FMO DATABASE

FMODB ID: 89VMY

Calculation Name: 2RKQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2RKQ

Chain ID: A

ChEMBL ID:

UniProt ID: Q9VS97

Base Structure: X-ray

Registration Date: 2023-09-23

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1722476.027516
FMO2-HF: Nuclear repulsion	1657573.732587
FMO2-HF: Total energy	-64902.294929
FMO2-MP2: Total energy	-65091.143988

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:11:GLU)

Summations of interaction energy for fragment #1(A:11:GLU)

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.
29.838	34.725	3.099	-3.375	-4.61	-0.012

Interaction energy analysis for fragmet #1(A:11:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.958 / q_NPA : -0.991

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].
3	A	13	PRO	0	-0.026	-0.013	3.803	-1.617	0.106	-0.018	-0.831	-0.874	0.003
4	A	14	ILE	0	-0.008	-0.007	5.825	-1.258	-1.258	0.000	0.000	0.000	0.000
5	A	15	VAL	0	-0.032	-0.013	8.650	-0.834	-0.834	0.000	0.000	0.000	0.000
6	A	16	THR	0	0.021	-0.022	11.729	-1.139	-1.139	0.000	0.000	0.000	0.000
7	A	17	ARG	1	0.788	0.845	13.670	-15.104	-15.104	0.000	0.000	0.000	0.000
8	A	18	ALA	0	-0.012	-0.006	17.146	-0.731	-0.731	0.000	0.000	0.000	0.000
9	A	19	GLU	-1	-0.845	-0.900	12.833	18.616	18.616	0.000	0.000	0.000	0.000
10	A	20	TRP	0	-0.081	-0.032	15.938	-1.020	-1.020	0.000	0.000	0.000	0.000
11	A	21	ASN	0	-0.074	-0.033	18.889	-0.665	-0.665	0.000	0.000	0.000	0.000
12	A	22	ALA	0	0.004	0.015	20.096	-0.560	-0.560	0.000	0.000	0.000	0.000
13	A	23	LYS	1	0.921	0.957	22.084	-10.376	-10.376	0.000	0.000	0.000	0.000
14	A	24	PRO	0	0.024	0.021	23.781	0.479	0.479	0.000	0.000	0.000	0.000
15	A	25	PRO	0	0.032	0.000	23.349	-0.299	-0.299	0.000	0.000	0.000	0.000
16	A	26	ASN	0	-0.056	-0.032	26.169	-0.037	-0.037	0.000	0.000	0.000	0.000
17	A	26	GLY	0	0.082	0.040	29.908	-0.206	-0.206	0.000	0.000	0.000	0.000
18	A	27	ALA	0	-0.031	-0.010	28.544	0.356	0.356	0.000	0.000	0.000	0.000
19	A	28	ILE	0	-0.027	-0.020	23.587	-0.073	-0.073	0.000	0.000	0.000	0.000
20	A	29	ASP	-1	-0.853	-0.910	26.505	10.373	10.373	0.000	0.000	0.000	0.000
21	A	30	SER	0	-0.006	-0.006	23.627	0.399	0.399	0.000	0.000	0.000	0.000
22	A	31	MET	0	-0.095	-0.022	19.147	-0.575	-0.575	0.000	0.000	0.000	0.000
23	A	32	VAL	0	0.005	0.002	20.967	0.285	0.285	0.000	0.000	0.000	0.000
24	A	33	THR	0	-0.007	0.019	15.490	-0.027	-0.027	0.000	0.000	0.000	0.000
25	A	34	PRO	0	-0.024	-0.015	14.467	-0.446	-0.446	0.000	0.000	0.000	0.000
26	A	35	LEU	0	-0.049	-0.039	15.535	-1.125	-1.125	0.000	0.000	0.000	0.000
27	A	36	PRO	0	0.019	0.006	16.664	0.842	0.842	0.000	0.000	0.000	0.000
28	A	37	ARG	1	0.912	0.972	18.435	-12.839	-12.839	0.000	0.000	0.000	0.000
29	A	38	ALA	0	0.031	0.031	14.389	0.460	0.460	0.000	0.000	0.000	0.000
30	A	39	VAL	0	-0.022	-0.007	16.389	-0.638	-0.638	0.000	0.000	0.000	0.000
31	A	40	ILE	0	0.026	0.016	14.645	0.382	0.382	0.000	0.000	0.000	0.000
32	A	41	ALA	0	-0.017	-0.019	18.212	-0.936	-0.936	0.000	0.000	0.000	0.000
33	A	42	HIS	0	0.014	0.028	19.427	0.703	0.703	0.000	0.000	0.000	0.000
34	A	43	THR	0	0.009	-0.002	20.927	-0.336	-0.336	0.000	0.000	0.000	0.000
35	A	44	ALA	0	-0.033	-0.001	23.454	-0.451	-0.451	0.000	0.000	0.000	0.000
36	A	45	GLY	0	0.024	0.019	25.638	-0.450	-0.450	0.000	0.000	0.000	0.000
37	A	46	GLY	0	-0.003	-0.007	26.559	0.069	0.069	0.000	0.000	0.000	0.000
38	A	47	ALA	0	0.035	0.004	23.280	0.362	0.362	0.000	0.000	0.000	0.000
39	A	48	CYS	0	-0.075	-0.002	18.412	-0.279	-0.279	0.000	0.000	0.000	0.000
40	A	49	ALA	0	0.036	0.008	20.642	0.458	0.458	0.000	0.000	0.000	0.000
41	A	50	ASP	-1	-0.788	-0.874	20.186	12.074	12.074	0.000	0.000	0.000	0.000
42	A	51	ASP	-1	-0.776	-0.897	16.907	16.006	16.006	0.000	0.000	0.000	0.000
43	A	52	VAL	0	-0.038	-0.004	19.194	0.021	0.021	0.000	0.000	0.000	0.000
44	A	53	THR	0	-0.008	-0.029	22.599	0.002	0.002	0.000	0.000	0.000	0.000
45	A	55	SER	0	0.077	0.057	19.305	-0.113	-0.113	0.000	0.000	0.000	0.000
46	A	56	GLN	0	-0.011	-0.008	20.390	-0.142	-0.142	0.000	0.000	0.000	0.000
47	A	57	HIS	0	-0.046	-0.033	22.282	-0.572	-0.572	0.000	0.000	0.000	0.000
48	A	58	MET	0	0.009	0.034	17.570	-0.208	-0.208	0.000	0.000	0.000	0.000
49	A	59	ARG	1	0.844	0.906	21.481	-12.264	-12.264	0.000	0.000	0.000	0.000
50	A	60	ASN	0	-0.030	-0.011	24.237	-0.406	-0.406	0.000	0.000	0.000	0.000
51	A	61	LEU	0	0.019	0.018	21.697	-0.404	-0.404	0.000	0.000	0.000	0.000
52	A	62	GLN	0	0.027	0.004	23.164	-0.293	-0.293	0.000	0.000	0.000	0.000
53	A	63	ASN	0	0.017	-0.001	24.912	-0.170	-0.170	0.000	0.000	0.000	0.000
54	A	64	PHE	0	-0.024	-0.011	28.276	-0.438	-0.438	0.000	0.000	0.000	0.000
55	A	65	GLN	0	0.065	0.031	24.180	0.086	0.086	0.000	0.000	0.000	0.000
56	A	66	MET	0	-0.051	0.013	26.867	-0.095	-0.095	0.000	0.000	0.000	0.000
57	A	67	SER	0	-0.051	-0.021	29.493	-0.408	-0.408	0.000	0.000	0.000	0.000
58	A	68	LYS	1	0.861	0.919	32.169	-8.568	-8.568	0.000	0.000	0.000	0.000
59	A	69	GLN	0	0.016	0.000	28.585	0.027	0.027	0.000	0.000	0.000	0.000
60	A	70	LYS	1	0.876	0.962	32.049	-8.232	-8.232	0.000	0.000	0.000	0.000
61	A	71	PHE	0	0.002	0.001	26.112	-0.018	-0.018	0.000	0.000	0.000	0.000
62	A	72	SER	0	0.039	0.011	27.044	-0.160	-0.160	0.000	0.000	0.000	0.000
63	A	73	ASP	-1	-0.728	-0.854	21.903	13.089	13.089	0.000	0.000	0.000	0.000
64	A	74	ILE	0	0.002	0.006	20.034	-0.281	-0.281	0.000	0.000	0.000	0.000
65	A	75	GLY	0	-0.020	-0.004	22.033	0.241	0.241	0.000	0.000	0.000	0.000
66	A	76	TYR	0	-0.014	-0.004	17.625	-0.239	-0.239	0.000	0.000	0.000	0.000
67	A	77	HIS	0	0.023	0.020	14.667	0.043	0.043	0.000	0.000	0.000	0.000
68	A	78	TYR	0	-0.019	-0.014	9.958	0.755	0.755	0.000	0.000	0.000	0.000
69	A	79	LEU	0	-0.040	-0.023	13.821	-1.051	-1.051	0.000	0.000	0.000	0.000
70	A	80	ILE	0	-0.002	0.017	11.773	0.734	0.734	0.000	0.000	0.000	0.000
71	A	81	GLY	0	0.025	0.010	14.437	-1.110	-1.110	0.000	0.000	0.000	0.000
72	A	82	GLY	0	0.042	0.008	15.876	0.656	0.656	0.000	0.000	0.000	0.000
73	A	83	ASN	0	-0.034	-0.040	16.021	0.202	0.202	0.000	0.000	0.000	0.000
74	A	84	GLY	0	0.007	0.001	12.981	0.417	0.417	0.000	0.000	0.000	0.000
75	A	85	LYS	1	0.860	0.944	11.239	-16.348	-16.348	0.000	0.000	0.000	0.000
76	A	86	VAL	0	0.067	0.035	8.290	-1.450	-1.450	0.000	0.000	0.000	0.000
77	A	87	TYR	0	-0.027	-0.017	11.108	0.171	0.171	0.000	0.000	0.000	0.000
78	A	88	GLU	-1	-0.834	-0.924	12.688	18.900	18.900	0.000	0.000	0.000	0.000
79	A	89	GLY	0	-0.004	-0.001	13.962	-1.173	-1.173	0.000	0.000	0.000	0.000
80	A	90	ARG	1	0.796	0.871	17.036	-12.533	-12.533	0.000	0.000	0.000	0.000
81	A	91	SER	0	0.085	0.035	15.947	1.153	1.153	0.000	0.000	0.000	0.000
82	A	92	PRO	0	0.075	0.026	12.868	-0.908	-0.908	0.000	0.000	0.000	0.000
83	A	93	SER	0	0.006	0.009	15.946	-0.327	-0.327	0.000	0.000	0.000	0.000
84	A	94	GLN	0	-0.024	-0.009	18.908	-0.439	-0.439	0.000	0.000	0.000	0.000
85	A	95	ARG	1	0.927	0.965	20.311	-10.571	-10.571	0.000	0.000	0.000	0.000
86	A	96	GLY	0	0.040	0.023	21.390	-0.044	-0.044	0.000	0.000	0.000	0.000
87	A	97	ALA	0	-0.082	-0.046	22.036	-0.528	-0.528	0.000	0.000	0.000	0.000
88	A	98	PHE	0	-0.022	-0.024	20.086	-0.109	-0.109	0.000	0.000	0.000	0.000
89	A	99	ALA	0	-0.004	0.002	24.709	-0.197	-0.197	0.000	0.000	0.000	0.000
90	A	100	GLY	0	0.018	0.022	26.608	-0.240	-0.240	0.000	0.000	0.000	0.000
91	A	101	PRO	0	0.016	-0.001	28.436	0.244	0.244	0.000	0.000	0.000	0.000
92	A	102	ASN	0	-0.022	-0.019	26.319	0.081	0.081	0.000	0.000	0.000	0.000
93	A	103	ASN	0	0.032	0.020	24.059	0.702	0.702	0.000	0.000	0.000	0.000
94	A	104	ASP	-1	-0.867	-0.935	22.978	11.730	11.730	0.000	0.000	0.000	0.000
95	A	105	GLY	0	0.002	0.001	21.242	0.080	0.080	0.000	0.000	0.000	0.000
96	A	106	SER	0	-0.009	-0.018	19.139	0.433	0.433	0.000	0.000	0.000	0.000
97	A	107	LEU	0	0.021	0.015	11.598	-0.347	-0.347	0.000	0.000	0.000	0.000
98	A	108	GLY	0	0.002	-0.011	16.276	-0.100	-0.100	0.000	0.000	0.000	0.000
99	A	109	ILE	0	0.018	0.005	11.920	0.325	0.325	0.000	0.000	0.000	0.000
100	A	110	ALA	0	-0.018	-0.011	15.388	-0.683	-0.683	0.000	0.000	0.000	0.000
101	A	111	PHE	0	0.042	0.015	14.494	0.526	0.526	0.000	0.000	0.000	0.000
102	A	112	ILE	0	-0.017	-0.035	17.828	-0.954	-0.954	0.000	0.000	0.000	0.000
103	A	113	GLY	0	0.003	-0.007	20.087	0.137	0.137	0.000	0.000	0.000	0.000
104	A	114	ASN	0	-0.069	-0.035	23.190	0.074	0.074	0.000	0.000	0.000	0.000
105	A	115	PHE	0	0.004	-0.010	20.644	0.005	0.005	0.000	0.000	0.000	0.000
106	A	116	GLU	-1	-0.793	-0.898	24.619	10.116	10.116	0.000	0.000	0.000	0.000
107	A	117	GLU	-1	-0.937	-0.968	27.875	9.145	9.145	0.000	0.000	0.000	0.000
108	A	118	ARG	1	0.919	0.975	24.134	-11.340	-11.340	0.000	0.000	0.000	0.000
109	A	119	ALA	0	0.047	0.016	20.407	0.094	0.094	0.000	0.000	0.000	0.000
110	A	120	PRO	0	-0.026	-0.012	17.450	-0.264	-0.264	0.000	0.000	0.000	0.000
111	A	121	ASN	0	-0.017	-0.014	17.233	-0.504	-0.504	0.000	0.000	0.000	0.000
112	A	122	LYS	1	0.909	0.929	12.359	-19.169	-19.169	0.000	0.000	0.000	0.000
113	A	123	GLU	-1	-0.869	-0.930	12.256	17.613	17.613	0.000	0.000	0.000	0.000
114	A	124	ALA	0	-0.020	-0.004	11.536	1.271	1.271	0.000	0.000	0.000	0.000
115	A	125	LEU	0	-0.039	-0.035	12.445	0.868	0.868	0.000	0.000	0.000	0.000
116	A	126	ASP	-1	-0.845	-0.902	8.781	22.252	22.252	0.000	0.000	0.000	0.000
117	A	127	ALA	0	0.070	0.044	7.889	2.313	2.313	0.000	0.000	0.000	0.000
118	A	128	ALA	0	-0.024	-0.023	7.975	1.961	1.961	0.000	0.000	0.000	0.000
119	A	129	LYS	1	0.916	0.959	9.109	-19.846	-19.846	0.000	0.000	0.000	0.000
120	A	130	GLU	-1	-0.853	-0.926	4.028	34.127	34.381	0.000	-0.044	-0.209	0.000
121	A	131	LEU	0	-0.029	-0.016	4.554	5.258	5.418	-0.001	-0.009	-0.150	0.000
122	A	132	LEU	0	-0.053	-0.026	6.394	0.063	0.063	0.000	0.000	0.000	0.000
123	A	133	GLU	-1	-0.835	-0.906	4.993	58.390	58.607	-0.001	-0.011	-0.204	0.000
124	A	134	GLN	0	0.026	0.011	2.431	8.010	9.595	3.117	-2.096	-2.607	-0.018
125	A	135	ALA	0	0.000	-0.008	4.567	-2.416	-2.380	-0.001	-0.010	-0.025	0.000
126	A	136	VAL	0	-0.022	-0.008	8.143	-2.245	-2.245	0.000	0.000	0.000	0.000
127	A	137	LYS	1	0.867	0.930	3.625	-74.838	-73.981	0.004	-0.368	-0.493	0.003
128	A	138	GLN	0	-0.060	-0.024	4.359	-5.247	-5.192	-0.001	-0.006	-0.048	0.000
129	A	139	ALA	0	-0.026	-0.002	8.121	-2.928	-2.928	0.000	0.000	0.000	0.000
130	A	140	GLN	0	0.064	0.037	9.751	-2.534	-2.534	0.000	0.000	0.000	0.000
131	A	141	LEU	0	-0.052	-0.007	11.389	-2.126	-2.126	0.000	0.000	0.000	0.000
132	A	142	VAL	0	-0.020	-0.004	12.874	1.209	1.209	0.000	0.000	0.000	0.000
133	A	143	GLU	-1	-0.858	-0.951	13.185	23.071	23.071	0.000	0.000	0.000	0.000
134	A	144	GLY	0	-0.032	-0.002	14.584	-0.008	-0.008	0.000	0.000	0.000	0.000
135	A	145	TYR	0	-0.042	-0.030	12.249	-0.757	-0.757	0.000	0.000	0.000	0.000
136	A	146	LYS	1	0.949	0.976	17.153	-14.158	-14.158	0.000	0.000	0.000	0.000
137	A	147	LEU	0	0.010	0.005	15.025	0.353	0.353	0.000	0.000	0.000	0.000
138	A	148	LEU	0	-0.017	-0.008	18.170	-0.690	-0.690	0.000	0.000	0.000	0.000
139	A	149	GLY	0	0.037	0.005	19.911	0.540	0.540	0.000	0.000	0.000	0.000
140	A	150	HIS	0	-0.019	-0.037	22.052	-0.245	-0.245	0.000	0.000	0.000	0.000
141	A	151	ARG	1	0.803	0.895	23.514	-11.010	-11.010	0.000	0.000	0.000	0.000
142	A	152	GLN	0	0.025	0.014	23.736	0.109	0.109	0.000	0.000	0.000	0.000
143	A	153	VAL	0	0.005	0.010	23.795	-0.199	-0.199	0.000	0.000	0.000	0.000
144	A	154	SER	0	-0.021	-0.002	26.756	-0.368	-0.368	0.000	0.000	0.000	0.000
145	A	155	ALA	0	0.041	0.028	28.688	0.035	0.035	0.000	0.000	0.000	0.000
146	A	156	THR	0	-0.026	-0.014	26.813	-0.130	-0.130	0.000	0.000	0.000	0.000
147	A	157	LYS	1	0.890	0.942	29.205	-9.544	-9.544	0.000	0.000	0.000	0.000
148	A	158	SER	0	-0.024	0.006	23.769	0.398	0.398	0.000	0.000	0.000	0.000
149	A	159	PRO	0	0.017	-0.009	21.199	-0.150	-0.150	0.000	0.000	0.000	0.000
150	A	160	GLY	0	0.029	0.006	23.161	0.166	0.166	0.000	0.000	0.000	0.000
151	A	161	GLU	-1	-0.800	-0.924	24.961	10.441	10.441	0.000	0.000	0.000	0.000
152	A	162	ALA	0	-0.018	0.011	24.591	0.229	0.229	0.000	0.000	0.000	0.000
153	A	163	LEU	0	-0.033	-0.014	17.936	0.418	0.418	0.000	0.000	0.000	0.000
154	A	164	TYR	0	-0.007	-0.016	20.992	0.641	0.641	0.000	0.000	0.000	0.000
155	A	165	ALA	0	0.063	0.029	22.779	0.278	0.278	0.000	0.000	0.000	0.000
156	A	166	LEU	0	-0.036	-0.015	18.570	0.230	0.230	0.000	0.000	0.000	0.000
157	A	167	ILE	0	-0.033	-0.011	17.199	0.502	0.502	0.000	0.000	0.000	0.000
158	A	168	GLN	0	-0.032	-0.025	19.078	0.280	0.280	0.000	0.000	0.000	0.000
159	A	169	GLN	0	-0.043	-0.023	19.592	0.393	0.393	0.000	0.000	0.000	0.000
160	A	170	TRP	0	-0.073	-0.025	13.764	1.026	1.026	0.000	0.000	0.000	0.000
161	A	171	PRO	0	0.036	0.002	13.692	-0.837	-0.837	0.000	0.000	0.000	0.000
162	A	172	ASN	0	-0.016	-0.006	15.178	-0.297	-0.297	0.000	0.000	0.000	0.000
163	A	173	TRP	0	-0.002	0.023	18.327	-0.556	-0.556	0.000	0.000	0.000	0.000
164	A	174	SER	0	-0.024	-0.010	20.251	-0.480	-0.480	0.000	0.000	0.000	0.000
165	A	175	GLU	-1	-0.896	-0.957	23.352	10.617	10.617	0.000	0.000	0.000	0.000
166	A	176	GLU	-1	-0.982	-0.979	24.710	11.737	11.737	0.000	0.000	0.000	0.000
167	A	177	MET	0	-0.025	-0.005	27.123	0.371	0.371	0.000	0.000	0.000	0.000
168	A	178	LEU	0	-0.049	-0.018	25.971	-0.355	-0.355	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:11:GLU)