FMO DATABASE

FMODB ID: 98V92

Calculation Name: 2RK5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2RK5

Chain ID: A

ChEMBL ID:

UniProt ID: O68574

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	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	86
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-599748.002713
FMO2-HF: Nuclear repulsion	565871.936587
FMO2-HF: Total energy	-33876.066126
FMO2-MP2: Total energy	-33976.197123

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:3:GLN)

Summations of interaction energy for fragment #1(A:3:GLN)

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.
-25.001	-19.129	13.086	-6.853	-12.103	0.049

Interaction energy analysis for fragmet #1(A:3:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.053 / q_NPA : 0.004

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

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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	5	ARG	1	0.879	0.955	3.896	0.202	1.523	-0.014	-0.658	-0.649	0.001
4	A	6	GLU	-1	-0.777	-0.865	6.362	0.138	0.138	0.000	0.000	0.000	0.000
5	A	7	ILE	0	-0.139	-0.091	10.168	-0.048	-0.048	0.000	0.000	0.000	0.000
6	A	8	ALA	0	-0.012	-0.003	12.778	-0.008	-0.008	0.000	0.000	0.000	0.000
7	A	9	ASP	-1	-0.823	-0.909	15.003	0.073	0.073	0.000	0.000	0.000	0.000
8	A	10	ASN	0	-0.030	0.000	15.289	0.017	0.017	0.000	0.000	0.000	0.000
9	A	11	THR	0	-0.043	-0.014	14.304	0.052	0.052	0.000	0.000	0.000	0.000
10	A	12	TYR	0	-0.002	-0.031	8.766	-0.041	-0.041	0.000	0.000	0.000	0.000
11	A	13	ILE	0	-0.084	-0.044	7.486	0.124	0.124	0.000	0.000	0.000	0.000
12	A	14	VAL	0	0.038	0.020	4.581	-0.642	-0.574	-0.001	-0.028	-0.039	0.000
13	A	15	LEU	0	-0.043	-0.019	2.519	-3.926	-1.357	2.576	-1.638	-3.507	0.016
14	A	16	GLY	0	0.016	-0.010	4.605	0.962	1.128	-0.001	-0.012	-0.152	0.000
15	A	17	THR	0	-0.039	-0.041	1.918	-11.990	-12.937	5.866	-2.653	-2.266	0.035
16	A	18	MET	0	-0.038	0.019	2.206	-3.103	-1.158	4.564	-1.751	-4.757	-0.003
17	A	19	THR	0	0.013	-0.025	3.563	-1.876	-1.644	0.093	0.076	-0.401	0.001
18	A	20	LEU	0	0.033	0.004	6.329	-0.290	-0.290	0.000	0.000	0.000	0.000
19	A	21	ASN	0	-0.009	0.006	8.351	-0.125	-0.125	0.000	0.000	0.000	0.000
20	A	22	ASP	-1	-0.828	-0.891	3.894	-2.420	-1.902	0.003	-0.189	-0.332	-0.001
21	A	23	PHE	0	-0.015	-0.024	5.956	0.096	0.096	0.000	0.000	0.000	0.000
22	A	24	ASN	0	0.020	0.015	6.866	0.021	0.021	0.000	0.000	0.000	0.000
23	A	25	GLU	-1	-0.950	-0.961	8.062	-0.565	-0.565	0.000	0.000	0.000	0.000
24	A	26	TYR	0	-0.072	-0.046	5.632	0.125	0.125	0.000	0.000	0.000	0.000
25	A	27	PHE	0	-0.044	-0.032	7.077	0.049	0.049	0.000	0.000	0.000	0.000
26	A	28	GLU	-1	-0.902	-0.921	10.832	0.043	0.043	0.000	0.000	0.000	0.000
27	A	29	THR	0	-0.039	-0.033	12.209	0.022	0.022	0.000	0.000	0.000	0.000
28	A	30	ASP	-1	-0.843	-0.892	14.035	0.164	0.164	0.000	0.000	0.000	0.000
29	A	31	LEU	0	-0.037	-0.008	11.468	0.026	0.026	0.000	0.000	0.000	0.000
30	A	32	GLU	-1	-0.923	-0.960	13.511	0.289	0.289	0.000	0.000	0.000	0.000
31	A	33	SER	0	-0.008	-0.027	15.708	0.000	0.000	0.000	0.000	0.000	0.000
32	A	34	ASP	-1	-0.914	-0.939	17.134	0.333	0.333	0.000	0.000	0.000	0.000
33	A	35	ASN	0	-0.105	-0.070	17.537	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	36	VAL	0	-0.009	0.004	12.765	0.103	0.103	0.000	0.000	0.000	0.000
35	A	37	ASP	-1	-0.862	-0.913	10.679	0.772	0.772	0.000	0.000	0.000	0.000
36	A	38	THR	0	-0.092	-0.066	6.706	-0.276	-0.276	0.000	0.000	0.000	0.000
37	A	39	ILE	0	0.054	0.037	5.914	-0.316	-0.316	0.000	0.000	0.000	0.000
38	A	40	ALA	0	-0.040	-0.009	8.273	-0.343	-0.343	0.000	0.000	0.000	0.000
39	A	41	GLY	0	-0.024	-0.003	10.133	-0.317	-0.317	0.000	0.000	0.000	0.000
40	A	42	PHE	0	0.070	0.049	11.772	-0.191	-0.191	0.000	0.000	0.000	0.000
41	A	43	TYR	0	-0.035	-0.041	12.395	-0.090	-0.090	0.000	0.000	0.000	0.000
42	A	44	LEU	0	-0.028	-0.023	13.360	-0.098	-0.098	0.000	0.000	0.000	0.000
43	A	45	THR	0	-0.046	-0.043	16.036	-0.122	-0.122	0.000	0.000	0.000	0.000
44	A	46	GLY	0	0.007	0.012	17.024	-0.079	-0.079	0.000	0.000	0.000	0.000
45	A	47	VAL	0	-0.065	-0.026	17.960	-0.055	-0.055	0.000	0.000	0.000	0.000
46	A	48	GLY	0	-0.009	0.008	20.024	-0.051	-0.051	0.000	0.000	0.000	0.000
47	A	49	THR	0	-0.069	-0.065	20.469	-0.017	-0.017	0.000	0.000	0.000	0.000
48	A	50	ILE	0	-0.038	-0.025	17.993	0.080	0.080	0.000	0.000	0.000	0.000
49	A	51	PRO	0	0.017	0.027	17.148	-0.041	-0.041	0.000	0.000	0.000	0.000
50	A	52	SER	0	0.001	-0.028	18.920	0.049	0.049	0.000	0.000	0.000	0.000
51	A	53	GLN	0	-0.042	-0.031	18.769	0.067	0.067	0.000	0.000	0.000	0.000
52	A	54	GLU	-1	-0.879	-0.928	20.259	0.351	0.351	0.000	0.000	0.000	0.000
53	A	55	GLU	-1	-0.943	-0.967	23.220	0.299	0.299	0.000	0.000	0.000	0.000
54	A	56	LYS	1	0.776	0.888	16.220	-0.520	-0.520	0.000	0.000	0.000	0.000
55	A	57	GLU	-1	-0.772	-0.869	19.019	0.407	0.407	0.000	0.000	0.000	0.000
56	A	58	HIS	1	0.777	0.881	18.245	-0.344	-0.344	0.000	0.000	0.000	0.000
57	A	59	PHE	0	0.033	0.033	15.575	-0.013	-0.013	0.000	0.000	0.000	0.000
58	A	60	GLU	-1	-0.888	-0.939	17.179	0.313	0.313	0.000	0.000	0.000	0.000
59	A	61	VAL	0	-0.032	-0.010	15.478	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	62	GLU	-1	-0.915	-0.966	18.559	0.162	0.162	0.000	0.000	0.000	0.000
61	A	63	SER	0	0.020	-0.026	16.488	0.002	0.002	0.000	0.000	0.000	0.000
62	A	64	ASN	0	-0.060	-0.035	17.459	-0.033	-0.033	0.000	0.000	0.000	0.000
63	A	65	GLY	0	0.004	0.007	19.670	-0.020	-0.020	0.000	0.000	0.000	0.000
64	A	66	LYS	1	0.745	0.878	15.703	-0.103	-0.103	0.000	0.000	0.000	0.000
65	A	67	HIS	0	-0.003	-0.008	18.109	0.014	0.014	0.000	0.000	0.000	0.000
66	A	68	LEU	0	-0.015	-0.017	12.682	0.000	0.000	0.000	0.000	0.000	0.000
67	A	69	GLU	-1	-0.803	-0.877	16.274	0.378	0.378	0.000	0.000	0.000	0.000
68	A	70	LEU	0	-0.029	-0.019	11.183	0.059	0.059	0.000	0.000	0.000	0.000
69	A	71	ILE	0	0.005	0.005	13.619	-0.040	-0.040	0.000	0.000	0.000	0.000
70	A	72	ASN	0	0.036	0.025	13.205	0.094	0.094	0.000	0.000	0.000	0.000
71	A	73	ASP	-1	-0.867	-0.922	11.135	0.549	0.549	0.000	0.000	0.000	0.000
72	A	74	LYS	1	0.853	0.903	12.155	-0.687	-0.687	0.000	0.000	0.000	0.000
73	A	75	VAL	0	0.047	0.026	12.411	0.264	0.264	0.000	0.000	0.000	0.000
74	A	76	LYS	1	0.867	0.924	10.598	-1.144	-1.144	0.000	0.000	0.000	0.000
75	A	77	ASP	-1	-0.891	-0.943	15.123	0.611	0.611	0.000	0.000	0.000	0.000
76	A	78	GLY	0	0.054	0.037	17.381	0.017	0.017	0.000	0.000	0.000	0.000
77	A	79	ARG	1	0.930	0.983	8.868	-2.070	-2.070	0.000	0.000	0.000	0.000
78	A	80	VAL	0	0.058	0.023	10.935	0.006	0.006	0.000	0.000	0.000	0.000
79	A	81	THR	0	-0.059	-0.048	8.717	0.278	0.278	0.000	0.000	0.000	0.000
80	A	82	LYS	1	0.831	0.925	7.432	0.101	0.101	0.000	0.000	0.000	0.000
81	A	83	LEU	0	0.037	0.029	8.382	-0.281	-0.281	0.000	0.000	0.000	0.000
82	A	84	LYS	1	0.911	0.965	9.364	-0.407	-0.407	0.000	0.000	0.000	0.000
83	A	85	ILE	0	0.020	0.008	8.908	0.071	0.071	0.000	0.000	0.000	0.000
84	A	86	LEU	0	-0.031	-0.013	12.107	-0.074	-0.074	0.000	0.000	0.000	0.000
85	A	87	VAL	0	0.041	0.018	13.296	0.022	0.022	0.000	0.000	0.000	0.000
86	A	88	SER	0	-0.037	-0.016	16.074	-0.033	-0.033	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:GLN)