FMO DATABASE

FMODB ID: 1Y4QZ

Calculation Name: 3C5R-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3C5R

Chain ID: A

ChEMBL ID:

UniProt ID: Q99728

Base Structure: X-ray

Registration Date: 2025-10-04

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	125
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1041352.966818
FMO2-HF: Nuclear repulsion	993642.545705
FMO2-HF: Total energy	-47710.421113
FMO2-MP2: Total energy	-47851.910166

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:-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.
-64.143	-62.068	-0.007	-0.922	-1.146	-0.002

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 : 1 / q_Mulliken : 0.874 / q_NPA : 0.916

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

Sort

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	0.008	0.018	3.585	-5.962	-4.070	-0.005	-0.894	-0.993	-0.002
9	A	430	THR	0	0.033	-0.016	4.189	-2.084	-1.975	-0.001	-0.023	-0.085	0.000
35	A	456	VAL	0	-0.027	-0.011	4.427	-2.118	-2.044	-0.001	-0.005	-0.068	0.000
4	A	425	ASN	0	-0.037	-0.023	6.075	2.920	2.920	0.000	0.000	0.000	0.000
5	A	426	HIS	0	0.037	0.001	9.454	-3.062	-3.062	0.000	0.000	0.000	0.000
6	A	427	ARG	1	0.838	0.882	11.988	21.870	21.870	0.000	0.000	0.000	0.000
7	A	428	GLY	0	0.058	0.041	7.964	0.887	0.887	0.000	0.000	0.000	0.000
8	A	429	GLU	-1	-0.790	-0.847	7.692	-25.986	-25.986	0.000	0.000	0.000	0.000
10	A	431	LEU	0	0.005	-0.008	6.382	4.425	4.425	0.000	0.000	0.000	0.000
11	A	432	LEU	0	0.082	0.048	7.616	3.294	3.294	0.000	0.000	0.000	0.000
12	A	433	HIS	0	0.043	0.049	7.825	0.424	0.424	0.000	0.000	0.000	0.000
13	A	434	ILE	0	-0.012	-0.011	10.239	2.701	2.701	0.000	0.000	0.000	0.000
14	A	435	ALA	0	-0.014	-0.004	12.089	1.890	1.890	0.000	0.000	0.000	0.000
15	A	436	SER	0	0.014	-0.020	12.967	1.881	1.881	0.000	0.000	0.000	0.000
16	A	437	ILE	0	-0.032	-0.012	13.971	1.222	1.222	0.000	0.000	0.000	0.000
17	A	438	LYS	1	0.905	0.950	15.906	19.570	19.570	0.000	0.000	0.000	0.000
18	A	439	GLY	0	0.039	0.040	18.279	0.821	0.821	0.000	0.000	0.000	0.000
19	A	440	ASP	-1	-0.884	-0.921	16.475	-17.113	-17.113	0.000	0.000	0.000	0.000
20	A	441	ILE	0	0.035	0.005	17.001	-1.000	-1.000	0.000	0.000	0.000	0.000
21	A	442	PRO	0	0.015	0.009	18.102	-0.596	-0.596	0.000	0.000	0.000	0.000
22	A	443	SER	0	-0.023	-0.032	13.777	-0.781	-0.781	0.000	0.000	0.000	0.000
23	A	444	VAL	0	-0.030	-0.019	13.416	-1.770	-1.770	0.000	0.000	0.000	0.000
24	A	445	GLU	-1	-0.932	-0.969	13.782	-16.019	-16.019	0.000	0.000	0.000	0.000
25	A	446	TYR	0	0.022	0.018	12.583	-0.786	-0.786	0.000	0.000	0.000	0.000
26	A	447	LEU	0	-0.017	-0.013	8.402	-1.227	-1.227	0.000	0.000	0.000	0.000
27	A	448	LEU	0	-0.039	-0.010	10.052	-2.096	-2.096	0.000	0.000	0.000	0.000
28	A	449	GLN	0	0.001	0.001	12.180	-0.239	-0.239	0.000	0.000	0.000	0.000
29	A	450	ASN	0	-0.121	-0.065	10.644	0.903	0.903	0.000	0.000	0.000	0.000
30	A	451	GLY	0	-0.005	0.006	9.451	-1.867	-1.867	0.000	0.000	0.000	0.000
31	A	452	SER	0	-0.088	-0.050	6.457	-4.672	-4.672	0.000	0.000	0.000	0.000
32	A	453	ASP	-1	-0.832	-0.919	6.603	-27.523	-27.523	0.000	0.000	0.000	0.000
33	A	454	PRO	0	0.005	0.001	7.680	-3.205	-3.205	0.000	0.000	0.000	0.000
34	A	455	ASN	0	-0.097	-0.042	10.018	2.413	2.413	0.000	0.000	0.000	0.000
36	A	457	LYS	1	0.863	0.916	7.581	23.942	23.942	0.000	0.000	0.000	0.000
37	A	458	ASP	-1	-0.830	-0.897	7.912	-27.401	-27.401	0.000	0.000	0.000	0.000
38	A	459	HIS	0	-0.011	-0.029	8.494	0.530	0.530	0.000	0.000	0.000	0.000
39	A	460	ALA	0	-0.050	-0.008	12.057	1.532	1.532	0.000	0.000	0.000	0.000
40	A	461	GLY	0	0.004	-0.003	13.276	1.405	1.405	0.000	0.000	0.000	0.000
41	A	462	TRP	0	-0.018	-0.015	13.572	0.784	0.784	0.000	0.000	0.000	0.000
42	A	463	THR	0	0.022	-0.011	11.346	-2.130	-2.130	0.000	0.000	0.000	0.000
43	A	464	PRO	0	-0.005	-0.012	9.769	1.640	1.640	0.000	0.000	0.000	0.000
44	A	465	LEU	0	0.049	0.033	12.658	1.394	1.394	0.000	0.000	0.000	0.000
45	A	466	HIS	0	0.000	0.029	15.544	-0.042	-0.042	0.000	0.000	0.000	0.000
46	A	467	GLU	-1	-0.841	-0.938	14.299	-17.423	-17.423	0.000	0.000	0.000	0.000
47	A	468	ALA	0	-0.015	-0.002	16.704	0.897	0.897	0.000	0.000	0.000	0.000
48	A	469	CYS	0	-0.072	-0.025	18.453	1.032	1.032	0.000	0.000	0.000	0.000
49	A	470	ASN	0	-0.071	-0.039	20.264	0.764	0.764	0.000	0.000	0.000	0.000
50	A	471	HIS	1	0.837	0.907	19.029	16.286	16.286	0.000	0.000	0.000	0.000
51	A	472	GLY	0	0.062	0.049	22.390	0.274	0.274	0.000	0.000	0.000	0.000
52	A	473	HIS	0	-0.015	-0.005	19.576	0.695	0.695	0.000	0.000	0.000	0.000
53	A	474	LEU	0	0.023	0.012	21.458	-0.686	-0.686	0.000	0.000	0.000	0.000
54	A	475	LYS	1	0.899	0.946	21.878	13.231	13.231	0.000	0.000	0.000	0.000
55	A	476	VAL	0	0.012	0.013	16.476	-0.423	-0.423	0.000	0.000	0.000	0.000
56	A	477	VAL	0	0.018	0.002	18.013	-0.847	-0.847	0.000	0.000	0.000	0.000
57	A	478	GLU	-1	-0.876	-0.935	19.447	-13.110	-13.110	0.000	0.000	0.000	0.000
58	A	479	LEU	0	-0.017	-0.001	17.231	-0.238	-0.238	0.000	0.000	0.000	0.000
59	A	480	LEU	0	0.015	0.006	13.020	-0.867	-0.867	0.000	0.000	0.000	0.000
60	A	481	LEU	0	-0.020	-0.006	16.065	-0.503	-0.503	0.000	0.000	0.000	0.000
61	A	482	GLN	0	-0.030	-0.011	18.765	-0.265	-0.265	0.000	0.000	0.000	0.000
62	A	483	HIS	0	-0.090	-0.048	13.796	0.105	0.105	0.000	0.000	0.000	0.000
63	A	484	LYS	1	0.933	0.960	14.267	15.461	15.461	0.000	0.000	0.000	0.000
64	A	485	ALA	0	0.022	0.026	14.160	-0.808	-0.808	0.000	0.000	0.000	0.000
65	A	486	LEU	0	-0.003	-0.010	14.667	1.621	1.621	0.000	0.000	0.000	0.000
66	A	487	VAL	0	0.030	0.018	16.977	-0.254	-0.254	0.000	0.000	0.000	0.000
67	A	488	ASN	0	-0.037	-0.015	19.835	0.567	0.567	0.000	0.000	0.000	0.000
68	A	489	THR	0	-0.046	-0.023	14.498	-0.019	-0.019	0.000	0.000	0.000	0.000
69	A	490	THR	0	-0.009	0.002	17.923	-0.030	-0.030	0.000	0.000	0.000	0.000
70	A	491	GLY	0	0.035	0.007	16.370	-1.212	-1.212	0.000	0.000	0.000	0.000
71	A	492	TYR	0	0.023	0.022	17.378	0.403	0.403	0.000	0.000	0.000	0.000
72	A	493	GLN	0	-0.017	-0.021	18.684	0.872	0.872	0.000	0.000	0.000	0.000
73	A	494	ASN	0	0.010	-0.002	20.545	0.064	0.064	0.000	0.000	0.000	0.000
74	A	495	ASP	-1	-0.767	-0.859	21.654	-12.351	-12.351	0.000	0.000	0.000	0.000
75	A	496	SER	0	0.003	-0.022	20.313	-0.858	-0.858	0.000	0.000	0.000	0.000
76	A	497	PRO	0	0.038	-0.001	18.150	0.355	0.355	0.000	0.000	0.000	0.000
77	A	498	LEU	0	0.042	0.020	20.820	0.378	0.378	0.000	0.000	0.000	0.000
78	A	499	HIS	0	-0.026	0.009	23.899	0.088	0.088	0.000	0.000	0.000	0.000
79	A	500	ASP	-1	-0.838	-0.922	20.474	-14.412	-14.412	0.000	0.000	0.000	0.000
80	A	501	ALA	0	-0.008	-0.005	23.728	0.327	0.327	0.000	0.000	0.000	0.000
81	A	502	ALA	0	0.008	-0.012	25.481	0.393	0.393	0.000	0.000	0.000	0.000
82	A	503	LYS	1	0.862	0.933	24.027	13.020	13.020	0.000	0.000	0.000	0.000
83	A	504	ASN	0	-0.071	-0.036	25.190	-0.055	-0.055	0.000	0.000	0.000	0.000
84	A	505	GLY	0	0.029	0.026	28.010	0.102	0.102	0.000	0.000	0.000	0.000
85	A	506	HIS	0	0.013	0.014	25.502	0.520	0.520	0.000	0.000	0.000	0.000
86	A	507	VAL	0	0.042	-0.005	28.578	-0.208	-0.208	0.000	0.000	0.000	0.000
87	A	508	ASP	-1	-0.860	-0.930	28.677	-11.032	-11.032	0.000	0.000	0.000	0.000
88	A	509	ILE	0	-0.006	-0.002	23.301	-0.189	-0.189	0.000	0.000	0.000	0.000
89	A	510	VAL	0	0.006	0.002	26.061	-0.248	-0.248	0.000	0.000	0.000	0.000
90	A	511	LYS	1	0.920	0.966	28.135	9.218	9.218	0.000	0.000	0.000	0.000
91	A	512	LEU	0	-0.001	0.015	23.387	0.029	0.029	0.000	0.000	0.000	0.000
92	A	513	LEU	0	0.036	0.013	21.393	-0.162	-0.162	0.000	0.000	0.000	0.000
93	A	514	LEU	0	-0.024	-0.015	25.017	-0.054	-0.054	0.000	0.000	0.000	0.000
94	A	515	SER	0	-0.099	-0.055	27.343	0.095	0.095	0.000	0.000	0.000	0.000
95	A	516	TYR	0	0.011	0.000	22.405	-0.146	-0.146	0.000	0.000	0.000	0.000
96	A	517	GLY	0	0.001	0.010	24.504	-0.357	-0.357	0.000	0.000	0.000	0.000
97	A	518	ALA	0	-0.029	-0.006	24.476	-0.211	-0.211	0.000	0.000	0.000	0.000
98	A	519	SER	0	-0.010	-0.023	25.362	0.663	0.663	0.000	0.000	0.000	0.000
99	A	520	ARG	1	0.891	0.935	27.362	9.011	9.011	0.000	0.000	0.000	0.000
100	A	521	ASN	0	-0.042	-0.021	30.162	0.198	0.198	0.000	0.000	0.000	0.000
101	A	522	ALA	0	0.027	0.018	25.937	0.139	0.139	0.000	0.000	0.000	0.000
102	A	523	VAL	0	-0.036	-0.021	27.553	0.140	0.140	0.000	0.000	0.000	0.000
103	A	524	ASN	0	0.000	-0.006	25.053	-0.100	-0.100	0.000	0.000	0.000	0.000
104	A	525	ILE	0	-0.036	-0.039	24.012	0.301	0.301	0.000	0.000	0.000	0.000
105	A	526	PHE	0	-0.057	-0.022	26.536	0.299	0.299	0.000	0.000	0.000	0.000
106	A	527	GLY	0	-0.011	0.002	29.522	0.392	0.392	0.000	0.000	0.000	0.000
107	A	528	LEU	0	-0.022	0.006	30.129	0.236	0.236	0.000	0.000	0.000	0.000
108	A	529	ARG	1	0.960	0.976	29.023	8.691	8.691	0.000	0.000	0.000	0.000
109	A	530	PRO	0	-0.023	-0.022	26.983	0.109	0.109	0.000	0.000	0.000	0.000
110	A	531	VAL	0	0.012	-0.003	29.278	0.037	0.037	0.000	0.000	0.000	0.000
111	A	532	ASP	-1	-0.840	-0.903	32.568	-9.093	-9.093	0.000	0.000	0.000	0.000
112	A	533	TYR	0	-0.054	-0.019	28.853	-0.046	-0.046	0.000	0.000	0.000	0.000
113	A	534	THR	0	-0.017	-0.013	32.035	0.001	0.001	0.000	0.000	0.000	0.000
114	A	535	ASP	-1	-0.838	-0.921	34.296	-7.710	-7.710	0.000	0.000	0.000	0.000
115	A	536	ASP	-1	-0.810	-0.892	35.928	-8.374	-8.374	0.000	0.000	0.000	0.000
116	A	537	GLU	-1	-0.826	-0.928	37.542	-7.780	-7.780	0.000	0.000	0.000	0.000
117	A	538	SER	0	-0.062	-0.019	36.991	0.046	0.046	0.000	0.000	0.000	0.000
118	A	539	MET	0	-0.040	0.013	30.245	-0.152	-0.152	0.000	0.000	0.000	0.000
119	A	540	LYS	1	0.814	0.904	34.776	7.774	7.774	0.000	0.000	0.000	0.000
120	A	541	SER	0	-0.080	-0.041	37.057	-0.013	-0.013	0.000	0.000	0.000	0.000
121	A	542	LEU	0	-0.041	-0.020	32.321	0.003	0.003	0.000	0.000	0.000	0.000
122	A	543	LEU	0	-0.023	-0.021	30.392	-0.235	-0.235	0.000	0.000	0.000	0.000
123	A	544	LEU	0	-0.022	0.001	34.322	-0.038	-0.038	0.000	0.000	0.000	0.000
124	A	545	LEU	0	-0.088	-0.050	37.927	-0.155	-0.155	0.000	0.000	0.000	0.000
125	A	546	PRO	-1	-0.899	-0.933	40.489	-7.085	-7.085	0.000	0.000	0.000	0.000

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