FMO DATABASE

FMODB ID: L73M9

Calculation Name: 2XG8-D-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2XG8

Chain ID: D

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	168
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-578722.462999
FMO2-HF: Nuclear repulsion	542900.62444
FMO2-HF: Total energy	-35821.838559
FMO2-MP2: Total energy	-35927.058738

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(D:3:SER)

Summations of interaction energy for fragment #1(D: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.
-1.712	0.197	-0.01	-0.665	-1.233	0.003

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.070 / 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	D	4	GLU	-1	-0.957	-0.785	3.976	-0.264	0.203	0.000	-0.131	-0.336	0.000
5	D	5	ASN	0	0.051	-0.096	3.837	-0.131	1.438	-0.009	-0.813	-0.746	0.004
6	D	5	ASN	0	-0.091	0.090	3.606	-2.187	-2.314	-0.001	0.279	-0.151	-0.001
7	D	6	TYR	0	0.069	-0.126	6.197	0.025	0.025	0.000	0.000	0.000	0.000
8	D	6	TYR	0	-0.126	0.064	7.881	-0.083	-0.083	0.000	0.000	0.000	0.000
9	D	7	LEU	0	0.115	-0.106	9.888	0.042	0.042	0.000	0.000	0.000	0.000
10	D	7	LEU	0	-0.086	0.118	12.132	-0.003	-0.003	0.000	0.000	0.000	0.000
11	D	8	ASN	0	0.066	-0.077	13.293	0.005	0.005	0.000	0.000	0.000	0.000
12	D	8	ASN	0	-0.083	0.078	16.468	0.007	0.007	0.000	0.000	0.000	0.000
13	D	9	HIS	0	0.170	-0.082	17.009	-0.001	-0.001	0.000	0.000	0.000	0.000
14	D	9	HIS	0	-0.065	0.113	18.680	0.007	0.007	0.000	0.000	0.000	0.000
15	D	10	PRO	0	-0.062	-0.129	19.566	0.027	0.027	0.000	0.000	0.000	0.000
16	D	11	THR	0	0.014	0.033	22.938	0.030	0.030	0.000	0.000	0.000	0.000
17	D	11	THR	0	-0.024	0.051	24.685	-0.004	-0.004	0.000	0.000	0.000	0.000
18	D	12	PHE	0	0.019	-0.080	21.416	0.033	0.033	0.000	0.000	0.000	0.000
19	D	12	PHE	0	-0.085	0.074	20.660	-0.005	-0.005	0.000	0.000	0.000	0.000
20	D	13	GLY	0	0.056	-0.090	20.082	-0.003	-0.003	0.000	0.000	0.000	0.000
21	D	14	LEU	0	0.192	0.029	15.986	-0.044	-0.044	0.000	0.000	0.000	0.000
22	D	14	LEU	0	-0.108	0.113	13.293	0.009	0.009	0.000	0.000	0.000	0.000
23	D	15	LEU	0	-0.010	-0.145	14.283	0.066	0.066	0.000	0.000	0.000	0.000
24	D	15	LEU	0	-0.092	0.102	14.033	-0.001	-0.001	0.000	0.000	0.000	0.000
25	D	16	TYR	0	0.091	-0.064	10.193	-0.018	-0.018	0.000	0.000	0.000	0.000
26	D	16	TYR	0	-0.044	0.094	9.653	0.151	0.151	0.000	0.000	0.000	0.000
27	D	17	GLN	0	0.085	-0.112	7.734	0.486	0.486	0.000	0.000	0.000	0.000
28	D	17	GLN	0	-0.107	0.089	6.521	-0.682	-0.682	0.000	0.000	0.000	0.000
29	D	18	ILE	0	0.050	-0.085	8.412	-0.239	-0.239	0.000	0.000	0.000	0.000
30	D	18	ILE	0	-0.136	0.060	11.241	0.082	0.082	0.000	0.000	0.000	0.000
31	D	19	CYS	0	0.063	-0.089	8.331	-0.155	-0.155	0.000	0.000	0.000	0.000
32	D	19	CYS	0	-0.157	0.062	10.073	0.146	0.146	0.000	0.000	0.000	0.000
33	D	20	SER	0	0.126	-0.062	9.107	-0.020	-0.020	0.000	0.000	0.000	0.000
34	D	20	SER	0	-0.054	0.061	8.215	0.111	0.111	0.000	0.000	0.000	0.000
35	D	21	PHE	0	-0.011	-0.093	9.947	0.113	0.113	0.000	0.000	0.000	0.000
36	D	21	PHE	0	-0.125	0.064	13.870	0.023	0.023	0.000	0.000	0.000	0.000
37	D	22	GLY	0	0.049	-0.112	12.383	0.085	0.085	0.000	0.000	0.000	0.000
38	D	23	ASP	0	0.074	0.030	13.099	-0.010	-0.010	0.000	0.000	0.000	0.000
39	D	23	ASP	-1	-0.862	-0.791	13.496	-0.594	-0.594	0.000	0.000	0.000	0.000
40	D	24	SER	0	0.016	-0.080	14.055	0.030	0.030	0.000	0.000	0.000	0.000
41	D	24	SER	0	-0.057	0.043	15.842	0.037	0.037	0.000	0.000	0.000	0.000
42	D	25	LYS	0	0.042	-0.120	14.702	0.047	0.047	0.000	0.000	0.000	0.000
43	D	25	LYS	1	0.818	1.010	15.766	0.566	0.566	0.000	0.000	0.000	0.000
44	D	26	GLU	0	0.038	-0.081	10.973	-0.028	-0.028	0.000	0.000	0.000	0.000
45	D	26	GLU	-1	-0.829	-0.774	9.361	-1.940	-1.940	0.000	0.000	0.000	0.000
46	D	27	LEU	0	0.105	-0.087	11.232	0.206	0.206	0.000	0.000	0.000	0.000
47	D	27	LEU	0	-0.123	0.076	12.372	0.037	0.037	0.000	0.000	0.000	0.000
48	D	28	PHE	0	0.076	-0.098	11.202	-0.307	-0.307	0.000	0.000	0.000	0.000
49	D	28	PHE	0	-0.048	0.108	9.398	-0.010	-0.010	0.000	0.000	0.000	0.000
50	D	29	ALA	0	0.084	-0.099	12.920	0.142	0.142	0.000	0.000	0.000	0.000
51	D	29	ALA	0	-0.068	0.097	14.463	0.013	0.013	0.000	0.000	0.000	0.000
52	D	30	THR	0	0.039	-0.080	14.573	-0.091	-0.091	0.000	0.000	0.000	0.000
53	D	30	THR	0	-0.067	0.064	18.793	0.021	0.021	0.000	0.000	0.000	0.000
54	D	31	LEU	0	0.086	-0.101	15.120	0.016	0.016	0.000	0.000	0.000	0.000
55	D	31	LEU	0	-0.086	0.116	12.714	-0.001	-0.001	0.000	0.000	0.000	0.000
56	D	32	TYR	0	0.058	-0.125	16.015	0.040	0.040	0.000	0.000	0.000	0.000
57	D	32	TYR	0	-0.009	0.139	18.010	-0.007	-0.007	0.000	0.000	0.000	0.000
58	D	33	ALA	0	0.135	-0.052	19.627	0.047	0.047	0.000	0.000	0.000	0.000
59	D	33	ALA	0	-0.064	0.103	21.396	0.000	0.000	0.000	0.000	0.000	0.000
60	D	34	GLN	0	0.017	-0.104	19.953	-0.063	-0.063	0.000	0.000	0.000	0.000
61	D	34	GLN	0	-0.088	0.109	20.194	-0.027	-0.027	0.000	0.000	0.000	0.000
62	D	35	ARG	0	0.124	-0.103	19.768	0.046	0.046	0.000	0.000	0.000	0.000
63	D	35	ARG	1	0.740	0.987	15.358	0.524	0.524	0.000	0.000	0.000	0.000
64	D	36	LEU	0	-0.002	-0.126	20.114	0.025	0.025	0.000	0.000	0.000	0.000
65	D	36	LEU	0	-0.034	0.114	21.059	0.001	0.001	0.000	0.000	0.000	0.000
66	D	37	PHE	0	0.077	-0.077	17.536	-0.053	-0.053	0.000	0.000	0.000	0.000
67	D	37	PHE	0	-0.052	0.085	16.121	0.012	0.012	0.000	0.000	0.000	0.000
68	D	38	PHE	0	0.051	-0.109	16.693	0.088	0.088	0.000	0.000	0.000	0.000
69	D	38	PHE	0	-0.040	0.106	16.707	0.013	0.013	0.000	0.000	0.000	0.000
70	D	39	LEU	0	0.174	-0.047	15.617	-0.140	-0.140	0.000	0.000	0.000	0.000
71	D	39	LEU	0	-0.110	0.083	15.753	0.013	0.013	0.000	0.000	0.000	0.000
72	D	40	VAL	0	0.048	-0.118	14.594	0.122	0.122	0.000	0.000	0.000	0.000
73	D	40	VAL	0	-0.064	0.123	13.651	-0.016	-0.016	0.000	0.000	0.000	0.000
74	D	41	ALA	0	0.142	-0.086	15.065	-0.106	-0.106	0.000	0.000	0.000	0.000
75	D	41	ALA	0	-0.080	0.095	17.771	0.018	0.018	0.000	0.000	0.000	0.000
76	D	42	PHE	0	0.032	-0.107	16.835	0.049	0.049	0.000	0.000	0.000	0.000
77	D	42	PHE	0	-0.067	0.110	12.229	0.026	0.026	0.000	0.000	0.000	0.000
78	D	43	ASP	0	0.063	-0.061	17.897	0.006	0.006	0.000	0.000	0.000	0.000
79	D	43	ASP	-1	-0.839	-0.824	21.785	-0.375	-0.375	0.000	0.000	0.000	0.000
80	D	44	ALA	0	0.049	-0.109	20.499	0.027	0.027	0.000	0.000	0.000	0.000
81	D	44	ALA	0	-0.070	0.103	19.893	-0.006	-0.006	0.000	0.000	0.000	0.000
82	D	45	ARG	0	0.070	-0.097	21.612	0.011	0.011	0.000	0.000	0.000	0.000
83	D	45	ARG	1	0.809	1.014	24.633	0.296	0.296	0.000	0.000	0.000	0.000
84	D	46	GLY	0	-0.013	-0.125	21.810	0.024	0.024	0.000	0.000	0.000	0.000
85	D	47	THR	0	-0.013	0.039	18.248	0.020	0.020	0.000	0.000	0.000	0.000
86	D	47	THR	0	-0.056	0.072	17.249	-0.036	-0.036	0.000	0.000	0.000	0.000
87	D	48	ARG	0	0.125	-0.101	18.983	0.012	0.012	0.000	0.000	0.000	0.000
88	D	48	ARG	1	0.784	0.984	20.036	0.458	0.458	0.000	0.000	0.000	0.000
89	D	49	PHE	0	0.056	-0.074	18.236	-0.078	-0.078	0.000	0.000	0.000	0.000
90	D	49	PHE	0	-0.067	0.083	16.458	-0.009	-0.009	0.000	0.000	0.000	0.000
91	D	50	GLU	0	0.122	-0.086	19.563	0.054	0.054	0.000	0.000	0.000	0.000
92	D	50	GLU	-1	-0.906	-0.750	19.860	-0.487	-0.487	0.000	0.000	0.000	0.000
93	D	51	PRO	0	-0.031	-0.129	20.321	-0.046	-0.046	0.000	0.000	0.000	0.000
94	D	52	ILE	0	0.053	0.007	21.193	0.039	0.039	0.000	0.000	0.000	0.000
95	D	52	ILE	0	-0.075	0.117	18.148	-0.009	-0.009	0.000	0.000	0.000	0.000
96	D	53	GLY	0	0.044	-0.092	22.159	-0.001	-0.001	0.000	0.000	0.000	0.000
97	D	54	ARG	0	0.084	0.004	20.961	-0.034	-0.034	0.000	0.000	0.000	0.000
98	D	54	ARG	1	0.912	1.084	21.349	0.340	0.340	0.000	0.000	0.000	0.000
99	D	55	ASN	0	0.066	-0.084	21.034	-0.031	-0.031	0.000	0.000	0.000	0.000
100	D	55	ASN	0	-0.067	0.053	25.053	-0.006	-0.006	0.000	0.000	0.000	0.000
101	D	56	GLU	0	0.182	-0.089	22.529	0.003	0.003	0.000	0.000	0.000	0.000
102	D	56	GLU	-1	-0.965	-0.798	21.924	-0.390	-0.390	0.000	0.000	0.000	0.000
103	D	57	ALA	0	0.114	-0.103	18.628	-0.009	-0.009	0.000	0.000	0.000	0.000
104	D	57	ALA	0	-0.065	0.102	17.635	-0.006	-0.006	0.000	0.000	0.000	0.000
105	D	58	ARG	0	0.057	-0.095	17.583	-0.075	-0.075	0.000	0.000	0.000	0.000
106	D	58	ARG	1	0.759	0.998	18.093	0.367	0.367	0.000	0.000	0.000	0.000
107	D	59	MET	0	0.083	-0.106	18.577	-0.018	-0.018	0.000	0.000	0.000	0.000
108	D	59	MET	0	-0.064	0.104	22.109	0.015	0.015	0.000	0.000	0.000	0.000
109	D	60	LEU	0	0.009	-0.104	17.888	0.042	0.042	0.000	0.000	0.000	0.000
110	D	60	LEU	0	-0.032	0.110	17.184	-0.012	-0.012	0.000	0.000	0.000	0.000
111	D	61	VAL	0	0.138	-0.077	14.461	-0.029	-0.029	0.000	0.000	0.000	0.000
112	D	61	VAL	0	-0.090	0.103	13.168	-0.005	-0.005	0.000	0.000	0.000	0.000
113	D	62	ASP	0	0.109	-0.086	15.273	-0.019	-0.019	0.000	0.000	0.000	0.000
114	D	62	ASP	-1	-0.896	-0.771	18.713	-0.346	-0.346	0.000	0.000	0.000	0.000
115	D	63	ASN	0	0.098	-0.081	17.862	0.045	0.045	0.000	0.000	0.000	0.000
116	D	63	ASN	0	-0.133	0.054	19.312	0.031	0.031	0.000	0.000	0.000	0.000
117	D	64	ARG	0	0.092	-0.091	14.249	0.080	0.080	0.000	0.000	0.000	0.000
118	D	64	ARG	1	0.778	1.018	10.703	1.002	1.002	0.000	0.000	0.000	0.000
119	D	65	LEU	0	0.101	-0.115	13.794	-0.015	-0.015	0.000	0.000	0.000	0.000
120	D	65	LEU	0	-0.088	0.118	12.862	0.006	0.006	0.000	0.000	0.000	0.000
121	D	66	ARG	0	0.038	-0.107	14.772	0.056	0.056	0.000	0.000	0.000	0.000
122	D	66	ARG	1	0.755	0.977	19.198	0.296	0.296	0.000	0.000	0.000	0.000
123	D	67	GLN	0	0.075	-0.074	17.295	0.062	0.062	0.000	0.000	0.000	0.000
124	D	67	GLN	0	-0.086	0.099	15.623	-0.071	-0.071	0.000	0.000	0.000	0.000
125	D	68	LEU	0	0.118	-0.108	12.671	0.070	0.070	0.000	0.000	0.000	0.000
126	D	68	LEU	0	-0.060	0.110	10.102	-0.019	-0.019	0.000	0.000	0.000	0.000
127	D	69	ARG	0	0.127	-0.074	13.982	0.071	0.071	0.000	0.000	0.000	0.000
128	D	69	ARG	1	0.739	1.029	15.182	0.025	0.025	0.000	0.000	0.000	0.000
129	D	70	ARG	0	0.004	-0.098	15.987	0.057	0.057	0.000	0.000	0.000	0.000
130	D	70	ARG	1	0.797	1.035	18.631	0.224	0.224	0.000	0.000	0.000	0.000
131	D	71	ASP	0	0.121	-0.111	14.292	0.007	0.007	0.000	0.000	0.000	0.000
132	D	71	ASP	-1	-0.885	-0.827	13.130	-0.153	-0.153	0.000	0.000	0.000	0.000
133	D	72	ALA	0	0.039	-0.110	15.790	0.042	0.042	0.000	0.000	0.000	0.000
134	D	72	ALA	0	-0.051	0.117	17.179	-0.001	-0.001	0.000	0.000	0.000	0.000
135	D	73	SER	0	0.065	-0.088	13.494	0.023	0.023	0.000	0.000	0.000	0.000
136	D	73	SER	0	-0.036	0.091	12.811	-0.011	-0.011	0.000	0.000	0.000	0.000
137	D	74	LEU	0	0.142	-0.071	12.033	0.170	0.170	0.000	0.000	0.000	0.000
138	D	74	LEU	0	-0.117	0.076	10.398	-0.028	-0.028	0.000	0.000	0.000	0.000
139	D	75	GLN	0	-0.011	-0.142	12.825	0.063	0.063	0.000	0.000	0.000	0.000
140	D	75	GLN	0	-0.045	0.124	16.971	0.005	0.005	0.000	0.000	0.000	0.000
141	D	76	GLU	0	0.136	-0.103	16.443	0.012	0.012	0.000	0.000	0.000	0.000
142	D	76	GLU	-1	-1.002	-0.810	15.587	0.305	0.305	0.000	0.000	0.000	0.000
143	D	77	TYR	0	0.101	-0.094	12.708	-0.006	-0.006	0.000	0.000	0.000	0.000
144	D	77	TYR	0	-0.114	0.081	11.826	0.124	0.124	0.000	0.000	0.000	0.000
145	D	78	ASN	0	0.086	-0.069	14.241	0.051	0.051	0.000	0.000	0.000	0.000
146	D	78	ASN	0	-0.125	0.040	13.491	0.050	0.050	0.000	0.000	0.000	0.000
147	D	79	GLN	0	0.131	-0.076	15.654	0.010	0.010	0.000	0.000	0.000	0.000
148	D	79	GLN	0	-0.091	0.097	19.466	-0.010	-0.010	0.000	0.000	0.000	0.000
149	D	80	LEU	0	0.093	-0.105	17.728	-0.034	-0.034	0.000	0.000	0.000	0.000
150	D	80	LEU	0	-0.078	0.119	16.198	0.007	0.007	0.000	0.000	0.000	0.000
151	D	81	GLN	0	0.125	-0.092	16.145	-0.004	-0.004	0.000	0.000	0.000	0.000
152	D	81	GLN	0	-0.085	0.106	13.806	0.103	0.103	0.000	0.000	0.000	0.000
153	D	82	GLN	0	-0.004	-0.144	17.366	0.005	0.005	0.000	0.000	0.000	0.000
154	D	82	GLN	0	-0.091	0.090	19.050	-0.013	-0.013	0.000	0.000	0.000	0.000
155	D	83	VAL	0	0.073	-0.086	20.555	-0.022	-0.022	0.000	0.000	0.000	0.000
156	D	83	VAL	0	-0.072	0.124	22.013	-0.003	-0.003	0.000	0.000	0.000	0.000
157	D	84	PHE	0	0.149	-0.064	20.232	-0.036	-0.036	0.000	0.000	0.000	0.000
158	D	84	PHE	0	-0.074	0.093	19.708	0.016	0.016	0.000	0.000	0.000	0.000
159	D	85	LYS	0	0.141	-0.073	21.659	-0.007	-0.007	0.000	0.000	0.000	0.000
160	D	85	LYS	1	0.866	1.058	22.090	-0.253	-0.253	0.000	0.000	0.000	0.000
161	D	86	GLN	0	0.037	-0.080	23.349	-0.003	-0.003	0.000	0.000	0.000	0.000
162	D	86	GLN	0	-0.107	0.071	24.707	-0.018	-0.018	0.000	0.000	0.000	0.000
163	D	87	THR	0	-0.005	-0.089	25.252	-0.023	-0.023	0.000	0.000	0.000	0.000
164	D	87	THR	0	-0.069	0.047	24.834	-0.006	-0.006	0.000	0.000	0.000	0.000
165	D	88	PHE	0	0.019	-0.099	24.969	-0.021	-0.021	0.000	0.000	0.000	0.000
166	D	88	PHE	0	-0.088	0.081	22.934	0.006	0.006	0.000	0.000	0.000	0.000
167	D	89	LEU	0	-0.071	-0.130	24.614	-0.025	-0.025	0.000	0.000	0.000	0.000
168	D	89	LEU	0	0.003	0.003	22.113	0.005	0.005	0.000	0.000	0.000	0.000

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