FMO DATABASE

FMODB ID: QYV3Y

Calculation Name: 2RF4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2RF4

Chain ID: A

ChEMBL ID:

UniProt ID: P50106

Base Structure: X-ray

Registration Date: 2023-06-22

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

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

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	175
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1608250.690279
FMO2-HF: Nuclear repulsion	1540351.240299
FMO2-HF: Total energy	-67899.44998
FMO2-MP2: Total energy	-68098.79508

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(A:22:LYS)

Summations of interaction energy for fragment #1(A:22:LYS)

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.
-20.399	-17.516	-0.024	-1.373	-1.488	0

Interaction energy analysis for fragmet #1(A:22:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.972 / q_NPA : 0.974

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].
3	A	24	VAL	0	-0.013	0.020	3.864	-1.579	0.931	-0.020	-1.329	-1.161
4	A	25	THR	0	-0.010	-0.028	6.479	1.535	1.535	0.000	0.000	0.000
5	A	26	ASN	0	-0.011	-0.019	9.032	0.199	0.199	0.000	0.000	0.000
6	A	27	PRO	0	-0.012	0.011	11.442	0.800	0.800	0.000	0.000	0.000
7	A	28	ILE	0	0.028	-0.004	14.962	0.216	0.216	0.000	0.000	0.000
8	A	29	ASP	-1	-0.943	-0.975	17.574	-14.336	-14.336	0.000	0.000	0.000
9	A	30	GLU	-1	-0.813	-0.903	20.867	-11.208	-11.208	0.000	0.000	0.000
10	A	31	LYS	1	0.939	0.973	24.398	10.088	10.088	0.000	0.000	0.000
11	A	32	ASN	0	-0.050	-0.044	23.709	0.455	0.455	0.000	0.000	0.000
12	A	33	GLY	0	0.001	0.031	22.179	-0.013	-0.013	0.000	0.000	0.000
13	A	34	THR	0	-0.040	-0.028	18.670	0.027	0.027	0.000	0.000	0.000
14	A	35	SER	0	-0.025	-0.052	13.538	0.373	0.373	0.000	0.000	0.000
15	A	36	ASN	0	0.023	0.019	15.609	0.032	0.032	0.000	0.000	0.000
16	A	37	CYS	0	-0.052	-0.008	11.288	-1.215	-1.215	0.000	0.000	0.000
17	A	38	ILE	0	-0.036	-0.010	12.045	-1.266	-1.266	0.000	0.000	0.000
18	A	39	VAL	0	0.010	0.014	9.302	0.558	0.558	0.000	0.000	0.000
19	A	40	ARG	1	0.850	0.912	12.813	18.019	18.019	0.000	0.000	0.000
20	A	41	VAL	0	-0.008	-0.009	8.420	-0.628	-0.628	0.000	0.000	0.000
21	A	42	PRO	0	-0.020	-0.009	11.876	0.794	0.794	0.000	0.000	0.000
22	A	43	ILE	0	-0.043	-0.018	9.421	-2.493	-2.493	0.000	0.000	0.000
23	A	44	ALA	0	0.041	0.031	12.128	1.934	1.934	0.000	0.000	0.000
24	A	45	LEU	0	-0.072	-0.046	12.612	-1.872	-1.872	0.000	0.000	0.000
25	A	46	TYR	0	0.028	0.025	14.586	1.324	1.324	0.000	0.000	0.000
26	A	47	VAL	0	-0.016	-0.022	16.603	-0.714	-0.714	0.000	0.000	0.000
27	A	48	SER	0	0.036	0.009	19.153	0.732	0.732	0.000	0.000	0.000
28	A	49	LEU	0	-0.052	-0.016	22.085	0.104	0.104	0.000	0.000	0.000
29	A	50	ALA	0	0.041	0.023	24.791	0.388	0.388	0.000	0.000	0.000
30	A	51	PRO	0	0.051	0.009	27.420	0.094	0.094	0.000	0.000	0.000
31	A	52	MET	0	-0.047	-0.016	30.664	0.143	0.143	0.000	0.000	0.000
32	A	53	TYR	0	0.014	-0.006	27.749	0.045	0.045	0.000	0.000	0.000
33	A	54	LEU	0	0.073	0.035	29.535	-0.294	-0.294	0.000	0.000	0.000
34	A	55	GLU	-1	-0.936	-0.951	31.411	-8.411	-8.411	0.000	0.000	0.000
35	A	56	ASN	0	-0.033	-0.023	30.394	-0.305	-0.305	0.000	0.000	0.000
36	A	57	PRO	0	0.081	0.036	26.135	-0.225	-0.225	0.000	0.000	0.000
37	A	58	LEU	0	-0.015	0.002	24.968	-0.556	-0.556	0.000	0.000	0.000
38	A	59	GLN	0	0.075	0.014	25.272	-0.451	-0.451	0.000	0.000	0.000
39	A	60	GLY	0	0.005	0.013	26.091	-0.031	-0.031	0.000	0.000	0.000
40	A	61	VAL	0	0.019	0.003	19.931	-0.365	-0.365	0.000	0.000	0.000
41	A	62	MET	0	-0.002	0.000	21.158	-0.460	-0.460	0.000	0.000	0.000
42	A	63	LYS	1	0.817	0.912	22.714	10.972	10.972	0.000	0.000	0.000
43	A	64	GLN	0	-0.029	0.000	17.679	0.252	0.252	0.000	0.000	0.000
44	A	65	HIS	0	0.039	0.001	15.281	-1.133	-1.133	0.000	0.000	0.000
45	A	66	LEU	0	0.011	0.006	18.941	-0.325	-0.325	0.000	0.000	0.000
46	A	67	ASN	0	0.016	0.012	20.553	-0.760	-0.760	0.000	0.000	0.000
47	A	68	PRO	0	-0.024	-0.011	18.541	-0.200	-0.200	0.000	0.000	0.000
48	A	69	LEU	0	-0.019	0.006	13.769	-1.086	-1.086	0.000	0.000	0.000
49	A	70	VAL	0	0.024	0.015	16.436	-0.444	-0.444	0.000	0.000	0.000
50	A	71	MET	0	-0.010	-0.002	17.232	0.392	0.392	0.000	0.000	0.000
51	A	72	LYS	1	0.822	0.915	15.509	15.466	15.466	0.000	0.000	0.000
52	A	73	TYR	0	0.027	0.019	5.714	-1.265	-1.265	0.000	0.000	0.000
53	A	74	ASN	0	0.000	-0.004	9.427	-1.837	-1.837	0.000	0.000	0.000
54	A	75	ASN	0	0.065	0.006	6.669	-1.765	-1.765	0.000	0.000	0.000
55	A	76	LYS	1	0.904	0.955	4.790	24.025	24.149	-0.001	-0.002	-0.121
56	A	77	VAL	0	-0.020	-0.009	4.579	-7.546	-7.454	-0.001	-0.009	-0.082
57	A	78	GLY	0	0.013	0.022	4.216	0.609	0.740	-0.001	-0.030	-0.101
58	A	79	GLY	0	0.049	0.005	5.024	1.789	1.815	-0.001	-0.003	-0.023
59	A	80	VAL	0	-0.048	-0.009	8.434	0.162	0.162	0.000	0.000	0.000
60	A	81	VAL	0	0.004	0.011	12.166	-0.273	-0.273	0.000	0.000	0.000
61	A	82	LEU	0	0.021	0.004	14.016	1.346	1.346	0.000	0.000	0.000
62	A	83	GLY	0	0.012	0.005	16.737	1.214	1.214	0.000	0.000	0.000
63	A	84	TYR	0	-0.036	-0.019	17.060	-1.067	-1.067	0.000	0.000	0.000
64	A	85	GLU	-1	-0.753	-0.841	18.550	-14.419	-14.419	0.000	0.000	0.000
65	A	86	GLY	0	0.019	0.007	19.363	-0.694	-0.694	0.000	0.000	0.000
66	A	87	LEU	0	-0.064	-0.023	19.196	-0.370	-0.370	0.000	0.000	0.000
67	A	88	LYS	1	0.830	0.889	20.670	15.502	15.502	0.000	0.000	0.000
68	A	89	ILE	0	0.028	-0.006	21.419	-0.547	-0.547	0.000	0.000	0.000
69	A	90	LEU	0	0.032	0.008	23.578	0.025	0.025	0.000	0.000	0.000
70	A	91	ASP	-1	-0.840	-0.881	20.711	-15.006	-15.006	0.000	0.000	0.000
71	A	92	ALA	0	-0.013	-0.029	22.738	-0.372	-0.372	0.000	0.000	0.000
72	A	93	ASP	-1	-0.866	-0.899	25.416	-9.840	-9.840	0.000	0.000	0.000
73	A	94	PRO	0	-0.104	-0.056	28.945	0.077	0.077	0.000	0.000	0.000
74	A	112	PRO	0	0.034	-0.003	32.925	0.058	0.058	0.000	0.000	0.000
75	A	113	PHE	0	-0.022	-0.016	28.403	-0.117	-0.117	0.000	0.000	0.000
76	A	114	GLY	0	0.043	0.031	27.527	-0.161	-0.161	0.000	0.000	0.000
77	A	115	PHE	0	-0.070	-0.037	20.953	-0.443	-0.443	0.000	0.000	0.000
78	A	116	THR	0	0.007	0.006	22.022	0.663	0.663	0.000	0.000	0.000
79	A	117	TRP	0	0.021	0.018	14.570	-1.136	-1.136	0.000	0.000	0.000
80	A	118	CYS	0	-0.068	-0.016	18.198	0.675	0.675	0.000	0.000	0.000
81	A	119	HIS	0	0.070	0.034	15.075	-1.280	-1.280	0.000	0.000	0.000
82	A	120	VAL	0	-0.021	-0.006	15.066	1.120	1.120	0.000	0.000	0.000
83	A	121	ASN	0	0.004	-0.011	14.894	-1.594	-1.594	0.000	0.000	0.000
84	A	122	LEU	0	0.011	0.011	11.257	1.209	1.209	0.000	0.000	0.000
85	A	123	TYR	0	-0.018	-0.037	14.205	-0.955	-0.955	0.000	0.000	0.000
86	A	124	VAL	0	-0.038	-0.027	8.868	0.264	0.264	0.000	0.000	0.000
87	A	125	TRP	0	0.062	0.040	12.112	-0.149	-0.149	0.000	0.000	0.000
88	A	126	GLN	0	-0.026	-0.027	6.185	-4.554	-4.554	0.000	0.000	0.000
89	A	127	PRO	0	0.010	0.023	8.311	-1.045	-1.045	0.000	0.000	0.000
90	A	128	GLN	0	0.007	-0.011	5.080	-0.686	-0.686	0.000	0.000	0.000
91	A	129	VAL	0	-0.022	-0.029	6.994	2.207	2.207	0.000	0.000	0.000
92	A	130	GLY	0	-0.002	0.002	8.993	-0.845	-0.845	0.000	0.000	0.000
93	A	131	ASP	-1	-0.726	-0.809	10.333	-21.496	-21.496	0.000	0.000	0.000
94	A	132	VAL	0	-0.006	-0.003	12.818	0.890	0.890	0.000	0.000	0.000
95	A	133	LEU	0	-0.007	-0.002	13.437	-0.073	-0.073	0.000	0.000	0.000
96	A	134	GLU	-1	-0.777	-0.884	17.698	-11.010	-11.010	0.000	0.000	0.000
97	A	135	GLY	0	-0.030	-0.014	20.810	-0.429	-0.429	0.000	0.000	0.000
98	A	136	TYR	0	0.032	0.020	22.471	0.325	0.325	0.000	0.000	0.000
99	A	137	ILE	0	0.003	0.001	25.067	-0.397	-0.397	0.000	0.000	0.000
100	A	138	PHE	0	-0.039	-0.003	24.543	0.154	0.154	0.000	0.000	0.000
101	A	139	ILE	0	-0.006	-0.009	25.341	0.327	0.327	0.000	0.000	0.000
102	A	140	GLN	0	-0.006	0.004	27.486	-0.264	-0.264	0.000	0.000	0.000
103	A	141	SER	0	-0.018	-0.014	28.858	0.221	0.221	0.000	0.000	0.000
104	A	142	ALA	0	0.018	0.017	30.347	-0.128	-0.128	0.000	0.000	0.000
105	A	143	SER	0	-0.043	-0.033	28.087	-0.039	-0.039	0.000	0.000	0.000
106	A	144	HIS	0	-0.036	-0.005	22.681	-0.414	-0.414	0.000	0.000	0.000
107	A	145	ILE	0	0.064	0.037	24.801	0.339	0.339	0.000	0.000	0.000
108	A	146	GLY	0	0.010	0.004	22.985	-0.501	-0.501	0.000	0.000	0.000
109	A	147	LEU	0	-0.013	-0.007	21.337	0.398	0.398	0.000	0.000	0.000
110	A	148	LEU	0	0.002	0.012	21.286	-0.493	-0.493	0.000	0.000	0.000
111	A	149	ILE	0	0.002	-0.007	15.813	0.195	0.195	0.000	0.000	0.000
112	A	150	HIS	0	-0.042	-0.033	17.160	0.334	0.334	0.000	0.000	0.000
113	A	151	ASP	-1	-0.902	-0.948	21.542	-10.709	-10.709	0.000	0.000	0.000
114	A	152	ALA	0	-0.026	-0.004	20.454	0.198	0.198	0.000	0.000	0.000
115	A	153	PHE	0	-0.032	-0.026	16.272	-0.619	-0.619	0.000	0.000	0.000
116	A	154	ASN	0	0.032	0.019	18.386	0.036	0.036	0.000	0.000	0.000
117	A	155	ALA	0	0.032	0.029	17.235	-0.886	-0.886	0.000	0.000	0.000
118	A	156	SER	0	-0.006	0.010	18.316	0.743	0.743	0.000	0.000	0.000
119	A	157	ILE	0	0.033	0.031	19.005	-0.565	-0.565	0.000	0.000	0.000
120	A	158	LYS	1	0.857	0.891	18.340	13.700	13.700	0.000	0.000	0.000
121	A	159	LYS	1	0.957	0.968	22.935	8.840	8.840	0.000	0.000	0.000
122	A	160	ASN	0	-0.037	-0.025	22.834	0.103	0.103	0.000	0.000	0.000
123	A	161	ASN	0	-0.006	0.011	19.402	-0.214	-0.214	0.000	0.000	0.000
124	A	162	ILE	0	0.059	0.044	22.889	-0.275	-0.275	0.000	0.000	0.000
125	A	163	PRO	0	0.022	0.012	26.026	0.056	0.056	0.000	0.000	0.000
126	A	164	VAL	0	-0.078	-0.026	28.351	0.191	0.191	0.000	0.000	0.000
127	A	165	ASP	-1	-0.824	-0.896	30.987	-8.311	-8.311	0.000	0.000	0.000
128	A	166	TRP	0	0.007	0.006	27.265	0.044	0.044	0.000	0.000	0.000
129	A	167	THR	0	0.022	0.017	33.341	0.001	0.001	0.000	0.000	0.000
130	A	168	PHE	0	-0.054	-0.027	32.820	-0.014	-0.014	0.000	0.000	0.000
131	A	169	VAL	0	0.034	0.025	35.592	0.156	0.156	0.000	0.000	0.000
132	A	170	HIS	0	-0.005	-0.020	37.724	-0.160	-0.160	0.000	0.000	0.000
133	A	171	ASN	0	0.022	-0.009	40.252	0.029	0.029	0.000	0.000	0.000
134	A	172	ASP	-1	-0.839	-0.925	42.424	-6.556	-6.556	0.000	0.000	0.000
135	A	210	GLY	0	-0.044	0.000	41.872	0.056	0.056	0.000	0.000	0.000
136	A	211	ASN	0	-0.069	-0.062	41.649	-0.016	-0.016	0.000	0.000	0.000
137	A	212	ARG	1	0.993	0.995	40.626	6.609	6.609	0.000	0.000	0.000
138	A	213	SER	0	-0.064	-0.035	37.359	0.037	0.037	0.000	0.000	0.000
139	A	214	LEU	0	0.036	0.024	38.048	-0.108	-0.108	0.000	0.000	0.000
140	A	215	GLY	0	-0.016	0.005	37.038	0.059	0.059	0.000	0.000	0.000
141	A	216	HIS	0	-0.002	-0.002	34.566	-0.217	-0.217	0.000	0.000	0.000
142	A	217	TRP	0	-0.122	-0.082	29.025	-0.262	-0.262	0.000	0.000	0.000
143	A	218	VAL	0	0.072	0.062	33.386	-0.178	-0.178	0.000	0.000	0.000
144	A	219	ASP	-1	-0.737	-0.858	33.583	-8.038	-8.038	0.000	0.000	0.000
145	A	220	SER	0	-0.062	-0.060	34.721	0.199	0.199	0.000	0.000	0.000
146	A	221	ASN	0	-0.119	-0.075	36.245	0.348	0.348	0.000	0.000	0.000
147	A	222	GLY	0	-0.024	-0.023	38.277	0.216	0.216	0.000	0.000	0.000
148	A	223	GLU	-1	-0.909	-0.950	36.520	-7.272	-7.272	0.000	0.000	0.000
149	A	224	PRO	0	-0.060	-0.040	35.937	-0.197	-0.197	0.000	0.000	0.000
150	A	225	ILE	0	-0.074	-0.034	30.132	-0.120	-0.120	0.000	0.000	0.000
151	A	226	ASP	-1	-0.869	-0.929	30.503	-9.349	-9.349	0.000	0.000	0.000
152	A	227	GLY	0	0.067	0.044	30.389	0.209	0.209	0.000	0.000	0.000
153	A	228	LYS	1	0.766	0.870	24.317	11.065	11.065	0.000	0.000	0.000
154	A	229	LEU	0	0.033	0.020	24.407	0.100	0.100	0.000	0.000	0.000
155	A	230	ARG	1	0.827	0.902	20.869	11.746	11.746	0.000	0.000	0.000
156	A	231	PHE	0	-0.040	-0.028	15.925	0.151	0.151	0.000	0.000	0.000
157	A	232	THR	0	0.023	0.008	16.172	-0.294	-0.294	0.000	0.000	0.000
158	A	233	VAL	0	-0.030	-0.017	10.784	0.525	0.525	0.000	0.000	0.000
159	A	234	ARG	1	0.916	0.941	12.698	12.993	12.993	0.000	0.000	0.000
160	A	235	ASN	0	-0.048	-0.051	10.469	-0.934	-0.934	0.000	0.000	0.000
161	A	236	VAL	0	0.022	0.020	8.277	0.745	0.745	0.000	0.000	0.000
162	A	237	HIS	0	-0.007	-0.003	9.619	-1.742	-1.742	0.000	0.000	0.000
163	A	238	THR	0	-0.008	-0.014	8.400	1.306	1.306	0.000	0.000	0.000
164	A	239	THR	0	0.006	-0.003	11.113	-0.100	-0.100	0.000	0.000	0.000
165	A	240	GLY	0	-0.003	0.008	14.340	0.974	0.974	0.000	0.000	0.000
166	A	241	ARG	1	0.885	0.936	16.375	13.562	13.562	0.000	0.000	0.000
167	A	242	VAL	0	0.023	0.012	15.895	-0.846	-0.846	0.000	0.000	0.000
168	A	243	VAL	0	-0.017	0.008	10.625	0.220	0.220	0.000	0.000	0.000
169	A	244	SER	0	-0.057	-0.028	13.952	0.833	0.833	0.000	0.000	0.000
170	A	245	VAL	0	0.016	0.005	12.607	-0.748	-0.748	0.000	0.000	0.000
171	A	246	ASP	-1	-0.811	-0.877	13.766	-13.036	-13.036	0.000	0.000	0.000
172	A	247	GLY	0	0.038	0.015	14.561	-0.917	-0.917	0.000	0.000	0.000
173	A	248	THR	0	-0.116	-0.069	17.106	0.686	0.686	0.000	0.000	0.000
174	A	249	LEU	0	0.071	0.032	19.836	-0.352	-0.352	0.000	0.000	0.000
175	A	250	ILE	0	-0.030	0.009	20.592	0.410	0.410	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:22:LYS)