FMO DATABASE

FMODB ID: JL5Z9

Calculation Name: 3RHE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3RHE

Chain ID: A

ChEMBL ID:

UniProt ID: Q5ZTJ2

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	118
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1000619.618905
FMO2-HF: Nuclear repulsion	952299.717551
FMO2-HF: Total energy	-48319.901354
FMO2-MP2: Total energy	-48458.950803

3D Structure Molmil

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:PRO)

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

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.
-6.495	0.116	1.716	-3.692	-4.634	-0.017

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.070 / q_NPA : 0.020

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	7	LEU	0	-0.023	0.004	3.648	-1.507	0.391	-0.002	-1.031	-0.866	0.001
4	A	8	VAL	0	0.020	0.037	6.391	0.096	0.096	0.000	0.000	0.000	0.000
5	A	9	LEU	0	0.006	0.010	9.972	0.110	0.110	0.000	0.000	0.000	0.000
6	A	10	PHE	0	0.006	-0.006	12.403	0.015	0.015	0.000	0.000	0.000	0.000
7	A	11	TYR	0	0.009	-0.014	16.035	0.038	0.038	0.000	0.000	0.000	0.000
8	A	12	VAL	0	-0.024	-0.017	18.962	0.012	0.012	0.000	0.000	0.000	0.000
9	A	13	LYS	1	0.975	0.981	21.483	0.087	0.087	0.000	0.000	0.000	0.000
10	A	14	ASN	0	-0.007	-0.014	23.689	0.015	0.015	0.000	0.000	0.000	0.000
11	A	15	PRO	0	0.081	0.060	19.637	0.002	0.002	0.000	0.000	0.000	0.000
12	A	16	ALA	0	0.038	0.032	21.062	0.006	0.006	0.000	0.000	0.000	0.000
13	A	17	LYS	1	0.963	0.969	23.436	0.024	0.024	0.000	0.000	0.000	0.000
14	A	18	SER	0	-0.004	-0.002	20.277	-0.001	-0.001	0.000	0.000	0.000	0.000
15	A	19	GLH	0	-0.030	-0.049	18.609	0.000	0.000	0.000	0.000	0.000	0.000
16	A	20	GLU	-1	-0.845	-0.892	20.170	0.043	0.043	0.000	0.000	0.000	0.000
17	A	21	PHE	0	-0.051	-0.016	21.278	0.003	0.003	0.000	0.000	0.000	0.000
18	A	22	TYR	0	0.044	0.002	17.507	-0.009	-0.009	0.000	0.000	0.000	0.000
19	A	23	LYS	1	0.868	0.947	19.370	-0.049	-0.049	0.000	0.000	0.000	0.000
20	A	24	ASN	0	-0.062	-0.032	20.670	0.013	0.013	0.000	0.000	0.000	0.000
21	A	25	LEU	0	-0.057	-0.023	19.128	0.001	0.001	0.000	0.000	0.000	0.000
22	A	26	LEU	0	-0.054	-0.041	15.190	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	27	ASP	-1	-0.910	-0.941	19.094	0.066	0.066	0.000	0.000	0.000	0.000
24	A	28	THR	0	-0.031	-0.002	15.782	0.020	0.020	0.000	0.000	0.000	0.000
25	A	29	GLN	0	0.036	0.003	18.569	-0.023	-0.023	0.000	0.000	0.000	0.000
26	A	30	PRO	0	-0.047	-0.012	14.879	0.021	0.021	0.000	0.000	0.000	0.000
27	A	31	ILE	0	-0.034	-0.028	9.513	0.030	0.030	0.000	0.000	0.000	0.000
28	A	32	GLU	-1	-0.859	-0.931	13.731	0.124	0.124	0.000	0.000	0.000	0.000
29	A	33	SER	0	-0.020	-0.014	15.449	-0.034	-0.034	0.000	0.000	0.000	0.000
30	A	34	SER	0	-0.014	-0.005	17.839	0.002	0.002	0.000	0.000	0.000	0.000
31	A	35	PRO	0	-0.041	-0.040	20.498	-0.012	-0.012	0.000	0.000	0.000	0.000
32	A	36	THR	0	-0.037	-0.034	18.448	-0.014	-0.014	0.000	0.000	0.000	0.000
33	A	37	PHE	0	0.010	-0.006	11.091	-0.043	-0.043	0.000	0.000	0.000	0.000
34	A	38	ALA	0	0.063	0.029	15.764	0.027	0.027	0.000	0.000	0.000	0.000
35	A	39	MET	0	-0.030	0.004	9.055	-0.032	-0.032	0.000	0.000	0.000	0.000
36	A	40	PHE	0	0.031	0.009	12.164	0.077	0.077	0.000	0.000	0.000	0.000
37	A	41	VAL	0	-0.006	-0.016	7.805	-0.033	-0.033	0.000	0.000	0.000	0.000
38	A	42	MET	0	0.005	0.023	10.084	0.031	0.031	0.000	0.000	0.000	0.000
39	A	43	LYS	1	0.985	0.982	10.812	-0.117	-0.117	0.000	0.000	0.000	0.000
40	A	44	THR	0	-0.023	-0.024	11.510	0.051	0.051	0.000	0.000	0.000	0.000
41	A	45	GLY	0	0.003	0.010	7.760	-0.032	-0.032	0.000	0.000	0.000	0.000
42	A	46	LEU	0	-0.012	0.002	6.143	-0.028	-0.028	0.000	0.000	0.000	0.000
43	A	47	ARG	1	0.848	0.904	3.390	0.285	1.212	0.049	-0.350	-0.627	0.000
44	A	48	LEU	0	-0.007	-0.004	7.330	-0.223	-0.223	0.000	0.000	0.000	0.000
45	A	49	GLY	0	0.014	0.014	10.543	0.112	0.112	0.000	0.000	0.000	0.000
46	A	50	LEU	0	-0.052	-0.027	12.149	-0.043	-0.043	0.000	0.000	0.000	0.000
47	A	51	TRP	0	0.012	0.006	14.527	0.019	0.019	0.000	0.000	0.000	0.000
48	A	52	ALA	0	0.044	0.009	17.147	-0.011	-0.011	0.000	0.000	0.000	0.000
49	A	53	GLN	0	-0.037	-0.018	20.551	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	54	GLU	-1	-0.909	-0.964	22.299	-0.082	-0.082	0.000	0.000	0.000	0.000
51	A	55	GLU	-1	-0.879	-0.908	19.705	-0.050	-0.050	0.000	0.000	0.000	0.000
52	A	56	ILE	0	-0.093	-0.016	17.277	-0.012	-0.012	0.000	0.000	0.000	0.000
53	A	57	GLU	-1	-0.801	-0.906	18.344	-0.111	-0.111	0.000	0.000	0.000	0.000
54	A	58	PRO	0	0.034	0.016	17.860	-0.029	-0.029	0.000	0.000	0.000	0.000
55	A	59	LYS	1	0.838	0.932	20.753	0.093	0.093	0.000	0.000	0.000	0.000
56	A	60	ALA	0	0.021	0.026	21.112	-0.012	-0.012	0.000	0.000	0.000	0.000
57	A	61	HIS	0	0.010	0.012	22.511	0.028	0.028	0.000	0.000	0.000	0.000
58	A	62	GLN	0	-0.032	-0.032	24.721	0.012	0.012	0.000	0.000	0.000	0.000
59	A	63	THR	0	-0.033	-0.027	24.249	-0.008	-0.008	0.000	0.000	0.000	0.000
60	A	64	GLY	0	0.085	0.061	21.475	0.003	0.003	0.000	0.000	0.000	0.000
61	A	65	GLY	0	0.057	0.034	19.951	-0.028	-0.028	0.000	0.000	0.000	0.000
62	A	66	GLY	0	-0.071	-0.048	20.597	0.013	0.013	0.000	0.000	0.000	0.000
63	A	67	MET	0	-0.054	-0.027	13.801	0.011	0.011	0.000	0.000	0.000	0.000
64	A	68	GLU	-1	-0.702	-0.800	12.529	-0.437	-0.437	0.000	0.000	0.000	0.000
65	A	69	LEU	0	-0.042	-0.011	7.731	-0.030	-0.030	0.000	0.000	0.000	0.000
66	A	70	SER	0	-0.025	-0.020	8.148	0.056	0.056	0.000	0.000	0.000	0.000
67	A	71	PHE	0	-0.008	-0.023	3.956	-0.879	-0.680	0.000	-0.055	-0.144	0.000
68	A	72	GLN	0	0.029	0.040	2.453	0.107	1.164	0.563	-0.645	-0.974	0.001
69	A	73	VAL	0	-0.032	-0.032	2.559	-3.868	-1.354	1.107	-1.608	-2.012	-0.019
70	A	74	ASN	0	-0.021	-0.022	4.977	0.276	0.292	-0.001	-0.003	-0.011	0.000
71	A	75	SER	0	-0.016	-0.045	7.746	0.080	0.080	0.000	0.000	0.000	0.000
72	A	76	ASN	0	0.033	0.004	10.381	-0.102	-0.102	0.000	0.000	0.000	0.000
73	A	77	GLU	-1	-0.781	-0.880	12.917	-0.080	-0.080	0.000	0.000	0.000	0.000
74	A	78	MET	0	-0.034	-0.002	7.579	-0.041	-0.041	0.000	0.000	0.000	0.000
75	A	79	VAL	0	-0.024	-0.008	9.366	-0.099	-0.099	0.000	0.000	0.000	0.000
76	A	80	ASP	-1	-0.798	-0.881	10.924	-0.193	-0.193	0.000	0.000	0.000	0.000
77	A	81	GLU	-1	-0.807	-0.873	12.442	-0.235	-0.235	0.000	0.000	0.000	0.000
78	A	82	ILE	0	-0.036	-0.022	7.511	-0.019	-0.019	0.000	0.000	0.000	0.000
79	A	83	HIS	0	0.030	0.018	11.792	0.011	0.011	0.000	0.000	0.000	0.000
80	A	84	ARG	1	0.873	0.926	14.653	0.195	0.195	0.000	0.000	0.000	0.000
81	A	85	GLN	0	-0.018	-0.024	13.254	-0.021	-0.021	0.000	0.000	0.000	0.000
82	A	86	TRP	0	-0.017	-0.023	9.858	0.002	0.002	0.000	0.000	0.000	0.000
83	A	87	SER	0	-0.006	-0.010	15.861	0.023	0.023	0.000	0.000	0.000	0.000
84	A	88	ASP	-1	-0.963	-0.988	18.872	-0.181	-0.181	0.000	0.000	0.000	0.000
85	A	89	LYS	1	0.776	0.889	14.124	0.356	0.356	0.000	0.000	0.000	0.000
86	A	90	GLU	-1	-0.953	-0.970	19.501	-0.164	-0.164	0.000	0.000	0.000	0.000
87	A	91	ILE	0	-0.039	-0.005	14.881	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	92	SER	0	0.020	0.009	18.759	0.011	0.011	0.000	0.000	0.000	0.000
89	A	93	ILE	0	-0.017	-0.014	16.628	-0.036	-0.036	0.000	0.000	0.000	0.000
90	A	94	ILE	0	-0.029	-0.014	18.257	0.029	0.029	0.000	0.000	0.000	0.000
91	A	95	GLN	0	0.015	-0.007	16.953	-0.005	-0.005	0.000	0.000	0.000	0.000
92	A	96	PRO	0	0.038	0.026	17.270	-0.035	-0.035	0.000	0.000	0.000	0.000
93	A	97	PRO	0	0.021	0.013	15.492	-0.006	-0.006	0.000	0.000	0.000	0.000
94	A	98	THR	0	-0.047	-0.022	16.346	0.041	0.041	0.000	0.000	0.000	0.000
95	A	99	GLN	0	-0.021	-0.012	16.432	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	100	MET	0	0.003	0.017	15.822	0.005	0.005	0.000	0.000	0.000	0.000
97	A	101	ASP	-1	-0.856	-0.926	17.020	-0.023	-0.023	0.000	0.000	0.000	0.000
98	A	102	PHE	0	0.025	0.009	11.553	0.031	0.031	0.000	0.000	0.000	0.000
99	A	103	GLY	0	-0.033	-0.037	12.468	0.053	0.053	0.000	0.000	0.000	0.000
100	A	104	TYR	0	-0.096	-0.061	12.321	0.014	0.014	0.000	0.000	0.000	0.000
101	A	105	THR	0	-0.031	-0.037	11.724	-0.053	-0.053	0.000	0.000	0.000	0.000
102	A	106	PHE	0	0.052	0.045	11.555	0.056	0.056	0.000	0.000	0.000	0.000
103	A	107	VAL	0	-0.001	-0.009	12.582	-0.094	-0.094	0.000	0.000	0.000	0.000
104	A	108	GLY	0	0.044	0.021	14.347	0.063	0.063	0.000	0.000	0.000	0.000
105	A	109	VAL	0	-0.053	-0.014	15.768	-0.036	-0.036	0.000	0.000	0.000	0.000
106	A	110	ASP	-1	-0.804	-0.887	16.114	-0.315	-0.315	0.000	0.000	0.000	0.000
107	A	111	PRO	0	-0.042	-0.043	17.857	0.018	0.018	0.000	0.000	0.000	0.000
108	A	112	ASP	-1	-0.948	-0.961	20.474	-0.183	-0.183	0.000	0.000	0.000	0.000
109	A	113	GLU	-1	-0.964	-0.986	20.484	-0.212	-0.212	0.000	0.000	0.000	0.000
110	A	114	HIS	0	-0.088	-0.046	16.104	0.005	0.005	0.000	0.000	0.000	0.000
111	A	115	ARG	1	0.839	0.899	15.499	0.232	0.232	0.000	0.000	0.000	0.000
112	A	116	LEU	0	-0.021	-0.011	11.256	-0.082	-0.082	0.000	0.000	0.000	0.000
113	A	117	ARG	1	0.780	0.840	10.435	0.456	0.456	0.000	0.000	0.000	0.000
114	A	118	ILE	0	0.023	0.024	7.333	-0.311	-0.311	0.000	0.000	0.000	0.000
115	A	119	PHE	0	-0.005	-0.013	6.323	0.239	0.239	0.000	0.000	0.000	0.000
116	A	120	CYS	0	-0.011	0.025	7.048	-0.104	-0.104	0.000	0.000	0.000	0.000
117	A	121	LEU	0	0.001	0.005	8.139	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	122	LYS	1	0.815	0.927	10.483	0.055	0.055	0.000	0.000	0.000	0.000

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