FMO DATABASE

FMODB ID: VRN41

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1213864.019657
FMO2-HF: Nuclear repulsion	1156846.256015
FMO2-HF: Total energy	-57017.763641
FMO2-MP2: Total energy	-57187.125562

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.
-4.401	-0.217	3.291	-2.732	-4.741	-0.008

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 : -0.043 / q_NPA : -0.036

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	-0.028	-0.031	3.803	-1.445	-0.317	-0.014	-0.399	-0.715	0.002
4	A	5	GLY	0	0.009	0.015	6.049	0.479	0.479	0.000	0.000	0.000	0.000
5	A	6	ASP	-1	-0.830	-0.880	5.622	0.169	0.169	0.000	0.000	0.000	0.000
6	A	7	VAL	0	-0.018	-0.027	6.951	-0.418	-0.418	0.000	0.000	0.000	0.000
7	A	8	SER	0	-0.077	-0.052	8.238	0.040	0.040	0.000	0.000	0.000	0.000
8	A	9	LEU	0	-0.034	-0.013	2.456	-0.690	-0.207	1.075	-0.438	-1.120	-0.005
9	A	10	PRO	0	0.016	0.001	4.992	0.008	0.008	0.000	0.000	0.000	0.000
10	A	11	PRO	0	0.049	0.020	5.628	-1.005	-1.005	0.000	0.000	0.000	0.000
11	A	12	GLU	-1	-0.888	-0.942	7.264	-1.879	-1.879	0.000	0.000	0.000	0.000
12	A	13	ASP	-1	-0.869	-0.928	2.121	-5.724	-5.065	1.486	-0.894	-1.251	0.003
13	A	14	ARG	1	0.785	0.902	2.874	-0.757	0.399	0.447	-0.684	-0.918	-0.007
14	A	15	VAL	0	-0.007	-0.012	4.570	0.568	0.564	-0.001	-0.002	0.008	0.000
15	A	16	ARG	1	0.811	0.876	4.532	3.271	3.369	-0.001	-0.004	-0.093	0.000
16	A	17	ALA	0	0.044	0.039	2.531	0.723	1.273	0.299	-0.284	-0.565	-0.001
17	A	18	LEU	0	0.024	0.014	4.329	1.252	1.366	0.000	-0.027	-0.087	0.000
18	A	19	SER	0	-0.066	-0.033	7.890	0.463	0.463	0.000	0.000	0.000	0.000
19	A	20	GLN	0	-0.031	-0.015	6.192	0.579	0.579	0.000	0.000	0.000	0.000
20	A	21	LEU	0	0.021	0.026	6.905	0.385	0.385	0.000	0.000	0.000	0.000
21	A	22	GLY	0	-0.018	-0.014	9.312	0.175	0.175	0.000	0.000	0.000	0.000
22	A	23	SER	0	-0.069	-0.040	10.883	0.115	0.115	0.000	0.000	0.000	0.000
23	A	24	ALA	0	0.035	0.025	11.701	0.093	0.093	0.000	0.000	0.000	0.000
24	A	25	VAL	0	-0.083	-0.048	13.626	0.009	0.009	0.000	0.000	0.000	0.000
25	A	26	GLU	-1	-0.788	-0.889	17.411	0.029	0.029	0.000	0.000	0.000	0.000
26	A	27	VAL	0	-0.050	-0.022	20.183	-0.013	-0.013	0.000	0.000	0.000	0.000
27	A	28	ASN	0	0.015	0.006	23.833	0.014	0.014	0.000	0.000	0.000	0.000
28	A	29	GLU	-1	-0.749	-0.892	26.601	0.009	0.009	0.000	0.000	0.000	0.000
29	A	30	ASP	-1	-0.891	-0.917	29.334	0.031	0.031	0.000	0.000	0.000	0.000
30	A	31	ILE	0	-0.098	-0.042	28.110	-0.005	-0.005	0.000	0.000	0.000	0.000
31	A	32	PRO	0	0.022	0.006	31.282	-0.006	-0.006	0.000	0.000	0.000	0.000
32	A	33	PRO	0	0.105	0.048	30.143	-0.007	-0.007	0.000	0.000	0.000	0.000
33	A	34	ARG	1	0.831	0.885	30.594	0.051	0.051	0.000	0.000	0.000	0.000
34	A	35	ARG	1	0.944	0.972	30.765	0.012	0.012	0.000	0.000	0.000	0.000
35	A	36	TYR	0	0.122	0.061	24.233	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	37	PHE	0	-0.014	-0.013	27.705	-0.014	-0.014	0.000	0.000	0.000	0.000
37	A	38	ARG	1	0.836	0.917	29.901	0.054	0.054	0.000	0.000	0.000	0.000
38	A	39	SER	0	0.041	0.017	26.753	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	40	GLY	0	0.023	0.015	25.155	-0.009	-0.009	0.000	0.000	0.000	0.000
40	A	41	VAL	0	-0.042	-0.032	25.646	-0.022	-0.022	0.000	0.000	0.000	0.000
41	A	42	GLU	-1	-0.907	-0.958	26.340	-0.106	-0.106	0.000	0.000	0.000	0.000
42	A	43	ILE	0	-0.019	0.005	20.477	-0.011	-0.011	0.000	0.000	0.000	0.000
43	A	44	ILE	0	-0.003	-0.006	22.492	-0.024	-0.024	0.000	0.000	0.000	0.000
44	A	45	ARG	1	0.911	0.952	24.091	0.122	0.122	0.000	0.000	0.000	0.000
45	A	46	MET	0	0.051	0.026	22.541	0.000	0.000	0.000	0.000	0.000	0.000
46	A	47	ALA	0	-0.011	0.003	20.173	-0.017	-0.017	0.000	0.000	0.000	0.000
47	A	48	SER	0	-0.019	-0.016	21.380	-0.028	-0.028	0.000	0.000	0.000	0.000
48	A	49	ILE	0	0.016	0.021	24.179	-0.004	-0.004	0.000	0.000	0.000	0.000
49	A	50	TYR	0	-0.007	0.001	19.478	0.000	0.000	0.000	0.000	0.000	0.000
50	A	51	SER	0	-0.008	-0.020	20.493	-0.033	-0.033	0.000	0.000	0.000	0.000
51	A	52	GLU	-1	-1.037	-1.014	21.438	-0.232	-0.232	0.000	0.000	0.000	0.000
52	A	53	GLU	-1	-0.926	-0.965	22.929	-0.236	-0.236	0.000	0.000	0.000	0.000
53	A	54	GLY	0	-0.012	0.005	21.437	0.006	0.006	0.000	0.000	0.000	0.000
54	A	55	ASN	0	-0.021	-0.001	16.739	-0.119	-0.119	0.000	0.000	0.000	0.000
55	A	56	ILE	0	0.024	-0.015	15.104	-0.007	-0.007	0.000	0.000	0.000	0.000
56	A	57	GLU	-1	-0.774	-0.849	10.936	-1.301	-1.301	0.000	0.000	0.000	0.000
57	A	58	HIS	0	0.005	0.006	13.296	0.029	0.029	0.000	0.000	0.000	0.000
58	A	59	ALA	0	0.027	0.013	15.413	0.037	0.037	0.000	0.000	0.000	0.000
59	A	60	PHE	0	-0.003	0.007	10.107	0.077	0.077	0.000	0.000	0.000	0.000
60	A	61	ILE	0	0.021	0.032	10.709	0.043	0.043	0.000	0.000	0.000	0.000
61	A	62	LEU	0	-0.016	-0.009	13.626	0.077	0.077	0.000	0.000	0.000	0.000
62	A	63	TYR	0	0.029	0.000	17.319	0.061	0.061	0.000	0.000	0.000	0.000
63	A	64	ASN	0	-0.028	-0.026	13.286	0.032	0.032	0.000	0.000	0.000	0.000
64	A	65	LYS	1	0.922	0.991	15.771	0.196	0.196	0.000	0.000	0.000	0.000
65	A	66	TYR	0	-0.025	-0.025	17.104	0.052	0.052	0.000	0.000	0.000	0.000
66	A	67	ILE	0	0.007	-0.009	18.226	0.041	0.041	0.000	0.000	0.000	0.000
67	A	68	THR	0	-0.005	-0.006	16.021	0.027	0.027	0.000	0.000	0.000	0.000
68	A	69	LEU	0	-0.019	0.002	18.582	0.043	0.043	0.000	0.000	0.000	0.000
69	A	70	PHE	0	-0.043	-0.036	21.335	0.031	0.031	0.000	0.000	0.000	0.000
70	A	71	ILE	0	-0.048	-0.018	21.108	0.017	0.017	0.000	0.000	0.000	0.000
71	A	72	GLU	-1	-0.871	-0.922	17.728	-0.114	-0.114	0.000	0.000	0.000	0.000
72	A	73	LYS	1	0.844	0.914	16.199	0.083	0.083	0.000	0.000	0.000	0.000
73	A	74	LEU	0	-0.014	-0.008	22.108	0.022	0.022	0.000	0.000	0.000	0.000
74	A	75	PRO	0	-0.071	-0.049	24.565	0.017	0.017	0.000	0.000	0.000	0.000
75	A	76	LYS	1	0.859	0.923	20.840	0.089	0.089	0.000	0.000	0.000	0.000
76	A	77	HIS	0	-0.035	0.007	26.650	0.012	0.012	0.000	0.000	0.000	0.000
77	A	78	ARG	1	0.913	0.931	28.456	-0.033	-0.033	0.000	0.000	0.000	0.000
78	A	79	ASP	-1	-0.913	-0.959	31.761	-0.012	-0.012	0.000	0.000	0.000	0.000
79	A	80	TYR	0	-0.053	-0.030	30.009	-0.010	-0.010	0.000	0.000	0.000	0.000
80	A	81	LYS	1	0.935	0.963	32.328	0.051	0.051	0.000	0.000	0.000	0.000
81	A	82	SER	0	0.013	-0.001	34.740	-0.004	-0.004	0.000	0.000	0.000	0.000
82	A	83	ALA	0	-0.005	0.025	34.644	0.001	0.001	0.000	0.000	0.000	0.000
83	A	84	VAL	0	0.009	0.005	36.785	-0.007	-0.007	0.000	0.000	0.000	0.000
84	A	85	ILE	0	-0.055	-0.042	32.717	0.001	0.001	0.000	0.000	0.000	0.000
85	A	86	PRO	0	0.012	0.000	36.346	-0.007	-0.007	0.000	0.000	0.000	0.000
86	A	87	GLU	-1	-0.712	-0.840	33.491	-0.077	-0.077	0.000	0.000	0.000	0.000
87	A	88	LYS	1	0.939	0.990	31.666	0.079	0.079	0.000	0.000	0.000	0.000
88	A	89	LYS	1	0.985	0.997	32.347	0.098	0.098	0.000	0.000	0.000	0.000
89	A	90	ASP	-1	-0.824	-0.914	33.379	-0.149	-0.149	0.000	0.000	0.000	0.000
90	A	91	THR	0	0.009	0.008	27.867	-0.011	-0.011	0.000	0.000	0.000	0.000
91	A	92	VAL	0	0.003	0.001	28.487	-0.016	-0.016	0.000	0.000	0.000	0.000
92	A	93	LYS	1	0.884	0.934	29.128	0.133	0.133	0.000	0.000	0.000	0.000
93	A	94	LYS	1	0.957	0.986	27.609	0.183	0.183	0.000	0.000	0.000	0.000
94	A	95	LEU	0	0.008	0.006	23.435	-0.021	-0.021	0.000	0.000	0.000	0.000
95	A	96	LYS	1	0.858	0.930	24.617	0.173	0.173	0.000	0.000	0.000	0.000
96	A	97	GLU	-1	-0.836	-0.927	26.545	-0.227	-0.227	0.000	0.000	0.000	0.000
97	A	98	ILE	0	-0.063	-0.024	24.999	0.000	0.000	0.000	0.000	0.000	0.000
98	A	99	ALA	0	-0.020	-0.009	21.731	-0.024	-0.024	0.000	0.000	0.000	0.000
99	A	100	PHE	0	0.026	0.007	19.395	-0.034	-0.034	0.000	0.000	0.000	0.000
100	A	101	PRO	0	0.062	0.037	20.447	-0.046	-0.046	0.000	0.000	0.000	0.000
101	A	102	LYS	1	0.842	0.921	21.037	0.375	0.375	0.000	0.000	0.000	0.000
102	A	103	ALA	0	-0.004	0.001	16.577	-0.049	-0.049	0.000	0.000	0.000	0.000
103	A	104	GLU	-1	-0.934	-0.977	16.424	-0.569	-0.569	0.000	0.000	0.000	0.000
104	A	105	GLU	-1	-0.857	-0.919	17.700	-0.472	-0.472	0.000	0.000	0.000	0.000
105	A	106	LEU	0	-0.021	-0.025	15.850	-0.036	-0.036	0.000	0.000	0.000	0.000
106	A	107	LYS	1	0.968	1.002	11.808	0.965	0.965	0.000	0.000	0.000	0.000
107	A	108	ALA	0	0.016	0.005	13.810	-0.115	-0.115	0.000	0.000	0.000	0.000
108	A	109	GLU	-1	-0.794	-0.876	16.365	-0.595	-0.595	0.000	0.000	0.000	0.000
109	A	110	LEU	0	-0.008	-0.003	11.105	0.018	0.018	0.000	0.000	0.000	0.000
110	A	111	LEU	0	0.022	0.016	10.513	-0.087	-0.087	0.000	0.000	0.000	0.000
111	A	112	LYS	1	0.862	0.945	12.828	0.571	0.571	0.000	0.000	0.000	0.000
112	A	113	ARG	1	0.807	0.879	13.781	0.732	0.732	0.000	0.000	0.000	0.000
113	A	114	TYR	0	0.002	-0.042	8.234	-0.114	-0.114	0.000	0.000	0.000	0.000
114	A	115	THR	0	-0.021	-0.032	11.562	-0.006	-0.006	0.000	0.000	0.000	0.000
115	A	116	LYS	1	0.799	0.894	13.263	0.513	0.513	0.000	0.000	0.000	0.000
116	A	117	GLU	-1	-0.796	-0.899	11.704	-1.021	-1.021	0.000	0.000	0.000	0.000
117	A	118	TYR	0	0.024	0.016	9.291	0.092	0.092	0.000	0.000	0.000	0.000
118	A	119	THR	0	-0.010	-0.006	12.203	0.089	0.089	0.000	0.000	0.000	0.000
119	A	120	GLU	-1	-0.794	-0.876	15.712	-0.347	-0.347	0.000	0.000	0.000	0.000
120	A	121	TYR	0	0.034	0.028	12.404	0.077	0.077	0.000	0.000	0.000	0.000
121	A	122	ASN	0	-0.045	-0.051	12.044	0.157	0.157	0.000	0.000	0.000	0.000
122	A	123	GLU	-1	-0.978	-0.981	15.870	-0.254	-0.254	0.000	0.000	0.000	0.000
123	A	124	GLU	-1	-0.891	-0.927	18.396	-0.148	-0.148	0.000	0.000	0.000	0.000
124	A	125	LYS	1	0.764	0.858	15.648	0.166	0.166	0.000	0.000	0.000	0.000
125	A	126	LYS	1	0.862	0.930	18.810	0.171	0.171	0.000	0.000	0.000	0.000
126	A	127	LYS	1	0.934	0.966	21.116	0.119	0.119	0.000	0.000	0.000	0.000
127	A	128	GLU	-1	-0.855	-0.916	20.185	-0.052	-0.052	0.000	0.000	0.000	0.000
128	A	129	ALA	0	-0.009	-0.007	21.761	0.022	0.022	0.000	0.000	0.000	0.000
129	A	130	GLU	-1	-0.887	-0.942	23.750	-0.089	-0.089	0.000	0.000	0.000	0.000
130	A	131	GLU	-1	-0.918	-0.959	26.704	-0.046	-0.046	0.000	0.000	0.000	0.000
131	A	132	LEU	0	-0.018	-0.001	24.965	0.009	0.009	0.000	0.000	0.000	0.000
132	A	133	ALA	0	0.007	-0.003	27.710	0.009	0.009	0.000	0.000	0.000	0.000
133	A	134	ARG	1	0.936	0.972	29.362	0.032	0.032	0.000	0.000	0.000	0.000
134	A	135	ASN	0	-0.046	-0.049	30.649	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	136	MET	0	-0.030	-0.002	29.097	0.005	0.005	0.000	0.000	0.000	0.000
136	A	137	ALA	0	-0.031	-0.006	33.131	0.003	0.003	0.000	0.000	0.000	0.000
137	A	138	ILE	0	-0.083	-0.031	35.572	-0.002	-0.002	0.000	0.000	0.000	0.000
138	A	139	GLN	0	0.004	-0.009	38.056	0.006	0.006	0.000	0.000	0.000	0.000
139	A	140	GLN	0	0.021	0.004	40.813	-0.003	-0.003	0.000	0.000	0.000	0.000
140	A	141	GLU	-1	-0.905	-0.938	42.473	0.023	0.023	0.000	0.000	0.000	0.000
141	A	142	LEU	0	-0.106	-0.039	42.856	-0.002	-0.002	0.000	0.000	0.000	0.000

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