FMO DATABASE

FMODB ID: 37V3L

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

Total energy (hartree)

FMO2-HF: Electronic energy	-577528.458539
FMO2-HF: Nuclear repulsion	541706.976656
FMO2-HF: Total energy	-35821.481883
FMO2-MP2: Total energy	-35926.724039

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.
-2.321	0.01	-0.011	-1.139	-1.181	0.005

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 : 0.064 / q_NPA : 0.022

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	-0.952	-0.782	3.693	0.003	0.561	0.003	-0.166	-0.393	0.000
5	D	5	ASN	0	0.053	-0.096	3.829	-0.762	1.012	-0.013	-0.968	-0.794	0.005
6	D	5	ASN	0	-0.098	0.087	4.181	-1.713	-1.714	-0.001	-0.005	0.006	0.000
7	D	6	TYR	0	0.095	-0.097	6.549	0.021	0.021	0.000	0.000	0.000	0.000
8	D	6	TYR	0	-0.168	0.039	7.811	-0.086	-0.086	0.000	0.000	0.000	0.000
9	D	7	LEU	0	0.124	-0.129	10.125	0.016	0.016	0.000	0.000	0.000	0.000
10	D	7	LEU	0	-0.083	0.128	12.273	0.002	0.002	0.000	0.000	0.000	0.000
11	D	8	ASN	0	0.075	-0.065	13.466	0.020	0.020	0.000	0.000	0.000	0.000
12	D	8	ASN	0	-0.092	0.077	16.997	0.013	0.013	0.000	0.000	0.000	0.000
13	D	9	HIS	0	0.167	-0.091	17.113	-0.008	-0.008	0.000	0.000	0.000	0.000
14	D	9	HIS	0	-0.082	0.109	18.647	0.016	0.016	0.000	0.000	0.000	0.000
15	D	10	PRO	0	-0.063	-0.125	19.559	0.028	0.028	0.000	0.000	0.000	0.000
16	D	11	THR	0	0.027	0.038	23.096	0.028	0.028	0.000	0.000	0.000	0.000
17	D	11	THR	0	-0.048	0.043	24.343	-0.005	-0.005	0.000	0.000	0.000	0.000
18	D	12	PHE	0	0.016	-0.088	21.478	0.031	0.031	0.000	0.000	0.000	0.000
19	D	12	PHE	0	-0.081	0.078	20.724	-0.001	-0.001	0.000	0.000	0.000	0.000
20	D	13	GLY	0	0.078	-0.080	19.953	-0.003	-0.003	0.000	0.000	0.000	0.000
21	D	14	LEU	0	0.158	0.030	15.857	-0.049	-0.049	0.000	0.000	0.000	0.000
22	D	14	LEU	0	-0.097	0.113	13.341	0.007	0.007	0.000	0.000	0.000	0.000
23	D	15	LEU	0	0.007	-0.137	14.135	0.075	0.075	0.000	0.000	0.000	0.000
24	D	15	LEU	0	-0.110	0.097	13.842	-0.004	-0.004	0.000	0.000	0.000	0.000
25	D	16	TYR	0	0.107	-0.070	10.161	-0.081	-0.081	0.000	0.000	0.000	0.000
26	D	16	TYR	0	-0.061	0.086	9.406	0.136	0.136	0.000	0.000	0.000	0.000
27	D	17	GLN	0	0.091	-0.118	7.824	0.479	0.479	0.000	0.000	0.000	0.000
28	D	17	GLN	0	-0.054	0.131	6.146	-0.833	-0.833	0.000	0.000	0.000	0.000
29	D	18	ILE	0	0.079	-0.063	7.652	-0.247	-0.247	0.000	0.000	0.000	0.000
30	D	18	ILE	0	-0.139	0.056	10.898	0.077	0.077	0.000	0.000	0.000	0.000
31	D	19	CYS	0	0.056	-0.093	7.850	-0.172	-0.172	0.000	0.000	0.000	0.000
32	D	19	CYS	0	-0.133	0.057	9.403	0.145	0.145	0.000	0.000	0.000	0.000
33	D	20	SER	0	0.105	-0.084	8.915	0.035	0.035	0.000	0.000	0.000	0.000
34	D	20	SER	0	-0.060	0.049	8.742	0.088	0.088	0.000	0.000	0.000	0.000
35	D	21	PHE	0	-0.049	-0.079	10.541	0.129	0.129	0.000	0.000	0.000	0.000
36	D	21	PHE	0	-0.120	0.053	14.321	0.027	0.027	0.000	0.000	0.000	0.000
37	D	22	GLY	0	0.072	-0.113	12.919	0.087	0.087	0.000	0.000	0.000	0.000
38	D	23	ASP	0	0.048	-0.002	13.313	-0.013	-0.013	0.000	0.000	0.000	0.000
39	D	23	ASP	-1	-0.871	-0.796	13.866	-0.636	-0.636	0.000	0.000	0.000	0.000
40	D	24	SER	0	0.041	-0.069	14.172	0.042	0.042	0.000	0.000	0.000	0.000
41	D	24	SER	0	-0.063	0.049	15.758	0.036	0.036	0.000	0.000	0.000	0.000
42	D	25	LYS	0	0.049	-0.121	14.319	0.039	0.039	0.000	0.000	0.000	0.000
43	D	25	LYS	1	0.819	1.018	15.836	0.579	0.579	0.000	0.000	0.000	0.000
44	D	26	GLU	0	0.039	-0.087	10.894	-0.008	-0.008	0.000	0.000	0.000	0.000
45	D	26	GLU	-1	-0.879	-0.780	9.827	-1.865	-1.865	0.000	0.000	0.000	0.000
46	D	27	LEU	0	0.131	-0.074	11.854	0.173	0.173	0.000	0.000	0.000	0.000
47	D	27	LEU	0	-0.144	0.074	12.424	0.035	0.035	0.000	0.000	0.000	0.000
48	D	28	PHE	0	0.031	-0.116	11.465	-0.265	-0.265	0.000	0.000	0.000	0.000
49	D	28	PHE	0	-0.048	0.113	9.936	-0.004	-0.004	0.000	0.000	0.000	0.000
50	D	29	ALA	0	0.107	-0.087	13.220	0.131	0.131	0.000	0.000	0.000	0.000
51	D	29	ALA	0	-0.080	0.096	13.817	0.016	0.016	0.000	0.000	0.000	0.000
52	D	30	THR	0	0.064	-0.090	14.675	-0.079	-0.079	0.000	0.000	0.000	0.000
53	D	30	THR	0	-0.077	0.060	18.710	0.014	0.014	0.000	0.000	0.000	0.000
54	D	31	LEU	0	0.079	-0.095	15.212	0.016	0.016	0.000	0.000	0.000	0.000
55	D	31	LEU	0	-0.089	0.121	12.706	-0.002	-0.002	0.000	0.000	0.000	0.000
56	D	32	TYR	0	0.080	-0.116	16.022	0.045	0.045	0.000	0.000	0.000	0.000
57	D	32	TYR	0	-0.033	0.125	18.055	-0.011	-0.011	0.000	0.000	0.000	0.000
58	D	33	ALA	0	0.145	-0.057	19.671	0.042	0.042	0.000	0.000	0.000	0.000
59	D	33	ALA	0	-0.057	0.105	21.339	-0.001	-0.001	0.000	0.000	0.000	0.000
60	D	34	GLN	0	-0.012	-0.133	19.551	-0.054	-0.054	0.000	0.000	0.000	0.000
61	D	34	GLN	0	-0.093	0.118	19.595	-0.021	-0.021	0.000	0.000	0.000	0.000
62	D	35	ARG	0	0.193	-0.053	19.557	0.040	0.040	0.000	0.000	0.000	0.000
63	D	35	ARG	1	0.750	0.996	15.122	0.402	0.402	0.000	0.000	0.000	0.000
64	D	36	LEU	0	-0.050	-0.154	19.681	0.026	0.026	0.000	0.000	0.000	0.000
65	D	36	LEU	0	-0.037	0.119	20.963	0.001	0.001	0.000	0.000	0.000	0.000
66	D	37	PHE	0	0.071	-0.068	17.418	-0.043	-0.043	0.000	0.000	0.000	0.000
67	D	37	PHE	0	-0.042	0.081	15.699	0.018	0.018	0.000	0.000	0.000	0.000
68	D	38	PHE	0	0.047	-0.108	16.817	0.078	0.078	0.000	0.000	0.000	0.000
69	D	38	PHE	0	-0.048	0.093	17.044	0.011	0.011	0.000	0.000	0.000	0.000
70	D	39	LEU	0	0.199	-0.059	16.103	-0.127	-0.127	0.000	0.000	0.000	0.000
71	D	39	LEU	0	-0.157	0.088	16.113	0.013	0.013	0.000	0.000	0.000	0.000
72	D	40	VAL	0	0.054	-0.129	15.125	0.119	0.119	0.000	0.000	0.000	0.000
73	D	40	VAL	0	-0.064	0.117	14.134	-0.011	-0.011	0.000	0.000	0.000	0.000
74	D	41	ALA	0	0.146	-0.079	15.353	-0.105	-0.105	0.000	0.000	0.000	0.000
75	D	41	ALA	0	-0.074	0.091	17.807	0.019	0.019	0.000	0.000	0.000	0.000
76	D	42	PHE	0	0.023	-0.114	16.894	0.044	0.044	0.000	0.000	0.000	0.000
77	D	42	PHE	0	-0.053	0.110	12.152	0.021	0.021	0.000	0.000	0.000	0.000
78	D	43	ASP	0	-0.023	-0.043	18.047	0.001	0.001	0.000	0.000	0.000	0.000
79	D	43	ASP	-1	-0.807	-0.824	22.054	-0.404	-0.404	0.000	0.000	0.000	0.000
80	D	44	ALA	0	0.109	-0.120	20.724	0.026	0.026	0.000	0.000	0.000	0.000
81	D	44	ALA	0	-0.065	0.109	19.957	-0.010	-0.010	0.000	0.000	0.000	0.000
82	D	45	ARG	0	0.082	-0.071	22.001	0.013	0.013	0.000	0.000	0.000	0.000
83	D	45	ARG	1	0.792	1.004	24.962	0.319	0.319	0.000	0.000	0.000	0.000
84	D	46	GLY	0	0.002	-0.139	22.683	0.021	0.021	0.000	0.000	0.000	0.000
85	D	47	THR	0	-0.153	0.005	18.752	0.022	0.022	0.000	0.000	0.000	0.000
86	D	47	THR	0	-0.035	0.075	17.678	-0.039	-0.039	0.000	0.000	0.000	0.000
87	D	48	ARG	0	0.205	-0.072	19.632	0.010	0.010	0.000	0.000	0.000	0.000
88	D	48	ARG	1	0.788	0.977	20.519	0.460	0.460	0.000	0.000	0.000	0.000
89	D	49	PHE	0	0.062	-0.075	18.877	-0.067	-0.067	0.000	0.000	0.000	0.000
90	D	49	PHE	0	-0.049	0.093	16.850	-0.004	-0.004	0.000	0.000	0.000	0.000
91	D	50	GLU	0	0.070	-0.094	20.089	0.049	0.049	0.000	0.000	0.000	0.000
92	D	50	GLU	-1	-0.885	-0.755	20.690	-0.479	-0.479	0.000	0.000	0.000	0.000
93	D	51	PRO	0	-0.005	-0.103	20.688	-0.045	-0.045	0.000	0.000	0.000	0.000
94	D	52	ILE	0	0.046	-0.011	21.292	0.036	0.036	0.000	0.000	0.000	0.000
95	D	52	ILE	0	-0.044	0.136	18.284	-0.007	-0.007	0.000	0.000	0.000	0.000
96	D	53	GLY	0	0.047	-0.086	21.588	-0.008	-0.008	0.000	0.000	0.000	0.000
97	D	54	ARG	0	0.108	0.011	20.589	-0.030	-0.030	0.000	0.000	0.000	0.000
98	D	54	ARG	1	0.913	1.078	20.888	0.266	0.266	0.000	0.000	0.000	0.000
99	D	55	ASN	0	0.071	-0.060	20.795	-0.023	-0.023	0.000	0.000	0.000	0.000
100	D	55	ASN	0	-0.064	0.059	24.869	-0.003	-0.003	0.000	0.000	0.000	0.000
101	D	56	GLU	0	0.187	-0.094	22.294	0.011	0.011	0.000	0.000	0.000	0.000
102	D	56	GLU	-1	-0.983	-0.810	21.655	-0.357	-0.357	0.000	0.000	0.000	0.000
103	D	57	ALA	0	0.124	-0.086	18.194	-0.008	-0.008	0.000	0.000	0.000	0.000
104	D	57	ALA	0	-0.080	0.099	17.186	-0.005	-0.005	0.000	0.000	0.000	0.000
105	D	58	ARG	0	0.057	-0.115	17.377	-0.056	-0.056	0.000	0.000	0.000	0.000
106	D	58	ARG	1	0.753	1.001	17.945	0.257	0.257	0.000	0.000	0.000	0.000
107	D	59	MET	0	0.073	-0.109	18.512	0.000	0.000	0.000	0.000	0.000	0.000
108	D	59	MET	0	-0.080	0.102	21.831	0.012	0.012	0.000	0.000	0.000	0.000
109	D	60	LEU	0	0.005	-0.123	17.726	0.038	0.038	0.000	0.000	0.000	0.000
110	D	60	LEU	0	-0.027	0.113	17.130	-0.011	-0.011	0.000	0.000	0.000	0.000
111	D	61	VAL	0	0.126	-0.087	14.276	-0.037	-0.037	0.000	0.000	0.000	0.000
112	D	61	VAL	0	-0.083	0.101	12.813	-0.004	-0.004	0.000	0.000	0.000	0.000
113	D	62	ASP	0	0.130	-0.051	14.897	-0.009	-0.009	0.000	0.000	0.000	0.000
114	D	62	ASP	-1	-0.912	-0.786	18.565	-0.242	-0.242	0.000	0.000	0.000	0.000
115	D	63	ASN	0	0.079	-0.097	17.412	0.037	0.037	0.000	0.000	0.000	0.000
116	D	63	ASN	0	-0.113	0.062	19.052	0.028	0.028	0.000	0.000	0.000	0.000
117	D	64	ARG	0	0.091	-0.094	13.956	0.063	0.063	0.000	0.000	0.000	0.000
118	D	64	ARG	1	0.822	1.051	11.076	0.895	0.895	0.000	0.000	0.000	0.000
119	D	65	LEU	0	0.085	-0.119	13.478	-0.005	-0.005	0.000	0.000	0.000	0.000
120	D	65	LEU	0	-0.087	0.113	12.492	0.009	0.009	0.000	0.000	0.000	0.000
121	D	66	ARG	0	0.035	-0.122	14.481	0.063	0.063	0.000	0.000	0.000	0.000
122	D	66	ARG	1	0.774	0.999	18.932	0.198	0.198	0.000	0.000	0.000	0.000
123	D	67	GLN	0	0.037	-0.095	17.027	0.064	0.064	0.000	0.000	0.000	0.000
124	D	67	GLN	0	-0.065	0.103	15.536	-0.067	-0.067	0.000	0.000	0.000	0.000
125	D	68	LEU	0	0.096	-0.110	12.612	0.028	0.028	0.000	0.000	0.000	0.000
126	D	68	LEU	0	-0.057	0.107	10.062	-0.016	-0.016	0.000	0.000	0.000	0.000
127	D	69	ARG	0	0.157	-0.052	13.872	0.069	0.069	0.000	0.000	0.000	0.000
128	D	69	ARG	1	0.764	1.033	15.169	-0.096	-0.096	0.000	0.000	0.000	0.000
129	D	70	ARG	0	0.040	-0.086	15.770	0.058	0.058	0.000	0.000	0.000	0.000
130	D	70	ARG	1	0.792	1.042	18.493	0.177	0.177	0.000	0.000	0.000	0.000
131	D	71	ASP	0	0.090	-0.128	14.566	-0.006	-0.006	0.000	0.000	0.000	0.000
132	D	71	ASP	-1	-0.896	-0.832	13.617	-0.167	-0.167	0.000	0.000	0.000	0.000
133	D	72	ALA	0	0.046	-0.100	15.758	0.059	0.059	0.000	0.000	0.000	0.000
134	D	72	ALA	0	-0.045	0.111	17.518	-0.004	-0.004	0.000	0.000	0.000	0.000
135	D	73	SER	0	0.104	-0.051	13.391	0.054	0.054	0.000	0.000	0.000	0.000
136	D	73	SER	0	-0.007	0.102	12.642	-0.031	-0.031	0.000	0.000	0.000	0.000
137	D	74	LEU	0	0.116	-0.063	12.007	0.167	0.167	0.000	0.000	0.000	0.000
138	D	74	LEU	0	-0.126	0.081	10.694	-0.020	-0.020	0.000	0.000	0.000	0.000
139	D	75	GLN	0	0.002	-0.141	12.874	0.112	0.112	0.000	0.000	0.000	0.000
140	D	75	GLN	0	-0.053	0.096	16.977	0.000	0.000	0.000	0.000	0.000	0.000
141	D	76	GLU	0	0.072	-0.118	16.428	0.030	0.030	0.000	0.000	0.000	0.000
142	D	76	GLU	-1	-0.993	-0.828	15.926	0.245	0.245	0.000	0.000	0.000	0.000
143	D	77	TYR	0	0.088	-0.088	12.982	-0.011	-0.011	0.000	0.000	0.000	0.000
144	D	77	TYR	0	-0.126	0.081	11.928	0.132	0.132	0.000	0.000	0.000	0.000
145	D	78	ASN	0	0.111	-0.072	14.510	0.044	0.044	0.000	0.000	0.000	0.000
146	D	78	ASN	0	-0.126	0.030	13.326	0.071	0.071	0.000	0.000	0.000	0.000
147	D	79	GLN	0	0.101	-0.085	15.574	0.007	0.007	0.000	0.000	0.000	0.000
148	D	79	GLN	0	-0.090	0.097	19.462	-0.011	-0.011	0.000	0.000	0.000	0.000
149	D	80	LEU	0	0.106	-0.103	17.998	-0.032	-0.032	0.000	0.000	0.000	0.000
150	D	80	LEU	0	-0.058	0.130	16.415	0.005	0.005	0.000	0.000	0.000	0.000
151	D	81	GLN	0	0.115	-0.080	16.362	-0.007	-0.007	0.000	0.000	0.000	0.000
152	D	81	GLN	0	-0.097	0.089	13.982	0.113	0.113	0.000	0.000	0.000	0.000
153	D	82	GLN	0	0.002	-0.137	17.594	0.000	0.000	0.000	0.000	0.000	0.000
154	D	82	GLN	0	-0.107	0.083	19.271	-0.020	-0.020	0.000	0.000	0.000	0.000
155	D	83	VAL	0	0.061	-0.098	20.605	-0.016	-0.016	0.000	0.000	0.000	0.000
156	D	83	VAL	0	-0.088	0.111	22.169	-0.004	-0.004	0.000	0.000	0.000	0.000
157	D	84	PHE	0	0.144	-0.070	20.398	-0.042	-0.042	0.000	0.000	0.000	0.000
158	D	84	PHE	0	-0.059	0.091	19.872	0.018	0.018	0.000	0.000	0.000	0.000
159	D	85	LYS	0	0.157	-0.059	21.816	-0.011	-0.011	0.000	0.000	0.000	0.000
160	D	85	LYS	1	0.840	1.041	22.424	-0.301	-0.301	0.000	0.000	0.000	0.000
161	D	86	GLN	0	0.056	-0.065	23.661	-0.006	-0.006	0.000	0.000	0.000	0.000
162	D	86	GLN	0	-0.084	0.073	25.475	-0.018	-0.018	0.000	0.000	0.000	0.000
163	D	87	THR	0	-0.003	-0.086	25.559	-0.023	-0.023	0.000	0.000	0.000	0.000
164	D	87	THR	0	-0.073	0.055	24.904	-0.005	-0.005	0.000	0.000	0.000	0.000
165	D	88	PHE	0	0.032	-0.054	25.245	-0.025	-0.025	0.000	0.000	0.000	0.000
166	D	88	PHE	0	-0.134	0.045	23.129	0.005	0.005	0.000	0.000	0.000	0.000
167	D	89	LEU	0	-0.007	-0.135	24.612	-0.043	-0.043	0.000	0.000	0.000	0.000
168	D	89	LEU	0	-0.017	0.009	22.251	0.008	0.008	0.000	0.000	0.000	0.000

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