	-0.002	0.000	0.000	0.000	0.000
135	A	136	PRO	0	0.054	-0.006	42.480	-0.003	-0.003	0.000	0.000	0.000	0.000
136	A	137	ASP	-1	-0.860	-0.906	41.078	-0.043	-0.043	0.000	0.000	0.000	0.000
137	A	138	GLY	0	0.017	0.006	38.099	-0.003	-0.003	0.000	0.000	0.000	0.000
138	A	139	LEU	0	-0.037	-0.017	37.556	-0.005	-0.005	0.000	0.000	0.000	0.000
139	A	140	LYS	1	0.822	0.893	38.499	0.045	0.045	0.000	0.000	0.000	0.000
140	A	141	LEU	0	0.014	0.007	33.372	-0.004	-0.004	0.000	0.000	0.000	0.000
141	A	142	ALA	0	0.012	-0.003	33.270	-0.006	-0.006	0.000	0.000	0.000	0.000
142	A	143	ALA	0	0.032	0.017	32.842	-0.008	-0.008	0.000	0.000	0.000	0.000
143	A	144	ALA	0	-0.027	-0.001	33.653	-0.004	-0.004	0.000	0.000	0.000	0.000
144	A	145	LEU	0	-0.066	-0.031	28.657	-0.006	-0.006	0.000	0.000	0.000	0.000
145	A	146	GLU	-1	-0.919	-0.954	28.276	-0.118	-0.118	0.000	0.000	0.000	0.000
146	A	147	HIS	0	-0.026	-0.026	24.321	0.008	0.008	0.000	0.000	0.000	0.000

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