FMO DATABASE

FMODB ID: L75Q9

Calculation Name: 2RF4-B-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2RF4

Chain ID: B

ChEMBL ID:

UniProt ID: P50106

Base Structure: X-ray

Registration Date: 2025-07-11

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	117
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-290826.978663
FMO2-HF: Nuclear repulsion	267048.051455
FMO2-HF: Total energy	-23778.927209
FMO2-MP2: Total energy	-23849.645388

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(B:16:LEU)

Summations of interaction energy for fragment #1(B:16:LEU)

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.
-3.361	-0.923	-0.01	-1.264	-1.165	0.001

Interaction energy analysis for fragmet #1(B:16:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.167 / q_NPA : 0.024

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	B	17	ASN	0	-0.084	0.060	4.281	-0.781	-0.329	0.000	-0.177	-0.275	0.000
5	B	18	THR	0	0.072	-0.114	3.780	-1.200	0.680	-0.009	-1.079	-0.793	0.001
6	B	18	THR	0	-0.037	0.100	5.712	0.291	0.291	0.000	0.000	0.000	0.000
7	B	19	PRO	0	-0.027	-0.101	4.797	-1.397	-1.291	-0.001	-0.008	-0.097	0.000
8	B	20	VAL	0	0.091	-0.006	6.240	0.277	0.277	0.000	0.000	0.000	0.000
9	B	20	VAL	0	-0.057	0.126	8.027	-0.023	-0.023	0.000	0.000	0.000	0.000
10	B	21	VAL	0	0.067	-0.111	9.152	0.033	0.033	0.000	0.000	0.000	0.000
11	B	21	VAL	0	-0.074	0.097	12.562	0.019	0.019	0.000	0.000	0.000	0.000
12	B	22	ILE	0	0.048	-0.111	12.674	-0.022	-0.022	0.000	0.000	0.000	0.000
13	B	22	ILE	0	-0.046	0.110	11.523	0.006	0.006	0.000	0.000	0.000	0.000
14	B	23	HIS	0	0.034	-0.105	14.898	0.030	0.030	0.000	0.000	0.000	0.000
15	B	23	HIS	0	-0.054	0.093	17.086	0.027	0.027	0.000	0.000	0.000	0.000
16	B	24	ALA	0	0.130	-0.095	18.694	-0.019	-0.019	0.000	0.000	0.000	0.000
17	B	24	ALA	0	-0.089	0.123	21.575	0.004	0.004	0.000	0.000	0.000	0.000
18	B	25	THR	0	0.033	-0.084	21.649	0.024	0.024	0.000	0.000	0.000	0.000
19	B	25	THR	0	-0.061	0.054	21.476	-0.001	-0.001	0.000	0.000	0.000	0.000
20	B	26	GLN	0	0.044	-0.102	23.799	0.019	0.019	0.000	0.000	0.000	0.000
21	B	26	GLN	0	-0.052	0.097	25.876	0.011	0.011	0.000	0.000	0.000	0.000
22	B	27	LEU	0	0.101	-0.087	24.862	-0.021	-0.021	0.000	0.000	0.000	0.000
23	B	27	LEU	0	-0.070	0.119	28.046	0.003	0.003	0.000	0.000	0.000	0.000
24	B	28	PRO	0	-0.053	-0.147	23.507	0.001	0.001	0.000	0.000	0.000	0.000
25	B	29	GLN	0	0.129	0.025	26.021	0.014	0.014	0.000	0.000	0.000	0.000
26	B	29	GLN	0	-0.120	0.085	28.613	0.000	0.000	0.000	0.000	0.000	0.000
27	B	30	HIS	0	0.077	-0.084	28.021	-0.013	-0.013	0.000	0.000	0.000	0.000
28	B	30	HIS	0	-0.083	0.076	29.198	0.001	0.001	0.000	0.000	0.000	0.000
29	B	31	VAL	0	0.016	-0.095	30.054	0.006	0.006	0.000	0.000	0.000	0.000
30	B	31	VAL	0	-0.040	0.112	28.530	-0.001	-0.001	0.000	0.000	0.000	0.000
31	B	32	SER	0	0.039	-0.102	31.237	0.002	0.002	0.000	0.000	0.000	0.000
32	B	32	SER	0	-0.060	0.025	34.858	0.002	0.002	0.000	0.000	0.000	0.000
33	B	33	THR	0	0.021	-0.087	32.623	-0.009	-0.009	0.000	0.000	0.000	0.000
34	B	33	THR	0	0.008	0.086	34.998	0.001	0.001	0.000	0.000	0.000	0.000
35	B	34	ASP	0	0.044	-0.122	34.121	-0.001	-0.001	0.000	0.000	0.000	0.000
36	B	34	ASP	-1	-0.959	-0.835	36.602	-0.097	-0.097	0.000	0.000	0.000	0.000
37	B	35	GLU	0	0.072	-0.105	32.251	-0.001	-0.001	0.000	0.000	0.000	0.000
38	B	35	GLU	-1	-0.853	-0.765	31.295	-0.127	-0.127	0.000	0.000	0.000	0.000
39	B	36	VAL	0	0.095	-0.092	28.950	-0.010	-0.010	0.000	0.000	0.000	0.000
40	B	36	VAL	0	-0.085	0.117	27.395	-0.001	-0.001	0.000	0.000	0.000	0.000
41	B	37	LEU	0	0.081	-0.116	29.309	-0.010	-0.010	0.000	0.000	0.000	0.000
42	B	37	LEU	0	-0.089	0.110	32.825	0.001	0.001	0.000	0.000	0.000	0.000
43	B	38	GLN	0	0.123	-0.086	31.359	-0.002	-0.002	0.000	0.000	0.000	0.000
44	B	38	GLN	0	-0.104	0.097	32.478	-0.003	-0.003	0.000	0.000	0.000	0.000
45	B	39	PHE	0	0.061	-0.093	27.759	0.000	0.000	0.000	0.000	0.000	0.000
46	B	39	PHE	0	-0.105	0.073	22.371	-0.003	-0.003	0.000	0.000	0.000	0.000
47	B	40	LEU	0	0.054	-0.089	26.460	-0.014	-0.014	0.000	0.000	0.000	0.000
48	B	40	LEU	0	-0.072	0.083	25.122	0.000	0.000	0.000	0.000	0.000	0.000
49	B	41	GLU	0	0.096	-0.107	27.480	-0.007	-0.007	0.000	0.000	0.000	0.000
50	B	41	GLU	-1	-0.883	-0.764	31.618	-0.107	-0.107	0.000	0.000	0.000	0.000
51	B	42	SER	0	0.081	-0.076	28.903	0.001	0.001	0.000	0.000	0.000	0.000
52	B	42	SER	0	-0.030	0.080	28.296	0.003	0.003	0.000	0.000	0.000	0.000
53	B	43	PHE	0	0.093	-0.065	24.403	-0.002	-0.002	0.000	0.000	0.000	0.000
54	B	43	PHE	0	-0.131	0.058	19.042	-0.009	-0.009	0.000	0.000	0.000	0.000
55	B	44	ILE	0	0.029	-0.082	24.178	-0.018	-0.018	0.000	0.000	0.000	0.000
56	B	44	ILE	0	-0.120	0.048	25.493	0.003	0.003	0.000	0.000	0.000	0.000
57	B	45	ASP	0	0.089	-0.096	25.959	-0.003	-0.003	0.000	0.000	0.000	0.000
58	B	45	ASP	-1	-1.001	-0.861	29.157	-0.135	-0.135	0.000	0.000	0.000	0.000
59	B	46	GLU	0	0.101	-0.110	25.453	0.007	0.007	0.000	0.000	0.000	0.000
60	B	46	GLU	-1	-0.970	-0.818	23.220	-0.257	-0.257	0.000	0.000	0.000	0.000
61	B	47	LYS	0	-0.009	-0.105	22.052	-0.016	-0.016	0.000	0.000	0.000	0.000
62	B	47	LYS	1	0.687	0.944	19.471	0.275	0.275	0.000	0.000	0.000	0.000
63	B	48	GLU	0	0.151	-0.051	22.652	-0.011	-0.011	0.000	0.000	0.000	0.000
64	B	48	GLU	-1	-0.901	-0.805	25.624	-0.121	-0.121	0.000	0.000	0.000	0.000
65	B	49	ASN	0	0.087	-0.074	25.455	0.015	0.015	0.000	0.000	0.000	0.000
66	B	49	ASN	0	-0.094	0.072	26.781	0.010	0.010	0.000	0.000	0.000	0.000
67	B	50	ILE	0	0.067	-0.082	25.408	-0.012	-0.012	0.000	0.000	0.000	0.000
68	B	50	ILE	0	-0.108	0.065	27.567	0.002	0.002	0.000	0.000	0.000	0.000
69	B	51	ILE	0	0.035	-0.093	24.411	-0.001	-0.001	0.000	0.000	0.000	0.000
70	B	51	ILE	0	-0.107	0.066	23.150	0.001	0.001	0.000	0.000	0.000	0.000
71	B	52	ASP	0	0.130	-0.091	22.378	-0.022	-0.022	0.000	0.000	0.000	0.000
72	B	52	ASP	-1	-0.958	-0.830	22.058	-0.172	-0.172	0.000	0.000	0.000	0.000
73	B	78	ILE	0	0.057	-0.118	17.815	0.008	0.008	0.000	0.000	0.000	0.000
74	B	78	ILE	0	-0.156	0.081	14.487	-0.013	-0.013	0.000	0.000	0.000	0.000
75	B	79	ASP	0	0.122	-0.076	18.309	-0.031	-0.031	0.000	0.000	0.000	0.000
76	B	79	ASP	-1	-0.942	-0.845	18.578	-0.146	-0.146	0.000	0.000	0.000	0.000
77	B	80	THR	0	-0.079	-0.112	14.562	0.009	0.009	0.000	0.000	0.000	0.000
78	B	80	THR	0	0.005	0.072	12.464	-0.011	-0.011	0.000	0.000	0.000	0.000
79	B	81	ASN	0	0.100	-0.028	14.956	-0.050	-0.050	0.000	0.000	0.000	0.000
80	B	81	ASN	0	-0.075	0.064	15.052	0.038	0.038	0.000	0.000	0.000	0.000
81	B	82	LEU	0	0.153	-0.113	16.960	0.010	0.010	0.000	0.000	0.000	0.000
82	B	82	LEU	0	-0.050	0.145	16.571	-0.010	-0.010	0.000	0.000	0.000	0.000
83	B	83	SER	0	0.078	-0.062	17.914	0.005	0.005	0.000	0.000	0.000	0.000
84	B	83	SER	0	-0.015	0.087	21.017	0.003	0.003	0.000	0.000	0.000	0.000
85	B	84	SER	0	0.016	-0.086	20.420	0.010	0.010	0.000	0.000	0.000	0.000
86	B	84	SER	0	-0.061	0.043	19.077	-0.004	-0.004	0.000	0.000	0.000	0.000
87	B	85	SER	0	0.035	-0.089	18.890	0.028	0.028	0.000	0.000	0.000	0.000
88	B	85	SER	0	-0.054	0.065	17.846	-0.017	-0.017	0.000	0.000	0.000	0.000
89	B	86	ILE	0	0.057	-0.127	20.269	0.002	0.002	0.000	0.000	0.000	0.000
90	B	86	ILE	0	-0.039	0.167	21.256	0.000	0.000	0.000	0.000	0.000	0.000
91	B	87	SER	0	0.089	-0.053	23.034	0.009	0.009	0.000	0.000	0.000	0.000
92	B	87	SER	0	-0.076	0.050	24.868	0.004	0.004	0.000	0.000	0.000	0.000
93	B	88	GLN	0	0.050	-0.106	23.360	0.016	0.016	0.000	0.000	0.000	0.000
94	B	88	GLN	0	-0.108	0.091	21.377	-0.014	-0.014	0.000	0.000	0.000	0.000
95	B	89	LEU	0	0.056	-0.129	23.625	0.014	0.014	0.000	0.000	0.000	0.000
96	B	89	LEU	0	-0.028	0.122	20.908	-0.001	-0.001	0.000	0.000	0.000	0.000
97	B	90	LYS	0	0.112	-0.090	24.872	0.003	0.003	0.000	0.000	0.000	0.000
98	B	90	LYS	1	0.712	0.969	27.324	0.119	0.119	0.000	0.000	0.000	0.000
99	B	91	ARG	0	0.030	-0.076	27.835	0.007	0.007	0.000	0.000	0.000	0.000
100	B	91	ARG	1	0.845	1.035	27.420	0.073	0.073	0.000	0.000	0.000	0.000
101	B	92	ILE	0	0.111	-0.075	27.313	0.013	0.013	0.000	0.000	0.000	0.000
102	B	92	ILE	0	-0.079	0.094	24.577	-0.001	-0.001	0.000	0.000	0.000	0.000
103	B	93	GLN	0	0.139	-0.103	28.658	0.005	0.005	0.000	0.000	0.000	0.000
104	B	93	GLN	0	-0.100	0.108	28.923	0.008	0.008	0.000	0.000	0.000	0.000
105	B	94	ARG	0	0.116	-0.076	30.382	0.004	0.004	0.000	0.000	0.000	0.000
106	B	94	ARG	1	0.793	1.031	32.735	0.067	0.067	0.000	0.000	0.000	0.000
107	B	95	ASP	0	0.033	-0.099	32.241	0.006	0.006	0.000	0.000	0.000	0.000
108	B	95	ASP	-1	-1.028	-0.873	31.796	-0.076	-0.076	0.000	0.000	0.000	0.000
109	B	96	PHE	0	0.142	-0.071	32.332	0.007	0.007	0.000	0.000	0.000	0.000
110	B	96	PHE	0	-0.122	0.067	30.047	-0.003	-0.003	0.000	0.000	0.000	0.000
111	B	97	LYS	0	0.001	-0.110	33.683	0.002	0.002	0.000	0.000	0.000	0.000
112	B	97	LYS	1	0.711	0.946	33.846	0.099	0.099	0.000	0.000	0.000	0.000
113	B	98	GLY	0	-0.012	-0.114	36.292	0.004	0.004	0.000	0.000	0.000	0.000
114	B	99	LEU	0	0.039	-0.003	37.060	0.006	0.006	0.000	0.000	0.000	0.000
115	B	99	LEU	0	-0.057	0.121	33.822	0.000	0.000	0.000	0.000	0.000	0.000
116	B	100	PRO	0	-0.073	-0.123	38.240	0.002	0.002	0.000	0.000	0.000	0.000
117	B	101	PRO	0	-0.008	-0.003	39.954	-0.005	-0.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:16:LEU)