FMO DATABASE

FMODB ID: J2969

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	OptH
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	-497181.66445
FMO2-HF: Nuclear repulsion	464535.665623
FMO2-HF: Total energy	-32645.998827
FMO2-MP2: Total energy	-32741.986479

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.
-3.358	-1.364	-0.013	-1.061	-0.919	0.004

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 : 0.079 / q_NPA : 0.025

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	-0.940	-0.779	3.694	0.639	1.170	0.002	-0.158	-0.376	0.000
5	F	5	ASN	0	0.078	-0.092	3.836	-0.485	1.149	-0.013	-0.882	-0.738	0.004
6	F	5	ASN	0	-0.069	0.096	4.127	-2.096	-2.198	-0.001	-0.017	0.120	0.000
7	F	6	TYR	0	0.078	-0.101	6.548	0.029	0.029	0.000	0.000	0.000	0.000
8	F	6	TYR	0	-0.169	0.039	7.702	-0.130	-0.130	0.000	0.000	0.000	0.000
9	F	7	LEU	0	0.135	-0.141	10.127	0.016	0.016	0.000	0.000	0.000	0.000
10	F	7	LEU	0	-0.089	0.142	11.933	0.020	0.020	0.000	0.000	0.000	0.000
11	F	8	ASN	0	0.082	-0.065	13.469	0.026	0.026	0.000	0.000	0.000	0.000
12	F	8	ASN	0	-0.105	0.080	17.378	0.023	0.023	0.000	0.000	0.000	0.000
13	F	9	HIS	0	0.138	-0.103	17.114	-0.010	-0.010	0.000	0.000	0.000	0.000
14	F	9	HIS	0	-0.072	0.090	18.690	0.020	0.020	0.000	0.000	0.000	0.000
15	F	10	PRO	0	-0.042	-0.114	19.592	0.029	0.029	0.000	0.000	0.000	0.000
16	F	11	THR	0	0.055	0.032	23.120	0.031	0.031	0.000	0.000	0.000	0.000
17	F	11	THR	0	-0.045	0.056	24.280	-0.005	-0.005	0.000	0.000	0.000	0.000
18	F	12	PHE	0	0.006	-0.094	21.482	0.034	0.034	0.000	0.000	0.000	0.000
19	F	12	PHE	0	-0.081	0.088	20.706	0.000	0.000	0.000	0.000	0.000	0.000
20	F	13	GLY	0	0.055	-0.070	19.967	-0.003	-0.003	0.000	0.000	0.000	0.000
21	F	14	LEU	0	0.178	0.015	15.826	-0.056	-0.056	0.000	0.000	0.000	0.000
22	F	14	LEU	0	-0.107	0.114	13.324	0.007	0.007	0.000	0.000	0.000	0.000
23	F	15	LEU	0	-0.015	-0.151	14.159	0.082	0.082	0.000	0.000	0.000	0.000
24	F	15	LEU	0	-0.093	0.111	13.892	-0.005	-0.005	0.000	0.000	0.000	0.000
25	F	16	TYR	0	0.105	-0.067	10.190	-0.081	-0.081	0.000	0.000	0.000	0.000
26	F	16	TYR	0	-0.092	0.081	9.300	0.120	0.120	0.000	0.000	0.000	0.000
27	F	17	GLN	0	0.152	-0.139	7.800	0.519	0.519	0.000	0.000	0.000	0.000
28	F	17	GLN	0	-0.087	0.138	5.676	-1.030	-1.099	-0.001	-0.004	0.075	0.000
29	F	18	ILE	0	0.030	-0.085	7.812	-0.246	-0.246	0.000	0.000	0.000	0.000
30	F	18	ILE	0	-0.127	0.066	10.975	0.078	0.078	0.000	0.000	0.000	0.000
31	F	19	CYS	0	0.015	-0.099	7.914	-0.123	-0.123	0.000	0.000	0.000	0.000
32	F	19	CYS	0	-0.114	0.072	9.362	0.138	0.138	0.000	0.000	0.000	0.000
33	F	20	SER	0	0.149	-0.086	8.994	0.067	0.067	0.000	0.000	0.000	0.000
34	F	20	SER	0	-0.035	0.095	8.445	-0.069	-0.069	0.000	0.000	0.000	0.000
35	F	21	PHE	0	0.016	-0.110	10.194	0.128	0.128	0.000	0.000	0.000	0.000
36	F	21	PHE	0	-0.078	0.081	14.672	0.019	0.019	0.000	0.000	0.000	0.000
37	F	22	GLY	0	-0.022	-0.102	13.043	0.179	0.179	0.000	0.000	0.000	0.000
38	F	23	ASP	0	-0.027	-0.145	12.367	-0.226	-0.226	0.000	0.000	0.000	0.000
39	F	23	ASP	-1	-0.841	-0.806	15.984	-0.646	-0.646	0.000	0.000	0.000	0.000
40	F	24	SER	0	-0.034	0.001	13.741	0.036	0.036	0.000	0.000	0.000	0.000
41	F	24	SER	0	-0.049	0.064	16.473	0.010	0.010	0.000	0.000	0.000	0.000
42	F	25	LYS	0	0.133	-0.042	14.628	-0.026	-0.026	0.000	0.000	0.000	0.000
43	F	25	LYS	1	0.847	1.043	15.801	0.638	0.638	0.000	0.000	0.000	0.000
44	F	26	GLU	0	-0.011	-0.147	11.036	-0.023	-0.023	0.000	0.000	0.000	0.000
45	F	26	GLU	-1	-0.901	-0.805	8.361	-2.736	-2.736	0.000	0.000	0.000	0.000
46	F	27	LEU	0	0.137	-0.072	11.841	0.178	0.178	0.000	0.000	0.000	0.000
47	F	27	LEU	0	-0.156	0.069	12.650	0.035	0.035	0.000	0.000	0.000	0.000
48	F	28	PHE	0	0.050	-0.109	11.587	-0.284	-0.284	0.000	0.000	0.000	0.000
49	F	28	PHE	0	-0.058	0.120	9.700	0.043	0.043	0.000	0.000	0.000	0.000
50	F	29	ALA	0	0.088	-0.100	13.263	0.140	0.140	0.000	0.000	0.000	0.000
51	F	29	ALA	0	-0.077	0.100	13.650	0.015	0.015	0.000	0.000	0.000	0.000
52	F	30	THR	0	0.093	-0.084	14.592	-0.076	-0.076	0.000	0.000	0.000	0.000
53	F	30	THR	0	-0.096	0.048	18.610	0.012	0.012	0.000	0.000	0.000	0.000
54	F	31	LEU	0	0.077	-0.111	15.188	0.011	0.011	0.000	0.000	0.000	0.000
55	F	31	LEU	0	-0.083	0.139	12.764	-0.005	-0.005	0.000	0.000	0.000	0.000
56	F	32	TYR	0	0.081	-0.129	15.960	0.048	0.048	0.000	0.000	0.000	0.000
57	F	32	TYR	0	-0.056	0.129	18.560	-0.010	-0.010	0.000	0.000	0.000	0.000
58	F	33	ALA	0	0.118	-0.081	19.614	0.044	0.044	0.000	0.000	0.000	0.000
59	F	33	ALA	0	-0.055	0.126	21.205	-0.002	-0.002	0.000	0.000	0.000	0.000
60	F	34	GLN	0	0.049	-0.121	19.469	-0.056	-0.056	0.000	0.000	0.000	0.000
61	F	34	GLN	0	-0.116	0.111	19.362	-0.008	-0.008	0.000	0.000	0.000	0.000
62	F	35	ARG	0	0.172	-0.095	19.535	0.041	0.041	0.000	0.000	0.000	0.000
63	F	35	ARG	1	0.785	1.049	15.980	0.392	0.392	0.000	0.000	0.000	0.000
64	F	36	LEU	0	-0.073	-0.150	19.612	0.026	0.026	0.000	0.000	0.000	0.000
65	F	36	LEU	0	-0.027	0.124	20.915	0.000	0.000	0.000	0.000	0.000	0.000
66	F	37	PHE	0	0.083	-0.080	17.607	-0.043	-0.043	0.000	0.000	0.000	0.000
67	F	37	PHE	0	-0.061	0.093	15.841	0.023	0.023	0.000	0.000	0.000	0.000
68	F	38	PHE	0	0.036	-0.121	16.994	0.082	0.082	0.000	0.000	0.000	0.000
69	F	38	PHE	0	-0.053	0.105	17.068	0.013	0.013	0.000	0.000	0.000	0.000
70	F	39	LEU	0	0.184	-0.092	16.154	-0.133	-0.133	0.000	0.000	0.000	0.000
71	F	39	LEU	0	-0.156	0.101	16.149	0.006	0.006	0.000	0.000	0.000	0.000
72	F	40	VAL	0	0.103	-0.125	15.174	0.128	0.128	0.000	0.000	0.000	0.000
73	F	40	VAL	0	-0.073	0.129	14.156	-0.006	-0.006	0.000	0.000	0.000	0.000
74	F	41	ALA	0	0.166	-0.081	15.396	-0.113	-0.113	0.000	0.000	0.000	0.000
75	F	41	ALA	0	-0.102	0.093	17.475	0.018	0.018	0.000	0.000	0.000	0.000
76	F	42	PHE	0	0.070	-0.077	16.903	0.052	0.052	0.000	0.000	0.000	0.000
77	F	42	PHE	0	-0.109	0.085	12.558	0.022	0.022	0.000	0.000	0.000	0.000
78	F	43	ASP	0	0.154	-0.061	18.231	-0.044	-0.044	0.000	0.000	0.000	0.000
79	F	43	ASP	-1	-0.905	-0.803	20.810	-0.437	-0.437	0.000	0.000	0.000	0.000
80	F	44	ALA	0	0.102	-0.112	21.208	0.020	0.020	0.000	0.000	0.000	0.000
81	F	44	ALA	0	-0.185	0.111	23.467	0.001	0.001	0.000	0.000	0.000	0.000
82	F	45	ARG	0	0.133	-0.144	21.649	-0.041	-0.041	0.000	0.000	0.000	0.000
83	F	45	ARG	1	0.801	1.103	25.574	0.309	0.309	0.000	0.000	0.000	0.000
84	F	46	GLY	0	0.016	-0.124	22.589	0.035	0.035	0.000	0.000	0.000	0.000
85	F	47	THR	0	0.094	0.019	18.568	0.011	0.011	0.000	0.000	0.000	0.000
86	F	47	THR	0	-0.048	0.089	17.627	-0.038	-0.038	0.000	0.000	0.000	0.000
87	F	48	ARG	0	0.122	-0.068	19.530	0.028	0.028	0.000	0.000	0.000	0.000
88	F	48	ARG	1	0.761	1.011	20.485	0.453	0.453	0.000	0.000	0.000	0.000
89	F	49	PHE	0	0.014	-0.126	18.617	-0.084	-0.084	0.000	0.000	0.000	0.000
90	F	49	PHE	0	-0.028	0.094	16.605	-0.006	-0.006	0.000	0.000	0.000	0.000
91	F	50	GLU	0	0.071	-0.130	20.056	0.053	0.053	0.000	0.000	0.000	0.000
92	F	50	GLU	-1	-0.992	-0.813	20.761	-0.484	-0.484	0.000	0.000	0.000	0.000
93	F	51	PRO	0	-0.021	-0.096	20.688	-0.049	-0.049	0.000	0.000	0.000	0.000
94	F	52	ILE	0	0.038	-0.037	21.491	0.038	0.038	0.000	0.000	0.000	0.000
95	F	52	ILE	0	-0.037	0.147	18.495	-0.001	-0.001	0.000	0.000	0.000	0.000
96	F	53	GLY	0	0.046	-0.086	21.777	-0.006	-0.006	0.000	0.000	0.000	0.000
97	F	54	ARG	0	0.139	0.001	20.767	-0.032	-0.032	0.000	0.000	0.000	0.000
98	F	54	ARG	1	0.905	1.082	20.293	0.294	0.294	0.000	0.000	0.000	0.000
99	F	55	ASN	0	0.041	-0.077	20.970	-0.023	-0.023	0.000	0.000	0.000	0.000
100	F	55	ASN	0	-0.020	0.090	25.037	0.001	0.001	0.000	0.000	0.000	0.000
101	F	56	GLU	0	0.102	-0.053	22.539	0.012	0.012	0.000	0.000	0.000	0.000
102	F	56	GLU	-1	-0.928	-0.863	21.512	-0.384	-0.384	0.000	0.000	0.000	0.000
103	F	57	ALA	0	0.142	-0.081	18.386	-0.012	-0.012	0.000	0.000	0.000	0.000
104	F	57	ALA	0	-0.079	0.106	17.383	-0.004	-0.004	0.000	0.000	0.000	0.000
105	F	58	ARG	0	0.071	-0.084	17.552	-0.063	-0.063	0.000	0.000	0.000	0.000
106	F	58	ARG	1	0.775	1.009	19.372	0.273	0.273	0.000	0.000	0.000	0.000
107	F	59	MET	0	0.106	-0.109	18.632	-0.002	-0.002	0.000	0.000	0.000	0.000
108	F	59	MET	0	-0.084	0.115	21.680	0.003	0.003	0.000	0.000	0.000	0.000
109	F	60	LEU	0	0.020	-0.122	17.881	0.033	0.033	0.000	0.000	0.000	0.000
110	F	60	LEU	0	-0.051	0.120	17.242	-0.021	-0.021	0.000	0.000	0.000	0.000
111	F	61	VAL	0	0.093	-0.107	14.416	-0.044	-0.044	0.000	0.000	0.000	0.000
112	F	61	VAL	0	-0.055	0.107	12.750	-0.009	-0.009	0.000	0.000	0.000	0.000
113	F	62	ASP	0	0.117	-0.077	15.028	-0.024	-0.024	0.000	0.000	0.000	0.000
114	F	62	ASP	-1	-0.994	-0.852	18.849	-0.281	-0.281	0.000	0.000	0.000	0.000
115	F	63	ASN	0	0.032	-0.103	17.460	0.030	0.030	0.000	0.000	0.000	0.000
116	F	63	ASN	0	-0.074	0.079	19.059	0.040	0.040	0.000	0.000	0.000	0.000
117	F	64	ARG	0	0.135	-0.084	14.006	0.059	0.059	0.000	0.000	0.000	0.000
118	F	64	ARG	1	0.864	1.083	10.763	1.003	1.003	0.000	0.000	0.000	0.000
119	F	65	LEU	0	0.087	-0.104	13.561	-0.025	-0.025	0.000	0.000	0.000	0.000
120	F	65	LEU	0	-0.125	0.098	12.329	0.012	0.012	0.000	0.000	0.000	0.000
121	F	66	ARG	0	0.057	-0.089	14.574	0.061	0.061	0.000	0.000	0.000	0.000
122	F	66	ARG	1	0.767	1.025	18.902	0.238	0.238	0.000	0.000	0.000	0.000
123	F	67	GLN	0	0.151	-0.082	16.450	0.057	0.057	0.000	0.000	0.000	0.000
124	F	67	GLN	0	-0.056	0.116	15.375	-0.056	-0.056	0.000	0.000	0.000	0.000
125	F	68	LEU	0	0.022	-0.105	13.021	0.066	0.066	0.000	0.000	0.000	0.000
126	F	68	LEU	0	-0.132	0.064	9.803	-0.030	-0.030	0.000	0.000	0.000	0.000
127	F	69	ARG	0	0.104	-0.081	13.323	0.032	0.032	0.000	0.000	0.000	0.000
128	F	69	ARG	1	0.793	1.054	13.639	0.102	0.102	0.000	0.000	0.000	0.000
129	F	70	ARG	0	0.005	-0.137	14.989	0.043	0.043	0.000	0.000	0.000	0.000
130	F	70	ARG	1	0.951	1.007	14.820	0.017	0.017	0.000	0.000	0.000	0.000
131	F	79	GLN	0	0.197	0.023	22.870	-0.005	-0.005	0.000	0.000	0.000	0.000
132	F	79	GLN	0	-0.113	0.097	23.420	0.014	0.014	0.000	0.000	0.000	0.000
133	F	80	LEU	0	0.134	-0.091	23.059	0.002	0.002	0.000	0.000	0.000	0.000
134	F	80	LEU	0	-0.042	0.125	21.854	-0.001	-0.001	0.000	0.000	0.000	0.000
135	F	81	GLN	0	0.099	-0.093	23.516	-0.012	-0.012	0.000	0.000	0.000	0.000
136	F	81	GLN	0	-0.058	0.107	22.946	0.007	0.007	0.000	0.000	0.000	0.000
137	F	82	GLN	0	0.081	-0.090	24.833	-0.009	-0.009	0.000	0.000	0.000	0.000
138	F	82	GLN	0	-0.062	0.094	27.216	0.005	0.005	0.000	0.000	0.000	0.000
139	F	83	VAL	0	0.126	-0.160	27.456	0.001	0.001	0.000	0.000	0.000	0.000
140	F	83	VAL	0	-0.091	0.150	27.648	0.000	0.000	0.000	0.000	0.000	0.000
141	F	84	PHE	0	0.141	-0.099	27.407	0.001	0.001	0.000	0.000	0.000	0.000
142	F	84	PHE	0	-0.113	0.097	26.386	-0.002	-0.002	0.000	0.000	0.000	0.000
143	F	85	LYS	0	0.030	-0.055	28.668	-0.008	-0.008	0.000	0.000	0.000	0.000
144	F	85	LYS	1	0.857	1.019	26.808	0.035	0.035	0.000	0.000	0.000	0.000
145	F	86	GLN	0	0.067	-0.072	30.485	-0.001	-0.001	0.000	0.000	0.000	0.000
146	F	86	GLN	0	-0.085	0.094	32.254	0.004	0.004	0.000	0.000	0.000	0.000
147	F	87	THR	0	0.002	-0.110	32.097	0.005	0.005	0.000	0.000	0.000	0.000
148	F	87	THR	0	-0.058	0.054	31.781	0.000	0.000	0.000	0.000	0.000	0.000
149	F	88	PHE	0	0.028	-0.079	32.373	0.002	0.002	0.000	0.000	0.000	0.000
150	F	88	PHE	0	-0.113	0.076	30.185	-0.003	-0.003	0.000	0.000	0.000	0.000
151	F	89	LEU	0	-0.041	-0.096	32.744	-0.002	-0.002	0.000	0.000	0.000	0.000
152	F	89	LEU	0	0.014	0.011	30.455	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)