FMO DATABASE

FMODB ID: KGQR3

Calculation Name: 3RHI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3RHI

Chain ID: A

ChEMBL ID:

UniProt ID: A0A2A7

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:

Apendix: None

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	87
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-444023.09915
FMO2-HF: Nuclear repulsion	411599.466114
FMO2-HF: Total energy	-32423.633037
FMO2-MP2: Total energy	-32519.477146

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:4:THR)

Summations of interaction energy for fragment #1(A:4: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.
-2.735	1.371	1.863	-2.282	-3.688	0

Interaction energy analysis for fragmet #1(A:4:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.002 / q_NPA : -0.021

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	6	LEU	0	-0.002	0.003	2.736	-3.658	-1.278	0.132	-1.045	-1.468	0.001
4	A	7	ILE	0	0.000	-0.009	2.256	-1.129	-0.049	1.726	-1.091	-1.715	-0.001
5	A	8	LYS	1	0.953	0.969	3.670	1.010	1.527	0.006	-0.133	-0.389	0.000
6	A	9	ASN	0	0.064	0.039	5.734	0.393	0.393	0.000	0.000	0.000	0.000
7	A	10	VAL	0	-0.026	0.005	7.242	0.168	0.168	0.000	0.000	0.000	0.000
8	A	11	ALA	0	-0.008	-0.014	7.911	0.132	0.132	0.000	0.000	0.000	0.000
9	A	12	GLN	0	-0.005	-0.002	9.548	0.111	0.111	0.000	0.000	0.000	0.000
10	A	13	ASN	0	-0.027	-0.017	11.421	0.094	0.094	0.000	0.000	0.000	0.000
11	A	14	ALA	0	-0.057	-0.034	12.549	0.043	0.043	0.000	0.000	0.000	0.000
12	A	15	GLU	-1	-0.977	-0.954	13.577	-0.178	-0.178	0.000	0.000	0.000	0.000
13	A	16	ILE	0	0.040	0.027	11.495	-0.007	-0.007	0.000	0.000	0.000	0.000
14	A	17	SER	0	0.021	0.006	12.064	-0.054	-0.054	0.000	0.000	0.000	0.000
15	A	18	GLN	0	0.035	-0.003	4.176	0.212	0.341	-0.001	-0.013	-0.116	0.000
16	A	19	LYS	1	0.968	0.990	7.794	0.177	0.177	0.000	0.000	0.000	0.000
17	A	20	GLU	-1	-0.874	-0.949	9.863	-0.486	-0.486	0.000	0.000	0.000	0.000
18	A	21	ALA	0	0.033	0.031	7.589	-0.018	-0.018	0.000	0.000	0.000	0.000
19	A	22	THR	0	-0.092	-0.058	6.495	-0.247	-0.247	0.000	0.000	0.000	0.000
20	A	23	VAL	0	0.024	0.018	7.992	0.024	0.024	0.000	0.000	0.000	0.000
21	A	24	VAL	0	0.048	0.019	11.328	0.036	0.036	0.000	0.000	0.000	0.000
22	A	25	VAL	0	-0.018	-0.016	6.781	0.048	0.048	0.000	0.000	0.000	0.000
23	A	26	GLN	0	-0.009	-0.019	9.195	0.121	0.121	0.000	0.000	0.000	0.000
24	A	27	THR	0	0.027	0.036	11.608	0.105	0.105	0.000	0.000	0.000	0.000
25	A	28	VAL	0	-0.024	-0.007	11.752	0.073	0.073	0.000	0.000	0.000	0.000
26	A	29	VAL	0	-0.019	-0.019	9.888	0.059	0.059	0.000	0.000	0.000	0.000
27	A	30	GLU	-1	-0.877	-0.918	12.909	-0.314	-0.314	0.000	0.000	0.000	0.000
28	A	31	SER	0	-0.007	-0.013	16.287	0.058	0.058	0.000	0.000	0.000	0.000
29	A	32	ILE	0	-0.028	-0.007	13.943	0.048	0.048	0.000	0.000	0.000	0.000
30	A	33	THR	0	-0.024	-0.038	15.496	0.037	0.037	0.000	0.000	0.000	0.000
31	A	34	ASN	0	-0.012	-0.013	18.106	0.035	0.035	0.000	0.000	0.000	0.000
32	A	35	THR	0	-0.044	-0.011	21.010	0.027	0.027	0.000	0.000	0.000	0.000
33	A	36	LEU	0	-0.054	-0.033	18.272	0.020	0.020	0.000	0.000	0.000	0.000
34	A	37	ALA	0	-0.048	-0.016	22.015	0.020	0.020	0.000	0.000	0.000	0.000
35	A	38	ALA	0	-0.026	-0.005	23.697	0.014	0.014	0.000	0.000	0.000	0.000
36	A	39	GLY	0	-0.042	-0.020	25.763	0.013	0.013	0.000	0.000	0.000	0.000
37	A	40	GLU	-1	-0.937	-0.952	25.842	-0.114	-0.114	0.000	0.000	0.000	0.000
38	A	41	LYS	1	0.868	0.917	23.636	0.092	0.092	0.000	0.000	0.000	0.000
39	A	42	VAL	0	0.044	0.037	18.089	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	43	GLN	0	-0.032	-0.033	20.775	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	44	LEU	0	0.015	0.013	16.184	-0.004	-0.004	0.000	0.000	0.000	0.000
42	A	45	ILE	0	0.019	-0.004	20.207	0.013	0.013	0.000	0.000	0.000	0.000
43	A	46	GLY	0	0.036	0.027	20.730	-0.007	-0.007	0.000	0.000	0.000	0.000
44	A	47	PHE	0	0.023	0.022	12.978	0.003	0.003	0.000	0.000	0.000	0.000
45	A	48	GLY	0	-0.001	-0.008	18.575	0.023	0.023	0.000	0.000	0.000	0.000
46	A	49	THR	0	-0.053	-0.017	19.563	-0.017	-0.017	0.000	0.000	0.000	0.000
47	A	50	PHE	0	0.012	0.019	14.500	0.012	0.012	0.000	0.000	0.000	0.000
48	A	51	GLU	-1	-0.825	-0.927	20.172	-0.090	-0.090	0.000	0.000	0.000	0.000
49	A	52	VAL	0	0.047	0.027	22.599	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	53	ARG	1	0.884	0.954	24.173	0.094	0.094	0.000	0.000	0.000	0.000
51	A	54	GLU	-1	-0.871	-0.926	26.998	-0.097	-0.097	0.000	0.000	0.000	0.000
52	A	55	ARG	1	0.873	0.926	30.023	0.065	0.065	0.000	0.000	0.000	0.000
53	A	56	ALA	0	0.078	0.045	32.696	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	57	ALA	0	0.003	0.003	36.014	0.002	0.002	0.000	0.000	0.000	0.000
55	A	58	ARG	1	0.956	0.971	35.057	0.047	0.047	0.000	0.000	0.000	0.000
56	A	59	THR	0	0.015	0.016	39.900	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	60	GLY	0	-0.046	-0.030	41.211	0.001	0.001	0.000	0.000	0.000	0.000
58	A	61	ARG	1	0.944	0.954	41.837	0.021	0.021	0.000	0.000	0.000	0.000
59	A	62	ASN	0	0.045	0.031	41.775	0.002	0.002	0.000	0.000	0.000	0.000
60	A	63	PRO	0	-0.028	-0.025	38.955	0.002	0.002	0.000	0.000	0.000	0.000
61	A	64	GLN	0	-0.027	-0.005	40.019	0.004	0.004	0.000	0.000	0.000	0.000
62	A	65	THR	0	0.066	0.028	44.166	0.001	0.001	0.000	0.000	0.000	0.000
63	A	66	GLY	0	-0.040	0.002	46.271	0.001	0.001	0.000	0.000	0.000	0.000
64	A	67	GLU	-1	-0.943	-0.988	46.110	-0.024	-0.024	0.000	0.000	0.000	0.000
65	A	68	GLU	-1	-0.935	-0.963	45.662	-0.028	-0.028	0.000	0.000	0.000	0.000
66	A	69	MET	0	-0.001	0.004	38.554	0.000	0.000	0.000	0.000	0.000	0.000
67	A	70	GLN	0	0.012	0.016	40.115	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	71	ILE	0	-0.042	-0.013	35.439	0.000	0.000	0.000	0.000	0.000	0.000
69	A	72	ALA	0	0.039	0.012	33.754	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	73	ALA	0	-0.007	-0.006	33.733	0.001	0.001	0.000	0.000	0.000	0.000
71	A	74	SER	0	-0.055	-0.035	28.745	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	75	LYS	1	1.005	0.992	26.401	0.120	0.120	0.000	0.000	0.000	0.000
73	A	76	VAL	0	-0.017	-0.003	22.883	-0.007	-0.007	0.000	0.000	0.000	0.000
74	A	77	PRO	0	0.061	0.039	19.033	0.007	0.007	0.000	0.000	0.000	0.000
75	A	78	ALA	0	-0.042	-0.025	20.566	0.012	0.012	0.000	0.000	0.000	0.000
76	A	79	PHE	0	0.071	0.031	16.737	-0.012	-0.012	0.000	0.000	0.000	0.000
77	A	80	LYS	1	0.771	0.880	19.328	0.104	0.104	0.000	0.000	0.000	0.000
78	A	81	ALA	0	0.035	0.022	18.879	-0.008	-0.008	0.000	0.000	0.000	0.000
79	A	82	GLY	0	0.014	-0.008	20.283	0.006	0.006	0.000	0.000	0.000	0.000
80	A	83	LYS	1	0.913	0.934	22.074	0.001	0.001	0.000	0.000	0.000	0.000
81	A	84	GLU	-1	-0.834	-0.916	21.217	-0.027	-0.027	0.000	0.000	0.000	0.000
82	A	85	LEU	0	0.016	0.016	15.321	0.012	0.012	0.000	0.000	0.000	0.000
83	A	86	LYS	1	0.885	0.919	19.207	0.034	0.034	0.000	0.000	0.000	0.000
84	A	87	GLU	-1	-0.975	-0.987	21.668	0.052	0.052	0.000	0.000	0.000	0.000
85	A	88	ALA	0	0.019	0.022	18.518	0.009	0.009	0.000	0.000	0.000	0.000
86	A	89	VAL	0	-0.047	-0.012	16.983	0.020	0.020	0.000	0.000	0.000	0.000
87	A	90	LYS	1	0.944	0.991	19.441	-0.027	-0.027	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:THR)