FMO DATABASE

FMODB ID: MVQ8Z

Calculation Name: 2RK0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2RK0

Chain ID: A

ChEMBL ID:

UniProt ID: A8LBF3

Base Structure: X-ray

Registration Date: 2023-09-20

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	OptHSide
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	135
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1115889.576039
FMO2-HF: Nuclear repulsion	1063664.607984
FMO2-HF: Total energy	-52224.968055
FMO2-MP2: Total energy	-52378.528883

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:2:SER)

Summations of interaction energy for fragment #1(A:2:SER)

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.
-9.428	-5.565	0.391	-2.26	-1.996	-0.01

Interaction energy analysis for fragmet #1(A:2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.017 / q_NPA : 0.007

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	4	SER	0	-0.005	-0.017	2.597	-8.691	-4.964	0.392	-2.253	-1.867	-0.010
4	A	5	GLY	0	0.039	0.030	5.222	0.952	1.088	-0.001	-0.007	-0.129	0.000
5	A	6	VAL	0	-0.006	-0.001	8.158	0.002	0.002	0.000	0.000	0.000	0.000
6	A	7	SER	0	-0.037	-0.004	11.525	0.054	0.054	0.000	0.000	0.000	0.000
7	A	8	HIS	0	-0.004	-0.026	13.032	0.148	0.148	0.000	0.000	0.000	0.000
8	A	9	VAL	0	0.036	0.029	16.236	-0.016	-0.016	0.000	0.000	0.000	0.000
9	A	10	SER	0	-0.006	-0.005	18.551	0.034	0.034	0.000	0.000	0.000	0.000
10	A	11	LEU	0	-0.002	0.004	21.598	0.015	0.015	0.000	0.000	0.000	0.000
11	A	12	THR	0	-0.037	-0.018	24.485	0.008	0.008	0.000	0.000	0.000	0.000
12	A	13	VAL	0	-0.021	-0.013	27.662	0.003	0.003	0.000	0.000	0.000	0.000
13	A	14	ARG	1	0.860	0.918	30.770	0.137	0.137	0.000	0.000	0.000	0.000
14	A	15	ASP	-1	-0.878	-0.937	34.478	-0.161	-0.161	0.000	0.000	0.000	0.000
15	A	16	LEU	0	0.034	0.007	30.126	-0.010	-0.010	0.000	0.000	0.000	0.000
16	A	17	ASP	-1	-0.797	-0.872	33.233	-0.201	-0.201	0.000	0.000	0.000	0.000
17	A	18	ILE	0	-0.044	-0.025	35.604	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	19	SER	0	0.059	0.028	30.576	0.000	0.000	0.000	0.000	0.000	0.000
19	A	20	CYS	0	-0.078	-0.030	30.930	-0.019	-0.019	0.000	0.000	0.000	0.000
20	A	21	ARG	1	0.844	0.916	32.008	0.171	0.171	0.000	0.000	0.000	0.000
21	A	22	TRP	0	0.050	0.039	28.649	-0.008	-0.008	0.000	0.000	0.000	0.000
22	A	23	TYR	0	0.001	-0.047	25.378	-0.016	-0.016	0.000	0.000	0.000	0.000
23	A	24	THR	0	-0.085	-0.055	29.600	-0.015	-0.015	0.000	0.000	0.000	0.000
24	A	25	GLU	-1	-0.995	-0.995	31.394	-0.190	-0.190	0.000	0.000	0.000	0.000
25	A	26	ILE	0	-0.017	-0.004	30.068	0.002	0.002	0.000	0.000	0.000	0.000
26	A	27	LEU	0	-0.025	-0.013	25.090	-0.005	-0.005	0.000	0.000	0.000	0.000
27	A	28	ASP	-1	-0.826	-0.872	27.129	-0.313	-0.313	0.000	0.000	0.000	0.000
28	A	29	TRP	0	-0.065	-0.031	24.599	-0.010	-0.010	0.000	0.000	0.000	0.000
29	A	30	LYS	1	0.962	0.971	26.496	0.372	0.372	0.000	0.000	0.000	0.000
30	A	31	GLU	-1	-0.799	-0.872	26.594	-0.299	-0.299	0.000	0.000	0.000	0.000
31	A	32	LEU	0	-0.085	-0.055	22.890	0.011	0.011	0.000	0.000	0.000	0.000
32	A	33	VAL	0	-0.022	-0.016	25.481	0.018	0.018	0.000	0.000	0.000	0.000
33	A	34	ARG	1	0.798	0.875	27.545	0.217	0.217	0.000	0.000	0.000	0.000
34	A	35	GLY	0	-0.032	-0.020	29.495	0.011	0.011	0.000	0.000	0.000	0.000
35	A	36	ARG	1	0.711	0.822	30.301	0.176	0.176	0.000	0.000	0.000	0.000
36	A	37	GLY	0	0.004	-0.009	28.617	-0.012	-0.012	0.000	0.000	0.000	0.000
37	A	38	ASP	-1	-0.916	-0.960	28.938	-0.142	-0.142	0.000	0.000	0.000	0.000
38	A	39	THR	0	0.002	0.002	30.452	0.007	0.007	0.000	0.000	0.000	0.000
39	A	40	THR	0	-0.011	0.008	28.373	-0.010	-0.010	0.000	0.000	0.000	0.000
40	A	41	SER	0	0.034	0.035	30.991	0.002	0.002	0.000	0.000	0.000	0.000
41	A	42	PHE	0	-0.043	-0.025	25.739	-0.009	-0.009	0.000	0.000	0.000	0.000
42	A	43	ALA	0	0.082	0.037	27.622	0.013	0.013	0.000	0.000	0.000	0.000
43	A	44	HIS	0	-0.030	-0.011	20.262	0.021	0.021	0.000	0.000	0.000	0.000
44	A	45	GLY	0	0.093	0.038	24.196	0.026	0.026	0.000	0.000	0.000	0.000
45	A	46	VAL	0	-0.102	-0.043	20.734	-0.052	-0.052	0.000	0.000	0.000	0.000
46	A	47	LEU	0	0.042	0.034	21.406	0.049	0.049	0.000	0.000	0.000	0.000
47	A	48	PRO	0	0.039	0.027	22.318	-0.050	-0.050	0.000	0.000	0.000	0.000
48	A	49	GLY	0	0.013	0.002	20.414	-0.010	-0.010	0.000	0.000	0.000	0.000
49	A	50	GLY	0	-0.052	-0.030	18.310	-0.084	-0.084	0.000	0.000	0.000	0.000
50	A	51	LEU	0	0.002	0.012	15.858	-0.073	-0.073	0.000	0.000	0.000	0.000
51	A	52	SER	0	0.026	0.018	17.552	0.110	0.110	0.000	0.000	0.000	0.000
52	A	53	ILE	0	0.020	0.006	18.954	-0.037	-0.037	0.000	0.000	0.000	0.000
53	A	54	VAL	0	-0.037	-0.023	21.010	0.032	0.032	0.000	0.000	0.000	0.000
54	A	55	LEU	0	0.025	0.030	23.609	0.007	0.007	0.000	0.000	0.000	0.000
55	A	56	ARG	1	0.889	0.925	23.453	0.332	0.332	0.000	0.000	0.000	0.000
56	A	57	GLU	-1	-0.808	-0.877	28.131	-0.174	-0.174	0.000	0.000	0.000	0.000
57	A	58	HIS	0	-0.022	-0.039	27.295	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	59	ASP	-1	-0.740	-0.836	32.309	-0.148	-0.148	0.000	0.000	0.000	0.000
59	A	60	GLY	0	-0.053	-0.024	34.718	0.009	0.009	0.000	0.000	0.000	0.000
60	A	61	GLY	0	-0.002	0.003	33.936	0.003	0.003	0.000	0.000	0.000	0.000
61	A	62	GLY	0	0.016	-0.005	34.644	0.006	0.006	0.000	0.000	0.000	0.000
62	A	63	THR	0	-0.057	-0.030	36.560	0.004	0.004	0.000	0.000	0.000	0.000
63	A	64	ASP	-1	-0.922	-0.945	34.063	-0.097	-0.097	0.000	0.000	0.000	0.000
64	A	65	LEU	0	-0.030	-0.022	34.614	-0.007	-0.007	0.000	0.000	0.000	0.000
65	A	66	PHE	0	-0.001	0.007	26.162	0.000	0.000	0.000	0.000	0.000	0.000
66	A	67	ASP	-1	-0.771	-0.865	30.150	-0.086	-0.086	0.000	0.000	0.000	0.000
67	A	68	GLU	-1	-0.757	-0.866	27.613	-0.144	-0.144	0.000	0.000	0.000	0.000
68	A	69	THR	0	-0.141	-0.083	27.582	0.009	0.009	0.000	0.000	0.000	0.000
69	A	70	ARG	1	0.799	0.891	28.865	0.102	0.102	0.000	0.000	0.000	0.000
70	A	71	PRO	0	-0.030	-0.024	24.549	-0.010	-0.010	0.000	0.000	0.000	0.000
71	A	72	GLY	0	0.002	0.002	22.336	-0.007	-0.007	0.000	0.000	0.000	0.000
72	A	73	LEU	0	-0.061	-0.027	20.465	-0.006	-0.006	0.000	0.000	0.000	0.000
73	A	74	ASP	-1	-0.842	-0.893	22.189	-0.151	-0.151	0.000	0.000	0.000	0.000
74	A	75	HIS	0	-0.031	-0.057	22.176	-0.009	-0.009	0.000	0.000	0.000	0.000
75	A	76	LEU	0	-0.058	-0.019	18.247	-0.032	-0.032	0.000	0.000	0.000	0.000
76	A	77	SER	0	-0.015	-0.020	19.675	0.011	0.011	0.000	0.000	0.000	0.000
77	A	78	PHE	0	-0.017	-0.016	18.912	-0.073	-0.073	0.000	0.000	0.000	0.000
78	A	79	SER	0	-0.030	-0.017	18.099	0.030	0.030	0.000	0.000	0.000	0.000
79	A	80	VAL	0	-0.004	-0.007	20.230	-0.021	-0.021	0.000	0.000	0.000	0.000
80	A	81	GLU	-1	-0.957	-0.982	22.290	-0.422	-0.422	0.000	0.000	0.000	0.000
81	A	82	SER	0	-0.107	-0.075	24.374	0.030	0.030	0.000	0.000	0.000	0.000
82	A	83	MET	0	0.056	0.005	27.946	-0.008	-0.008	0.000	0.000	0.000	0.000
83	A	84	THR	0	0.020	0.018	30.727	0.003	0.003	0.000	0.000	0.000	0.000
84	A	85	ASP	-1	-0.835	-0.895	27.518	-0.298	-0.298	0.000	0.000	0.000	0.000
85	A	86	LEU	0	-0.021	-0.018	27.009	-0.002	-0.002	0.000	0.000	0.000	0.000
86	A	87	ASP	-1	-0.876	-0.939	30.477	-0.166	-0.166	0.000	0.000	0.000	0.000
87	A	88	VAL	0	-0.004	-0.011	32.168	0.008	0.008	0.000	0.000	0.000	0.000
88	A	89	LEU	0	-0.012	-0.003	27.358	0.004	0.004	0.000	0.000	0.000	0.000
89	A	90	GLU	-1	-0.753	-0.861	32.069	-0.151	-0.151	0.000	0.000	0.000	0.000
90	A	91	GLU	-1	-0.907	-0.928	34.811	-0.150	-0.150	0.000	0.000	0.000	0.000
91	A	92	ARG	1	0.730	0.825	30.505	0.264	0.264	0.000	0.000	0.000	0.000
92	A	93	LEU	0	0.028	0.015	31.375	0.006	0.006	0.000	0.000	0.000	0.000
93	A	94	ALA	0	-0.004	0.002	35.638	0.008	0.008	0.000	0.000	0.000	0.000
94	A	95	LYS	1	0.762	0.865	39.163	0.161	0.161	0.000	0.000	0.000	0.000
95	A	96	ALA	0	0.001	0.013	37.062	0.006	0.006	0.000	0.000	0.000	0.000
96	A	97	GLY	0	-0.072	-0.024	39.175	0.003	0.003	0.000	0.000	0.000	0.000
97	A	98	ALA	0	-0.036	-0.016	34.853	0.002	0.002	0.000	0.000	0.000	0.000
98	A	99	ALA	0	0.000	-0.004	35.076	0.008	0.008	0.000	0.000	0.000	0.000
99	A	100	PHE	0	-0.026	-0.029	33.330	-0.013	-0.013	0.000	0.000	0.000	0.000
100	A	101	THR	0	-0.037	-0.002	33.133	0.012	0.012	0.000	0.000	0.000	0.000
101	A	102	PRO	0	-0.019	-0.019	33.928	-0.008	-0.008	0.000	0.000	0.000	0.000
102	A	103	THR	0	-0.010	-0.030	30.671	-0.006	-0.006	0.000	0.000	0.000	0.000
103	A	104	GLN	0	-0.049	-0.021	31.315	0.008	0.008	0.000	0.000	0.000	0.000
104	A	105	GLU	-1	-0.826	-0.884	30.706	-0.129	-0.129	0.000	0.000	0.000	0.000
105	A	106	LEU	0	-0.025	-0.017	27.809	0.015	0.015	0.000	0.000	0.000	0.000
106	A	107	PRO	0	-0.034	-0.038	28.418	-0.004	-0.004	0.000	0.000	0.000	0.000
107	A	108	PHE	0	-0.017	-0.027	23.856	0.005	0.005	0.000	0.000	0.000	0.000
108	A	109	GLY	0	0.008	0.006	24.622	-0.021	-0.021	0.000	0.000	0.000	0.000
109	A	110	TRP	0	-0.040	-0.026	26.559	0.017	0.017	0.000	0.000	0.000	0.000
110	A	111	ILE	0	0.039	0.012	24.844	-0.021	-0.021	0.000	0.000	0.000	0.000
111	A	112	LEU	0	-0.006	0.027	27.505	0.018	0.018	0.000	0.000	0.000	0.000
112	A	113	ALA	0	0.034	0.016	27.971	-0.020	-0.020	0.000	0.000	0.000	0.000
113	A	114	PHE	0	0.002	-0.021	26.451	0.013	0.013	0.000	0.000	0.000	0.000
114	A	115	ARG	1	0.770	0.892	29.256	0.157	0.157	0.000	0.000	0.000	0.000
115	A	116	ASP	-1	-0.745	-0.852	28.459	-0.249	-0.249	0.000	0.000	0.000	0.000
116	A	117	ALA	0	-0.019	-0.017	31.123	0.015	0.015	0.000	0.000	0.000	0.000
117	A	118	ASP	-1	-0.853	-0.921	30.978	-0.186	-0.186	0.000	0.000	0.000	0.000
118	A	119	ASN	0	-0.056	-0.045	32.449	0.007	0.007	0.000	0.000	0.000	0.000
119	A	120	ILE	0	0.010	0.019	25.757	0.005	0.005	0.000	0.000	0.000	0.000
120	A	121	ALA	0	-0.025	-0.017	26.563	-0.003	-0.003	0.000	0.000	0.000	0.000
121	A	122	LEU	0	-0.028	-0.014	24.093	-0.030	-0.030	0.000	0.000	0.000	0.000
122	A	123	GLU	-1	-0.839	-0.915	23.600	-0.214	-0.214	0.000	0.000	0.000	0.000
123	A	124	ALA	0	-0.024	0.014	23.688	-0.039	-0.039	0.000	0.000	0.000	0.000
124	A	125	MET	0	-0.013	0.006	20.802	0.038	0.038	0.000	0.000	0.000	0.000
125	A	126	LEU	0	0.004	0.024	22.960	-0.028	-0.028	0.000	0.000	0.000	0.000
126	A	127	GLY	0	0.028	0.014	22.750	0.024	0.024	0.000	0.000	0.000	0.000
127	A	128	ARG	1	0.840	0.902	23.621	0.130	0.130	0.000	0.000	0.000	0.000
128	A	129	GLU	-1	-0.920	-0.971	23.600	-0.106	-0.106	0.000	0.000	0.000	0.000
129	A	130	GLY	0	-0.018	-0.008	23.599	-0.023	-0.023	0.000	0.000	0.000	0.000
130	A	131	HIS	0	-0.027	0.002	21.624	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	132	HIS	1	0.843	0.878	26.714	0.159	0.159	0.000	0.000	0.000	0.000
132	A	133	HIS	0	0.065	0.048	25.726	0.025	0.025	0.000	0.000	0.000	0.000
133	A	134	HIS	0	0.048	0.033	29.323	-0.001	-0.001	0.000	0.000	0.000	0.000
134	A	135	HIS	0	-0.066	-0.030	32.032	0.005	0.005	0.000	0.000	0.000	0.000
135	A	136	HIS	0	0.007	0.025	32.034	0.016	0.016	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:2:SER)