FMO DATABASE

FMODB ID: LJ4Y9

Calculation Name: 2RKH-A-Xray372

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: 2023-06-20

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	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	166
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1435095.561256
FMO2-HF: Nuclear repulsion	1370569.684286
FMO2-HF: Total energy	-64525.87697
FMO2-MP2: Total energy	-64711.232099

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:6:THR)

Summations of interaction energy for fragment #1(A:6:THR)

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.
-25.223	-16.467	9.764	-7.626	-10.895	-0.033

Interaction energy analysis for fragmet #1(A:6:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.079 / q_NPA : -0.061

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	8	THR	0	-0.018	-0.017	2.702	-3.001	-0.389	0.537	-1.422	-1.727	-0.012
4	A	9	PRO	0	0.070	0.012	5.385	0.255	0.309	-0.001	-0.001	-0.052	0.000
5	A	10	LYS	1	0.986	0.996	7.694	1.277	1.277	0.000	0.000	0.000	0.000
6	A	11	GLU	-1	-0.847	-0.920	6.314	-3.581	-3.581	0.000	0.000	0.000	0.000
7	A	12	ALA	0	0.034	0.026	6.807	0.292	0.292	0.000	0.000	0.000	0.000
8	A	13	VAL	0	0.021	0.014	8.593	0.323	0.323	0.000	0.000	0.000	0.000
9	A	14	ARG	1	0.859	0.928	11.718	0.993	0.993	0.000	0.000	0.000	0.000
10	A	15	LEU	0	0.002	0.017	8.654	0.180	0.180	0.000	0.000	0.000	0.000
11	A	16	CYS	0	-0.010	0.014	12.024	0.185	0.185	0.000	0.000	0.000	0.000
12	A	17	ALA	0	0.026	0.026	14.113	0.116	0.116	0.000	0.000	0.000	0.000
13	A	18	LEU	0	-0.003	-0.019	14.285	0.087	0.087	0.000	0.000	0.000	0.000
14	A	19	GLY	0	0.034	0.009	15.726	0.071	0.071	0.000	0.000	0.000	0.000
15	A	20	THR	0	-0.036	-0.046	16.962	0.063	0.063	0.000	0.000	0.000	0.000
16	A	21	ILE	0	-0.040	-0.031	19.693	0.042	0.042	0.000	0.000	0.000	0.000
17	A	22	ALA	0	-0.070	-0.029	19.542	0.033	0.033	0.000	0.000	0.000	0.000
18	A	23	SER	0	-0.064	-0.010	21.418	0.036	0.036	0.000	0.000	0.000	0.000
19	A	24	GLN	0	0.013	0.001	23.577	0.034	0.034	0.000	0.000	0.000	0.000
20	A	25	PRO	0	-0.004	-0.012	25.570	-0.020	-0.020	0.000	0.000	0.000	0.000
21	A	26	MET	0	-0.003	0.019	22.468	0.002	0.002	0.000	0.000	0.000	0.000
22	A	27	ARG	1	0.927	0.990	27.563	0.165	0.165	0.000	0.000	0.000	0.000
23	A	28	TYR	0	0.006	-0.003	23.373	-0.026	-0.026	0.000	0.000	0.000	0.000
24	A	29	SER	0	-0.037	-0.064	25.219	-0.026	-0.026	0.000	0.000	0.000	0.000
25	A	30	GLU	-1	-0.913	-0.952	26.223	-0.209	-0.209	0.000	0.000	0.000	0.000
26	A	31	LEU	0	-0.008	0.008	20.147	-0.015	-0.015	0.000	0.000	0.000	0.000
27	A	32	ALA	0	-0.012	-0.018	21.289	-0.036	-0.036	0.000	0.000	0.000	0.000
28	A	33	GLY	0	-0.034	-0.027	21.331	-0.025	-0.025	0.000	0.000	0.000	0.000
29	A	34	SER	0	0.014	0.017	21.196	-0.008	-0.008	0.000	0.000	0.000	0.000
30	A	35	VAL	0	0.041	0.015	15.835	-0.016	-0.016	0.000	0.000	0.000	0.000
31	A	36	ARG	1	0.967	1.000	17.240	0.290	0.290	0.000	0.000	0.000	0.000
32	A	37	HIS	0	0.008	0.018	18.879	-0.023	-0.023	0.000	0.000	0.000	0.000
33	A	38	PHE	0	0.052	0.021	13.506	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	39	THR	0	-0.028	-0.043	13.067	-0.005	-0.005	0.000	0.000	0.000	0.000
35	A	40	SER	0	-0.027	-0.019	14.682	0.012	0.012	0.000	0.000	0.000	0.000
36	A	41	ARG	1	0.878	0.946	17.291	0.312	0.312	0.000	0.000	0.000	0.000
37	A	42	ILE	0	0.027	0.024	12.039	0.025	0.025	0.000	0.000	0.000	0.000
38	A	43	MET	0	-0.044	-0.019	9.505	0.000	0.000	0.000	0.000	0.000	0.000
39	A	44	GLY	0	0.035	0.033	13.871	0.041	0.041	0.000	0.000	0.000	0.000
40	A	45	PRO	0	-0.029	-0.027	16.843	-0.057	-0.057	0.000	0.000	0.000	0.000
41	A	46	SER	0	0.006	-0.001	14.056	-0.037	-0.037	0.000	0.000	0.000	0.000
42	A	47	LEU	0	0.006	-0.010	15.680	-0.040	-0.040	0.000	0.000	0.000	0.000
43	A	48	GLU	-1	-0.894	-0.951	12.664	-0.681	-0.681	0.000	0.000	0.000	0.000
44	A	49	LEU	0	-0.037	-0.024	11.035	-0.078	-0.078	0.000	0.000	0.000	0.000
45	A	50	MET	0	-0.026	-0.008	14.907	0.014	0.014	0.000	0.000	0.000	0.000
46	A	51	GLY	0	-0.005	0.008	17.936	0.038	0.038	0.000	0.000	0.000	0.000
47	A	52	ILE	0	-0.069	-0.027	13.033	-0.009	-0.009	0.000	0.000	0.000	0.000
48	A	53	SER	0	0.002	0.006	16.365	0.000	0.000	0.000	0.000	0.000	0.000
49	A	54	ILE	0	0.040	-0.002	18.506	-0.034	-0.034	0.000	0.000	0.000	0.000
50	A	55	GLU	-1	-0.855	-0.901	20.440	-0.293	-0.293	0.000	0.000	0.000	0.000
51	A	56	LEU	0	-0.028	-0.006	17.275	0.004	0.004	0.000	0.000	0.000	0.000
52	A	57	LEU	0	0.005	-0.006	16.631	0.003	0.003	0.000	0.000	0.000	0.000
53	A	58	ARG	1	0.900	0.948	20.371	0.277	0.277	0.000	0.000	0.000	0.000
54	A	59	TYR	0	-0.102	-0.082	22.775	0.017	0.017	0.000	0.000	0.000	0.000
55	A	60	GLU	-1	-0.857	-0.931	17.473	-0.579	-0.579	0.000	0.000	0.000	0.000
56	A	61	GLY	0	-0.018	0.007	21.619	0.013	0.013	0.000	0.000	0.000	0.000
57	A	62	LEU	0	-0.014	0.013	16.655	0.018	0.018	0.000	0.000	0.000	0.000
58	A	63	VAL	0	0.024	0.007	20.658	0.011	0.011	0.000	0.000	0.000	0.000
59	A	64	GLU	-1	-0.950	-0.978	23.122	-0.192	-0.192	0.000	0.000	0.000	0.000
60	A	65	ALA	0	0.012	0.003	26.966	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	66	VAL	0	0.006	0.010	30.073	0.010	0.010	0.000	0.000	0.000	0.000
62	A	75	ASP	-1	-0.795	-0.880	29.844	-0.222	-0.222	0.000	0.000	0.000	0.000
63	A	76	ALA	0	0.020	-0.003	30.547	0.010	0.010	0.000	0.000	0.000	0.000
64	A	77	MET	0	-0.013	0.001	29.747	-0.016	-0.016	0.000	0.000	0.000	0.000
65	A	78	LEU	0	-0.040	-0.025	25.261	0.002	0.002	0.000	0.000	0.000	0.000
66	A	79	ALA	0	0.056	0.008	25.634	0.005	0.005	0.000	0.000	0.000	0.000
67	A	80	ILE	0	-0.019	0.018	18.873	-0.007	-0.007	0.000	0.000	0.000	0.000
68	A	81	SER	0	0.061	0.022	22.404	0.022	0.022	0.000	0.000	0.000	0.000
69	A	82	ALA	0	-0.006	-0.024	21.807	-0.015	-0.015	0.000	0.000	0.000	0.000
70	A	83	ALA	0	0.011	0.001	20.260	0.006	0.006	0.000	0.000	0.000	0.000
71	A	84	GLY	0	0.071	0.033	18.201	-0.032	-0.032	0.000	0.000	0.000	0.000
72	A	85	ARG	1	0.942	0.967	17.086	0.154	0.154	0.000	0.000	0.000	0.000
73	A	86	ARG	1	0.919	0.968	16.846	0.117	0.117	0.000	0.000	0.000	0.000
74	A	87	GLU	-1	-0.881	-0.933	11.943	-0.740	-0.740	0.000	0.000	0.000	0.000
75	A	88	LEU	0	-0.014	-0.002	12.369	-0.070	-0.070	0.000	0.000	0.000	0.000
76	A	89	HIS	0	0.008	-0.001	12.331	-0.061	-0.061	0.000	0.000	0.000	0.000
77	A	90	SER	0	-0.012	0.009	10.328	0.139	0.139	0.000	0.000	0.000	0.000
78	A	91	LEU	0	-0.012	-0.011	7.989	0.075	0.075	0.000	0.000	0.000	0.000
79	A	92	LEU	0	-0.023	-0.015	7.517	-0.157	-0.157	0.000	0.000	0.000	0.000
80	A	93	THR	0	-0.114	-0.063	9.346	0.083	0.083	0.000	0.000	0.000	0.000
81	A	94	ALA	0	0.055	0.039	4.333	0.358	0.412	-0.001	-0.007	-0.046	0.000
82	A	95	ARG	1	0.899	0.946	4.118	-3.259	-2.912	0.000	-0.084	-0.264	0.000
83	A	96	LEU	0	0.094	0.049	2.501	-6.807	-3.293	1.616	-2.509	-2.621	-0.025
84	A	97	ARG	1	0.882	0.927	2.323	-7.698	-6.809	6.987	-2.955	-4.921	0.006
85	A	98	PRO	0	0.046	0.041	3.867	-1.675	-1.397	0.020	-0.101	-0.197	0.001
86	A	99	GLY	0	-0.030	-0.011	5.419	-0.797	-0.797	0.000	0.000	0.000	0.000
87	A	100	SER	0	0.002	-0.021	2.630	0.012	0.937	0.607	-0.532	-1.000	-0.003
88	A	101	ASP	-1	-0.742	-0.890	4.435	0.597	0.680	-0.001	-0.015	-0.067	0.000
89	A	102	LEU	0	-0.013	-0.004	7.802	0.122	0.122	0.000	0.000	0.000	0.000
90	A	103	SER	0	0.091	0.032	10.330	0.015	0.015	0.000	0.000	0.000	0.000
91	A	104	LYS	1	0.888	0.971	9.753	-0.786	-0.786	0.000	0.000	0.000	0.000
92	A	105	LEU	0	-0.020	-0.007	12.769	0.008	0.008	0.000	0.000	0.000	0.000
93	A	106	VAL	0	0.021	0.002	14.485	-0.021	-0.021	0.000	0.000	0.000	0.000
94	A	107	VAL	0	0.047	0.023	16.418	-0.009	-0.009	0.000	0.000	0.000	0.000
95	A	108	ALA	0	0.007	0.008	17.311	-0.006	-0.006	0.000	0.000	0.000	0.000
96	A	109	LEU	0	-0.048	-0.035	17.664	-0.008	-0.008	0.000	0.000	0.000	0.000
97	A	110	LYS	1	0.881	0.934	20.409	-0.012	-0.012	0.000	0.000	0.000	0.000
98	A	111	MET	0	0.015	0.017	22.085	-0.007	-0.007	0.000	0.000	0.000	0.000
99	A	112	ARG	1	0.902	0.962	21.869	-0.193	-0.193	0.000	0.000	0.000	0.000
100	A	113	PHE	0	-0.036	-0.044	22.639	0.002	0.002	0.000	0.000	0.000	0.000
101	A	114	LEU	0	0.075	0.049	26.436	-0.013	-0.013	0.000	0.000	0.000	0.000
102	A	115	GLY	0	-0.015	-0.017	28.085	-0.009	-0.009	0.000	0.000	0.000	0.000
103	A	116	LEU	0	-0.062	-0.034	28.163	-0.004	-0.004	0.000	0.000	0.000	0.000
104	A	117	MET	0	-0.021	0.017	26.166	-0.009	-0.009	0.000	0.000	0.000	0.000
105	A	118	GLU	-1	-0.914	-0.949	31.402	0.002	0.002	0.000	0.000	0.000	0.000
106	A	119	ALA	0	-0.023	-0.039	33.439	0.000	0.000	0.000	0.000	0.000	0.000
107	A	120	GLU	-1	-0.871	-0.931	34.370	-0.003	-0.003	0.000	0.000	0.000	0.000
108	A	121	GLU	-1	-0.824	-0.904	29.015	-0.022	-0.022	0.000	0.000	0.000	0.000
109	A	122	ARG	1	0.820	0.914	29.576	-0.038	-0.038	0.000	0.000	0.000	0.000
110	A	123	ALA	0	0.042	0.017	29.493	0.002	0.002	0.000	0.000	0.000	0.000
111	A	124	HIS	0	0.063	0.042	28.842	0.001	0.001	0.000	0.000	0.000	0.000
112	A	125	GLN	0	-0.033	-0.030	24.659	-0.003	-0.003	0.000	0.000	0.000	0.000
113	A	126	ILE	0	-0.060	-0.033	25.499	0.000	0.000	0.000	0.000	0.000	0.000
114	A	127	ASP	-1	-0.811	-0.899	26.743	-0.016	-0.016	0.000	0.000	0.000	0.000
115	A	128	LEU	0	-0.016	-0.010	24.329	-0.008	-0.008	0.000	0.000	0.000	0.000
116	A	129	LEU	0	-0.100	-0.051	20.565	-0.006	-0.006	0.000	0.000	0.000	0.000
117	A	130	ILE	0	0.003	0.008	22.853	-0.003	-0.003	0.000	0.000	0.000	0.000
118	A	131	GLU	-1	-0.911	-0.937	25.251	-0.091	-0.091	0.000	0.000	0.000	0.000
119	A	132	GLY	0	-0.043	-0.029	21.291	-0.016	-0.016	0.000	0.000	0.000	0.000
120	A	133	VAL	0	-0.023	-0.019	20.543	-0.015	-0.015	0.000	0.000	0.000	0.000
121	A	134	ASP	-1	-0.843	-0.919	21.964	-0.060	-0.060	0.000	0.000	0.000	0.000
122	A	135	SER	0	-0.072	-0.042	22.344	-0.018	-0.018	0.000	0.000	0.000	0.000
123	A	136	GLU	-1	-0.989	-1.004	16.109	-0.158	-0.158	0.000	0.000	0.000	0.000
124	A	137	LEU	0	0.036	0.010	20.388	-0.017	-0.017	0.000	0.000	0.000	0.000
125	A	138	ALA	0	-0.002	0.011	22.718	-0.004	-0.004	0.000	0.000	0.000	0.000
126	A	139	ARG	1	0.807	0.921	16.905	0.233	0.233	0.000	0.000	0.000	0.000
127	A	140	LEU	0	0.022	0.009	16.644	-0.021	-0.021	0.000	0.000	0.000	0.000
128	A	141	ALA	0	0.041	0.019	20.680	0.000	0.000	0.000	0.000	0.000	0.000
129	A	142	ASP	-1	-0.964	-0.983	23.384	-0.188	-0.188	0.000	0.000	0.000	0.000
130	A	143	LEU	0	-0.086	-0.050	17.455	-0.009	-0.009	0.000	0.000	0.000	0.000
131	A	144	ARG	1	0.774	0.892	22.037	0.085	0.085	0.000	0.000	0.000	0.000
132	A	145	GLY	0	0.052	0.021	23.451	0.004	0.004	0.000	0.000	0.000	0.000
133	A	146	SER	0	-0.078	-0.058	27.023	0.010	0.010	0.000	0.000	0.000	0.000
134	A	147	ASP	-1	-0.899	-0.940	29.335	-0.053	-0.053	0.000	0.000	0.000	0.000
135	A	148	GLY	0	-0.031	-0.003	29.161	0.007	0.007	0.000	0.000	0.000	0.000
136	A	149	GLU	-1	-0.997	-0.997	28.825	-0.073	-0.073	0.000	0.000	0.000	0.000
137	A	150	GLY	0	0.020	0.012	26.582	-0.009	-0.009	0.000	0.000	0.000	0.000
138	A	151	GLY	0	0.002	-0.004	26.303	-0.001	-0.001	0.000	0.000	0.000	0.000
139	A	152	SER	0	-0.011	-0.005	21.953	0.004	0.004	0.000	0.000	0.000	0.000
140	A	153	ALA	0	0.040	0.006	18.282	0.008	0.008	0.000	0.000	0.000	0.000
141	A	154	LEU	0	-0.008	0.000	16.178	0.003	0.003	0.000	0.000	0.000	0.000
142	A	155	ALA	0	0.043	0.019	18.693	0.000	0.000	0.000	0.000	0.000	0.000
143	A	156	ALA	0	0.023	0.017	20.995	0.008	0.008	0.000	0.000	0.000	0.000
144	A	157	TRP	0	-0.029	-0.022	12.843	0.043	0.043	0.000	0.000	0.000	0.000
145	A	158	LEU	0	0.008	-0.005	17.204	0.006	0.006	0.000	0.000	0.000	0.000
146	A	159	ASP	-1	-0.793	-0.873	19.355	-0.054	-0.054	0.000	0.000	0.000	0.000
147	A	160	HIS	0	-0.062	-0.033	17.505	0.007	0.007	0.000	0.000	0.000	0.000
148	A	161	ASP	-1	-0.946	-0.984	15.965	-0.048	-0.048	0.000	0.000	0.000	0.000
149	A	162	MET	0	0.032	0.018	18.482	0.003	0.003	0.000	0.000	0.000	0.000
150	A	163	ALA	0	0.062	0.045	21.598	0.010	0.010	0.000	0.000	0.000	0.000
151	A	164	LEU	0	-0.074	-0.046	17.863	0.022	0.022	0.000	0.000	0.000	0.000
152	A	165	LEU	0	0.003	-0.005	17.864	0.018	0.018	0.000	0.000	0.000	0.000
153	A	166	GLU	-1	-0.901	-0.947	21.390	-0.021	-0.021	0.000	0.000	0.000	0.000
154	A	167	SER	0	-0.051	-0.023	23.823	0.008	0.008	0.000	0.000	0.000	0.000
155	A	168	ARG	1	0.867	0.935	16.919	-0.100	-0.100	0.000	0.000	0.000	0.000
156	A	169	LEU	0	0.044	0.026	23.241	0.006	0.006	0.000	0.000	0.000	0.000
157	A	170	ALA	0	0.072	0.043	25.624	0.002	0.002	0.000	0.000	0.000	0.000
158	A	171	TRP	0	-0.063	-0.033	24.657	0.006	0.006	0.000	0.000	0.000	0.000
159	A	172	LEU	0	-0.033	-0.034	22.498	0.006	0.006	0.000	0.000	0.000	0.000
160	A	173	GLU	-1	-0.869	-0.936	26.938	-0.007	-0.007	0.000	0.000	0.000	0.000
161	A	174	ASP	-1	-0.917	-0.946	30.336	0.051	0.051	0.000	0.000	0.000	0.000
162	A	175	PHE	0	-0.038	-0.036	27.552	0.002	0.002	0.000	0.000	0.000	0.000
163	A	176	ARG	1	0.871	0.921	30.386	-0.001	-0.001	0.000	0.000	0.000	0.000
164	A	177	ALA	0	-0.009	-0.001	31.824	-0.003	-0.003	0.000	0.000	0.000	0.000
165	A	178	ARG	1	0.821	0.920	33.120	-0.052	-0.052	0.000	0.000	0.000	0.000
166	A	179	LEU	0	-0.088	-0.016	30.892	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:THR)