FMO DATABASE

FMODB ID: 4JGNN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-444334.837423
FMO2-HF: Nuclear repulsion	411910.521301
FMO2-HF: Total energy	-32424.316122
FMO2-MP2: Total energy	-32520.121288

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.
-6.706	-2.107	1.147	-2.105	-3.643	0.006

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 : 0.007 / q_NPA : -0.019

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	0.009	0.017	3.162	-4.429	-1.857	0.120	-1.208	-1.485	0.007
4	A	7	ILE	0	0.001	-0.010	2.495	-3.662	-2.224	1.022	-0.735	-1.725	-0.001
5	A	8	LYS	1	0.955	0.971	3.675	1.439	1.950	0.006	-0.155	-0.363	0.000
6	A	9	ASN	0	0.018	0.011	5.752	-0.048	-0.048	0.000	0.000	0.000	0.000
7	A	10	VAL	0	-0.011	0.008	7.257	-0.111	-0.111	0.000	0.000	0.000	0.000
8	A	11	ALA	0	-0.016	-0.012	7.924	-0.080	-0.080	0.000	0.000	0.000	0.000
9	A	12	GLN	0	-0.012	-0.006	9.563	0.093	0.093	0.000	0.000	0.000	0.000
10	A	13	ASN	0	-0.036	-0.020	11.430	-0.055	-0.055	0.000	0.000	0.000	0.000
11	A	14	ALA	0	-0.046	-0.029	12.563	-0.001	-0.001	0.000	0.000	0.000	0.000
12	A	15	GLU	-1	-0.975	-0.955	13.596	-0.168	-0.168	0.000	0.000	0.000	0.000
13	A	16	ILE	0	0.030	0.022	11.404	-0.015	-0.015	0.000	0.000	0.000	0.000
14	A	17	SER	0	0.014	0.002	12.074	-0.103	-0.103	0.000	0.000	0.000	0.000
15	A	18	GLN	0	0.040	-0.002	4.314	0.187	0.265	-0.001	-0.007	-0.070	0.000
16	A	19	LYS	1	0.973	0.996	7.755	0.532	0.532	0.000	0.000	0.000	0.000
17	A	20	GLU	-1	-0.866	-0.935	9.702	-0.094	-0.094	0.000	0.000	0.000	0.000
18	A	21	ALA	0	0.023	0.021	7.651	0.092	0.092	0.000	0.000	0.000	0.000
19	A	22	THR	0	-0.081	-0.061	6.421	0.078	0.078	0.000	0.000	0.000	0.000
20	A	23	VAL	0	0.038	0.025	7.987	0.175	0.175	0.000	0.000	0.000	0.000
21	A	24	VAL	0	0.034	0.014	11.307	0.091	0.091	0.000	0.000	0.000	0.000
22	A	25	VAL	0	-0.019	-0.016	7.014	0.131	0.131	0.000	0.000	0.000	0.000
23	A	26	GLN	0	-0.017	-0.022	9.527	0.053	0.053	0.000	0.000	0.000	0.000
24	A	27	THR	0	0.026	0.030	11.643	-0.004	-0.004	0.000	0.000	0.000	0.000
25	A	28	VAL	0	-0.022	-0.007	12.260	0.002	0.002	0.000	0.000	0.000	0.000
26	A	29	VAL	0	-0.022	-0.023	10.017	0.011	0.011	0.000	0.000	0.000	0.000
27	A	30	GLU	-1	-0.859	-0.911	13.254	0.077	0.077	0.000	0.000	0.000	0.000
28	A	31	SER	0	-0.006	-0.002	16.485	-0.026	-0.026	0.000	0.000	0.000	0.000
29	A	32	ILE	0	-0.021	-0.006	14.663	-0.022	-0.022	0.000	0.000	0.000	0.000
30	A	33	THR	0	-0.020	-0.033	15.711	-0.012	-0.012	0.000	0.000	0.000	0.000
31	A	34	ASN	0	-0.036	-0.027	18.329	-0.028	-0.028	0.000	0.000	0.000	0.000
32	A	35	THR	0	-0.047	-0.015	21.386	-0.022	-0.022	0.000	0.000	0.000	0.000
33	A	36	LEU	0	-0.036	-0.024	18.513	-0.009	-0.009	0.000	0.000	0.000	0.000
34	A	37	ALA	0	-0.050	-0.018	22.234	-0.016	-0.016	0.000	0.000	0.000	0.000
35	A	38	ALA	0	-0.029	-0.005	23.832	-0.019	-0.019	0.000	0.000	0.000	0.000
36	A	39	GLY	0	-0.054	-0.028	26.031	-0.010	-0.010	0.000	0.000	0.000	0.000
37	A	40	GLU	-1	-0.920	-0.943	26.270	0.163	0.163	0.000	0.000	0.000	0.000
38	A	41	LYS	1	0.816	0.884	24.244	-0.209	-0.209	0.000	0.000	0.000	0.000
39	A	42	VAL	0	0.051	0.040	18.918	-0.006	-0.006	0.000	0.000	0.000	0.000
40	A	43	GLN	0	-0.025	-0.029	21.576	0.039	0.039	0.000	0.000	0.000	0.000
41	A	44	LEU	0	0.015	0.008	17.075	-0.007	-0.007	0.000	0.000	0.000	0.000
42	A	45	ILE	0	0.007	-0.011	21.189	0.020	0.020	0.000	0.000	0.000	0.000
43	A	46	GLY	0	0.032	0.025	21.664	0.021	0.021	0.000	0.000	0.000	0.000
44	A	47	PHE	0	0.037	0.026	13.958	0.040	0.040	0.000	0.000	0.000	0.000
45	A	48	GLY	0	0.001	-0.004	19.460	-0.009	-0.009	0.000	0.000	0.000	0.000
46	A	49	THR	0	-0.041	-0.011	20.505	-0.007	-0.007	0.000	0.000	0.000	0.000
47	A	50	PHE	0	0.016	0.020	15.048	0.004	0.004	0.000	0.000	0.000	0.000
48	A	51	GLU	-1	-0.734	-0.852	20.812	0.218	0.218	0.000	0.000	0.000	0.000
49	A	52	VAL	0	0.064	0.037	22.990	0.016	0.016	0.000	0.000	0.000	0.000
50	A	53	ARG	1	0.822	0.909	25.181	-0.257	-0.257	0.000	0.000	0.000	0.000
51	A	54	GLU	-1	-0.751	-0.846	27.283	0.128	0.128	0.000	0.000	0.000	0.000
52	A	55	ARG	1	0.879	0.930	30.222	-0.143	-0.143	0.000	0.000	0.000	0.000
53	A	56	ALA	0	0.077	0.042	32.818	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	57	ALA	0	0.018	0.004	36.085	0.002	0.002	0.000	0.000	0.000	0.000
55	A	58	ARG	1	0.918	0.960	35.020	-0.096	-0.096	0.000	0.000	0.000	0.000
56	A	59	THR	0	0.050	0.038	39.857	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	60	GLY	0	-0.056	-0.024	41.139	0.002	0.002	0.000	0.000	0.000	0.000
58	A	61	ARG	1	0.920	0.943	41.789	-0.056	-0.056	0.000	0.000	0.000	0.000
59	A	62	ASN	0	0.034	0.023	41.765	0.005	0.005	0.000	0.000	0.000	0.000
60	A	63	PRO	0	-0.030	-0.024	38.960	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	64	GLN	0	-0.023	0.001	40.022	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	65	THR	0	0.054	0.018	44.213	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	66	GLY	0	-0.031	0.010	46.289	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	67	GLU	-1	-0.873	-0.956	46.441	0.038	0.038	0.000	0.000	0.000	0.000
65	A	68	GLU	-1	-0.953	-0.976	45.634	0.051	0.051	0.000	0.000	0.000	0.000
66	A	69	MET	0	-0.009	-0.005	37.887	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	70	GLN	0	-0.011	-0.002	40.009	0.005	0.005	0.000	0.000	0.000	0.000
68	A	71	ILE	0	-0.042	-0.016	35.359	0.002	0.002	0.000	0.000	0.000	0.000
69	A	72	ALA	0	0.042	0.015	33.620	0.000	0.000	0.000	0.000	0.000	0.000
70	A	73	ALA	0	-0.017	-0.013	33.790	0.006	0.006	0.000	0.000	0.000	0.000
71	A	74	SER	0	-0.044	-0.029	28.584	0.001	0.001	0.000	0.000	0.000	0.000
72	A	75	LYS	1	0.892	0.919	26.651	-0.129	-0.129	0.000	0.000	0.000	0.000
73	A	76	VAL	0	-0.017	-0.007	23.053	0.001	0.001	0.000	0.000	0.000	0.000
74	A	77	PRO	0	0.046	0.033	19.288	0.005	0.005	0.000	0.000	0.000	0.000
75	A	78	ALA	0	-0.032	-0.016	20.818	0.013	0.013	0.000	0.000	0.000	0.000
76	A	79	PHE	0	0.058	0.024	17.480	0.011	0.011	0.000	0.000	0.000	0.000
77	A	80	LYS	1	0.767	0.869	19.930	-0.279	-0.279	0.000	0.000	0.000	0.000
78	A	81	ALA	0	0.058	0.037	19.644	0.004	0.004	0.000	0.000	0.000	0.000
79	A	82	GLY	0	0.039	0.004	21.069	-0.053	-0.053	0.000	0.000	0.000	0.000
80	A	83	LYS	1	0.849	0.898	22.826	-0.268	-0.268	0.000	0.000	0.000	0.000
81	A	84	GLU	-1	-0.835	-0.920	21.905	0.351	0.351	0.000	0.000	0.000	0.000
82	A	85	LEU	0	0.010	0.011	16.009	0.013	0.013	0.000	0.000	0.000	0.000
83	A	86	LYS	1	0.849	0.905	19.868	-0.338	-0.338	0.000	0.000	0.000	0.000
84	A	87	GLU	-1	-0.801	-0.875	22.250	0.281	0.281	0.000	0.000	0.000	0.000
85	A	88	ALA	0	0.012	0.019	18.963	-0.015	-0.015	0.000	0.000	0.000	0.000
86	A	89	VAL	0	-0.049	-0.012	17.090	0.012	0.012	0.000	0.000	0.000	0.000
87	A	90	LYS	1	0.829	0.912	19.636	-0.300	-0.300	0.000	0.000	0.000	0.000

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