FMO DATABASE

FMODB ID: 8NV8Y

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	OptHSide
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	-497299.440788
FMO2-HF: Nuclear repulsion	464651.461791
FMO2-HF: Total energy	-32647.978997
FMO2-MP2: Total energy	-32743.906587

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.
-3.189	-0.81	-0.013	-1.156	-1.212	0.005

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 : 0.068 / q_NPA : 0.023

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	-0.944	-0.786	3.686	0.054	0.587	0.002	-0.166	-0.370	0.000
5	F	5	ASN	0	0.089	-0.105	3.836	-0.789	0.993	-0.014	-0.983	-0.786	0.005
6	F	5	ASN	0	-0.081	0.097	4.547	-0.997	-0.933	-0.001	-0.007	-0.056	0.000
7	F	6	TYR	0	0.061	-0.085	6.548	0.051	0.051	0.000	0.000	0.000	0.000
8	F	6	TYR	0	-0.160	0.038	7.840	-0.081	-0.081	0.000	0.000	0.000	0.000
9	F	7	LEU	0	0.140	-0.130	10.127	0.017	0.017	0.000	0.000	0.000	0.000
10	F	7	LEU	0	-0.076	0.132	12.260	0.010	0.010	0.000	0.000	0.000	0.000
11	F	8	ASN	0	0.065	-0.055	13.469	0.023	0.023	0.000	0.000	0.000	0.000
12	F	8	ASN	0	-0.097	0.070	17.330	0.019	0.019	0.000	0.000	0.000	0.000
13	F	9	HIS	0	0.154	-0.101	17.114	-0.006	-0.006	0.000	0.000	0.000	0.000
14	F	9	HIS	0	-0.090	0.105	18.668	0.016	0.016	0.000	0.000	0.000	0.000
15	F	10	PRO	0	-0.042	-0.119	19.592	0.029	0.029	0.000	0.000	0.000	0.000
16	F	11	THR	0	0.052	0.045	23.120	0.030	0.030	0.000	0.000	0.000	0.000
17	F	11	THR	0	-0.059	0.040	24.351	-0.005	-0.005	0.000	0.000	0.000	0.000
18	F	12	PHE	0	0.020	-0.084	21.521	0.032	0.032	0.000	0.000	0.000	0.000
19	F	12	PHE	0	-0.084	0.074	20.756	-0.001	-0.001	0.000	0.000	0.000	0.000
20	F	13	GLY	0	0.056	-0.080	19.967	-0.004	-0.004	0.000	0.000	0.000	0.000
21	F	14	LEU	0	0.178	0.030	15.876	-0.052	-0.052	0.000	0.000	0.000	0.000
22	F	14	LEU	0	-0.113	0.109	13.344	0.008	0.008	0.000	0.000	0.000	0.000
23	F	15	LEU	0	-0.006	-0.138	14.159	0.077	0.077	0.000	0.000	0.000	0.000
24	F	15	LEU	0	-0.110	0.091	13.866	0.001	0.001	0.000	0.000	0.000	0.000
25	F	16	TYR	0	0.111	-0.072	10.186	-0.087	-0.087	0.000	0.000	0.000	0.000
26	F	16	TYR	0	-0.087	0.079	9.413	0.128	0.128	0.000	0.000	0.000	0.000
27	F	17	GLN	0	0.133	-0.120	7.815	0.509	0.509	0.000	0.000	0.000	0.000
28	F	17	GLN	0	-0.103	0.112	5.930	-1.034	-1.034	0.000	0.000	0.000	0.000
29	F	18	ILE	0	0.060	-0.071	7.721	-0.244	-0.244	0.000	0.000	0.000	0.000
30	F	18	ILE	0	-0.138	0.059	10.972	0.079	0.079	0.000	0.000	0.000	0.000
31	F	19	CYS	0	0.038	-0.101	7.850	-0.133	-0.133	0.000	0.000	0.000	0.000
32	F	19	CYS	0	-0.112	0.076	9.429	0.140	0.140	0.000	0.000	0.000	0.000
33	F	20	SER	0	0.140	-0.085	8.923	0.055	0.055	0.000	0.000	0.000	0.000
34	F	20	SER	0	-0.027	0.101	8.423	-0.062	-0.062	0.000	0.000	0.000	0.000
35	F	21	PHE	0	0.038	-0.097	10.186	0.140	0.140	0.000	0.000	0.000	0.000
36	F	21	PHE	0	-0.070	0.085	14.566	0.015	0.015	0.000	0.000	0.000	0.000
37	F	22	GLY	0	0.016	-0.075	13.069	0.160	0.160	0.000	0.000	0.000	0.000
38	F	23	ASP	0	-0.224	-0.063	12.361	-0.218	-0.218	0.000	0.000	0.000	0.000
39	F	23	ASP	-1	-0.902	-0.838	15.892	-0.617	-0.617	0.000	0.000	0.000	0.000
40	F	24	SER	0	0.240	-0.083	13.779	0.040	0.040	0.000	0.000	0.000	0.000
41	F	24	SER	0	-0.028	0.065	16.491	0.010	0.010	0.000	0.000	0.000	0.000
42	F	25	LYS	0	0.101	-0.010	14.611	-0.034	-0.034	0.000	0.000	0.000	0.000
43	F	25	LYS	1	0.803	1.017	15.880	0.585	0.585	0.000	0.000	0.000	0.000
44	F	26	GLU	0	-0.018	-0.177	11.078	-0.024	-0.024	0.000	0.000	0.000	0.000
45	F	26	GLU	-1	-0.879	-0.774	8.265	-2.688	-2.688	0.000	0.000	0.000	0.000
46	F	27	LEU	0	0.115	-0.065	11.843	0.166	0.166	0.000	0.000	0.000	0.000
47	F	27	LEU	0	-0.143	0.065	12.481	0.035	0.035	0.000	0.000	0.000	0.000
48	F	28	PHE	0	0.046	-0.104	11.508	-0.274	-0.274	0.000	0.000	0.000	0.000
49	F	28	PHE	0	-0.049	0.112	9.726	0.032	0.032	0.000	0.000	0.000	0.000
50	F	29	ALA	0	0.103	-0.090	13.275	0.140	0.140	0.000	0.000	0.000	0.000
51	F	29	ALA	0	-0.081	0.098	13.832	0.016	0.016	0.000	0.000	0.000	0.000
52	F	30	THR	0	0.084	-0.089	14.743	-0.076	-0.076	0.000	0.000	0.000	0.000
53	F	30	THR	0	-0.082	0.064	18.769	0.012	0.012	0.000	0.000	0.000	0.000
54	F	31	LEU	0	0.096	-0.077	15.266	0.018	0.018	0.000	0.000	0.000	0.000
55	F	31	LEU	0	-0.069	0.133	12.760	-0.006	-0.006	0.000	0.000	0.000	0.000
56	F	32	TYR	0	0.070	-0.118	16.086	0.045	0.045	0.000	0.000	0.000	0.000
57	F	32	TYR	0	-0.035	0.125	18.232	-0.012	-0.012	0.000	0.000	0.000	0.000
58	F	33	ALA	0	0.119	-0.070	19.728	0.042	0.042	0.000	0.000	0.000	0.000
59	F	33	ALA	0	-0.054	0.108	21.397	-0.002	-0.002	0.000	0.000	0.000	0.000
60	F	34	GLN	0	0.043	-0.120	19.619	-0.054	-0.054	0.000	0.000	0.000	0.000
61	F	34	GLN	0	-0.102	0.112	19.246	-0.016	-0.016	0.000	0.000	0.000	0.000
62	F	35	ARG	0	0.161	-0.078	19.684	0.040	0.040	0.000	0.000	0.000	0.000
63	F	35	ARG	1	0.740	0.984	16.240	0.402	0.402	0.000	0.000	0.000	0.000
64	F	36	LEU	0	-0.074	-0.141	19.789	0.027	0.027	0.000	0.000	0.000	0.000
65	F	36	LEU	0	-0.027	0.119	21.006	0.000	0.000	0.000	0.000	0.000	0.000
66	F	37	PHE	0	0.071	-0.074	17.467	-0.044	-0.044	0.000	0.000	0.000	0.000
67	F	37	PHE	0	-0.051	0.084	15.751	0.020	0.020	0.000	0.000	0.000	0.000
68	F	38	PHE	0	0.026	-0.117	16.871	0.081	0.081	0.000	0.000	0.000	0.000
69	F	38	PHE	0	-0.035	0.102	17.061	0.011	0.011	0.000	0.000	0.000	0.000
70	F	39	LEU	0	0.223	-0.056	16.138	-0.127	-0.127	0.000	0.000	0.000	0.000
71	F	39	LEU	0	-0.161	0.087	16.065	0.011	0.011	0.000	0.000	0.000	0.000
72	F	40	VAL	0	0.037	-0.149	15.112	0.129	0.129	0.000	0.000	0.000	0.000
73	F	40	VAL	0	-0.080	0.115	14.124	-0.005	-0.005	0.000	0.000	0.000	0.000
74	F	41	ALA	0	0.143	-0.073	15.378	-0.108	-0.108	0.000	0.000	0.000	0.000
75	F	41	ALA	0	-0.082	0.086	17.606	0.018	0.018	0.000	0.000	0.000	0.000
76	F	42	PHE	0	0.109	-0.085	16.883	0.051	0.051	0.000	0.000	0.000	0.000
77	F	42	PHE	0	-0.132	0.085	12.144	0.018	0.018	0.000	0.000	0.000	0.000
78	F	43	ASP	0	0.137	-0.026	18.210	-0.040	-0.040	0.000	0.000	0.000	0.000
79	F	43	ASP	-1	-0.914	-0.845	20.832	-0.421	-0.421	0.000	0.000	0.000	0.000
80	F	44	ALA	0	0.087	-0.050	21.187	0.014	0.014	0.000	0.000	0.000	0.000
81	F	44	ALA	0	-0.103	0.090	23.909	0.006	0.006	0.000	0.000	0.000	0.000
82	F	45	ARG	0	0.072	-0.118	21.626	-0.043	-0.043	0.000	0.000	0.000	0.000
83	F	45	ARG	1	0.868	1.070	25.905	0.308	0.308	0.000	0.000	0.000	0.000
84	F	46	GLY	0	-0.037	-0.145	22.574	0.035	0.035	0.000	0.000	0.000	0.000
85	F	47	THR	0	0.069	0.032	18.505	0.015	0.015	0.000	0.000	0.000	0.000
86	F	47	THR	0	-0.044	0.086	17.437	-0.033	-0.033	0.000	0.000	0.000	0.000
87	F	48	ARG	0	0.123	-0.085	19.486	0.024	0.024	0.000	0.000	0.000	0.000
88	F	48	ARG	1	0.740	1.010	20.519	0.443	0.443	0.000	0.000	0.000	0.000
89	F	49	PHE	0	0.015	-0.141	18.595	-0.082	-0.082	0.000	0.000	0.000	0.000
90	F	49	PHE	0	-0.022	0.100	16.793	-0.008	-0.008	0.000	0.000	0.000	0.000
91	F	50	GLU	0	0.070	-0.093	20.028	0.051	0.051	0.000	0.000	0.000	0.000
92	F	50	GLU	-1	-0.911	-0.800	20.866	-0.467	-0.467	0.000	0.000	0.000	0.000
93	F	51	PRO	0	-0.011	-0.099	20.671	-0.047	-0.047	0.000	0.000	0.000	0.000
94	F	52	ILE	0	0.037	-0.029	21.374	0.037	0.037	0.000	0.000	0.000	0.000
95	F	52	ILE	0	-0.038	0.139	18.371	-0.001	-0.001	0.000	0.000	0.000	0.000
96	F	53	GLY	0	0.053	-0.081	21.653	-0.007	-0.007	0.000	0.000	0.000	0.000
97	F	54	ARG	0	0.132	0.017	20.639	-0.030	-0.030	0.000	0.000	0.000	0.000
98	F	54	ARG	1	0.913	1.078	20.864	0.275	0.275	0.000	0.000	0.000	0.000
99	F	55	ASN	0	0.022	-0.069	20.846	-0.021	-0.021	0.000	0.000	0.000	0.000
100	F	55	ASN	0	-0.023	0.078	24.934	0.001	0.001	0.000	0.000	0.000	0.000
101	F	56	GLU	0	0.170	-0.067	22.439	0.012	0.012	0.000	0.000	0.000	0.000
102	F	56	GLU	-1	-0.978	-0.834	21.493	-0.357	-0.357	0.000	0.000	0.000	0.000
103	F	57	ALA	0	0.126	-0.087	18.301	-0.008	-0.008	0.000	0.000	0.000	0.000
104	F	57	ALA	0	-0.075	0.098	17.259	-0.005	-0.005	0.000	0.000	0.000	0.000
105	F	58	ARG	0	0.077	-0.095	17.453	-0.057	-0.057	0.000	0.000	0.000	0.000
106	F	58	ARG	1	0.779	1.011	19.054	0.257	0.257	0.000	0.000	0.000	0.000
107	F	59	MET	0	0.093	-0.092	18.539	-0.001	-0.001	0.000	0.000	0.000	0.000
108	F	59	MET	0	-0.074	0.106	21.780	0.006	0.006	0.000	0.000	0.000	0.000
109	F	60	LEU	0	0.002	-0.134	17.825	0.033	0.033	0.000	0.000	0.000	0.000
110	F	60	LEU	0	-0.050	0.114	17.164	-0.020	-0.020	0.000	0.000	0.000	0.000
111	F	61	VAL	0	0.114	-0.102	14.339	-0.038	-0.038	0.000	0.000	0.000	0.000
112	F	61	VAL	0	-0.091	0.096	12.840	-0.007	-0.007	0.000	0.000	0.000	0.000
113	F	62	ASP	0	0.111	-0.065	14.970	-0.016	-0.016	0.000	0.000	0.000	0.000
114	F	62	ASP	-1	-0.950	-0.806	19.082	-0.232	-0.232	0.000	0.000	0.000	0.000
115	F	63	ASN	0	0.108	-0.073	17.422	0.029	0.029	0.000	0.000	0.000	0.000
116	F	63	ASN	0	-0.067	0.089	19.198	0.033	0.033	0.000	0.000	0.000	0.000
117	F	64	ARG	0	0.136	-0.095	14.049	0.062	0.062	0.000	0.000	0.000	0.000
118	F	64	ARG	1	0.764	1.027	11.415	0.912	0.912	0.000	0.000	0.000	0.000
119	F	65	LEU	0	0.101	-0.099	13.547	-0.011	-0.011	0.000	0.000	0.000	0.000
120	F	65	LEU	0	-0.112	0.097	12.515	0.022	0.022	0.000	0.000	0.000	0.000
121	F	66	ARG	0	0.060	-0.093	14.549	0.061	0.061	0.000	0.000	0.000	0.000
122	F	66	ARG	1	0.708	0.960	18.996	0.218	0.218	0.000	0.000	0.000	0.000
123	F	67	GLN	0	0.140	-0.084	16.580	0.056	0.056	0.000	0.000	0.000	0.000
124	F	67	GLN	0	-0.069	0.131	15.504	-0.073	-0.073	0.000	0.000	0.000	0.000
125	F	68	LEU	0	0.004	-0.122	12.867	0.066	0.066	0.000	0.000	0.000	0.000
126	F	68	LEU	0	-0.074	0.092	9.495	-0.024	-0.024	0.000	0.000	0.000	0.000
127	F	69	ARG	0	0.104	-0.070	13.382	0.045	0.045	0.000	0.000	0.000	0.000
128	F	69	ARG	1	0.795	1.036	13.882	0.077	0.077	0.000	0.000	0.000	0.000
129	F	70	ARG	0	-0.057	-0.142	15.026	0.045	0.045	0.000	0.000	0.000	0.000
130	F	70	ARG	1	0.968	1.000	15.004	-0.030	-0.030	0.000	0.000	0.000	0.000
131	F	79	GLN	0	0.193	0.021	22.976	-0.003	-0.003	0.000	0.000	0.000	0.000
132	F	79	GLN	0	-0.108	0.103	23.542	0.014	0.014	0.000	0.000	0.000	0.000
133	F	80	LEU	0	0.127	-0.103	23.072	-0.001	-0.001	0.000	0.000	0.000	0.000
134	F	80	LEU	0	-0.045	0.127	21.868	0.000	0.000	0.000	0.000	0.000	0.000
135	F	81	GLN	0	0.101	-0.088	23.528	-0.013	-0.013	0.000	0.000	0.000	0.000
136	F	81	GLN	0	-0.062	0.107	22.931	0.005	0.005	0.000	0.000	0.000	0.000
137	F	82	GLN	0	0.097	-0.091	24.844	-0.011	-0.011	0.000	0.000	0.000	0.000
138	F	82	GLN	0	-0.072	0.101	27.199	0.008	0.008	0.000	0.000	0.000	0.000
139	F	83	VAL	0	0.099	-0.131	27.450	-0.001	-0.001	0.000	0.000	0.000	0.000
140	F	83	VAL	0	-0.089	0.130	27.950	0.000	0.000	0.000	0.000	0.000	0.000
141	F	84	PHE	0	0.154	-0.063	27.378	-0.001	-0.001	0.000	0.000	0.000	0.000
142	F	84	PHE	0	-0.119	0.084	26.702	-0.003	-0.003	0.000	0.000	0.000	0.000
143	F	85	LYS	0	0.085	-0.084	28.677	-0.008	-0.008	0.000	0.000	0.000	0.000
144	F	85	LYS	1	0.837	1.043	26.806	0.017	0.017	0.000	0.000	0.000	0.000
145	F	86	GLN	0	0.066	-0.087	30.494	-0.002	-0.002	0.000	0.000	0.000	0.000
146	F	86	GLN	0	-0.081	0.088	32.281	0.005	0.005	0.000	0.000	0.000	0.000
147	F	87	THR	0	-0.001	-0.095	32.107	0.003	0.003	0.000	0.000	0.000	0.000
148	F	87	THR	0	-0.095	0.029	31.764	0.001	0.001	0.000	0.000	0.000	0.000
149	F	88	PHE	0	0.051	-0.077	32.378	0.001	0.001	0.000	0.000	0.000	0.000
150	F	88	PHE	0	-0.103	0.072	29.786	-0.003	-0.003	0.000	0.000	0.000	0.000
151	F	89	LEU	0	-0.045	-0.095	32.676	-0.003	-0.003	0.000	0.000	0.000	0.000
152	F	89	LEU	0	0.009	0.010	30.349	0.000	0.000	0.000	0.000	0.000	0.000

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