FMO DATABASE

FMODB ID: 66V2Z

Calculation Name: 1NYH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NYH

Chain ID: A

ChEMBL ID:

UniProt ID: P11978

Base Structure: X-ray

Registration Date: 2023-06-20

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	OptH
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	76
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-326538.090419
FMO2-HF: Nuclear repulsion	296340.648636
FMO2-HF: Total energy	-30197.441783
FMO2-MP2: Total energy	-30284.459959

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:1271:LEU)

Summations of interaction energy for fragment #1(A:1271:LEU)

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.
-7.498	-1.629	1.325	-3.074	-4.121	-0.022

Interaction energy analysis for fragmet #1(A:1271:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : -0.003

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	1273	PHE	0	0.072	0.016	3.705	0.573	1.863	0.000	-0.555	-0.736	0.003
4	A	1274	VAL	0	0.010	0.004	6.357	0.343	0.343	0.000	0.000	0.000	0.000
5	A	1275	ASP	-1	-0.835	-0.929	2.614	-6.667	-2.618	1.318	-2.375	-2.991	-0.026
6	A	1276	ILE	0	-0.074	-0.024	3.746	-0.322	0.208	0.007	-0.144	-0.394	0.001
7	A	1277	VAL	0	-0.024	-0.023	6.105	-0.290	-0.290	0.000	0.000	0.000	0.000
8	A	1278	LEU	0	0.048	0.020	7.746	-0.031	-0.031	0.000	0.000	0.000	0.000
9	A	1279	SER	0	0.012	0.022	6.408	-0.130	-0.130	0.000	0.000	0.000	0.000
10	A	1280	LYS	1	0.912	0.957	8.825	-0.863	-0.863	0.000	0.000	0.000	0.000
11	A	1281	ALA	0	-0.001	0.009	11.697	-0.090	-0.090	0.000	0.000	0.000	0.000
12	A	1282	ALA	0	0.008	-0.004	11.785	-0.053	-0.053	0.000	0.000	0.000	0.000
13	A	1283	SER	0	0.016	0.003	12.800	-0.025	-0.025	0.000	0.000	0.000	0.000
14	A	1284	ALA	0	0.002	0.007	14.574	-0.045	-0.045	0.000	0.000	0.000	0.000
15	A	1285	LEU	0	-0.030	-0.012	16.873	-0.034	-0.034	0.000	0.000	0.000	0.000
16	A	1286	ASP	-1	-0.817	-0.914	16.867	0.212	0.212	0.000	0.000	0.000	0.000
17	A	1287	GLU	-1	-0.934	-0.972	18.311	0.267	0.267	0.000	0.000	0.000	0.000
18	A	1288	LYS	1	0.806	0.895	20.685	-0.156	-0.156	0.000	0.000	0.000	0.000
19	A	1289	GLU	-1	-0.887	-0.951	21.767	0.091	0.091	0.000	0.000	0.000	0.000
20	A	1290	LYS	1	0.882	0.946	19.808	-0.222	-0.222	0.000	0.000	0.000	0.000
21	A	1291	GLN	0	-0.017	-0.004	24.800	-0.006	-0.006	0.000	0.000	0.000	0.000
22	A	1292	LEU	0	0.012	0.008	26.659	-0.010	-0.010	0.000	0.000	0.000	0.000
23	A	1293	ALA	0	0.016	0.008	27.163	-0.009	-0.009	0.000	0.000	0.000	0.000
24	A	1294	VAL	0	-0.030	-0.012	28.793	-0.007	-0.007	0.000	0.000	0.000	0.000
25	A	1295	ALA	0	-0.009	-0.006	31.023	-0.006	-0.006	0.000	0.000	0.000	0.000
26	A	1296	ASN	0	0.013	-0.014	30.913	-0.009	-0.009	0.000	0.000	0.000	0.000
27	A	1297	GLU	-1	-0.865	-0.895	33.501	0.055	0.055	0.000	0.000	0.000	0.000
28	A	1298	ILE	0	0.003	-0.002	35.264	-0.005	-0.005	0.000	0.000	0.000	0.000
29	A	1299	ILE	0	-0.008	0.009	35.409	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	1300	ARG	1	0.888	0.939	36.684	-0.052	-0.052	0.000	0.000	0.000	0.000
31	A	1301	SER	0	-0.001	-0.018	39.308	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	1302	LEU	0	0.019	-0.001	41.189	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	1303	SER	0	-0.008	0.000	42.314	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	1304	ASP	-1	-0.927	-0.951	43.886	0.035	0.035	0.000	0.000	0.000	0.000
35	A	1305	GLU	-1	-1.009	-0.997	45.597	0.034	0.034	0.000	0.000	0.000	0.000
36	A	1306	VAL	0	0.011	-0.001	47.098	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	1307	MET	0	0.047	0.025	47.443	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	1308	ARG	1	0.892	0.932	46.234	-0.034	-0.034	0.000	0.000	0.000	0.000
39	A	1309	ASN	0	-0.022	-0.009	50.898	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	1310	GLU	-1	-0.931	-0.964	52.276	0.023	0.023	0.000	0.000	0.000	0.000
41	A	1311	ILE	0	-0.006	0.004	53.734	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	1312	ARG	1	0.955	0.971	55.924	-0.025	-0.025	0.000	0.000	0.000	0.000
43	A	1313	ILE	0	-0.035	-0.015	56.502	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	1314	THR	0	0.045	0.025	59.034	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	1315	SER	0	-0.033	-0.011	60.610	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	1316	LEU	0	0.023	0.018	61.049	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	1317	GLN	0	0.024	0.011	62.683	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	1318	GLY	0	0.001	0.018	65.080	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	1319	ASP	-1	-0.885	-0.957	65.860	0.016	0.016	0.000	0.000	0.000	0.000
50	A	1320	LEU	0	-0.082	-0.040	67.770	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	1321	THR	0	-0.043	-0.040	68.892	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	1322	PHE	0	0.041	0.016	71.098	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	1323	THR	0	0.025	0.010	71.816	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	1324	LYS	1	0.962	0.982	71.506	-0.015	-0.015	0.000	0.000	0.000	0.000
55	A	1325	LYS	1	0.970	1.007	75.510	-0.011	-0.011	0.000	0.000	0.000	0.000
56	A	1326	CYS	0	-0.042	-0.021	76.593	0.000	0.000	0.000	0.000	0.000	0.000
57	A	1327	LEU	0	-0.030	-0.018	78.114	0.000	0.000	0.000	0.000	0.000	0.000
58	A	1328	GLU	-1	-0.945	-0.983	79.579	0.011	0.011	0.000	0.000	0.000	0.000
59	A	1329	ASN	0	-0.003	-0.012	81.515	0.000	0.000	0.000	0.000	0.000	0.000
60	A	1330	ALA	0	0.023	0.009	82.900	0.000	0.000	0.000	0.000	0.000	0.000
61	A	1331	ARG	1	0.904	0.948	82.742	-0.011	-0.011	0.000	0.000	0.000	0.000
62	A	1332	SER	0	0.035	0.028	85.567	0.000	0.000	0.000	0.000	0.000	0.000
63	A	1333	GLN	0	-0.003	-0.006	86.004	0.000	0.000	0.000	0.000	0.000	0.000
64	A	1334	ILE	0	-0.026	0.002	86.710	0.000	0.000	0.000	0.000	0.000	0.000
65	A	1335	SER	0	0.074	0.034	89.945	0.000	0.000	0.000	0.000	0.000	0.000
66	A	1336	GLU	-1	-0.963	-0.978	91.702	0.008	0.008	0.000	0.000	0.000	0.000
67	A	1337	LYS	1	0.857	0.915	91.700	-0.009	-0.009	0.000	0.000	0.000	0.000
68	A	1338	ASP	-1	-0.837	-0.921	93.754	0.009	0.009	0.000	0.000	0.000	0.000
69	A	1339	ALA	0	-0.024	0.000	95.697	0.000	0.000	0.000	0.000	0.000	0.000
70	A	1340	LYS	1	0.897	0.926	97.994	-0.007	-0.007	0.000	0.000	0.000	0.000
71	A	1341	ILE	0	-0.003	0.012	97.511	0.000	0.000	0.000	0.000	0.000	0.000
72	A	1342	ASN	0	0.022	-0.008	99.043	0.000	0.000	0.000	0.000	0.000	0.000
73	A	1343	LYS	1	0.926	0.977	101.545	-0.007	-0.007	0.000	0.000	0.000	0.000
74	A	1344	LEU	0	-0.117	-0.050	103.301	0.000	0.000	0.000	0.000	0.000	0.000
75	A	1345	MET	0	0.017	0.008	102.093	0.000	0.000	0.000	0.000	0.000	0.000
76	A	1346	GLU	-1	-1.008	-0.982	106.254	0.006	0.006	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1271:LEU)