FMO DATABASE

FMODB ID: N9YMQ

Calculation Name: 3RHE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

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:

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	118
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1000113.055952
FMO2-HF: Nuclear repulsion	951793.369439
FMO2-HF: Total energy	-48319.686512
FMO2-MP2: Total energy	-48458.759097

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: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.
-6.305	-0.084	3.078	-3.781	-5.521	-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 : 0.077 / q_NPA : 0.029

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	-0.021	0.004	3.760	-1.595	0.547	-0.021	-1.006	-1.115	0.003
4	A	8	VAL	0	0.014	0.034	6.357	0.038	0.038	0.000	0.000	0.000	0.000
5	A	9	LEU	0	0.018	0.019	9.878	0.107	0.107	0.000	0.000	0.000	0.000
6	A	10	PHE	0	0.000	-0.009	12.419	0.014	0.014	0.000	0.000	0.000	0.000
7	A	11	TYR	0	0.000	-0.028	16.004	0.033	0.033	0.000	0.000	0.000	0.000
8	A	12	VAL	0	-0.023	-0.012	18.690	0.016	0.016	0.000	0.000	0.000	0.000
9	A	13	LYS	1	0.985	0.984	21.146	0.073	0.073	0.000	0.000	0.000	0.000
10	A	14	ASN	0	0.008	-0.001	24.024	0.011	0.011	0.000	0.000	0.000	0.000
11	A	15	PRO	0	0.099	0.058	19.434	0.004	0.004	0.000	0.000	0.000	0.000
12	A	16	ALA	0	0.020	0.021	21.254	0.010	0.010	0.000	0.000	0.000	0.000
13	A	17	LYS	1	0.968	0.964	23.732	0.023	0.023	0.000	0.000	0.000	0.000
14	A	18	SER	0	-0.018	-0.008	20.252	0.000	0.000	0.000	0.000	0.000	0.000
15	A	19	GLH	0	-0.027	-0.047	18.819	0.006	0.006	0.000	0.000	0.000	0.000
16	A	20	GLU	-1	-0.846	-0.888	20.294	0.051	0.051	0.000	0.000	0.000	0.000
17	A	21	PHE	0	-0.057	-0.019	21.059	0.005	0.005	0.000	0.000	0.000	0.000
18	A	22	TYR	0	0.058	0.007	17.458	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	23	LYS	1	0.892	0.971	19.372	-0.060	-0.060	0.000	0.000	0.000	0.000
20	A	24	ASN	0	-0.068	-0.040	20.442	0.013	0.013	0.000	0.000	0.000	0.000
21	A	25	LEU	0	-0.054	-0.018	18.998	0.002	0.002	0.000	0.000	0.000	0.000
22	A	26	LEU	0	-0.052	-0.044	15.104	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	27	ASP	-1	-0.901	-0.936	19.062	0.080	0.080	0.000	0.000	0.000	0.000
24	A	28	THR	0	-0.069	-0.027	15.412	0.022	0.022	0.000	0.000	0.000	0.000
25	A	29	GLN	0	0.035	0.008	18.287	-0.024	-0.024	0.000	0.000	0.000	0.000
26	A	30	PRO	0	-0.034	-0.002	15.097	0.024	0.024	0.000	0.000	0.000	0.000
27	A	31	ILE	0	-0.037	-0.031	9.781	0.022	0.022	0.000	0.000	0.000	0.000
28	A	32	GLU	-1	-0.895	-0.958	13.371	0.099	0.099	0.000	0.000	0.000	0.000
29	A	33	SER	0	-0.015	-0.006	15.376	-0.029	-0.029	0.000	0.000	0.000	0.000
30	A	34	SER	0	0.016	0.014	17.562	0.002	0.002	0.000	0.000	0.000	0.000
31	A	35	PRO	0	-0.037	-0.036	20.036	-0.009	-0.009	0.000	0.000	0.000	0.000
32	A	36	THR	0	-0.028	-0.044	18.425	-0.011	-0.011	0.000	0.000	0.000	0.000
33	A	37	PHE	0	0.009	0.002	10.703	-0.040	-0.040	0.000	0.000	0.000	0.000
34	A	38	ALA	0	0.033	0.022	15.741	0.031	0.031	0.000	0.000	0.000	0.000
35	A	39	MET	0	0.003	0.012	8.914	-0.026	-0.026	0.000	0.000	0.000	0.000
36	A	40	PHE	0	0.000	-0.008	11.918	0.068	0.068	0.000	0.000	0.000	0.000
37	A	41	VAL	0	0.009	-0.002	7.726	-0.033	-0.033	0.000	0.000	0.000	0.000
38	A	42	MET	0	-0.013	0.007	9.785	0.014	0.014	0.000	0.000	0.000	0.000
39	A	43	LYS	1	1.001	0.996	10.339	-0.160	-0.160	0.000	0.000	0.000	0.000
40	A	44	THR	0	-0.041	-0.039	11.481	0.056	0.056	0.000	0.000	0.000	0.000
41	A	45	GLY	0	0.025	0.014	7.637	0.012	0.012	0.000	0.000	0.000	0.000
42	A	46	LEU	0	-0.032	0.001	6.004	0.001	0.001	0.000	0.000	0.000	0.000
43	A	47	ARG	1	0.857	0.910	3.072	0.082	1.158	0.306	-0.442	-0.940	-0.002
44	A	48	LEU	0	-0.001	0.000	7.244	-0.203	-0.203	0.000	0.000	0.000	0.000
45	A	49	GLY	0	0.023	0.015	10.497	0.094	0.094	0.000	0.000	0.000	0.000
46	A	50	LEU	0	-0.064	-0.028	12.107	-0.034	-0.034	0.000	0.000	0.000	0.000
47	A	51	TRP	0	0.037	0.010	14.278	0.010	0.010	0.000	0.000	0.000	0.000
48	A	52	ALA	0	0.039	0.010	16.734	-0.007	-0.007	0.000	0.000	0.000	0.000
49	A	53	GLN	0	-0.029	-0.004	20.201	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	54	GLU	-1	-0.942	-0.981	21.792	-0.084	-0.084	0.000	0.000	0.000	0.000
51	A	55	GLU	-1	-0.896	-0.924	19.359	-0.066	-0.066	0.000	0.000	0.000	0.000
52	A	56	ILE	0	-0.111	-0.025	16.973	-0.015	-0.015	0.000	0.000	0.000	0.000
53	A	57	GLU	-1	-0.828	-0.901	18.381	-0.123	-0.123	0.000	0.000	0.000	0.000
54	A	58	PRO	0	0.055	0.013	17.791	-0.031	-0.031	0.000	0.000	0.000	0.000
55	A	59	LYS	1	0.886	0.954	20.676	0.109	0.109	0.000	0.000	0.000	0.000
56	A	60	ALA	0	0.019	0.025	20.891	-0.009	-0.009	0.000	0.000	0.000	0.000
57	A	61	HIS	0	0.027	0.029	22.607	0.026	0.026	0.000	0.000	0.000	0.000
58	A	62	GLN	0	-0.022	-0.037	24.528	0.012	0.012	0.000	0.000	0.000	0.000
59	A	63	THR	0	-0.035	-0.029	23.972	-0.008	-0.008	0.000	0.000	0.000	0.000
60	A	64	GLY	0	0.063	0.054	21.661	0.001	0.001	0.000	0.000	0.000	0.000
61	A	65	GLY	0	0.059	0.029	19.884	-0.025	-0.025	0.000	0.000	0.000	0.000
62	A	66	GLY	0	-0.068	-0.039	20.418	0.008	0.008	0.000	0.000	0.000	0.000
63	A	67	MET	0	-0.050	-0.024	13.604	0.008	0.008	0.000	0.000	0.000	0.000
64	A	68	GLU	-1	-0.707	-0.797	12.485	-0.424	-0.424	0.000	0.000	0.000	0.000
65	A	69	LEU	0	-0.031	-0.003	7.838	-0.019	-0.019	0.000	0.000	0.000	0.000
66	A	70	SER	0	-0.028	-0.025	7.714	0.039	0.039	0.000	0.000	0.000	0.000
67	A	71	PHE	0	-0.005	-0.018	3.690	-0.709	-0.528	0.002	-0.058	-0.126	0.000
68	A	72	GLN	0	0.022	0.033	2.392	-0.310	1.039	0.851	-0.904	-1.297	-0.001
69	A	73	VAL	0	-0.023	-0.029	2.430	-3.091	-1.630	1.941	-1.368	-2.035	-0.017
70	A	74	ASN	0	-0.018	-0.023	4.896	0.246	0.258	-0.001	-0.003	-0.008	0.000
71	A	75	SER	0	-0.012	-0.046	7.301	0.100	0.100	0.000	0.000	0.000	0.000
72	A	76	ASN	0	0.071	0.014	10.415	-0.104	-0.104	0.000	0.000	0.000	0.000
73	A	77	GLU	-1	-0.795	-0.878	13.001	-0.145	-0.145	0.000	0.000	0.000	0.000
74	A	78	MET	0	-0.040	-0.005	7.799	-0.031	-0.031	0.000	0.000	0.000	0.000
75	A	79	VAL	0	-0.024	-0.015	9.593	-0.091	-0.091	0.000	0.000	0.000	0.000
76	A	80	ASP	-1	-0.816	-0.889	11.206	-0.237	-0.237	0.000	0.000	0.000	0.000
77	A	81	GLU	-1	-0.834	-0.892	12.759	-0.274	-0.274	0.000	0.000	0.000	0.000
78	A	82	ILE	0	-0.029	-0.025	7.711	-0.014	-0.014	0.000	0.000	0.000	0.000
79	A	83	HIS	0	0.027	0.017	12.028	0.021	0.021	0.000	0.000	0.000	0.000
80	A	84	ARG	1	0.893	0.939	14.678	0.229	0.229	0.000	0.000	0.000	0.000
81	A	85	GLN	0	-0.049	-0.035	12.835	-0.016	-0.016	0.000	0.000	0.000	0.000
82	A	86	TRP	0	-0.003	-0.025	9.670	0.015	0.015	0.000	0.000	0.000	0.000
83	A	87	SER	0	-0.008	-0.006	15.734	0.025	0.025	0.000	0.000	0.000	0.000
84	A	88	ASP	-1	-0.952	-0.968	19.059	-0.190	-0.190	0.000	0.000	0.000	0.000
85	A	89	LYS	1	0.794	0.900	13.899	0.390	0.390	0.000	0.000	0.000	0.000
86	A	90	GLU	-1	-0.962	-0.969	19.341	-0.159	-0.159	0.000	0.000	0.000	0.000
87	A	91	ILE	0	-0.051	-0.017	14.568	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	92	SER	0	0.015	0.009	18.419	0.007	0.007	0.000	0.000	0.000	0.000
89	A	93	ILE	0	-0.014	-0.014	16.477	-0.034	-0.034	0.000	0.000	0.000	0.000
90	A	94	ILE	0	-0.031	-0.010	18.166	0.029	0.029	0.000	0.000	0.000	0.000
91	A	95	GLN	0	0.014	-0.002	16.750	-0.009	-0.009	0.000	0.000	0.000	0.000
92	A	96	PRO	0	0.029	0.023	17.193	-0.036	-0.036	0.000	0.000	0.000	0.000
93	A	97	PRO	0	0.046	0.022	15.891	-0.004	-0.004	0.000	0.000	0.000	0.000
94	A	98	THR	0	-0.048	-0.029	16.509	0.044	0.044	0.000	0.000	0.000	0.000
95	A	99	GLN	0	-0.026	-0.025	16.518	-0.009	-0.009	0.000	0.000	0.000	0.000
96	A	100	MET	0	-0.008	0.021	15.694	0.022	0.022	0.000	0.000	0.000	0.000
97	A	101	ASP	-1	-0.845	-0.934	17.368	-0.054	-0.054	0.000	0.000	0.000	0.000
98	A	102	PHE	0	-0.016	-0.013	11.548	0.028	0.028	0.000	0.000	0.000	0.000
99	A	103	GLY	0	-0.031	-0.029	12.936	0.031	0.031	0.000	0.000	0.000	0.000
100	A	104	TYR	0	-0.102	-0.051	12.849	0.003	0.003	0.000	0.000	0.000	0.000
101	A	105	THR	0	-0.028	-0.035	11.699	-0.065	-0.065	0.000	0.000	0.000	0.000
102	A	106	PHE	0	0.057	0.044	11.805	0.058	0.058	0.000	0.000	0.000	0.000
103	A	107	VAL	0	-0.017	-0.018	12.566	-0.083	-0.083	0.000	0.000	0.000	0.000
104	A	108	GLY	0	0.047	0.027	13.808	0.056	0.056	0.000	0.000	0.000	0.000
105	A	109	VAL	0	-0.034	-0.020	15.438	-0.029	-0.029	0.000	0.000	0.000	0.000
106	A	110	ASP	-1	-0.828	-0.900	16.060	-0.296	-0.296	0.000	0.000	0.000	0.000
107	A	111	PRO	0	-0.014	-0.026	17.876	0.016	0.016	0.000	0.000	0.000	0.000
108	A	112	ASP	-1	-0.964	-0.972	20.323	-0.166	-0.166	0.000	0.000	0.000	0.000
109	A	113	GLU	-1	-0.980	-0.992	20.401	-0.204	-0.204	0.000	0.000	0.000	0.000
110	A	114	HIS	0	-0.076	-0.034	16.022	0.008	0.008	0.000	0.000	0.000	0.000
111	A	115	ARG	1	0.836	0.895	15.130	0.230	0.230	0.000	0.000	0.000	0.000
112	A	116	LEU	0	-0.023	-0.009	11.080	-0.070	-0.070	0.000	0.000	0.000	0.000
113	A	117	ARG	1	0.779	0.836	10.169	0.461	0.461	0.000	0.000	0.000	0.000
114	A	118	ILE	0	0.019	0.027	7.346	-0.312	-0.312	0.000	0.000	0.000	0.000
115	A	119	PHE	0	0.000	-0.012	5.939	0.231	0.231	0.000	0.000	0.000	0.000
116	A	120	CYS	0	0.008	0.039	7.163	-0.153	-0.153	0.000	0.000	0.000	0.000
117	A	121	LEU	0	-0.038	-0.012	7.985	0.038	0.038	0.000	0.000	0.000	0.000
118	A	122	LYS	1	0.863	0.953	10.372	0.121	0.121	0.000	0.000	0.000	0.000

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