FMO DATABASE

FMODB ID: 9M5L2

Calculation Name: 2RF4-B-Xray540

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

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	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

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	-291833.633869
FMO2-HF: Nuclear repulsion	268056.734918
FMO2-HF: Total energy	-23776.898951
FMO2-MP2: Total energy	-23847.826926

3D Structure

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.
-4.828	-0.159	-0.051	-2.439	-2.18	-0.004

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 : 0.180 / 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	B	17	ASN	0	-0.034	0.095	4.090	-0.924	-0.253	0.000	-0.297	-0.375	0.000
5	B	18	THR	0	0.038	-0.044	3.818	-2.803	1.119	-0.049	-2.140	-1.733	-0.004
6	B	18	THR	0	0.014	0.090	6.181	0.205	0.205	0.000	0.000	0.000	0.000
7	B	19	PRO	0	-0.035	-0.092	5.236	-0.983	-0.907	-0.002	-0.002	-0.072	0.000
8	B	20	VAL	0	0.126	-0.018	6.658	0.175	0.175	0.000	0.000	0.000	0.000
9	B	20	VAL	0	-0.053	0.145	7.911	-0.026	-0.026	0.000	0.000	0.000	0.000
10	B	21	VAL	0	0.055	-0.148	9.287	0.049	0.049	0.000	0.000	0.000	0.000
11	B	21	VAL	0	-0.077	0.129	12.429	0.016	0.016	0.000	0.000	0.000	0.000
12	B	22	ILE	0	0.040	-0.109	12.788	-0.015	-0.015	0.000	0.000	0.000	0.000
13	B	22	ILE	0	-0.032	0.105	12.097	0.002	0.002	0.000	0.000	0.000	0.000
14	B	23	HIS	0	0.039	-0.120	15.056	0.033	0.033	0.000	0.000	0.000	0.000
15	B	23	HIS	0	-0.082	0.111	18.401	0.012	0.012	0.000	0.000	0.000	0.000
16	B	24	ALA	0	0.139	-0.110	18.830	-0.019	-0.019	0.000	0.000	0.000	0.000
17	B	24	ALA	0	-0.075	0.137	21.563	0.004	0.004	0.000	0.000	0.000	0.000
18	B	25	THR	0	0.021	-0.074	21.580	0.012	0.012	0.000	0.000	0.000	0.000
19	B	25	THR	0	-0.055	0.054	21.998	0.001	0.001	0.000	0.000	0.000	0.000
20	B	26	GLN	0	0.018	-0.122	24.217	0.015	0.015	0.000	0.000	0.000	0.000
21	B	26	GLN	0	-0.028	0.109	26.156	0.009	0.009	0.000	0.000	0.000	0.000
22	B	27	LEU	0	0.096	-0.104	25.120	-0.017	-0.017	0.000	0.000	0.000	0.000
23	B	27	LEU	0	-0.089	0.128	28.076	0.002	0.002	0.000	0.000	0.000	0.000
24	B	28	PRO	0	-0.050	-0.137	23.939	0.001	0.001	0.000	0.000	0.000	0.000
25	B	29	GLN	0	0.151	-0.010	26.420	0.012	0.012	0.000	0.000	0.000	0.000
26	B	29	GLN	0	-0.069	0.137	29.047	-0.004	-0.004	0.000	0.000	0.000	0.000
27	B	30	HIS	0	0.061	-0.077	28.438	-0.010	-0.010	0.000	0.000	0.000	0.000
28	B	30	HIS	0	-0.091	0.068	29.772	0.002	0.002	0.000	0.000	0.000	0.000
29	B	31	VAL	0	0.047	-0.112	29.722	0.007	0.007	0.000	0.000	0.000	0.000
30	B	31	VAL	0	-0.043	0.127	28.325	-0.001	-0.001	0.000	0.000	0.000	0.000
31	B	32	SER	0	0.021	-0.094	31.053	0.002	0.002	0.000	0.000	0.000	0.000
32	B	32	SER	0	-0.047	0.073	35.107	0.002	0.002	0.000	0.000	0.000	0.000
33	B	33	THR	0	0.043	-0.083	32.865	-0.007	-0.007	0.000	0.000	0.000	0.000
34	B	33	THR	0	-0.022	0.070	34.928	-0.001	-0.001	0.000	0.000	0.000	0.000
35	B	34	ASP	0	0.109	-0.123	34.047	-0.003	-0.003	0.000	0.000	0.000	0.000
36	B	34	ASP	-1	-0.968	-0.829	36.927	-0.084	-0.084	0.000	0.000	0.000	0.000
37	B	35	GLU	0	0.069	-0.086	32.380	0.000	0.000	0.000	0.000	0.000	0.000
38	B	35	GLU	-1	-0.935	-0.827	31.607	-0.114	-0.114	0.000	0.000	0.000	0.000
39	B	36	VAL	0	0.095	-0.116	29.069	-0.009	-0.009	0.000	0.000	0.000	0.000
40	B	36	VAL	0	-0.104	0.110	27.822	-0.001	-0.001	0.000	0.000	0.000	0.000
41	B	37	LEU	0	0.086	-0.130	29.636	-0.010	-0.010	0.000	0.000	0.000	0.000
42	B	37	LEU	0	-0.106	0.143	32.554	0.001	0.001	0.000	0.000	0.000	0.000
43	B	38	GLN	0	0.104	-0.103	32.024	0.001	0.001	0.000	0.000	0.000	0.000
44	B	38	GLN	0	-0.084	0.113	32.347	-0.001	-0.001	0.000	0.000	0.000	0.000
45	B	39	PHE	0	0.057	-0.092	27.835	-0.002	-0.002	0.000	0.000	0.000	0.000
46	B	39	PHE	0	-0.133	0.055	22.546	-0.003	-0.003	0.000	0.000	0.000	0.000
47	B	40	LEU	0	0.042	-0.110	26.589	-0.013	-0.013	0.000	0.000	0.000	0.000
48	B	40	LEU	0	-0.063	0.097	25.664	0.000	0.000	0.000	0.000	0.000	0.000
49	B	41	GLU	0	0.088	-0.094	27.654	-0.008	-0.008	0.000	0.000	0.000	0.000
50	B	41	GLU	-1	-1.008	-0.850	31.584	-0.105	-0.105	0.000	0.000	0.000	0.000
51	B	42	SER	0	0.091	-0.074	28.890	0.000	0.000	0.000	0.000	0.000	0.000
52	B	42	SER	0	-0.038	0.080	28.119	0.001	0.001	0.000	0.000	0.000	0.000
53	B	43	PHE	0	0.081	-0.053	24.434	-0.005	-0.005	0.000	0.000	0.000	0.000
54	B	43	PHE	0	-0.152	0.041	19.217	-0.010	-0.010	0.000	0.000	0.000	0.000
55	B	44	ILE	0	0.050	-0.118	24.203	-0.018	-0.018	0.000	0.000	0.000	0.000
56	B	44	ILE	0	-0.107	0.068	25.512	0.002	0.002	0.000	0.000	0.000	0.000
57	B	45	ASP	0	0.056	-0.126	25.773	-0.007	-0.007	0.000	0.000	0.000	0.000
58	B	45	ASP	-1	-0.972	-0.825	29.254	-0.128	-0.128	0.000	0.000	0.000	0.000
59	B	46	GLU	0	0.125	-0.106	25.390	0.007	0.007	0.000	0.000	0.000	0.000
60	B	46	GLU	-1	-1.065	-0.863	23.712	-0.210	-0.210	0.000	0.000	0.000	0.000
61	B	47	LYS	0	0.004	-0.150	21.991	-0.003	-0.003	0.000	0.000	0.000	0.000
62	B	47	LYS	1	0.821	1.049	18.777	0.300	0.300	0.000	0.000	0.000	0.000
63	B	48	GLU	0	0.132	-0.043	22.743	-0.010	-0.010	0.000	0.000	0.000	0.000
64	B	48	GLU	-1	-0.961	-0.834	25.891	-0.117	-0.117	0.000	0.000	0.000	0.000
65	B	49	ASN	0	0.113	-0.091	25.350	0.014	0.014	0.000	0.000	0.000	0.000
66	B	49	ASN	0	-0.141	0.076	26.248	0.010	0.010	0.000	0.000	0.000	0.000
67	B	50	ILE	0	0.097	-0.076	25.165	-0.011	-0.011	0.000	0.000	0.000	0.000
68	B	50	ILE	0	-0.095	0.067	26.864	0.002	0.002	0.000	0.000	0.000	0.000
69	B	51	ILE	0	-0.055	-0.097	24.644	-0.003	-0.003	0.000	0.000	0.000	0.000
70	B	51	ILE	0	-0.079	0.061	23.728	0.002	0.002	0.000	0.000	0.000	0.000
71	B	52	ASP	0	0.049	-0.134	22.339	-0.019	-0.019	0.000	0.000	0.000	0.000
72	B	52	ASP	-1	-0.893	-0.804	21.714	-0.182	-0.182	0.000	0.000	0.000	0.000
73	B	78	ILE	0	0.023	-0.125	17.975	0.006	0.006	0.000	0.000	0.000	0.000
74	B	78	ILE	0	-0.177	0.077	15.550	-0.017	-0.017	0.000	0.000	0.000	0.000
75	B	79	ASP	0	0.201	-0.019	18.862	-0.014	-0.014	0.000	0.000	0.000	0.000
76	B	79	ASP	-1	-0.972	-0.872	18.558	-0.161	-0.161	0.000	0.000	0.000	0.000
77	B	80	THR	0	0.023	-0.097	14.612	-0.008	-0.008	0.000	0.000	0.000	0.000
78	B	80	THR	0	0.005	0.083	12.463	-0.016	-0.016	0.000	0.000	0.000	0.000
79	B	81	ASN	0	0.061	-0.050	15.351	-0.040	-0.040	0.000	0.000	0.000	0.000
80	B	81	ASN	0	-0.084	0.076	15.248	0.033	0.033	0.000	0.000	0.000	0.000
81	B	82	LEU	0	0.096	-0.155	17.172	0.008	0.008	0.000	0.000	0.000	0.000
82	B	82	LEU	0	-0.026	0.164	15.999	-0.007	-0.007	0.000	0.000	0.000	0.000
83	B	83	SER	0	0.069	-0.082	17.913	0.007	0.007	0.000	0.000	0.000	0.000
84	B	83	SER	0	-0.014	0.086	21.302	0.001	0.001	0.000	0.000	0.000	0.000
85	B	84	SER	0	0.005	-0.101	20.215	0.013	0.013	0.000	0.000	0.000	0.000
86	B	84	SER	0	-0.046	0.070	19.098	-0.005	-0.005	0.000	0.000	0.000	0.000
87	B	85	SER	0	0.042	-0.076	18.798	0.026	0.026	0.000	0.000	0.000	0.000
88	B	85	SER	0	-0.035	0.077	17.672	-0.017	-0.017	0.000	0.000	0.000	0.000
89	B	86	ILE	0	0.065	-0.129	20.092	0.006	0.006	0.000	0.000	0.000	0.000
90	B	86	ILE	0	-0.030	0.162	21.087	0.001	0.001	0.000	0.000	0.000	0.000
91	B	87	SER	0	0.046	-0.068	22.772	0.009	0.009	0.000	0.000	0.000	0.000
92	B	87	SER	0	-0.063	0.052	24.399	0.004	0.004	0.000	0.000	0.000	0.000
93	B	88	GLN	0	0.059	-0.106	23.250	0.016	0.016	0.000	0.000	0.000	0.000
94	B	88	GLN	0	-0.113	0.098	21.620	-0.009	-0.009	0.000	0.000	0.000	0.000
95	B	89	LEU	0	0.080	-0.108	23.654	0.016	0.016	0.000	0.000	0.000	0.000
96	B	89	LEU	0	-0.005	0.137	21.324	-0.001	-0.001	0.000	0.000	0.000	0.000
97	B	90	LYS	0	0.071	-0.103	25.058	0.004	0.004	0.000	0.000	0.000	0.000
98	B	90	LYS	1	0.768	1.009	26.934	0.111	0.111	0.000	0.000	0.000	0.000
99	B	91	ARG	0	-0.005	-0.112	27.574	0.008	0.008	0.000	0.000	0.000	0.000
100	B	91	ARG	1	0.858	1.039	27.390	0.066	0.066	0.000	0.000	0.000	0.000
101	B	92	ILE	0	0.130	-0.111	27.362	0.013	0.013	0.000	0.000	0.000	0.000
102	B	92	ILE	0	-0.109	0.117	24.502	-0.001	-0.001	0.000	0.000	0.000	0.000
103	B	93	GLN	0	0.175	-0.118	28.674	0.005	0.005	0.000	0.000	0.000	0.000
104	B	93	GLN	0	-0.100	0.126	29.427	0.001	0.001	0.000	0.000	0.000	0.000
105	B	94	ARG	0	0.079	-0.073	30.615	0.004	0.004	0.000	0.000	0.000	0.000
106	B	94	ARG	1	0.812	1.031	32.956	0.061	0.061	0.000	0.000	0.000	0.000
107	B	95	ASP	0	0.045	-0.105	32.264	0.005	0.005	0.000	0.000	0.000	0.000
108	B	95	ASP	-1	-1.018	-0.856	31.888	-0.066	-0.066	0.000	0.000	0.000	0.000
109	B	96	PHE	0	0.159	-0.106	32.504	0.006	0.006	0.000	0.000	0.000	0.000
110	B	96	PHE	0	-0.093	0.077	29.551	-0.002	-0.002	0.000	0.000	0.000	0.000
111	B	97	LYS	0	-0.002	-0.096	33.978	0.002	0.002	0.000	0.000	0.000	0.000
112	B	97	LYS	1	0.842	1.039	34.273	0.083	0.083	0.000	0.000	0.000	0.000
113	B	98	GLY	0	-0.045	-0.105	36.463	0.003	0.003	0.000	0.000	0.000	0.000
114	B	99	LEU	0	0.020	-0.011	37.131	0.006	0.006	0.000	0.000	0.000	0.000
115	B	99	LEU	0	-0.047	0.111	33.923	0.000	0.000	0.000	0.000	0.000	0.000
116	B	100	PRO	0	-0.050	-0.099	38.313	0.001	0.001	0.000	0.000	0.000	0.000
117	B	101	PRO	0	-0.015	-0.003	39.981	-0.004	-0.004	0.000	0.000	0.000	0.000

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