FMO DATABASE

FMODB ID: 2JLKR

Calculation Name: 3C5R-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3C5R

Chain ID: A

ChEMBL ID:

UniProt ID: Q99728

Base Structure: X-ray

Registration Date: 2023-06-22

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	125
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1040803.640838
FMO2-HF: Nuclear repulsion	993093.709582
FMO2-HF: Total energy	-47709.931256
FMO2-MP2: Total energy	-47851.508353

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:-2:PRO)

Summations of interaction energy for fragment #1(A:-2: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.
0.512	2.602	-0.01	-0.815	-1.265	0.003

Interaction energy analysis for fragmet #1(A:-2:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.048 / q_NPA : 0.018

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	0	THR	0	0.029	0.028	3.752	-0.979	0.957	-0.010	-0.780	-1.146	0.003
4	A	425	ASN	0	-0.047	-0.028	6.029	0.106	0.106	0.000	0.000	0.000	0.000
5	A	426	HIS	0	0.029	-0.004	9.227	-0.066	-0.066	0.000	0.000	0.000	0.000
6	A	427	ARG	1	0.837	0.880	11.535	0.286	0.286	0.000	0.000	0.000	0.000
7	A	428	GLY	0	0.053	0.036	7.380	0.115	0.115	0.000	0.000	0.000	0.000
8	A	429	GLU	-1	-0.810	-0.852	7.410	-0.069	-0.069	0.000	0.000	0.000	0.000
9	A	430	THR	0	0.040	-0.015	3.670	-0.459	-0.305	0.000	-0.035	-0.119	0.000
10	A	431	LEU	0	0.025	-0.007	6.121	0.168	0.168	0.000	0.000	0.000	0.000
11	A	432	LEU	0	0.064	0.040	7.413	0.055	0.055	0.000	0.000	0.000	0.000
12	A	433	HIS	0	0.052	0.051	7.719	-0.081	-0.081	0.000	0.000	0.000	0.000
13	A	434	ILE	0	-0.011	-0.001	10.086	0.001	0.001	0.000	0.000	0.000	0.000
14	A	435	ALA	0	-0.006	-0.009	11.893	0.011	0.011	0.000	0.000	0.000	0.000
15	A	436	SER	0	-0.013	-0.020	12.655	0.029	0.029	0.000	0.000	0.000	0.000
16	A	437	ILE	0	-0.030	-0.005	13.978	-0.005	-0.005	0.000	0.000	0.000	0.000
17	A	438	LYS	1	0.891	0.945	15.782	0.141	0.141	0.000	0.000	0.000	0.000
18	A	439	GLY	0	0.043	0.034	17.648	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	440	ASP	-1	-0.907	-0.935	16.459	-0.039	-0.039	0.000	0.000	0.000	0.000
20	A	441	ILE	0	0.042	0.000	16.923	0.014	0.014	0.000	0.000	0.000	0.000
21	A	442	PRO	0	0.013	0.009	17.910	0.018	0.018	0.000	0.000	0.000	0.000
22	A	443	SER	0	-0.024	-0.029	13.748	0.003	0.003	0.000	0.000	0.000	0.000
23	A	444	VAL	0	-0.029	-0.014	13.320	0.027	0.027	0.000	0.000	0.000	0.000
24	A	445	GLU	-1	-0.926	-0.973	13.860	0.155	0.155	0.000	0.000	0.000	0.000
25	A	446	TYR	0	-0.015	0.000	12.161	0.017	0.017	0.000	0.000	0.000	0.000
26	A	447	LEU	0	0.007	-0.004	8.396	0.009	0.009	0.000	0.000	0.000	0.000
27	A	448	LEU	0	-0.033	-0.014	10.803	0.105	0.105	0.000	0.000	0.000	0.000
28	A	449	GLN	0	-0.018	-0.009	12.823	0.022	0.022	0.000	0.000	0.000	0.000
29	A	450	ASN	0	-0.107	-0.053	11.131	-0.042	-0.042	0.000	0.000	0.000	0.000
30	A	451	GLY	0	-0.008	0.008	9.865	-0.008	-0.008	0.000	0.000	0.000	0.000
31	A	452	SER	0	-0.079	-0.040	6.884	0.195	0.195	0.000	0.000	0.000	0.000
32	A	453	ASP	-1	-0.831	-0.926	6.855	1.125	1.125	0.000	0.000	0.000	0.000
33	A	454	PRO	0	-0.004	-0.001	7.929	0.178	0.178	0.000	0.000	0.000	0.000
34	A	455	ASN	0	-0.102	-0.043	10.391	-0.267	-0.267	0.000	0.000	0.000	0.000
35	A	456	VAL	0	0.000	-0.001	5.171	0.194	0.194	0.000	0.000	0.000	0.000
36	A	457	LYS	1	0.857	0.920	8.265	-0.673	-0.673	0.000	0.000	0.000	0.000
37	A	458	ASP	-1	-0.803	-0.893	7.979	0.151	0.151	0.000	0.000	0.000	0.000
38	A	459	HIS	0	-0.030	-0.034	8.216	0.130	0.130	0.000	0.000	0.000	0.000
39	A	460	ALA	0	-0.051	-0.015	11.492	0.027	0.027	0.000	0.000	0.000	0.000
40	A	461	GLY	0	-0.010	-0.010	12.997	0.009	0.009	0.000	0.000	0.000	0.000
41	A	462	TRP	0	-0.030	-0.018	13.745	0.065	0.065	0.000	0.000	0.000	0.000
42	A	463	THR	0	0.015	-0.011	11.639	0.051	0.051	0.000	0.000	0.000	0.000
43	A	464	PRO	0	0.023	-0.003	9.858	-0.092	-0.092	0.000	0.000	0.000	0.000
44	A	465	LEU	0	0.027	0.019	12.644	-0.064	-0.064	0.000	0.000	0.000	0.000
45	A	466	HIS	0	-0.017	0.022	15.692	-0.006	-0.006	0.000	0.000	0.000	0.000
46	A	467	GLU	-1	-0.850	-0.935	13.857	0.031	0.031	0.000	0.000	0.000	0.000
47	A	468	ALA	0	0.001	0.006	16.742	-0.029	-0.029	0.000	0.000	0.000	0.000
48	A	469	CYS	0	-0.076	-0.032	18.505	-0.017	-0.017	0.000	0.000	0.000	0.000
49	A	470	ASN	0	-0.052	-0.024	20.360	-0.026	-0.026	0.000	0.000	0.000	0.000
50	A	471	HIS	0	-0.045	-0.036	18.797	-0.030	-0.030	0.000	0.000	0.000	0.000
51	A	472	GLY	0	0.016	0.025	22.240	-0.009	-0.009	0.000	0.000	0.000	0.000
52	A	473	HIS	0	0.006	0.005	19.404	0.000	0.000	0.000	0.000	0.000	0.000
53	A	474	LEU	0	0.012	0.006	21.369	0.020	0.020	0.000	0.000	0.000	0.000
54	A	475	LYS	1	0.903	0.943	21.722	-0.107	-0.107	0.000	0.000	0.000	0.000
55	A	476	VAL	0	0.035	0.021	16.379	0.014	0.014	0.000	0.000	0.000	0.000
56	A	477	VAL	0	0.022	0.002	17.994	0.035	0.035	0.000	0.000	0.000	0.000
57	A	478	GLU	-1	-0.893	-0.938	19.439	0.156	0.156	0.000	0.000	0.000	0.000
58	A	479	LEU	0	0.000	0.004	17.349	0.016	0.016	0.000	0.000	0.000	0.000
59	A	480	LEU	0	0.024	0.019	13.106	0.044	0.044	0.000	0.000	0.000	0.000
60	A	481	LEU	0	-0.033	-0.019	16.344	0.043	0.043	0.000	0.000	0.000	0.000
61	A	482	GLN	0	-0.057	-0.026	19.197	0.016	0.016	0.000	0.000	0.000	0.000
62	A	483	HIS	0	-0.092	-0.047	14.619	-0.008	-0.008	0.000	0.000	0.000	0.000
63	A	484	LYS	1	0.921	0.955	14.902	-0.270	-0.270	0.000	0.000	0.000	0.000
64	A	485	ALA	0	0.029	0.034	14.772	0.057	0.057	0.000	0.000	0.000	0.000
65	A	486	LEU	0	-0.017	-0.015	15.681	-0.079	-0.079	0.000	0.000	0.000	0.000
66	A	487	VAL	0	0.024	0.006	17.815	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	488	ASN	0	-0.028	-0.018	20.620	-0.031	-0.031	0.000	0.000	0.000	0.000
68	A	489	THR	0	-0.042	0.000	15.002	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	490	THR	0	0.027	0.017	18.492	-0.012	-0.012	0.000	0.000	0.000	0.000
70	A	491	GLY	0	0.044	0.015	16.357	0.051	0.051	0.000	0.000	0.000	0.000
71	A	492	TYR	0	0.011	0.009	17.321	-0.018	-0.018	0.000	0.000	0.000	0.000
72	A	493	GLN	0	0.007	-0.004	18.660	-0.012	-0.012	0.000	0.000	0.000	0.000
73	A	494	ASN	0	-0.003	-0.008	20.540	0.003	0.003	0.000	0.000	0.000	0.000
74	A	495	ASP	-1	-0.763	-0.854	21.539	0.102	0.102	0.000	0.000	0.000	0.000
75	A	496	SER	0	-0.001	-0.026	20.521	0.028	0.028	0.000	0.000	0.000	0.000
76	A	497	PRO	0	0.038	-0.001	18.740	-0.021	-0.021	0.000	0.000	0.000	0.000
77	A	498	LEU	0	0.022	0.009	21.269	-0.017	-0.017	0.000	0.000	0.000	0.000
78	A	499	HIS	0	-0.022	0.006	24.311	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	500	ASP	-1	-0.783	-0.886	20.610	0.106	0.106	0.000	0.000	0.000	0.000
80	A	501	ALA	0	-0.005	0.011	23.764	-0.012	-0.012	0.000	0.000	0.000	0.000
81	A	502	ALA	0	-0.034	-0.033	25.529	-0.010	-0.010	0.000	0.000	0.000	0.000
82	A	503	LYS	1	0.790	0.876	23.637	-0.091	-0.091	0.000	0.000	0.000	0.000
83	A	504	ASN	0	-0.063	-0.030	24.865	-0.007	-0.007	0.000	0.000	0.000	0.000
84	A	505	GLY	0	0.004	0.017	28.105	-0.005	-0.005	0.000	0.000	0.000	0.000
85	A	506	HIS	0	0.014	0.019	25.475	-0.003	-0.003	0.000	0.000	0.000	0.000
86	A	507	VAL	0	0.031	-0.013	28.646	0.009	0.009	0.000	0.000	0.000	0.000
87	A	508	ASP	-1	-0.868	-0.937	28.377	0.080	0.080	0.000	0.000	0.000	0.000
88	A	509	ILE	0	0.026	0.006	23.252	0.010	0.010	0.000	0.000	0.000	0.000
89	A	510	VAL	0	0.008	0.007	26.282	0.013	0.013	0.000	0.000	0.000	0.000
90	A	511	LYS	1	0.902	0.955	28.397	-0.065	-0.065	0.000	0.000	0.000	0.000
91	A	512	LEU	0	0.013	0.019	23.610	0.004	0.004	0.000	0.000	0.000	0.000
92	A	513	LEU	0	0.047	0.031	21.727	0.012	0.012	0.000	0.000	0.000	0.000
93	A	514	LEU	0	-0.011	-0.015	25.427	0.010	0.010	0.000	0.000	0.000	0.000
94	A	515	SER	0	-0.109	-0.051	27.650	0.002	0.002	0.000	0.000	0.000	0.000
95	A	516	TYR	0	0.024	0.005	22.751	0.007	0.007	0.000	0.000	0.000	0.000
96	A	517	GLY	0	-0.026	-0.011	25.322	0.015	0.015	0.000	0.000	0.000	0.000
97	A	518	ALA	0	-0.028	-0.009	25.067	0.006	0.006	0.000	0.000	0.000	0.000
98	A	519	SER	0	-0.026	-0.029	26.056	-0.016	-0.016	0.000	0.000	0.000	0.000
99	A	520	ARG	1	0.905	0.941	28.160	-0.088	-0.088	0.000	0.000	0.000	0.000
100	A	521	ASN	0	-0.055	-0.035	30.836	-0.009	-0.009	0.000	0.000	0.000	0.000
101	A	522	ALA	0	0.030	0.026	26.183	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	523	VAL	0	-0.033	-0.017	27.816	-0.008	-0.008	0.000	0.000	0.000	0.000
103	A	524	ASN	0	0.021	0.004	25.052	0.008	0.008	0.000	0.000	0.000	0.000
104	A	525	ILE	0	-0.040	-0.038	23.663	-0.003	-0.003	0.000	0.000	0.000	0.000
105	A	526	PHE	0	-0.057	-0.023	26.466	-0.007	-0.007	0.000	0.000	0.000	0.000
106	A	527	GLY	0	-0.023	-0.001	29.268	-0.005	-0.005	0.000	0.000	0.000	0.000
107	A	528	LEU	0	-0.025	0.004	30.056	-0.003	-0.003	0.000	0.000	0.000	0.000
108	A	529	ARG	1	0.944	0.963	29.380	-0.067	-0.067	0.000	0.000	0.000	0.000
109	A	530	PRO	0	-0.002	-0.003	27.643	-0.007	-0.007	0.000	0.000	0.000	0.000
110	A	531	VAL	0	0.011	-0.006	29.919	-0.005	-0.005	0.000	0.000	0.000	0.000
111	A	532	ASP	-1	-0.866	-0.915	32.821	0.061	0.061	0.000	0.000	0.000	0.000
112	A	533	TYR	0	-0.045	-0.019	29.283	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	534	THR	0	-0.009	-0.004	32.436	-0.004	-0.004	0.000	0.000	0.000	0.000
114	A	535	ASP	-1	-0.826	-0.915	34.687	0.034	0.034	0.000	0.000	0.000	0.000
115	A	536	ASP	-1	-0.817	-0.908	35.834	0.044	0.044	0.000	0.000	0.000	0.000
116	A	537	GLU	-1	-0.845	-0.928	37.778	0.045	0.045	0.000	0.000	0.000	0.000
117	A	538	SER	0	-0.031	-0.015	36.925	0.002	0.002	0.000	0.000	0.000	0.000
118	A	539	MET	0	-0.047	0.007	30.443	0.007	0.007	0.000	0.000	0.000	0.000
119	A	540	LYS	1	0.799	0.884	35.042	-0.035	-0.035	0.000	0.000	0.000	0.000
120	A	541	SER	0	-0.096	-0.042	37.311	0.003	0.003	0.000	0.000	0.000	0.000
121	A	542	LEU	0	-0.023	-0.011	32.798	0.002	0.002	0.000	0.000	0.000	0.000
122	A	543	LEU	0	0.005	-0.003	30.703	0.007	0.007	0.000	0.000	0.000	0.000
123	A	544	LEU	0	-0.019	0.018	34.731	0.003	0.003	0.000	0.000	0.000	0.000
124	A	545	LEU	0	-0.046	-0.028	38.250	0.002	0.002	0.000	0.000	0.000	0.000
125	A	546	PRO	0	0.028	0.024	40.842	-0.003	-0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-2:PRO)