FMO DATABASE

FMODB ID: YNRR2

Calculation Name: 2D68-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2D68

Chain ID: A

ChEMBL ID:

UniProt ID: O95684

Base Structure: X-ray

Registration Date: 2025-07-08

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	147
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-470628.399076
FMO2-HF: Nuclear repulsion	440932.597273
FMO2-HF: Total energy	-29695.801803
FMO2-MP2: Total energy	-29784.783008

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(A:58:VAL)

Summations of interaction energy for fragment #1(A:58:VAL)

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.
4.006	6.056	0.005	-1.024	-1.029	0.003

Interaction energy analysis for fragmet #1(A:58:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.138 / q_NPA : 0.031

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	A	59	ASN	0	-0.068	0.104	4.296	-0.752	-0.418	0.001	-0.191	-0.144	0.001
5	A	60	GLU	0	0.123	-0.083	3.819	-1.404	-0.274	-0.007	-0.610	-0.512	0.003
6	A	60	GLU	-1	-0.864	-0.766	5.914	-3.467	-3.467	0.000	0.000	0.000	0.000
7	A	61	SER	0	0.049	-0.068	6.246	0.162	0.162	0.000	0.000	0.000	0.000
8	A	61	SER	0	-0.035	0.059	9.362	0.044	0.044	0.000	0.000	0.000	0.000
9	A	62	LEU	0	0.104	-0.106	7.205	-0.026	-0.026	0.000	0.000	0.000	0.000
10	A	62	LEU	0	-0.072	0.131	5.952	0.074	0.074	0.000	0.000	0.000	0.000
11	A	63	LYS	0	0.122	-0.092	5.959	0.468	0.489	-0.002	0.000	-0.019	0.000
12	A	63	LYS	1	0.782	1.020	4.454	3.745	3.797	-0.001	-0.014	-0.037	0.000
13	A	64	LYS	0	0.047	-0.095	7.038	0.167	0.167	0.000	0.000	0.000	0.000
14	A	64	LYS	1	0.803	1.001	9.416	1.486	1.486	0.000	0.000	0.000	0.000
15	A	65	PHE	0	0.131	-0.071	10.363	0.068	0.068	0.000	0.000	0.000	0.000
16	A	65	PHE	0	-0.105	0.106	10.916	0.029	0.029	0.000	0.000	0.000	0.000
17	A	66	LEU	0	0.078	-0.110	10.238	0.159	0.159	0.000	0.000	0.000	0.000
18	A	66	LEU	0	-0.064	0.115	7.663	0.004	0.004	0.000	0.000	0.000	0.000
19	A	67	ASN	0	0.061	-0.048	11.442	0.088	0.088	0.000	0.000	0.000	0.000
20	A	67	ASN	0	-0.150	0.046	11.022	-0.054	-0.054	0.000	0.000	0.000	0.000
21	A	68	THR	0	-0.033	-0.100	12.778	0.014	0.014	0.000	0.000	0.000	0.000
22	A	68	THR	0	-0.060	0.044	14.633	0.044	0.044	0.000	0.000	0.000	0.000
23	A	69	LYS	0	0.116	-0.069	16.030	0.004	0.004	0.000	0.000	0.000	0.000
24	A	69	LYS	1	0.819	1.039	20.293	0.194	0.194	0.000	0.000	0.000	0.000
25	A	70	ASP	0	0.120	-0.133	18.841	0.012	0.012	0.000	0.000	0.000	0.000
26	A	70	ASP	-1	-0.985	-0.826	19.561	-0.181	-0.181	0.000	0.000	0.000	0.000
27	A	71	GLY	0	0.010	-0.107	14.962	0.046	0.046	0.000	0.000	0.000	0.000
28	A	72	ARG	0	0.129	0.022	14.575	0.057	0.057	0.000	0.000	0.000	0.000
29	A	72	ARG	1	0.738	0.988	14.304	0.274	0.274	0.000	0.000	0.000	0.000
30	A	73	LEU	0	0.033	-0.091	15.558	0.047	0.047	0.000	0.000	0.000	0.000
31	A	73	LEU	0	-0.052	0.100	19.932	0.000	0.000	0.000	0.000	0.000	0.000
32	A	74	VAL	0	0.065	-0.088	17.276	0.037	0.037	0.000	0.000	0.000	0.000
33	A	74	VAL	0	-0.066	0.099	15.985	0.003	0.003	0.000	0.000	0.000	0.000
34	A	75	ALA	0	0.117	-0.092	13.344	0.067	0.067	0.000	0.000	0.000	0.000
35	A	75	ALA	0	-0.040	0.100	12.712	-0.010	-0.010	0.000	0.000	0.000	0.000
36	A	76	SER	0	-0.007	-0.114	14.629	0.072	0.072	0.000	0.000	0.000	0.000
37	A	76	SER	0	-0.081	0.047	16.736	-0.012	-0.012	0.000	0.000	0.000	0.000
38	A	77	LEU	0	0.113	-0.065	17.155	0.027	0.027	0.000	0.000	0.000	0.000
39	A	77	LEU	0	-0.116	0.081	19.578	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	78	VAL	0	0.075	-0.082	16.341	0.006	0.006	0.000	0.000	0.000	0.000
41	A	78	VAL	0	-0.114	0.084	15.115	0.008	0.008	0.000	0.000	0.000	0.000
42	A	79	ALA	0	0.109	-0.088	16.163	0.044	0.044	0.000	0.000	0.000	0.000
43	A	79	ALA	0	-0.049	0.101	15.103	-0.004	-0.004	0.000	0.000	0.000	0.000
44	A	80	GLU	0	0.078	-0.105	16.928	0.027	0.027	0.000	0.000	0.000	0.000
45	A	80	GLU	-1	-0.840	-0.781	20.849	0.068	0.068	0.000	0.000	0.000	0.000
46	A	81	PHE	0	0.134	-0.052	20.366	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	81	PHE	0	-0.128	0.054	20.361	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	82	LEU	0	0.028	-0.120	18.612	-0.011	-0.011	0.000	0.000	0.000	0.000
49	A	82	LEU	0	-0.067	0.085	15.801	0.014	0.014	0.000	0.000	0.000	0.000
50	A	83	GLN	0	0.092	-0.085	20.089	0.016	0.016	0.000	0.000	0.000	0.000
51	A	83	GLN	0	-0.110	0.070	19.379	-0.011	-0.011	0.000	0.000	0.000	0.000
52	A	84	PHE	0	0.080	-0.068	21.728	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	84	PHE	0	-0.100	0.092	24.752	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	85	PHE	0	-0.015	-0.081	23.935	-0.014	-0.014	0.000	0.000	0.000	0.000
55	A	85	PHE	0	-0.124	0.053	24.215	-0.004	-0.004	0.000	0.000	0.000	0.000
56	A	86	ASN	0	0.117	-0.048	23.776	0.012	0.012	0.000	0.000	0.000	0.000
57	A	86	ASN	0	-0.125	0.050	25.550	-0.007	-0.007	0.000	0.000	0.000	0.000
58	A	87	LEU	0	0.179	-0.061	21.173	0.005	0.005	0.000	0.000	0.000	0.000
59	A	87	LEU	0	-0.154	0.069	20.555	0.008	0.008	0.000	0.000	0.000	0.000
60	A	88	ASP	0	0.112	-0.147	19.419	0.050	0.050	0.000	0.000	0.000	0.000
61	A	88	ASP	-1	-0.964	-0.815	21.277	0.239	0.239	0.000	0.000	0.000	0.000
62	A	89	PHE	0	0.069	-0.113	18.630	0.035	0.035	0.000	0.000	0.000	0.000
63	A	89	PHE	0	-0.098	0.090	19.551	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	90	THR	0	0.027	-0.078	16.573	0.089	0.089	0.000	0.000	0.000	0.000
65	A	90	THR	0	-0.026	0.060	15.943	-0.006	-0.006	0.000	0.000	0.000	0.000
66	A	91	LEU	0	0.118	-0.090	14.780	0.127	0.127	0.000	0.000	0.000	0.000
67	A	91	LEU	0	-0.065	0.126	15.741	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	92	ALA	0	0.089	-0.091	13.963	0.047	0.047	0.000	0.000	0.000	0.000
69	A	92	ALA	0	-0.076	0.099	16.154	-0.009	-0.009	0.000	0.000	0.000	0.000
70	A	93	VAL	0	0.000	-0.141	12.101	0.067	0.067	0.000	0.000	0.000	0.000
71	A	93	VAL	0	-0.067	0.113	11.447	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	94	PHE	0	0.160	-0.051	10.248	0.336	0.336	0.000	0.000	0.000	0.000
73	A	94	PHE	0	-0.098	0.081	12.404	-0.026	-0.026	0.000	0.000	0.000	0.000
74	A	95	GLN	0	0.075	-0.055	9.386	0.159	0.159	0.000	0.000	0.000	0.000
75	A	95	GLN	0	-0.035	0.106	11.575	-0.082	-0.082	0.000	0.000	0.000	0.000
76	A	96	PRO	0	-0.046	-0.131	7.777	-0.037	-0.037	0.000	0.000	0.000	0.000
77	A	97	GLU	0	0.080	-0.020	5.745	1.016	1.016	0.000	0.000	0.000	0.000
78	A	97	GLU	-1	-1.020	-0.836	7.096	1.779	1.779	0.000	0.000	0.000	0.000
79	A	98	THR	0	-0.080	-0.146	5.027	0.958	1.012	-0.002	-0.001	-0.051	0.000
80	A	98	THR	0	-0.064	0.060	7.802	-0.191	-0.191	0.000	0.000	0.000	0.000
81	A	99	SER	0	0.019	-0.055	4.686	-0.455	-0.416	-0.002	-0.003	-0.034	0.000
82	A	99	SER	0	-0.045	0.055	3.519	-0.784	-0.364	0.018	-0.205	-0.232	-0.001
83	A	100	THR	0	0.032	-0.090	5.791	-0.626	-0.626	0.000	0.000	0.000	0.000
84	A	100	THR	0	-0.079	0.055	8.596	-0.035	-0.035	0.000	0.000	0.000	0.000
85	A	101	LEU	0	0.075	-0.077	9.442	0.175	0.175	0.000	0.000	0.000	0.000
86	A	101	LEU	0	-0.085	0.104	8.687	-0.018	-0.018	0.000	0.000	0.000	0.000
87	A	102	GLN	0	0.078	-0.116	11.585	-0.070	-0.070	0.000	0.000	0.000	0.000
88	A	102	GLN	0	-0.086	0.078	14.244	0.043	0.043	0.000	0.000	0.000	0.000
89	A	103	GLY	0	0.027	-0.090	14.138	0.000	0.000	0.000	0.000	0.000	0.000
90	A	104	LEU	0	0.006	-0.023	14.799	-0.103	-0.103	0.000	0.000	0.000	0.000
91	A	104	LEU	0	-0.063	0.099	12.551	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	105	GLU	0	0.046	-0.134	15.599	0.011	0.011	0.000	0.000	0.000	0.000
93	A	105	GLU	-1	-0.853	-0.780	18.600	-0.174	-0.174	0.000	0.000	0.000	0.000
94	A	106	GLY	0	0.039	-0.057	19.267	0.028	0.028	0.000	0.000	0.000	0.000
95	A	107	ARG	0	0.115	0.009	21.778	-0.018	-0.018	0.000	0.000	0.000	0.000
96	A	107	ARG	1	0.696	0.936	24.601	-0.043	-0.043	0.000	0.000	0.000	0.000
97	A	108	GLU	0	0.123	-0.102	24.609	-0.003	-0.003	0.000	0.000	0.000	0.000
98	A	108	GLU	-1	-1.014	-0.846	27.284	-0.031	-0.031	0.000	0.000	0.000	0.000
99	A	109	ASN	0	0.063	-0.121	24.263	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	109	ASN	0	-0.073	0.073	22.756	0.007	0.007	0.000	0.000	0.000	0.000
101	A	110	LEU	0	0.119	-0.074	22.993	-0.019	-0.019	0.000	0.000	0.000	0.000
102	A	110	LEU	0	-0.117	0.115	20.710	0.000	0.000	0.000	0.000	0.000	0.000
103	A	111	ALA	0	0.086	-0.115	23.930	-0.006	-0.006	0.000	0.000	0.000	0.000
104	A	111	ALA	0	-0.063	0.117	27.953	0.002	0.002	0.000	0.000	0.000	0.000
105	A	112	ARG	0	0.120	-0.074	27.436	0.001	0.001	0.000	0.000	0.000	0.000
106	A	112	ARG	1	0.729	0.997	25.178	0.096	0.096	0.000	0.000	0.000	0.000
107	A	113	ASP	0	0.043	-0.093	24.693	0.000	0.000	0.000	0.000	0.000	0.000
108	A	113	ASP	-1	-0.909	-0.820	23.649	-0.142	-0.142	0.000	0.000	0.000	0.000
109	A	114	LEU	0	-0.034	-0.135	26.183	-0.013	-0.013	0.000	0.000	0.000	0.000
110	A	114	LEU	0	-0.085	0.092	23.346	0.002	0.002	0.000	0.000	0.000	0.000
111	A	115	GLY	0	0.022	-0.096	27.101	0.006	0.006	0.000	0.000	0.000	0.000
112	A	116	ILE	0	0.030	-0.025	29.938	0.003	0.003	0.000	0.000	0.000	0.000
113	A	116	ILE	0	-0.102	0.089	27.577	0.002	0.002	0.000	0.000	0.000	0.000
114	A	117	ILE	0	0.076	-0.100	31.290	-0.002	-0.002	0.000	0.000	0.000	0.000
115	A	117	ILE	0	-0.101	0.092	34.950	0.000	0.000	0.000	0.000	0.000	0.000
116	A	118	GLU	0	0.114	-0.110	33.003	0.004	0.004	0.000	0.000	0.000	0.000
117	A	118	GLU	-1	-0.892	-0.750	30.288	0.022	0.022	0.000	0.000	0.000	0.000
118	A	119	ALA	0	0.111	-0.089	33.796	-0.004	-0.004	0.000	0.000	0.000	0.000
119	A	119	ALA	0	-0.078	0.092	37.434	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	120	GLU	0	0.019	-0.146	36.024	0.005	0.005	0.000	0.000	0.000	0.000
121	A	120	GLU	-1	-0.902	-0.800	40.062	0.013	0.013	0.000	0.000	0.000	0.000
122	A	121	GLY	0	-0.048	-0.117	37.314	0.005	0.005	0.000	0.000	0.000	0.000
123	A	122	THR	0	-0.039	-0.020	33.094	0.005	0.005	0.000	0.000	0.000	0.000
124	A	122	THR	0	-0.002	0.074	32.010	-0.002	-0.002	0.000	0.000	0.000	0.000
125	A	123	VAL	0	0.054	-0.095	31.775	0.006	0.006	0.000	0.000	0.000	0.000
126	A	123	VAL	0	-0.049	0.127	33.032	0.000	0.000	0.000	0.000	0.000	0.000
127	A	124	GLY	0	-0.034	-0.115	31.934	0.006	0.006	0.000	0.000	0.000	0.000
128	A	125	GLY	0	-0.025	-0.012	30.133	0.009	0.009	0.000	0.000	0.000	0.000
129	A	126	PRO	0	0.022	0.034	24.784	-0.007	-0.007	0.000	0.000	0.000	0.000
130	A	127	LEU	0	0.120	-0.010	25.412	-0.003	-0.003	0.000	0.000	0.000	0.000
131	A	127	LEU	0	-0.065	0.116	24.392	-0.002	-0.002	0.000	0.000	0.000	0.000
132	A	128	LEU	0	0.113	-0.112	24.046	-0.016	-0.016	0.000	0.000	0.000	0.000
133	A	128	LEU	0	-0.078	0.120	21.677	0.002	0.002	0.000	0.000	0.000	0.000
134	A	129	LEU	0	0.057	-0.135	25.230	-0.003	-0.003	0.000	0.000	0.000	0.000
135	A	129	LEU	0	-0.074	0.116	28.692	0.002	0.002	0.000	0.000	0.000	0.000
136	A	130	GLU	0	0.101	-0.084	28.651	-0.001	-0.001	0.000	0.000	0.000	0.000
137	A	130	GLU	-1	-0.860	-0.767	29.604	0.015	0.015	0.000	0.000	0.000	0.000
138	A	131	VAL	0	0.019	-0.122	27.234	-0.006	-0.006	0.000	0.000	0.000	0.000
139	A	131	VAL	0	-0.077	0.090	25.687	-0.001	-0.001	0.000	0.000	0.000	0.000
140	A	132	ILE	0	0.052	-0.107	28.393	-0.009	-0.009	0.000	0.000	0.000	0.000
141	A	132	ILE	0	-0.101	0.092	26.106	0.002	0.002	0.000	0.000	0.000	0.000
142	A	133	ARG	0	0.133	-0.077	29.566	-0.001	-0.001	0.000	0.000	0.000	0.000
143	A	133	ARG	1	0.722	0.997	32.772	-0.035	-0.035	0.000	0.000	0.000	0.000
144	A	134	ARG	0	0.027	-0.119	32.223	0.001	0.001	0.000	0.000	0.000	0.000
145	A	134	ARG	1	0.788	1.016	32.696	0.006	0.006	0.000	0.000	0.000	0.000
146	A	135	TRP	0	-0.062	-0.125	31.260	-0.012	-0.012	0.000	0.000	0.000	0.000
147	A	135	TRP	0	-0.004	0.016	27.929	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:58:VAL)