FMO DATABASE

FMODB ID: 14YQZ

Calculation Name: 2XZE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2XZE

Chain ID: A

ChEMBL ID:

UniProt ID: Q9Y3E7

Base Structure: X-ray

Registration Date: 2023-03-14

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	141
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1217343.644213
FMO2-HF: Nuclear repulsion	1160325.477636
FMO2-HF: Total energy	-57018.166576
FMO2-MP2: Total energy	-57187.44444

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.
-3.294	0.269	5.521	-3.94	-5.146	-0.002

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 : -0.024 / 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	HIS	0	-0.054	-0.046	3.570	-2.539	-1.043	0.010	-0.691	-0.814	0.001
4	A	5	GLY	0	0.006	0.015	5.882	0.516	0.516	0.000	0.000	0.000	0.000
5	A	6	ASP	-1	-0.838	-0.910	5.188	0.492	0.492	0.000	0.000	0.000	0.000
6	A	7	VAL	0	-0.017	-0.016	6.488	-0.361	-0.361	0.000	0.000	0.000	0.000
7	A	8	SER	0	-0.081	-0.052	7.712	0.126	0.126	0.000	0.000	0.000	0.000
8	A	9	LEU	0	-0.032	-0.006	2.274	-0.358	-0.281	2.800	-1.247	-1.631	-0.006
9	A	10	PRO	0	0.016	0.001	4.841	-0.277	-0.277	0.000	0.000	0.000	0.000
10	A	11	PRO	0	0.030	0.012	5.698	-0.998	-0.998	0.000	0.000	0.000	0.000
11	A	12	GLU	-1	-0.849	-0.924	7.294	-1.611	-1.611	0.000	0.000	0.000	0.000
12	A	13	ASP	-1	-0.861	-0.918	1.853	-4.431	-4.117	2.272	-1.236	-1.350	0.008
13	A	14	ARG	1	0.796	0.911	3.143	-0.704	0.362	0.225	-0.537	-0.755	-0.004
14	A	15	VAL	0	-0.007	-0.005	4.377	0.526	0.529	-0.001	-0.002	0.001	0.000
15	A	16	ARG	1	0.763	0.851	4.663	2.766	2.861	-0.001	-0.003	-0.091	0.000
16	A	17	ALA	0	0.058	0.053	2.597	0.870	1.304	0.217	-0.206	-0.446	-0.001
17	A	18	LEU	0	0.026	0.016	4.452	1.121	1.199	-0.001	-0.018	-0.060	0.000
18	A	19	SER	0	-0.064	-0.046	7.969	0.551	0.551	0.000	0.000	0.000	0.000
19	A	20	GLN	0	-0.018	-0.003	6.760	0.604	0.604	0.000	0.000	0.000	0.000
20	A	21	LEU	0	0.028	0.018	7.654	0.410	0.410	0.000	0.000	0.000	0.000
21	A	22	GLY	0	-0.025	-0.015	10.138	0.214	0.214	0.000	0.000	0.000	0.000
22	A	23	SER	0	-0.068	-0.051	11.477	0.163	0.163	0.000	0.000	0.000	0.000
23	A	24	ALA	0	0.035	0.029	11.940	0.125	0.125	0.000	0.000	0.000	0.000
24	A	25	VAL	0	-0.080	-0.036	13.905	0.022	0.022	0.000	0.000	0.000	0.000
25	A	26	GLU	-1	-0.787	-0.893	17.767	-0.119	-0.119	0.000	0.000	0.000	0.000
26	A	27	VAL	0	-0.067	-0.035	20.496	-0.008	-0.008	0.000	0.000	0.000	0.000
27	A	28	ASN	0	0.014	0.003	24.304	0.017	0.017	0.000	0.000	0.000	0.000
28	A	29	GLU	-1	-0.738	-0.887	27.046	-0.053	-0.053	0.000	0.000	0.000	0.000
29	A	30	ASP	-1	-0.872	-0.906	29.697	-0.025	-0.025	0.000	0.000	0.000	0.000
30	A	31	ILE	0	-0.075	-0.029	28.722	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	32	PRO	0	0.028	0.008	31.590	-0.007	-0.007	0.000	0.000	0.000	0.000
32	A	33	PRO	0	0.077	0.034	30.636	-0.008	-0.008	0.000	0.000	0.000	0.000
33	A	34	ARG	1	0.838	0.889	30.954	0.087	0.087	0.000	0.000	0.000	0.000
34	A	35	ARG	1	0.942	0.976	31.077	0.074	0.074	0.000	0.000	0.000	0.000
35	A	36	TYR	0	0.105	0.051	24.527	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	37	PHE	0	-0.009	-0.017	28.030	-0.015	-0.015	0.000	0.000	0.000	0.000
37	A	38	ARG	1	0.825	0.914	29.927	0.100	0.100	0.000	0.000	0.000	0.000
38	A	39	SER	0	0.069	0.026	27.210	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	40	GLY	0	0.000	0.008	25.432	-0.017	-0.017	0.000	0.000	0.000	0.000
40	A	41	VAL	0	-0.048	-0.037	25.876	-0.022	-0.022	0.000	0.000	0.000	0.000
41	A	42	GLU	-1	-0.883	-0.940	26.868	-0.174	-0.174	0.000	0.000	0.000	0.000
42	A	43	ILE	0	0.001	0.010	20.817	-0.013	-0.013	0.000	0.000	0.000	0.000
43	A	44	ILE	0	0.002	-0.002	22.595	-0.025	-0.025	0.000	0.000	0.000	0.000
44	A	45	ARG	1	0.909	0.958	24.114	0.180	0.180	0.000	0.000	0.000	0.000
45	A	46	MET	0	0.045	0.027	22.445	0.004	0.004	0.000	0.000	0.000	0.000
46	A	47	ALA	0	-0.010	-0.002	20.176	-0.021	-0.021	0.000	0.000	0.000	0.000
47	A	48	SER	0	-0.015	-0.009	21.209	-0.026	-0.026	0.000	0.000	0.000	0.000
48	A	49	ILE	0	0.016	0.008	24.083	-0.004	-0.004	0.000	0.000	0.000	0.000
49	A	50	TYR	0	-0.020	-0.007	19.251	0.008	0.008	0.000	0.000	0.000	0.000
50	A	51	SER	0	-0.017	-0.026	20.571	-0.037	-0.037	0.000	0.000	0.000	0.000
51	A	52	GLU	-1	-1.022	-0.998	21.495	-0.267	-0.267	0.000	0.000	0.000	0.000
52	A	53	GLU	-1	-0.921	-0.969	22.453	-0.328	-0.328	0.000	0.000	0.000	0.000
53	A	54	GLY	0	0.001	0.013	21.126	0.003	0.003	0.000	0.000	0.000	0.000
54	A	55	ASN	0	-0.010	0.011	17.088	-0.128	-0.128	0.000	0.000	0.000	0.000
55	A	56	ILE	0	0.006	-0.031	14.736	-0.031	-0.031	0.000	0.000	0.000	0.000
56	A	57	GLU	-1	-0.773	-0.844	10.691	-1.438	-1.438	0.000	0.000	0.000	0.000
57	A	58	HIS	0	0.016	0.010	13.306	0.009	0.009	0.000	0.000	0.000	0.000
58	A	59	ALA	0	0.035	0.017	15.374	0.042	0.042	0.000	0.000	0.000	0.000
59	A	60	PHE	0	-0.008	0.009	10.133	0.082	0.082	0.000	0.000	0.000	0.000
60	A	61	ILE	0	0.024	0.030	10.721	0.053	0.053	0.000	0.000	0.000	0.000
61	A	62	LEU	0	-0.021	-0.009	13.699	0.081	0.081	0.000	0.000	0.000	0.000
62	A	63	TYR	0	0.031	0.003	17.426	0.074	0.074	0.000	0.000	0.000	0.000
63	A	64	ASN	0	-0.031	-0.028	13.314	0.041	0.041	0.000	0.000	0.000	0.000
64	A	65	LYS	1	0.887	0.967	15.568	0.459	0.459	0.000	0.000	0.000	0.000
65	A	66	TYR	0	-0.020	-0.021	17.448	0.063	0.063	0.000	0.000	0.000	0.000
66	A	67	ILE	0	0.002	-0.006	18.096	0.047	0.047	0.000	0.000	0.000	0.000
67	A	68	THR	0	0.002	-0.011	16.329	0.033	0.033	0.000	0.000	0.000	0.000
68	A	69	LEU	0	-0.016	0.005	18.735	0.050	0.050	0.000	0.000	0.000	0.000
69	A	70	PHE	0	-0.025	-0.027	21.748	0.039	0.039	0.000	0.000	0.000	0.000
70	A	71	ILE	0	-0.055	-0.018	21.149	0.023	0.023	0.000	0.000	0.000	0.000
71	A	72	GLU	-1	-0.860	-0.913	18.025	-0.219	-0.219	0.000	0.000	0.000	0.000
72	A	73	LYS	1	0.822	0.903	16.501	0.258	0.258	0.000	0.000	0.000	0.000
73	A	74	LEU	0	-0.012	-0.003	22.490	0.027	0.027	0.000	0.000	0.000	0.000
74	A	75	PRO	0	-0.070	-0.052	24.759	0.021	0.021	0.000	0.000	0.000	0.000
75	A	76	LYS	1	0.862	0.924	21.415	0.177	0.177	0.000	0.000	0.000	0.000
76	A	77	HIS	0	-0.039	0.011	27.248	0.013	0.013	0.000	0.000	0.000	0.000
77	A	78	ARG	1	0.869	0.908	29.055	0.029	0.029	0.000	0.000	0.000	0.000
78	A	79	ASP	-1	-0.868	-0.936	32.414	-0.056	-0.056	0.000	0.000	0.000	0.000
79	A	80	TYR	0	-0.047	-0.026	29.900	-0.007	-0.007	0.000	0.000	0.000	0.000
80	A	81	LYS	1	0.904	0.943	32.722	0.078	0.078	0.000	0.000	0.000	0.000
81	A	82	SER	0	-0.006	-0.004	35.355	0.000	0.000	0.000	0.000	0.000	0.000
82	A	83	ALA	0	0.009	0.009	35.193	0.002	0.002	0.000	0.000	0.000	0.000
83	A	84	VAL	0	0.004	0.010	36.916	-0.008	-0.008	0.000	0.000	0.000	0.000
84	A	85	ILE	0	-0.040	-0.036	33.265	0.001	0.001	0.000	0.000	0.000	0.000
85	A	86	PRO	0	0.020	0.007	36.233	-0.007	-0.007	0.000	0.000	0.000	0.000
86	A	87	GLU	-1	-0.716	-0.842	33.548	-0.118	-0.118	0.000	0.000	0.000	0.000
87	A	88	LYS	1	0.925	0.993	31.593	0.116	0.116	0.000	0.000	0.000	0.000
88	A	89	LYS	1	0.973	0.991	32.350	0.124	0.124	0.000	0.000	0.000	0.000
89	A	90	ASP	-1	-0.824	-0.909	33.447	-0.182	-0.182	0.000	0.000	0.000	0.000
90	A	91	THR	0	-0.003	-0.003	27.728	-0.013	-0.013	0.000	0.000	0.000	0.000
91	A	92	VAL	0	0.017	0.011	28.420	-0.018	-0.018	0.000	0.000	0.000	0.000
92	A	93	LYS	1	0.885	0.936	29.028	0.167	0.167	0.000	0.000	0.000	0.000
93	A	94	LYS	1	0.919	0.963	27.691	0.234	0.234	0.000	0.000	0.000	0.000
94	A	95	LEU	0	0.014	0.008	23.380	-0.024	-0.024	0.000	0.000	0.000	0.000
95	A	96	LYS	1	0.819	0.903	24.684	0.201	0.201	0.000	0.000	0.000	0.000
96	A	97	GLU	-1	-0.793	-0.897	26.546	-0.246	-0.246	0.000	0.000	0.000	0.000
97	A	98	ILE	0	-0.069	-0.030	24.827	0.004	0.004	0.000	0.000	0.000	0.000
98	A	99	ALA	0	0.000	-0.001	21.766	-0.027	-0.027	0.000	0.000	0.000	0.000
99	A	100	PHE	0	0.022	0.013	19.667	-0.041	-0.041	0.000	0.000	0.000	0.000
100	A	101	PRO	0	0.060	0.031	20.415	-0.046	-0.046	0.000	0.000	0.000	0.000
101	A	102	LYS	1	0.834	0.902	21.067	0.425	0.425	0.000	0.000	0.000	0.000
102	A	103	ALA	0	0.009	0.005	16.498	-0.052	-0.052	0.000	0.000	0.000	0.000
103	A	104	GLU	-1	-0.949	-0.989	16.307	-0.614	-0.614	0.000	0.000	0.000	0.000
104	A	105	GLU	-1	-0.867	-0.909	17.911	-0.509	-0.509	0.000	0.000	0.000	0.000
105	A	106	LEU	0	0.005	-0.007	16.024	-0.033	-0.033	0.000	0.000	0.000	0.000
106	A	107	LYS	1	0.959	0.992	12.455	0.899	0.899	0.000	0.000	0.000	0.000
107	A	108	ALA	0	0.013	0.006	13.842	-0.098	-0.098	0.000	0.000	0.000	0.000
108	A	109	GLU	-1	-0.808	-0.892	16.121	-0.597	-0.597	0.000	0.000	0.000	0.000
109	A	110	LEU	0	-0.023	-0.009	11.154	0.021	0.021	0.000	0.000	0.000	0.000
110	A	111	LEU	0	0.012	0.013	10.240	-0.049	-0.049	0.000	0.000	0.000	0.000
111	A	112	LYS	1	0.862	0.946	12.478	0.585	0.585	0.000	0.000	0.000	0.000
112	A	113	ARG	1	0.819	0.900	13.388	0.770	0.770	0.000	0.000	0.000	0.000
113	A	114	TYR	0	0.007	-0.042	8.014	-0.089	-0.089	0.000	0.000	0.000	0.000
114	A	115	THR	0	-0.025	-0.033	11.108	0.023	0.023	0.000	0.000	0.000	0.000
115	A	116	LYS	1	0.787	0.880	13.018	0.486	0.486	0.000	0.000	0.000	0.000
116	A	117	GLU	-1	-0.781	-0.896	11.499	-1.002	-1.002	0.000	0.000	0.000	0.000
117	A	118	TYR	0	0.016	0.019	9.217	0.068	0.068	0.000	0.000	0.000	0.000
118	A	119	THR	0	-0.027	-0.012	11.997	0.098	0.098	0.000	0.000	0.000	0.000
119	A	120	GLU	-1	-0.764	-0.856	15.566	-0.309	-0.309	0.000	0.000	0.000	0.000
120	A	121	TYR	0	0.036	0.022	12.201	0.064	0.064	0.000	0.000	0.000	0.000
121	A	122	ASN	0	-0.038	-0.038	11.938	0.170	0.170	0.000	0.000	0.000	0.000
122	A	123	GLU	-1	-0.960	-0.983	15.775	-0.185	-0.185	0.000	0.000	0.000	0.000
123	A	124	GLU	-1	-0.902	-0.934	18.242	-0.076	-0.076	0.000	0.000	0.000	0.000
124	A	125	LYS	1	0.773	0.857	15.311	0.045	0.045	0.000	0.000	0.000	0.000
125	A	126	LYS	1	0.801	0.891	18.648	0.072	0.072	0.000	0.000	0.000	0.000
126	A	127	LYS	1	0.905	0.944	20.938	0.053	0.053	0.000	0.000	0.000	0.000
127	A	128	GLU	-1	-0.849	-0.913	19.717	0.043	0.043	0.000	0.000	0.000	0.000
128	A	129	ALA	0	0.006	0.005	21.259	0.015	0.015	0.000	0.000	0.000	0.000
129	A	130	GLU	-1	-0.827	-0.901	23.273	-0.009	-0.009	0.000	0.000	0.000	0.000
130	A	131	GLU	-1	-0.915	-0.947	26.373	-0.003	-0.003	0.000	0.000	0.000	0.000
131	A	132	LEU	0	-0.011	-0.003	24.521	0.003	0.003	0.000	0.000	0.000	0.000
132	A	133	ALA	0	-0.004	-0.007	27.180	0.004	0.004	0.000	0.000	0.000	0.000
133	A	134	ARG	1	0.928	0.968	28.833	-0.017	-0.017	0.000	0.000	0.000	0.000
134	A	135	ASN	0	-0.020	-0.029	30.407	-0.007	-0.007	0.000	0.000	0.000	0.000
135	A	136	MET	0	-0.035	-0.016	28.740	0.001	0.001	0.000	0.000	0.000	0.000
136	A	137	ALA	0	0.005	0.017	32.616	0.003	0.003	0.000	0.000	0.000	0.000
137	A	138	ILE	0	-0.080	-0.032	35.364	-0.006	-0.006	0.000	0.000	0.000	0.000
138	A	139	GLN	0	-0.038	-0.026	37.835	0.005	0.005	0.000	0.000	0.000	0.000
139	A	140	GLN	0	0.013	-0.001	40.347	-0.005	-0.005	0.000	0.000	0.000	0.000
140	A	141	GLU	-1	-0.892	-0.934	42.068	0.051	0.051	0.000	0.000	0.000	0.000
141	A	142	LEU	0	-0.112	-0.043	42.791	-0.004	-0.004	0.000	0.000	0.000	0.000

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