FMO DATABASE

FMODB ID: V2471

Calculation Name: 2RKH-A-Xray316

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2RKH

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	169
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1447665.427813
FMO2-HF: Nuclear repulsion	1382817.594584
FMO2-HF: Total energy	-64847.833229
FMO2-MP2: Total energy	-65034.189562

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:5:ACE )

Summations of interaction energy for fragment #1(A:5:ACE )

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.
-0.213	1.248	0.375	-0.828	-1.008	0.001

Interaction energy analysis for fragmet #1(A:5:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / q_NPA : 0.001

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	7	LEU	0	0.032	0.047	3.875	0.531	1.407	-0.005	-0.384	-0.487	-0.001
4	A	8	THR	0	-0.021	-0.017	6.909	0.084	0.084	0.000	0.000	0.000	0.000
5	A	9	PRO	0	0.073	0.014	9.680	0.004	0.004	0.000	0.000	0.000	0.000
6	A	10	LYS	1	0.987	0.997	13.189	0.135	0.135	0.000	0.000	0.000	0.000
7	A	11	GLU	-1	-0.847	-0.921	8.067	-0.431	-0.431	0.000	0.000	0.000	0.000
8	A	12	ALA	0	0.035	0.026	11.758	0.012	0.012	0.000	0.000	0.000	0.000
9	A	13	VAL	0	0.028	0.017	12.709	0.045	0.045	0.000	0.000	0.000	0.000
10	A	14	ARG	1	0.853	0.926	14.120	0.141	0.141	0.000	0.000	0.000	0.000
11	A	15	LEU	0	0.006	0.017	11.265	0.038	0.038	0.000	0.000	0.000	0.000
12	A	16	CYS	0	-0.013	0.014	14.571	0.040	0.040	0.000	0.000	0.000	0.000
13	A	17	ALA	0	0.030	0.028	17.675	0.028	0.028	0.000	0.000	0.000	0.000
14	A	18	LEU	0	-0.005	-0.020	15.773	0.022	0.022	0.000	0.000	0.000	0.000
15	A	19	GLY	0	0.035	0.009	18.083	0.017	0.017	0.000	0.000	0.000	0.000
16	A	20	THR	0	-0.036	-0.045	19.257	0.014	0.014	0.000	0.000	0.000	0.000
17	A	21	ILE	0	-0.040	-0.031	21.900	0.013	0.013	0.000	0.000	0.000	0.000
18	A	22	ALA	0	-0.070	-0.029	21.125	0.012	0.012	0.000	0.000	0.000	0.000
19	A	23	SER	0	-0.065	-0.010	23.169	0.010	0.010	0.000	0.000	0.000	0.000
20	A	24	GLN	0	0.015	0.001	25.654	0.008	0.008	0.000	0.000	0.000	0.000
21	A	25	PRO	0	-0.007	-0.013	27.853	-0.005	-0.005	0.000	0.000	0.000	0.000
22	A	26	MET	0	0.002	0.019	25.362	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	27	ARG	1	0.922	0.988	29.925	0.047	0.047	0.000	0.000	0.000	0.000
24	A	28	TYR	0	0.010	-0.001	26.606	-0.008	-0.008	0.000	0.000	0.000	0.000
25	A	29	SER	0	-0.034	-0.062	28.684	-0.009	-0.009	0.000	0.000	0.000	0.000
26	A	30	GLU	-1	-0.918	-0.953	30.290	-0.066	-0.066	0.000	0.000	0.000	0.000
27	A	31	LEU	0	-0.008	0.008	23.059	-0.008	-0.008	0.000	0.000	0.000	0.000
28	A	32	ALA	0	-0.015	-0.019	25.276	-0.012	-0.012	0.000	0.000	0.000	0.000
29	A	33	GLY	0	-0.031	-0.025	25.881	-0.009	-0.009	0.000	0.000	0.000	0.000
30	A	34	SER	0	0.011	0.016	25.375	-0.009	-0.009	0.000	0.000	0.000	0.000
31	A	35	VAL	0	0.046	0.016	20.230	-0.011	-0.011	0.000	0.000	0.000	0.000
32	A	36	ARG	1	0.963	0.999	22.288	0.085	0.085	0.000	0.000	0.000	0.000
33	A	37	HIS	0	0.010	0.019	24.467	-0.009	-0.009	0.000	0.000	0.000	0.000
34	A	38	PHE	0	0.051	0.021	18.591	-0.007	-0.007	0.000	0.000	0.000	0.000
35	A	39	THR	0	-0.027	-0.045	18.318	-0.011	-0.011	0.000	0.000	0.000	0.000
36	A	40	SER	0	-0.029	-0.019	20.560	-0.009	-0.009	0.000	0.000	0.000	0.000
37	A	41	ARG	1	0.870	0.944	23.374	0.133	0.133	0.000	0.000	0.000	0.000
38	A	42	ILE	0	0.034	0.027	18.082	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	43	MET	0	-0.044	-0.020	16.003	-0.023	-0.023	0.000	0.000	0.000	0.000
40	A	44	GLY	0	0.038	0.035	20.238	0.010	0.010	0.000	0.000	0.000	0.000
41	A	45	PRO	0	-0.031	-0.027	23.220	-0.008	-0.008	0.000	0.000	0.000	0.000
42	A	46	SER	0	0.006	-0.001	20.395	-0.006	-0.006	0.000	0.000	0.000	0.000
43	A	47	LEU	0	0.007	-0.010	22.089	0.002	0.002	0.000	0.000	0.000	0.000
44	A	48	GLU	-1	-0.895	-0.951	18.835	-0.198	-0.198	0.000	0.000	0.000	0.000
45	A	49	LEU	0	-0.035	-0.024	16.878	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	50	MET	0	-0.028	-0.008	20.571	0.007	0.007	0.000	0.000	0.000	0.000
47	A	51	GLY	0	-0.005	0.008	23.141	0.010	0.010	0.000	0.000	0.000	0.000
48	A	52	ILE	0	-0.072	-0.028	17.515	0.008	0.008	0.000	0.000	0.000	0.000
49	A	53	SER	0	0.006	0.008	20.775	-0.007	-0.007	0.000	0.000	0.000	0.000
50	A	54	ILE	0	0.035	-0.004	22.058	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	55	GLU	-1	-0.850	-0.898	23.574	-0.044	-0.044	0.000	0.000	0.000	0.000
52	A	56	LEU	0	-0.028	-0.006	19.439	0.005	0.005	0.000	0.000	0.000	0.000
53	A	57	LEU	0	0.004	-0.006	18.416	0.007	0.007	0.000	0.000	0.000	0.000
54	A	58	ARG	1	0.899	0.948	21.811	0.038	0.038	0.000	0.000	0.000	0.000
55	A	59	TYR	0	-0.103	-0.083	24.003	0.008	0.008	0.000	0.000	0.000	0.000
56	A	60	GLU	-1	-0.859	-0.932	18.313	-0.033	-0.033	0.000	0.000	0.000	0.000
57	A	61	GLY	0	-0.018	0.006	22.032	0.007	0.007	0.000	0.000	0.000	0.000
58	A	62	LEU	0	-0.015	0.014	17.443	0.000	0.000	0.000	0.000	0.000	0.000
59	A	63	VAL	0	0.023	0.007	21.355	-0.006	-0.006	0.000	0.000	0.000	0.000
60	A	64	GLU	-1	-0.947	-0.976	24.287	-0.014	-0.014	0.000	0.000	0.000	0.000
61	A	65	ALA	0	0.006	-0.003	28.003	-0.004	-0.004	0.000	0.000	0.000	0.000
62	A	66	VAL	0	0.013	0.005	31.407	0.001	0.001	0.000	0.000	0.000	0.000
63	A	67	NME	0	-0.005	0.007	34.591	0.003	0.003	0.000	0.000	0.000	0.000
64	A	74	ACE	0	0.003	-0.011	36.815	0.001	0.001	0.000	0.000	0.000	0.000
65	A	75	ASP	-1	-0.773	-0.873	33.193	-0.059	-0.059	0.000	0.000	0.000	0.000
66	A	76	ALA	0	-0.008	-0.002	32.657	0.001	0.001	0.000	0.000	0.000	0.000
67	A	77	MET	0	-0.008	0.005	32.140	-0.005	-0.005	0.000	0.000	0.000	0.000
68	A	78	LEU	0	-0.040	-0.025	27.319	0.004	0.004	0.000	0.000	0.000	0.000
69	A	79	ALA	0	0.058	0.008	27.309	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	80	ILE	0	-0.018	0.019	19.931	0.003	0.003	0.000	0.000	0.000	0.000
71	A	81	SER	0	0.059	0.020	23.200	0.005	0.005	0.000	0.000	0.000	0.000
72	A	82	ALA	0	-0.005	-0.024	22.198	-0.005	-0.005	0.000	0.000	0.000	0.000
73	A	83	ALA	0	0.010	0.001	19.950	0.003	0.003	0.000	0.000	0.000	0.000
74	A	84	GLY	0	0.072	0.033	18.236	-0.002	-0.002	0.000	0.000	0.000	0.000
75	A	85	ARG	1	0.942	0.967	17.742	0.032	0.032	0.000	0.000	0.000	0.000
76	A	86	ARG	1	0.921	0.969	16.094	-0.071	-0.071	0.000	0.000	0.000	0.000
77	A	87	GLU	-1	-0.886	-0.934	12.342	-0.076	-0.076	0.000	0.000	0.000	0.000
78	A	88	LEU	0	-0.010	-0.001	12.804	-0.036	-0.036	0.000	0.000	0.000	0.000
79	A	89	HIS	0	0.008	0.000	13.299	-0.039	-0.039	0.000	0.000	0.000	0.000
80	A	90	SER	0	-0.012	0.009	9.691	-0.007	-0.007	0.000	0.000	0.000	0.000
81	A	91	LEU	0	-0.016	-0.013	8.565	-0.072	-0.072	0.000	0.000	0.000	0.000
82	A	92	LEU	0	-0.020	-0.014	9.156	-0.145	-0.145	0.000	0.000	0.000	0.000
83	A	93	THR	0	-0.115	-0.062	9.775	-0.024	-0.024	0.000	0.000	0.000	0.000
84	A	94	ALA	0	0.048	0.034	4.855	0.091	0.091	0.000	0.000	0.000	0.000
85	A	95	ARG	1	0.810	0.906	2.697	0.699	1.403	0.380	-0.419	-0.665	0.002
86	A	96	LEU	0	0.096	0.056	5.011	-0.918	-1.037	0.000	-0.025	0.144	0.000
87	A	97	ARG	1	0.885	0.928	4.876	0.492	0.492	0.000	0.000	0.000	0.000
88	A	98	PRO	0	0.058	0.046	7.389	0.116	0.116	0.000	0.000	0.000	0.000
89	A	99	GLY	0	-0.025	-0.008	9.112	0.131	0.131	0.000	0.000	0.000	0.000
90	A	100	SER	0	-0.005	-0.026	8.660	-0.248	-0.248	0.000	0.000	0.000	0.000
91	A	101	ASP	-1	-0.739	-0.888	10.731	-0.517	-0.517	0.000	0.000	0.000	0.000
92	A	102	LEU	0	-0.016	-0.006	14.214	0.049	0.049	0.000	0.000	0.000	0.000
93	A	103	SER	0	0.094	0.033	16.173	0.036	0.036	0.000	0.000	0.000	0.000
94	A	104	LYS	1	0.890	0.972	14.436	0.351	0.351	0.000	0.000	0.000	0.000
95	A	105	LEU	0	-0.022	-0.008	17.394	0.023	0.023	0.000	0.000	0.000	0.000
96	A	106	VAL	0	0.019	0.000	19.583	0.023	0.023	0.000	0.000	0.000	0.000
97	A	107	VAL	0	0.051	0.025	22.212	0.016	0.016	0.000	0.000	0.000	0.000
98	A	108	ALA	0	0.007	0.009	22.170	0.013	0.013	0.000	0.000	0.000	0.000
99	A	109	LEU	0	-0.052	-0.037	22.123	0.015	0.015	0.000	0.000	0.000	0.000
100	A	110	LYS	1	0.880	0.933	25.360	0.107	0.107	0.000	0.000	0.000	0.000
101	A	111	MET	0	0.021	0.021	27.465	0.010	0.010	0.000	0.000	0.000	0.000
102	A	112	ARG	1	0.897	0.960	25.495	0.064	0.064	0.000	0.000	0.000	0.000
103	A	113	PHE	0	-0.042	-0.048	26.773	0.007	0.007	0.000	0.000	0.000	0.000
104	A	114	LEU	0	0.083	0.053	31.222	0.003	0.003	0.000	0.000	0.000	0.000
105	A	115	GLY	0	-0.010	-0.013	33.340	0.003	0.003	0.000	0.000	0.000	0.000
106	A	116	LEU	0	-0.072	-0.040	32.646	0.003	0.003	0.000	0.000	0.000	0.000
107	A	117	MET	0	-0.024	0.014	31.813	0.000	0.000	0.000	0.000	0.000	0.000
108	A	118	GLU	-1	-0.920	-0.953	36.736	-0.039	-0.039	0.000	0.000	0.000	0.000
109	A	119	ALA	0	-0.012	-0.032	39.151	-0.003	-0.003	0.000	0.000	0.000	0.000
110	A	120	GLU	-1	-0.869	-0.930	40.309	-0.045	-0.045	0.000	0.000	0.000	0.000
111	A	121	GLU	-1	-0.829	-0.908	35.022	-0.064	-0.064	0.000	0.000	0.000	0.000
112	A	122	ARG	1	0.820	0.914	35.466	0.041	0.041	0.000	0.000	0.000	0.000
113	A	123	ALA	0	0.067	0.031	35.585	-0.004	-0.004	0.000	0.000	0.000	0.000
114	A	124	HIS	0	0.055	0.038	35.207	-0.002	-0.002	0.000	0.000	0.000	0.000
115	A	125	GLN	0	-0.041	-0.035	30.766	-0.013	-0.013	0.000	0.000	0.000	0.000
116	A	126	ILE	0	-0.054	-0.030	31.877	-0.008	-0.008	0.000	0.000	0.000	0.000
117	A	127	ASP	-1	-0.811	-0.899	33.141	-0.067	-0.067	0.000	0.000	0.000	0.000
118	A	128	LEU	0	-0.028	-0.016	30.900	-0.005	-0.005	0.000	0.000	0.000	0.000
119	A	129	LEU	0	-0.100	-0.051	26.938	-0.010	-0.010	0.000	0.000	0.000	0.000
120	A	130	ILE	0	0.011	0.012	29.321	-0.008	-0.008	0.000	0.000	0.000	0.000
121	A	131	GLU	-1	-0.915	-0.938	31.712	-0.088	-0.088	0.000	0.000	0.000	0.000
122	A	132	GLY	0	-0.046	-0.031	27.917	-0.004	-0.004	0.000	0.000	0.000	0.000
123	A	133	VAL	0	-0.022	-0.019	26.766	-0.010	-0.010	0.000	0.000	0.000	0.000
124	A	134	ASP	-1	-0.843	-0.919	28.324	-0.092	-0.092	0.000	0.000	0.000	0.000
125	A	135	SER	0	-0.072	-0.043	28.892	-0.003	-0.003	0.000	0.000	0.000	0.000
126	A	136	GLU	-1	-0.992	-1.005	22.247	-0.202	-0.202	0.000	0.000	0.000	0.000
127	A	137	LEU	0	0.035	0.010	26.667	-0.006	-0.006	0.000	0.000	0.000	0.000
128	A	138	ALA	0	-0.003	0.010	28.814	0.002	0.002	0.000	0.000	0.000	0.000
129	A	139	ARG	1	0.806	0.920	23.284	0.167	0.167	0.000	0.000	0.000	0.000
130	A	140	LEU	0	0.021	0.008	22.661	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	141	ALA	0	0.038	0.017	26.662	0.002	0.002	0.000	0.000	0.000	0.000
132	A	142	ASP	-1	-0.965	-0.982	29.436	-0.099	-0.099	0.000	0.000	0.000	0.000
133	A	143	LEU	0	-0.089	-0.051	23.011	0.001	0.001	0.000	0.000	0.000	0.000
134	A	144	ARG	1	0.774	0.889	27.712	0.102	0.102	0.000	0.000	0.000	0.000
135	A	145	GLY	0	0.048	0.011	28.843	0.005	0.005	0.000	0.000	0.000	0.000
136	A	146	SER	0	-0.119	-0.082	32.406	0.000	0.000	0.000	0.000	0.000	0.000
137	A	147	ASP	-1	-0.878	-0.932	35.517	-0.065	-0.065	0.000	0.000	0.000	0.000
138	A	148	GLY	0	0.005	0.027	34.152	-0.001	-0.001	0.000	0.000	0.000	0.000
139	A	149	GLU	-1	-0.991	-0.988	33.261	-0.067	-0.067	0.000	0.000	0.000	0.000
140	A	150	GLY	0	0.017	0.011	30.675	-0.006	-0.006	0.000	0.000	0.000	0.000
141	A	151	GLY	0	0.002	-0.004	29.880	0.004	0.004	0.000	0.000	0.000	0.000
142	A	152	SER	0	-0.014	-0.007	25.285	-0.006	-0.006	0.000	0.000	0.000	0.000
143	A	153	ALA	0	0.039	0.005	21.223	-0.002	-0.002	0.000	0.000	0.000	0.000
144	A	154	LEU	0	-0.010	-0.001	20.716	-0.010	-0.010	0.000	0.000	0.000	0.000
145	A	155	ALA	0	0.049	0.023	22.802	-0.005	-0.005	0.000	0.000	0.000	0.000
146	A	156	ALA	0	0.023	0.017	24.635	0.001	0.001	0.000	0.000	0.000	0.000
147	A	157	TRP	0	-0.032	-0.023	17.658	-0.002	-0.002	0.000	0.000	0.000	0.000
148	A	158	LEU	0	0.008	-0.004	22.623	-0.007	-0.007	0.000	0.000	0.000	0.000
149	A	159	ASP	-1	-0.795	-0.874	24.446	-0.104	-0.104	0.000	0.000	0.000	0.000
150	A	160	HIS	0	-0.062	-0.034	21.623	0.014	0.014	0.000	0.000	0.000	0.000
151	A	161	ASP	-1	-0.946	-0.984	21.268	-0.214	-0.214	0.000	0.000	0.000	0.000
152	A	162	MET	0	0.029	0.018	23.610	0.003	0.003	0.000	0.000	0.000	0.000
153	A	163	ALA	0	0.060	0.043	27.046	0.007	0.007	0.000	0.000	0.000	0.000
154	A	164	LEU	0	-0.074	-0.046	22.342	0.006	0.006	0.000	0.000	0.000	0.000
155	A	165	LEU	0	0.002	-0.006	23.797	0.007	0.007	0.000	0.000	0.000	0.000
156	A	166	GLU	-1	-0.901	-0.948	26.944	-0.089	-0.089	0.000	0.000	0.000	0.000
157	A	167	SER	0	-0.054	-0.024	28.719	0.009	0.009	0.000	0.000	0.000	0.000
158	A	168	ARG	1	0.866	0.935	22.460	0.153	0.153	0.000	0.000	0.000	0.000
159	A	169	LEU	0	0.045	0.026	28.834	0.002	0.002	0.000	0.000	0.000	0.000
160	A	170	ALA	0	0.066	0.040	31.545	0.005	0.005	0.000	0.000	0.000	0.000
161	A	171	TRP	0	-0.067	-0.034	30.314	0.003	0.003	0.000	0.000	0.000	0.000
162	A	172	LEU	0	-0.032	-0.035	28.629	0.003	0.003	0.000	0.000	0.000	0.000
163	A	173	GLU	-1	-0.875	-0.939	32.867	-0.068	-0.068	0.000	0.000	0.000	0.000
164	A	174	ASP	-1	-0.926	-0.951	35.972	-0.053	-0.053	0.000	0.000	0.000	0.000
165	A	175	PHE	0	-0.043	-0.040	32.850	0.004	0.004	0.000	0.000	0.000	0.000
166	A	176	ARG	1	0.882	0.926	36.213	0.059	0.059	0.000	0.000	0.000	0.000
167	A	177	ALA	0	-0.017	-0.004	37.881	0.003	0.003	0.000	0.000	0.000	0.000
168	A	178	ARG	1	0.784	0.897	38.432	0.052	0.052	0.000	0.000	0.000	0.000
169	A	179	LEU	-1	-1.008	-0.972	36.876	-0.042	-0.042	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:ACE )