FMO DATABASE

FMODB ID: 9MVN2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-577260.744194
FMO2-HF: Nuclear repulsion	541441.258284
FMO2-HF: Total energy	-35819.48591
FMO2-MP2: Total energy	-35924.772928

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.
-1.822	0.213	-0.013	-1.041	-0.981	0.004

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 : 0.078 / 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	D	4	GLU	-1	-0.952	-0.781	3.693	0.541	1.100	0.002	-0.157	-0.404	0.000
5	D	5	ASN	0	0.060	-0.088	3.829	-0.529	1.100	-0.013	-0.865	-0.751	0.004
6	D	5	ASN	0	-0.084	0.078	4.142	-1.947	-2.034	-0.001	-0.015	0.103	0.000
7	D	6	TYR	0	0.103	-0.097	6.549	0.021	0.021	0.000	0.000	0.000	0.000
8	D	6	TYR	0	-0.170	0.042	7.673	-0.131	-0.131	0.000	0.000	0.000	0.000
9	D	7	LEU	0	0.118	-0.140	10.125	0.016	0.016	0.000	0.000	0.000	0.000
10	D	7	LEU	0	-0.096	0.140	11.967	0.011	0.011	0.000	0.000	0.000	0.000
11	D	8	ASN	0	0.084	-0.079	13.466	0.021	0.021	0.000	0.000	0.000	0.000
12	D	8	ASN	0	-0.087	0.088	16.982	0.026	0.026	0.000	0.000	0.000	0.000
13	D	9	HIS	0	0.148	-0.093	17.113	-0.011	-0.011	0.000	0.000	0.000	0.000
14	D	9	HIS	0	-0.069	0.094	18.652	0.019	0.019	0.000	0.000	0.000	0.000
15	D	10	PRO	0	-0.062	-0.120	19.559	0.029	0.029	0.000	0.000	0.000	0.000
16	D	11	THR	0	0.031	0.022	23.096	0.029	0.029	0.000	0.000	0.000	0.000
17	D	11	THR	0	-0.036	0.062	24.261	-0.005	-0.005	0.000	0.000	0.000	0.000
18	D	12	PHE	0	-0.003	-0.093	21.441	0.032	0.032	0.000	0.000	0.000	0.000
19	D	12	PHE	0	-0.077	0.088	20.668	-0.001	-0.001	0.000	0.000	0.000	0.000
20	D	13	GLY	0	0.080	-0.071	19.953	-0.002	-0.002	0.000	0.000	0.000	0.000
21	D	14	LEU	0	0.166	0.012	15.789	-0.052	-0.052	0.000	0.000	0.000	0.000
22	D	14	LEU	0	-0.086	0.123	13.299	0.006	0.006	0.000	0.000	0.000	0.000
23	D	15	LEU	0	-0.019	-0.155	14.135	0.080	0.080	0.000	0.000	0.000	0.000
24	D	15	LEU	0	-0.089	0.119	13.858	-0.008	-0.008	0.000	0.000	0.000	0.000
25	D	16	TYR	0	0.104	-0.068	10.165	-0.076	-0.076	0.000	0.000	0.000	0.000
26	D	16	TYR	0	-0.075	0.082	9.258	0.112	0.112	0.000	0.000	0.000	0.000
27	D	17	GLN	0	0.120	-0.140	7.765	0.485	0.485	0.000	0.000	0.000	0.000
28	D	17	GLN	0	-0.064	0.140	5.705	-0.852	-0.918	-0.001	-0.004	0.071	0.000
29	D	18	ILE	0	0.053	-0.082	7.736	-0.246	-0.246	0.000	0.000	0.000	0.000
30	D	18	ILE	0	-0.131	0.073	10.892	0.073	0.073	0.000	0.000	0.000	0.000
31	D	19	CYS	0	0.043	-0.096	7.914	-0.169	-0.169	0.000	0.000	0.000	0.000
32	D	19	CYS	0	-0.143	0.059	9.363	0.148	0.148	0.000	0.000	0.000	0.000
33	D	20	SER	0	0.087	-0.077	8.985	0.041	0.041	0.000	0.000	0.000	0.000
34	D	20	SER	0	-0.038	0.068	8.766	0.045	0.045	0.000	0.000	0.000	0.000
35	D	21	PHE	0	-0.013	-0.086	10.550	0.122	0.122	0.000	0.000	0.000	0.000
36	D	21	PHE	0	-0.122	0.061	14.386	0.026	0.026	0.000	0.000	0.000	0.000
37	D	22	GLY	0	0.034	-0.119	12.927	0.091	0.091	0.000	0.000	0.000	0.000
38	D	23	ASP	0	0.015	-0.026	13.324	-0.030	-0.030	0.000	0.000	0.000	0.000
39	D	23	ASP	-1	-0.916	-0.830	13.862	-0.677	-0.677	0.000	0.000	0.000	0.000
40	D	24	SER	0	0.063	-0.059	14.182	0.046	0.046	0.000	0.000	0.000	0.000
41	D	24	SER	0	-0.033	0.081	16.087	0.036	0.036	0.000	0.000	0.000	0.000
42	D	25	LYS	0	0.043	-0.114	14.309	0.046	0.046	0.000	0.000	0.000	0.000
43	D	25	LYS	1	0.805	1.024	15.824	0.604	0.604	0.000	0.000	0.000	0.000
44	D	26	GLU	0	0.052	-0.072	10.844	-0.003	-0.003	0.000	0.000	0.000	0.000
45	D	26	GLU	-1	-0.925	-0.820	10.011	-1.762	-1.762	0.000	0.000	0.000	0.000
46	D	27	LEU	0	0.151	-0.096	11.854	0.180	0.180	0.000	0.000	0.000	0.000
47	D	27	LEU	0	-0.141	0.084	12.574	0.034	0.034	0.000	0.000	0.000	0.000
48	D	28	PHE	0	0.035	-0.115	11.570	-0.271	-0.271	0.000	0.000	0.000	0.000
49	D	28	PHE	0	-0.067	0.114	9.704	0.004	0.004	0.000	0.000	0.000	0.000
50	D	29	ALA	0	0.105	-0.109	13.207	0.132	0.132	0.000	0.000	0.000	0.000
51	D	29	ALA	0	-0.086	0.108	13.652	0.016	0.016	0.000	0.000	0.000	0.000
52	D	30	THR	0	0.085	-0.091	14.524	-0.078	-0.078	0.000	0.000	0.000	0.000
53	D	30	THR	0	-0.094	0.058	18.555	0.012	0.012	0.000	0.000	0.000	0.000
54	D	31	LEU	0	0.065	-0.107	15.147	0.014	0.014	0.000	0.000	0.000	0.000
55	D	31	LEU	0	-0.079	0.133	12.694	-0.001	-0.001	0.000	0.000	0.000	0.000
56	D	32	TYR	0	0.083	-0.128	15.908	0.046	0.046	0.000	0.000	0.000	0.000
57	D	32	TYR	0	-0.052	0.126	18.470	-0.011	-0.011	0.000	0.000	0.000	0.000
58	D	33	ALA	0	0.156	-0.071	19.567	0.040	0.040	0.000	0.000	0.000	0.000
59	D	33	ALA	0	-0.067	0.128	21.147	-0.002	-0.002	0.000	0.000	0.000	0.000
60	D	34	GLN	0	0.040	-0.142	19.415	-0.055	-0.055	0.000	0.000	0.000	0.000
61	D	34	GLN	0	-0.169	0.125	19.415	-0.004	-0.004	0.000	0.000	0.000	0.000
62	D	35	ARG	0	0.201	-0.082	19.467	0.039	0.039	0.000	0.000	0.000	0.000
63	D	35	ARG	1	0.787	1.040	15.953	0.382	0.382	0.000	0.000	0.000	0.000
64	D	36	LEU	0	-0.057	-0.166	19.522	0.026	0.026	0.000	0.000	0.000	0.000
65	D	36	LEU	0	-0.031	0.131	20.848	0.000	0.000	0.000	0.000	0.000	0.000
66	D	37	PHE	0	0.078	-0.072	17.554	-0.042	-0.042	0.000	0.000	0.000	0.000
67	D	37	PHE	0	-0.046	0.087	15.767	0.022	0.022	0.000	0.000	0.000	0.000
68	D	38	PHE	0	0.053	-0.105	16.939	0.079	0.079	0.000	0.000	0.000	0.000
69	D	38	PHE	0	-0.062	0.094	17.046	0.013	0.013	0.000	0.000	0.000	0.000
70	D	39	LEU	0	0.181	-0.062	16.119	-0.133	-0.133	0.000	0.000	0.000	0.000
71	D	39	LEU	0	-0.122	0.089	16.953	0.010	0.010	0.000	0.000	0.000	0.000
72	D	40	VAL	0	0.051	-0.139	15.172	0.119	0.119	0.000	0.000	0.000	0.000
73	D	40	VAL	0	-0.053	0.132	14.155	-0.011	-0.011	0.000	0.000	0.000	0.000
74	D	41	ALA	0	0.153	-0.085	15.372	-0.103	-0.103	0.000	0.000	0.000	0.000
75	D	41	ALA	0	-0.104	0.093	17.866	0.020	0.020	0.000	0.000	0.000	0.000
76	D	42	PHE	0	0.012	-0.131	16.914	0.044	0.044	0.000	0.000	0.000	0.000
77	D	42	PHE	0	-0.034	0.115	12.121	0.026	0.026	0.000	0.000	0.000	0.000
78	D	43	ASP	0	-0.049	-0.060	18.068	0.000	0.000	0.000	0.000	0.000	0.000
79	D	43	ASP	-1	-0.761	-0.802	21.639	-0.434	-0.434	0.000	0.000	0.000	0.000
80	D	44	ALA	0	0.118	-0.119	20.759	0.026	0.026	0.000	0.000	0.000	0.000
81	D	44	ALA	0	-0.062	0.126	19.982	-0.010	-0.010	0.000	0.000	0.000	0.000
82	D	45	ARG	0	0.047	-0.070	22.023	0.014	0.014	0.000	0.000	0.000	0.000
83	D	45	ARG	1	0.787	0.994	24.862	0.331	0.331	0.000	0.000	0.000	0.000
84	D	46	GLY	0	0.016	-0.137	22.714	0.022	0.022	0.000	0.000	0.000	0.000
85	D	47	THR	0	-0.118	-0.021	18.898	0.019	0.019	0.000	0.000	0.000	0.000
86	D	47	THR	0	-0.021	0.067	17.960	-0.037	-0.037	0.000	0.000	0.000	0.000
87	D	48	ARG	0	0.184	-0.019	19.655	0.011	0.011	0.000	0.000	0.000	0.000
88	D	48	ARG	1	0.834	1.030	20.609	0.479	0.479	0.000	0.000	0.000	0.000
89	D	49	PHE	0	0.082	-0.091	18.899	-0.068	-0.068	0.000	0.000	0.000	0.000
90	D	49	PHE	0	-0.052	0.099	16.956	-0.001	-0.001	0.000	0.000	0.000	0.000
91	D	50	GLU	0	0.064	-0.135	20.107	0.050	0.050	0.000	0.000	0.000	0.000
92	D	50	GLU	-1	-0.959	-0.779	20.770	-0.471	-0.471	0.000	0.000	0.000	0.000
93	D	51	PRO	0	-0.012	-0.098	20.705	-0.047	-0.047	0.000	0.000	0.000	0.000
94	D	52	ILE	0	0.038	-0.020	21.406	0.036	0.036	0.000	0.000	0.000	0.000
95	D	52	ILE	0	-0.032	0.147	18.526	-0.007	-0.007	0.000	0.000	0.000	0.000
96	D	53	GLY	0	0.050	-0.092	21.710	-0.007	-0.007	0.000	0.000	0.000	0.000
97	D	54	ARG	0	0.114	-0.005	20.715	-0.031	-0.031	0.000	0.000	0.000	0.000
98	D	54	ARG	1	0.916	1.081	20.216	0.281	0.281	0.000	0.000	0.000	0.000
99	D	55	ASN	0	0.082	-0.066	20.915	-0.025	-0.025	0.000	0.000	0.000	0.000
100	D	55	ASN	0	-0.068	0.072	24.963	0.001	0.001	0.000	0.000	0.000	0.000
101	D	56	GLU	0	0.143	-0.107	22.391	0.012	0.012	0.000	0.000	0.000	0.000
102	D	56	GLU	-1	-0.967	-0.812	21.664	-0.370	-0.370	0.000	0.000	0.000	0.000
103	D	57	ALA	0	0.142	-0.091	18.278	-0.012	-0.012	0.000	0.000	0.000	0.000
104	D	57	ALA	0	-0.089	0.105	17.298	-0.003	-0.003	0.000	0.000	0.000	0.000
105	D	58	ARG	0	0.069	-0.111	17.474	-0.060	-0.060	0.000	0.000	0.000	0.000
106	D	58	ARG	1	0.841	1.066	18.137	0.266	0.266	0.000	0.000	0.000	0.000
107	D	59	MET	0	0.054	-0.104	18.602	-0.002	-0.002	0.000	0.000	0.000	0.000
108	D	59	MET	0	-0.078	0.105	21.881	0.010	0.010	0.000	0.000	0.000	0.000
109	D	60	LEU	0	0.032	-0.122	17.796	0.036	0.036	0.000	0.000	0.000	0.000
110	D	60	LEU	0	-0.031	0.122	17.158	-0.012	-0.012	0.000	0.000	0.000	0.000
111	D	61	VAL	0	0.114	-0.095	14.351	-0.043	-0.043	0.000	0.000	0.000	0.000
112	D	61	VAL	0	-0.071	0.105	12.709	-0.004	-0.004	0.000	0.000	0.000	0.000
113	D	62	ASP	0	0.114	-0.065	14.952	-0.018	-0.018	0.000	0.000	0.000	0.000
114	D	62	ASP	-1	-0.988	-0.862	18.782	-0.264	-0.264	0.000	0.000	0.000	0.000
115	D	63	ASN	0	0.033	-0.110	17.449	0.034	0.034	0.000	0.000	0.000	0.000
116	D	63	ASN	0	-0.105	0.069	19.032	0.038	0.038	0.000	0.000	0.000	0.000
117	D	64	ARG	0	0.107	-0.095	13.944	0.059	0.059	0.000	0.000	0.000	0.000
118	D	64	ARG	1	0.903	1.100	10.748	0.949	0.949	0.000	0.000	0.000	0.000
119	D	65	LEU	0	0.068	-0.136	13.491	-0.017	-0.017	0.000	0.000	0.000	0.000
120	D	65	LEU	0	-0.109	0.110	12.264	0.008	0.008	0.000	0.000	0.000	0.000
121	D	66	ARG	0	0.061	-0.102	14.505	0.060	0.060	0.000	0.000	0.000	0.000
122	D	66	ARG	1	0.793	1.035	18.964	0.222	0.222	0.000	0.000	0.000	0.000
123	D	67	GLN	0	0.068	-0.131	17.041	0.065	0.065	0.000	0.000	0.000	0.000
124	D	67	GLN	0	-0.079	0.107	15.571	-0.050	-0.050	0.000	0.000	0.000	0.000
125	D	68	LEU	0	0.086	-0.120	12.615	0.026	0.026	0.000	0.000	0.000	0.000
126	D	68	LEU	0	-0.073	0.105	10.189	-0.024	-0.024	0.000	0.000	0.000	0.000
127	D	69	ARG	0	0.145	-0.063	13.831	0.063	0.063	0.000	0.000	0.000	0.000
128	D	69	ARG	1	0.787	1.057	14.552	-0.028	-0.028	0.000	0.000	0.000	0.000
129	D	70	ARG	0	0.034	-0.092	15.731	0.060	0.060	0.000	0.000	0.000	0.000
130	D	70	ARG	1	0.798	1.052	18.367	0.214	0.214	0.000	0.000	0.000	0.000
131	D	71	ASP	0	0.101	-0.102	14.520	0.002	0.002	0.000	0.000	0.000	0.000
132	D	71	ASP	-1	-0.922	-0.834	13.806	-0.292	-0.292	0.000	0.000	0.000	0.000
133	D	72	ALA	0	0.071	-0.127	15.661	0.058	0.058	0.000	0.000	0.000	0.000
134	D	72	ALA	0	-0.040	0.127	17.342	-0.003	-0.003	0.000	0.000	0.000	0.000
135	D	73	SER	0	0.048	-0.065	13.142	0.071	0.071	0.000	0.000	0.000	0.000
136	D	73	SER	0	0.025	0.096	12.275	-0.033	-0.033	0.000	0.000	0.000	0.000
137	D	74	LEU	0	0.131	-0.053	11.889	0.155	0.155	0.000	0.000	0.000	0.000
138	D	74	LEU	0	-0.133	0.084	10.551	-0.012	-0.012	0.000	0.000	0.000	0.000
139	D	75	GLN	0	0.047	-0.120	12.774	0.115	0.115	0.000	0.000	0.000	0.000
140	D	75	GLN	0	-0.106	0.081	17.052	-0.026	-0.026	0.000	0.000	0.000	0.000
141	D	76	GLU	0	0.088	-0.129	16.334	0.036	0.036	0.000	0.000	0.000	0.000
142	D	76	GLU	-1	-1.004	-0.826	15.799	0.198	0.198	0.000	0.000	0.000	0.000
143	D	77	TYR	0	0.084	-0.096	12.869	0.002	0.002	0.000	0.000	0.000	0.000
144	D	77	TYR	0	-0.108	0.095	11.660	0.114	0.114	0.000	0.000	0.000	0.000
145	D	78	ASN	0	0.106	-0.057	14.401	0.053	0.053	0.000	0.000	0.000	0.000
146	D	78	ASN	0	-0.129	0.027	13.589	0.075	0.075	0.000	0.000	0.000	0.000
147	D	79	GLN	0	0.125	-0.113	15.494	0.012	0.012	0.000	0.000	0.000	0.000
148	D	79	GLN	0	-0.093	0.116	19.379	-0.007	-0.007	0.000	0.000	0.000	0.000
149	D	80	LEU	0	0.093	-0.116	17.885	-0.028	-0.028	0.000	0.000	0.000	0.000
150	D	80	LEU	0	-0.068	0.138	16.349	0.006	0.006	0.000	0.000	0.000	0.000
151	D	81	GLN	0	0.110	-0.087	16.328	0.000	0.000	0.000	0.000	0.000	0.000
152	D	81	GLN	0	-0.108	0.086	14.242	0.045	0.045	0.000	0.000	0.000	0.000
153	D	82	GLN	0	0.002	-0.141	17.509	0.003	0.003	0.000	0.000	0.000	0.000
154	D	82	GLN	0	-0.110	0.078	19.375	-0.022	-0.022	0.000	0.000	0.000	0.000
155	D	83	VAL	0	0.035	-0.102	20.536	-0.013	-0.013	0.000	0.000	0.000	0.000
156	D	83	VAL	0	-0.066	0.119	22.055	-0.004	-0.004	0.000	0.000	0.000	0.000
157	D	84	PHE	0	0.142	-0.067	20.348	-0.040	-0.040	0.000	0.000	0.000	0.000
158	D	84	PHE	0	-0.070	0.088	19.775	0.018	0.018	0.000	0.000	0.000	0.000
159	D	85	LYS	0	0.141	-0.077	21.733	-0.009	-0.009	0.000	0.000	0.000	0.000
160	D	85	LYS	1	0.827	1.040	22.628	-0.300	-0.300	0.000	0.000	0.000	0.000
161	D	86	GLN	0	0.059	-0.078	23.661	-0.005	-0.005	0.000	0.000	0.000	0.000
162	D	86	GLN	0	-0.081	0.067	25.484	-0.016	-0.016	0.000	0.000	0.000	0.000
163	D	87	THR	0	-0.043	-0.090	25.470	-0.023	-0.023	0.000	0.000	0.000	0.000
164	D	87	THR	0	-0.040	0.061	24.780	-0.005	-0.005	0.000	0.000	0.000	0.000
165	D	88	PHE	0	0.065	-0.060	25.245	-0.025	-0.025	0.000	0.000	0.000	0.000
166	D	88	PHE	0	-0.126	0.058	23.103	0.004	0.004	0.000	0.000	0.000	0.000
167	D	89	LEU	0	-0.005	-0.104	24.706	-0.033	-0.033	0.000	0.000	0.000	0.000
168	D	89	LEU	0	-0.007	0.019	22.615	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)