FMO DATABASE

FMODB ID: N2GVQ

Calculation Name: 2XG8-F-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2XG8

Chain ID: F

ChEMBL ID:

UniProt ID: P0A3F4

Base Structure: X-ray

Registration Date: 2025-07-09

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	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	152
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-498301.963988
FMO2-HF: Nuclear repulsion	465653.573447
FMO2-HF: Total energy	-32648.390541
FMO2-MP2: Total energy	-32744.266518

3D Structure Molmil

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(F:3:SER)

Summations of interaction energy for fragment #1(F:3: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.
-1.884	0.467	-0.006	-1.122	-1.221	0.003

Interaction energy analysis for fragmet #1(F:3:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.076 / q_NPA : 0.032

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].
4	F	4	GLU	-1	-0.962	-0.799	3.389	-0.080	0.510	0.007	-0.174	-0.423	0.000
5	F	5	ASN	0	0.172	-0.071	3.861	0.363	2.045	-0.009	-0.933	-0.739	0.003
6	F	5	ASN	0	-0.145	0.066	4.524	-0.758	-0.621	-0.001	-0.010	-0.125	0.000
7	F	6	TYR	0	0.032	-0.133	5.978	0.029	0.034	-0.002	0.000	-0.004	0.000
8	F	6	TYR	0	-0.130	0.066	7.799	-0.087	-0.087	0.000	0.000	0.000	0.000
9	F	7	LEU	0	0.121	-0.107	9.490	0.079	0.079	0.000	0.000	0.000	0.000
10	F	7	LEU	0	-0.087	0.116	11.895	0.005	0.005	0.000	0.000	0.000	0.000
11	F	8	ASN	0	0.056	-0.072	12.902	0.010	0.010	0.000	0.000	0.000	0.000
12	F	8	ASN	0	-0.073	0.076	16.366	0.013	0.013	0.000	0.000	0.000	0.000
13	F	9	HIS	0	0.144	-0.093	16.621	-0.007	-0.007	0.000	0.000	0.000	0.000
14	F	9	HIS	0	-0.070	0.111	18.424	0.007	0.007	0.000	0.000	0.000	0.000
15	F	10	PRO	0	-0.055	-0.129	19.271	0.028	0.028	0.000	0.000	0.000	0.000
16	F	11	THR	0	0.038	0.035	22.591	0.031	0.031	0.000	0.000	0.000	0.000
17	F	11	THR	0	-0.037	0.049	24.370	-0.004	-0.004	0.000	0.000	0.000	0.000
18	F	12	PHE	0	0.030	-0.073	21.121	0.034	0.034	0.000	0.000	0.000	0.000
19	F	12	PHE	0	-0.090	0.072	20.363	-0.005	-0.005	0.000	0.000	0.000	0.000
20	F	13	GLY	0	0.037	-0.092	19.785	-0.001	-0.001	0.000	0.000	0.000	0.000
21	F	14	LEU	0	0.213	0.035	15.750	-0.050	-0.050	0.000	0.000	0.000	0.000
22	F	14	LEU	0	-0.117	0.111	13.020	0.011	0.011	0.000	0.000	0.000	0.000
23	F	15	LEU	0	-0.010	-0.143	13.969	0.070	0.070	0.000	0.000	0.000	0.000
24	F	15	LEU	0	-0.101	0.093	13.678	0.002	0.002	0.000	0.000	0.000	0.000
25	F	16	TYR	0	0.094	-0.064	9.889	-0.010	-0.010	0.000	0.000	0.000	0.000
26	F	16	TYR	0	-0.071	0.084	9.387	0.144	0.144	0.000	0.000	0.000	0.000
27	F	17	GLN	0	0.133	-0.106	7.451	0.548	0.548	0.000	0.000	0.000	0.000
28	F	17	GLN	0	-0.113	0.101	5.181	-1.378	-1.441	-0.001	-0.005	0.070	0.000
29	F	18	ILE	0	0.043	-0.088	8.300	-0.169	-0.169	0.000	0.000	0.000	0.000
30	F	18	ILE	0	-0.131	0.066	11.176	0.086	0.086	0.000	0.000	0.000	0.000
31	F	19	CYS	0	0.036	-0.113	8.001	-0.152	-0.152	0.000	0.000	0.000	0.000
32	F	19	CYS	0	-0.097	0.091	9.873	0.162	0.162	0.000	0.000	0.000	0.000
33	F	20	SER	0	0.140	-0.082	8.223	0.094	0.094	0.000	0.000	0.000	0.000
34	F	20	SER	0	-0.031	0.102	7.708	-0.043	-0.043	0.000	0.000	0.000	0.000
35	F	21	PHE	0	0.049	-0.098	9.354	0.143	0.143	0.000	0.000	0.000	0.000
36	F	21	PHE	0	-0.081	0.089	13.892	0.020	0.020	0.000	0.000	0.000	0.000
37	F	22	GLY	0	-0.006	-0.087	12.721	0.155	0.155	0.000	0.000	0.000	0.000
38	F	23	ASP	0	-0.063	-0.006	11.720	-0.255	-0.255	0.000	0.000	0.000	0.000
39	F	23	ASP	-1	-0.896	-0.840	15.435	-0.653	-0.653	0.000	0.000	0.000	0.000
40	F	24	SER	0	0.132	-0.085	14.252	-0.015	-0.015	0.000	0.000	0.000	0.000
41	F	24	SER	0	-0.067	0.067	16.529	0.012	0.012	0.000	0.000	0.000	0.000
42	F	25	LYS	0	0.050	-0.083	14.155	0.010	0.010	0.000	0.000	0.000	0.000
43	F	25	LYS	1	0.805	1.007	15.272	0.608	0.608	0.000	0.000	0.000	0.000
44	F	26	GLU	0	0.035	-0.134	10.427	-0.020	-0.020	0.000	0.000	0.000	0.000
45	F	26	GLU	-1	-0.866	-0.772	7.494	-2.982	-2.982	0.000	0.000	0.000	0.000
46	F	27	LEU	0	0.103	-0.086	11.330	0.190	0.190	0.000	0.000	0.000	0.000
47	F	27	LEU	0	-0.138	0.068	12.246	0.038	0.038	0.000	0.000	0.000	0.000
48	F	28	PHE	0	0.091	-0.085	11.004	-0.334	-0.334	0.000	0.000	0.000	0.000
49	F	28	PHE	0	-0.065	0.100	9.310	0.019	0.019	0.000	0.000	0.000	0.000
50	F	29	ALA	0	0.072	-0.105	12.702	0.151	0.151	0.000	0.000	0.000	0.000
51	F	29	ALA	0	-0.070	0.099	14.141	0.013	0.013	0.000	0.000	0.000	0.000
52	F	30	THR	0	0.063	-0.077	14.269	-0.084	-0.084	0.000	0.000	0.000	0.000
53	F	30	THR	0	-0.070	0.072	18.495	0.016	0.016	0.000	0.000	0.000	0.000
54	F	31	LEU	0	0.105	-0.084	14.874	0.007	0.007	0.000	0.000	0.000	0.000
55	F	31	LEU	0	-0.077	0.127	12.414	-0.003	-0.003	0.000	0.000	0.000	0.000
56	F	32	TYR	0	0.061	-0.126	15.726	0.039	0.039	0.000	0.000	0.000	0.000
57	F	32	TYR	0	-0.020	0.135	17.857	-0.008	-0.008	0.000	0.000	0.000	0.000
58	F	33	ALA	0	0.105	-0.071	19.349	0.044	0.044	0.000	0.000	0.000	0.000
59	F	33	ALA	0	-0.059	0.102	21.141	-0.001	-0.001	0.000	0.000	0.000	0.000
60	F	34	GLN	0	0.034	-0.110	19.588	-0.061	-0.061	0.000	0.000	0.000	0.000
61	F	34	GLN	0	-0.096	0.104	19.409	-0.024	-0.024	0.000	0.000	0.000	0.000
62	F	35	ARG	0	0.134	-0.105	19.523	0.046	0.046	0.000	0.000	0.000	0.000
63	F	35	ARG	1	0.729	0.992	16.083	0.493	0.493	0.000	0.000	0.000	0.000
64	F	36	LEU	0	-0.031	-0.123	19.822	0.024	0.024	0.000	0.000	0.000	0.000
65	F	36	LEU	0	-0.029	0.111	20.791	0.001	0.001	0.000	0.000	0.000	0.000
66	F	37	PHE	0	0.063	-0.083	17.272	-0.052	-0.052	0.000	0.000	0.000	0.000
67	F	37	PHE	0	-0.044	0.089	16.004	0.014	0.014	0.000	0.000	0.000	0.000
68	F	38	PHE	0	0.039	-0.101	16.437	0.091	0.091	0.000	0.000	0.000	0.000
69	F	38	PHE	0	-0.036	0.101	16.505	0.014	0.014	0.000	0.000	0.000	0.000
70	F	39	LEU	0	0.189	-0.048	15.374	-0.152	-0.152	0.000	0.000	0.000	0.000
71	F	39	LEU	0	-0.134	0.089	15.245	0.012	0.012	0.000	0.000	0.000	0.000
72	F	40	VAL	0	0.077	-0.124	14.608	0.125	0.125	0.000	0.000	0.000	0.000
73	F	40	VAL	0	-0.091	0.108	13.596	-0.007	-0.007	0.000	0.000	0.000	0.000
74	F	41	ALA	0	0.157	-0.080	14.877	-0.121	-0.121	0.000	0.000	0.000	0.000
75	F	41	ALA	0	-0.078	0.096	17.576	0.017	0.017	0.000	0.000	0.000	0.000
76	F	42	PHE	0	0.022	-0.097	16.623	0.048	0.048	0.000	0.000	0.000	0.000
77	F	42	PHE	0	-0.118	0.086	11.539	0.016	0.016	0.000	0.000	0.000	0.000
78	F	43	ASP	0	0.224	-0.025	17.782	-0.021	-0.021	0.000	0.000	0.000	0.000
79	F	43	ASP	-1	-0.931	-0.820	20.591	-0.382	-0.382	0.000	0.000	0.000	0.000
80	F	44	ALA	0	0.086	-0.063	20.805	0.003	0.003	0.000	0.000	0.000	0.000
81	F	44	ALA	0	-0.118	0.071	23.883	0.005	0.005	0.000	0.000	0.000	0.000
82	F	45	ARG	0	0.054	-0.104	21.488	-0.032	-0.032	0.000	0.000	0.000	0.000
83	F	45	ARG	1	0.833	1.052	24.942	0.291	0.291	0.000	0.000	0.000	0.000
84	F	46	GLY	0	0.004	-0.151	22.068	0.031	0.031	0.000	0.000	0.000	0.000
85	F	47	THR	0	0.080	0.056	18.093	0.007	0.007	0.000	0.000	0.000	0.000
86	F	47	THR	0	-0.045	0.082	17.034	-0.032	-0.032	0.000	0.000	0.000	0.000
87	F	48	ARG	0	0.089	-0.102	18.905	0.032	0.032	0.000	0.000	0.000	0.000
88	F	48	ARG	1	0.729	0.997	20.172	0.448	0.448	0.000	0.000	0.000	0.000
89	F	49	PHE	0	0.027	-0.117	18.318	-0.079	-0.079	0.000	0.000	0.000	0.000
90	F	49	PHE	0	-0.043	0.093	16.291	-0.006	-0.006	0.000	0.000	0.000	0.000
91	F	50	GLU	0	0.139	-0.092	19.432	0.054	0.054	0.000	0.000	0.000	0.000
92	F	50	GLU	-1	-0.888	-0.755	19.850	-0.494	-0.494	0.000	0.000	0.000	0.000
93	F	51	PRO	0	-0.040	-0.127	20.029	-0.054	-0.054	0.000	0.000	0.000	0.000
94	F	52	ILE	0	0.031	-0.020	20.955	0.040	0.040	0.000	0.000	0.000	0.000
95	F	52	ILE	0	-0.044	0.135	18.145	-0.003	-0.003	0.000	0.000	0.000	0.000
96	F	53	GLY	0	0.066	-0.081	21.800	-0.004	-0.004	0.000	0.000	0.000	0.000
97	F	54	ARG	0	0.097	-0.003	20.804	-0.028	-0.028	0.000	0.000	0.000	0.000
98	F	54	ARG	1	0.927	1.088	21.206	0.341	0.341	0.000	0.000	0.000	0.000
99	F	55	ASN	0	0.009	-0.079	21.181	-0.022	-0.022	0.000	0.000	0.000	0.000
100	F	55	ASN	0	-0.032	0.078	25.045	-0.004	-0.004	0.000	0.000	0.000	0.000
101	F	56	GLU	0	0.184	-0.071	22.517	0.005	0.005	0.000	0.000	0.000	0.000
102	F	56	GLU	-1	-0.973	-0.833	21.404	-0.414	-0.414	0.000	0.000	0.000	0.000
103	F	57	ALA	0	0.111	-0.091	18.401	-0.019	-0.019	0.000	0.000	0.000	0.000
104	F	57	ALA	0	-0.067	0.095	17.562	-0.003	-0.003	0.000	0.000	0.000	0.000
105	F	58	ARG	0	0.095	-0.080	17.438	-0.083	-0.083	0.000	0.000	0.000	0.000
106	F	58	ARG	1	0.768	1.017	18.984	0.353	0.353	0.000	0.000	0.000	0.000
107	F	59	MET	0	0.111	-0.083	18.598	-0.023	-0.023	0.000	0.000	0.000	0.000
108	F	59	MET	0	-0.058	0.111	22.273	0.011	0.011	0.000	0.000	0.000	0.000
109	F	60	LEU	0	0.025	-0.118	18.015	0.039	0.039	0.000	0.000	0.000	0.000
110	F	60	LEU	0	-0.059	0.113	17.247	-0.022	-0.022	0.000	0.000	0.000	0.000
111	F	61	VAL	0	0.112	-0.091	14.624	-0.034	-0.034	0.000	0.000	0.000	0.000
112	F	61	VAL	0	-0.085	0.096	13.239	-0.009	-0.009	0.000	0.000	0.000	0.000
113	F	62	ASP	0	0.107	-0.074	15.332	-0.038	-0.038	0.000	0.000	0.000	0.000
114	F	62	ASP	-1	-0.952	-0.809	19.057	-0.339	-0.339	0.000	0.000	0.000	0.000
115	F	63	ASN	0	0.083	-0.087	17.913	0.027	0.027	0.000	0.000	0.000	0.000
116	F	63	ASN	0	-0.100	0.070	19.752	0.036	0.036	0.000	0.000	0.000	0.000
117	F	64	ARG	0	0.141	-0.087	14.656	0.077	0.077	0.000	0.000	0.000	0.000
118	F	64	ARG	1	0.755	1.019	11.232	1.054	1.054	0.000	0.000	0.000	0.000
119	F	65	LEU	0	0.109	-0.113	13.861	-0.030	-0.030	0.000	0.000	0.000	0.000
120	F	65	LEU	0	-0.136	0.098	12.799	0.015	0.015	0.000	0.000	0.000	0.000
121	F	66	ARG	0	0.023	-0.128	14.836	0.051	0.051	0.000	0.000	0.000	0.000
122	F	66	ARG	1	0.740	0.967	19.474	0.321	0.321	0.000	0.000	0.000	0.000
123	F	67	GLN	0	0.142	-0.068	17.305	0.061	0.061	0.000	0.000	0.000	0.000
124	F	67	GLN	0	-0.090	0.122	15.900	-0.085	-0.085	0.000	0.000	0.000	0.000
125	F	68	LEU	0	0.100	-0.082	12.747	0.093	0.093	0.000	0.000	0.000	0.000
126	F	68	LEU	0	-0.090	0.113	9.361	-0.022	-0.022	0.000	0.000	0.000	0.000
127	F	69	ARG	0	0.021	-0.103	13.652	0.048	0.048	0.000	0.000	0.000	0.000
128	F	69	ARG	1	0.827	1.060	13.857	0.259	0.259	0.000	0.000	0.000	0.000
129	F	70	ARG	0	-0.057	-0.155	15.407	0.067	0.067	0.000	0.000	0.000	0.000
130	F	70	ARG	1	0.980	0.989	15.549	0.078	0.078	0.000	0.000	0.000	0.000
131	F	79	GLN	0	0.180	0.033	22.886	-0.001	-0.001	0.000	0.000	0.000	0.000
132	F	79	GLN	0	-0.093	0.095	23.985	0.012	0.012	0.000	0.000	0.000	0.000
133	F	80	LEU	0	0.115	-0.101	23.187	0.002	0.002	0.000	0.000	0.000	0.000
134	F	80	LEU	0	-0.049	0.118	21.984	-0.001	-0.001	0.000	0.000	0.000	0.000
135	F	81	GLN	0	0.101	-0.091	23.464	-0.013	-0.013	0.000	0.000	0.000	0.000
136	F	81	GLN	0	-0.057	0.105	22.836	0.007	0.007	0.000	0.000	0.000	0.000
137	F	82	GLN	0	0.090	-0.091	24.793	-0.007	-0.007	0.000	0.000	0.000	0.000
138	F	82	GLN	0	-0.075	0.091	27.386	0.007	0.007	0.000	0.000	0.000	0.000
139	F	83	VAL	0	0.101	-0.107	27.644	0.000	0.000	0.000	0.000	0.000	0.000
140	F	83	VAL	0	-0.085	0.109	27.923	0.000	0.000	0.000	0.000	0.000	0.000
141	F	84	PHE	0	0.141	-0.044	27.366	-0.002	-0.002	0.000	0.000	0.000	0.000
142	F	84	PHE	0	-0.125	0.072	26.702	-0.002	-0.002	0.000	0.000	0.000	0.000
143	F	85	LYS	0	0.086	-0.081	28.711	-0.007	-0.007	0.000	0.000	0.000	0.000
144	F	85	LYS	1	0.839	1.038	27.159	-0.012	-0.012	0.000	0.000	0.000	0.000
145	F	86	GLN	0	0.082	-0.081	30.634	0.000	0.000	0.000	0.000	0.000	0.000
146	F	86	GLN	0	-0.097	0.084	32.315	0.005	0.005	0.000	0.000	0.000	0.000
147	F	87	THR	0	-0.004	-0.086	32.214	0.003	0.003	0.000	0.000	0.000	0.000
148	F	87	THR	0	-0.090	0.031	31.992	0.000	0.000	0.000	0.000	0.000	0.000
149	F	88	PHE	0	0.046	-0.077	32.248	-0.001	-0.001	0.000	0.000	0.000	0.000
150	F	88	PHE	0	-0.095	0.073	29.758	-0.003	-0.003	0.000	0.000	0.000	0.000
151	F	89	LEU	0	-0.040	-0.104	32.847	-0.003	-0.003	0.000	0.000	0.000	0.000
152	F	89	LEU	0	0.030	0.013	30.531	0.001	0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(F:3:SER)