FMO DATABASE

FMODB ID: 3MM3L

Calculation Name: 2NQB-D-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2NQB

Chain ID: D

ChEMBL ID:

UniProt ID: P84051

Base Structure: X-ray

Registration Date: 2025-10-05

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	95
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-591939.23255
FMO2-HF: Nuclear repulsion	554855.01383
FMO2-HF: Total energy	-37084.21872
FMO2-MP2: Total energy	-37193.278495

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:1228:ARG)

Summations of interaction energy for fragment #1(A:1228:ARG)

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.
142.861	144.464	-0.01	-0.661	-0.932	-0.002

Interaction energy analysis for fragmet #1(A:1228:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.870 / q_NPA : 1.917

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	1230	ARG	1	0.906	0.942	3.695	62.175	63.752	-0.009	-0.660	-0.908	-0.002
4	A	1231	LYS	1	0.987	1.000	5.393	47.548	47.574	-0.001	-0.001	-0.024	0.000
5	A	1232	GLU	-1	-0.830	-0.894	9.205	-50.284	-50.284	0.000	0.000	0.000	0.000
6	A	1233	SER	0	-0.043	-0.027	11.836	2.322	2.322	0.000	0.000	0.000	0.000
7	A	1234	TYR	0	0.068	0.027	15.175	-1.271	-1.271	0.000	0.000	0.000	0.000
8	A	1235	ALA	0	0.031	0.000	16.435	1.159	1.159	0.000	0.000	0.000	0.000
9	A	1236	ILE	0	0.027	0.010	13.497	1.343	1.343	0.000	0.000	0.000	0.000
10	A	1237	TYR	0	0.024	0.027	14.991	0.896	0.896	0.000	0.000	0.000	0.000
11	A	1238	ILE	0	0.019	0.009	20.142	1.276	1.276	0.000	0.000	0.000	0.000
12	A	1239	TYR	0	-0.008	-0.008	20.275	1.419	1.419	0.000	0.000	0.000	0.000
13	A	1240	THR	0	-0.013	-0.020	19.983	0.849	0.849	0.000	0.000	0.000	0.000
14	A	1241	VAL	0	0.019	0.007	22.602	0.890	0.890	0.000	0.000	0.000	0.000
15	A	1242	LEU	0	-0.024	-0.016	25.380	0.838	0.838	0.000	0.000	0.000	0.000
16	A	1243	LYS	1	0.821	0.896	24.279	23.692	23.692	0.000	0.000	0.000	0.000
17	A	1244	GLN	0	-0.027	-0.010	26.231	0.521	0.521	0.000	0.000	0.000	0.000
18	A	1245	VAL	0	-0.046	-0.012	28.770	0.669	0.669	0.000	0.000	0.000	0.000
19	A	1246	HIS	0	-0.002	-0.001	30.321	0.684	0.684	0.000	0.000	0.000	0.000
20	A	1247	PRO	0	0.040	0.028	29.057	-0.652	-0.652	0.000	0.000	0.000	0.000
21	A	1248	ASP	-1	-0.865	-0.931	28.679	-19.755	-19.755	0.000	0.000	0.000	0.000
22	A	1249	THR	0	-0.032	0.000	29.572	0.142	0.142	0.000	0.000	0.000	0.000
23	A	1250	GLY	0	-0.005	0.005	26.488	-0.836	-0.836	0.000	0.000	0.000	0.000
24	A	1251	ILE	0	0.005	-0.013	23.127	0.501	0.501	0.000	0.000	0.000	0.000
25	A	1252	SER	0	0.037	0.024	23.960	-0.983	-0.983	0.000	0.000	0.000	0.000
26	A	1253	SER	0	0.048	0.010	19.293	0.163	0.163	0.000	0.000	0.000	0.000
27	A	1254	LYS	1	0.985	0.983	20.999	23.255	23.255	0.000	0.000	0.000	0.000
28	A	1255	ALA	0	0.055	0.036	23.301	0.055	0.055	0.000	0.000	0.000	0.000
29	A	1256	MET	0	0.023	0.036	19.504	0.103	0.103	0.000	0.000	0.000	0.000
30	A	1257	SER	0	-0.034	-0.016	19.964	-0.808	-0.808	0.000	0.000	0.000	0.000
31	A	1258	ILE	0	0.026	0.025	20.903	-0.110	-0.110	0.000	0.000	0.000	0.000
32	A	1259	MET	0	0.036	0.018	23.576	0.438	0.438	0.000	0.000	0.000	0.000
33	A	1260	ASN	0	0.014	-0.005	17.483	-0.599	-0.599	0.000	0.000	0.000	0.000
34	A	1261	SER	0	-0.015	-0.011	21.017	-0.449	-0.449	0.000	0.000	0.000	0.000
35	A	1262	PHE	0	0.014	0.010	22.738	0.350	0.350	0.000	0.000	0.000	0.000
36	A	1263	VAL	0	0.001	-0.002	22.410	0.467	0.467	0.000	0.000	0.000	0.000
37	A	1264	ASN	0	-0.046	-0.028	18.846	-0.371	-0.371	0.000	0.000	0.000	0.000
38	A	1265	ASP	-1	-0.750	-0.825	22.821	-20.510	-20.510	0.000	0.000	0.000	0.000
39	A	1266	ILE	0	-0.025	-0.013	26.312	0.750	0.750	0.000	0.000	0.000	0.000
40	A	1267	PHE	0	-0.007	-0.005	22.508	0.532	0.532	0.000	0.000	0.000	0.000
41	A	1268	GLU	-1	-0.915	-0.965	22.920	-24.832	-24.832	0.000	0.000	0.000	0.000
42	A	1269	ARG	1	0.789	0.856	26.523	20.402	20.402	0.000	0.000	0.000	0.000
43	A	1270	ILE	0	0.012	0.002	29.323	0.629	0.629	0.000	0.000	0.000	0.000
44	A	1271	ALA	0	0.011	0.006	26.915	0.520	0.520	0.000	0.000	0.000	0.000
45	A	1272	ALA	0	-0.016	-0.009	28.966	0.420	0.420	0.000	0.000	0.000	0.000
46	A	1273	GLU	-1	-0.857	-0.922	30.889	-16.377	-16.377	0.000	0.000	0.000	0.000
47	A	1274	ALA	0	-0.004	-0.006	31.373	0.456	0.456	0.000	0.000	0.000	0.000
48	A	1275	SER	0	-0.017	-0.002	30.854	0.501	0.501	0.000	0.000	0.000	0.000
49	A	1276	ARG	1	0.887	0.933	32.944	18.310	18.310	0.000	0.000	0.000	0.000
50	A	1277	LEU	0	0.008	0.014	36.216	0.472	0.472	0.000	0.000	0.000	0.000
51	A	1278	ALA	0	0.025	0.014	34.668	0.488	0.488	0.000	0.000	0.000	0.000
52	A	1279	HIS	0	0.010	0.011	36.236	0.479	0.479	0.000	0.000	0.000	0.000
53	A	1280	TYR	0	0.015	-0.002	37.903	0.383	0.383	0.000	0.000	0.000	0.000
54	A	1281	ASN	0	-0.092	-0.040	40.216	0.760	0.760	0.000	0.000	0.000	0.000
55	A	1282	LYS	1	0.928	0.961	40.268	13.948	13.948	0.000	0.000	0.000	0.000
56	A	1283	ARG	1	0.892	0.944	36.881	15.120	15.120	0.000	0.000	0.000	0.000
57	A	1284	SER	0	0.033	0.014	34.094	-0.213	-0.213	0.000	0.000	0.000	0.000
58	A	1285	THR	0	-0.026	-0.012	31.225	-0.658	-0.658	0.000	0.000	0.000	0.000
59	A	1286	ILE	0	0.010	0.012	29.555	0.518	0.518	0.000	0.000	0.000	0.000
60	A	1287	THR	0	0.002	-0.020	30.587	-0.402	-0.402	0.000	0.000	0.000	0.000
61	A	1288	SER	0	0.050	0.006	31.505	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	1289	ARG	1	0.966	0.993	32.649	15.364	15.364	0.000	0.000	0.000	0.000
63	A	1290	GLU	-1	-0.808	-0.888	34.066	-16.641	-16.641	0.000	0.000	0.000	0.000
64	A	1291	ILE	0	0.016	0.014	29.362	0.083	0.083	0.000	0.000	0.000	0.000
65	A	1292	GLN	0	0.004	-0.005	32.977	0.122	0.122	0.000	0.000	0.000	0.000
66	A	1293	THR	0	-0.062	-0.041	35.697	0.500	0.500	0.000	0.000	0.000	0.000
67	A	1294	ALA	0	0.048	0.020	33.882	0.241	0.241	0.000	0.000	0.000	0.000
68	A	1295	VAL	0	-0.016	-0.012	33.191	0.065	0.065	0.000	0.000	0.000	0.000
69	A	1296	ARG	1	0.887	0.937	35.566	15.430	15.430	0.000	0.000	0.000	0.000
70	A	1297	LEU	0	-0.018	0.014	38.123	0.384	0.384	0.000	0.000	0.000	0.000
71	A	1298	LEU	0	-0.027	-0.004	33.051	0.042	0.042	0.000	0.000	0.000	0.000
72	A	1299	LEU	0	-0.046	-0.012	33.507	-0.125	-0.125	0.000	0.000	0.000	0.000
73	A	1300	PRO	0	0.036	0.008	37.524	0.409	0.409	0.000	0.000	0.000	0.000
74	A	1301	GLY	0	0.035	0.012	40.811	-0.095	-0.095	0.000	0.000	0.000	0.000
75	A	1302	GLU	-1	-0.809	-0.895	41.834	-14.344	-14.344	0.000	0.000	0.000	0.000
76	A	1303	LEU	0	0.021	0.009	36.063	-0.247	-0.247	0.000	0.000	0.000	0.000
77	A	1304	ALA	0	0.015	0.020	37.195	-0.412	-0.412	0.000	0.000	0.000	0.000
78	A	1305	LYS	1	0.849	0.907	38.433	13.859	13.859	0.000	0.000	0.000	0.000
79	A	1306	HIS	0	0.043	0.033	36.939	-0.274	-0.274	0.000	0.000	0.000	0.000
80	A	1307	ALA	0	0.023	0.017	33.760	-0.316	-0.316	0.000	0.000	0.000	0.000
81	A	1308	VAL	0	-0.016	-0.014	34.270	-0.291	-0.291	0.000	0.000	0.000	0.000
82	A	1309	SER	0	-0.026	-0.005	36.426	0.060	0.060	0.000	0.000	0.000	0.000
83	A	1310	GLU	-1	-0.857	-0.930	32.016	-18.739	-18.739	0.000	0.000	0.000	0.000
84	A	1311	GLY	0	-0.002	0.002	31.413	-0.424	-0.424	0.000	0.000	0.000	0.000
85	A	1312	THR	0	-0.009	-0.019	32.437	-0.171	-0.171	0.000	0.000	0.000	0.000
86	A	1313	LYS	1	0.898	0.958	32.506	18.180	18.180	0.000	0.000	0.000	0.000
87	A	1314	ALA	0	-0.026	-0.008	28.728	-0.126	-0.126	0.000	0.000	0.000	0.000
88	A	1315	VAL	0	-0.001	-0.008	30.164	-0.294	-0.294	0.000	0.000	0.000	0.000
89	A	1316	THR	0	-0.013	-0.007	31.489	0.165	0.165	0.000	0.000	0.000	0.000
90	A	1317	LYS	1	0.965	0.982	28.822	19.885	19.885	0.000	0.000	0.000	0.000
91	A	1318	TYR	0	-0.037	-0.001	24.429	0.019	0.019	0.000	0.000	0.000	0.000
92	A	1319	THR	0	-0.002	-0.020	29.252	-0.127	-0.127	0.000	0.000	0.000	0.000
93	A	1320	SER	0	-0.103	-0.050	32.140	0.387	0.387	0.000	0.000	0.000	0.000
94	A	1321	SER	0	-0.094	-0.052	28.580	-0.097	-0.097	0.000	0.000	0.000	0.000
95	A	1322	LYS	0	0.076	0.049	24.062	3.058	3.058	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1228:ARG)