FMO DATABASE

FMODB ID: L7YJ9

Calculation Name: 1NYH-A-Xray540

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: 2025-07-09

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
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	151
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-325968.980451
FMO2-HF: Nuclear repulsion	295786.719002
FMO2-HF: Total energy	-30182.261448
FMO2-MP2: Total energy	-30268.756232

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.
-5.575	-3.576	0.343	-0.25	-2.091	0.006

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 : 0.209 / q_NPA : 0.067

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].
4	A	1272	SER	0	-0.048	0.063	4.983	0.586	0.747	-0.001	-0.062	-0.098	0.000
5	A	1273	PHE	0	0.090	-0.078	3.745	-1.757	0.199	-0.003	-1.242	-0.710	0.006
6	A	1273	PHE	0	-0.068	0.095	7.135	0.094	0.094	0.000	0.000	0.000	0.000
7	A	1274	VAL	0	0.066	-0.106	6.104	0.502	0.502	0.000	0.000	0.000	0.000
8	A	1274	VAL	0	-0.052	0.105	7.724	0.024	0.024	0.000	0.000	0.000	0.000
9	A	1275	ASP	0	0.100	-0.097	4.249	1.208	1.269	-0.001	0.005	-0.066	0.000
10	A	1275	ASP	-1	-0.859	-0.799	3.220	-7.749	-8.756	0.034	1.396	-0.423	-0.002
11	A	1276	ILE	0	0.052	-0.070	4.291	0.741	0.876	-0.001	-0.022	-0.111	0.000
12	A	1276	ILE	0	-0.073	0.101	2.764	-0.649	-0.003	0.317	-0.323	-0.639	0.002
13	A	1277	VAL	0	0.086	-0.094	5.103	0.423	0.470	-0.002	-0.002	-0.044	0.000
14	A	1277	VAL	0	-0.090	0.100	8.774	0.018	0.018	0.000	0.000	0.000	0.000
15	A	1278	LEU	0	0.075	-0.102	8.202	0.303	0.303	0.000	0.000	0.000	0.000
16	A	1278	LEU	0	-0.056	0.102	8.173	0.002	0.002	0.000	0.000	0.000	0.000
17	A	1279	SER	0	0.022	-0.115	7.177	0.087	0.087	0.000	0.000	0.000	0.000
18	A	1279	SER	0	-0.071	0.065	5.943	0.255	0.255	0.000	0.000	0.000	0.000
19	A	1280	LYS	0	0.061	-0.099	8.415	0.191	0.191	0.000	0.000	0.000	0.000
20	A	1280	LYS	1	0.733	1.020	9.718	-0.169	-0.169	0.000	0.000	0.000	0.000
21	A	1281	ALA	0	0.158	-0.078	10.699	0.101	0.101	0.000	0.000	0.000	0.000
22	A	1281	ALA	0	-0.095	0.100	12.541	-0.018	-0.018	0.000	0.000	0.000	0.000
23	A	1282	ALA	0	0.090	-0.097	12.032	0.045	0.045	0.000	0.000	0.000	0.000
24	A	1282	ALA	0	-0.075	0.100	11.689	-0.008	-0.008	0.000	0.000	0.000	0.000
25	A	1283	SER	0	0.040	-0.071	12.290	0.016	0.016	0.000	0.000	0.000	0.000
26	A	1283	SER	0	-0.109	0.009	11.961	0.050	0.050	0.000	0.000	0.000	0.000
27	A	1284	ALA	0	0.098	-0.090	13.842	0.034	0.034	0.000	0.000	0.000	0.000
28	A	1284	ALA	0	-0.092	0.098	15.624	-0.007	-0.007	0.000	0.000	0.000	0.000
29	A	1285	LEU	0	0.092	-0.096	16.310	0.017	0.017	0.000	0.000	0.000	0.000
30	A	1285	LEU	0	-0.084	0.106	17.096	-0.009	-0.009	0.000	0.000	0.000	0.000
31	A	1286	ASP	0	0.094	-0.090	16.925	-0.006	-0.006	0.000	0.000	0.000	0.000
32	A	1286	ASP	-1	-0.915	-0.810	16.438	0.143	0.143	0.000	0.000	0.000	0.000
33	A	1287	GLU	0	0.064	-0.114	17.842	0.010	0.010	0.000	0.000	0.000	0.000
34	A	1287	GLU	-1	-0.884	-0.783	15.598	0.140	0.140	0.000	0.000	0.000	0.000
35	A	1288	LYS	0	0.066	-0.116	19.644	0.011	0.011	0.000	0.000	0.000	0.000
36	A	1288	LYS	1	0.813	1.048	21.171	-0.005	-0.005	0.000	0.000	0.000	0.000
37	A	1289	GLU	0	0.109	-0.101	21.577	0.001	0.001	0.000	0.000	0.000	0.000
38	A	1289	GLU	-1	-0.983	-0.843	21.915	-0.040	-0.040	0.000	0.000	0.000	0.000
39	A	1290	LYS	0	0.082	-0.101	22.499	-0.005	-0.005	0.000	0.000	0.000	0.000
40	A	1290	LYS	1	0.726	0.997	19.023	-0.143	-0.143	0.000	0.000	0.000	0.000
41	A	1291	GLN	0	0.063	-0.095	24.248	0.006	0.006	0.000	0.000	0.000	0.000
42	A	1291	GLN	0	-0.068	0.090	24.283	-0.009	-0.009	0.000	0.000	0.000	0.000
43	A	1292	LEU	0	0.098	-0.092	26.077	0.004	0.004	0.000	0.000	0.000	0.000
44	A	1292	LEU	0	-0.086	0.125	26.716	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	1293	ALA	0	0.121	-0.093	27.086	-0.007	-0.007	0.000	0.000	0.000	0.000
46	A	1293	ALA	0	-0.084	0.106	27.160	0.002	0.002	0.000	0.000	0.000	0.000
47	A	1294	VAL	0	0.064	-0.092	28.477	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	1294	VAL	0	-0.087	0.085	28.208	0.002	0.002	0.000	0.000	0.000	0.000
49	A	1295	ALA	0	0.105	-0.098	30.333	0.002	0.002	0.000	0.000	0.000	0.000
50	A	1295	ALA	0	-0.082	0.104	31.244	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	1296	ASN	0	0.082	-0.069	31.835	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	1296	ASN	0	-0.141	0.033	31.034	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	1297	GLU	0	0.133	-0.099	33.012	-0.005	-0.005	0.000	0.000	0.000	0.000
54	A	1297	GLU	-1	-0.949	-0.793	33.248	0.035	0.035	0.000	0.000	0.000	0.000
55	A	1298	ILE	0	0.099	-0.083	34.678	0.001	0.001	0.000	0.000	0.000	0.000
56	A	1298	ILE	0	-0.107	0.087	33.895	0.000	0.000	0.000	0.000	0.000	0.000
57	A	1299	ILE	0	0.079	-0.101	36.336	0.001	0.001	0.000	0.000	0.000	0.000
58	A	1299	ILE	0	-0.082	0.103	35.290	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	1300	ARG	0	0.114	-0.068	37.547	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	1300	ARG	1	0.760	0.997	36.666	-0.029	-0.029	0.000	0.000	0.000	0.000
61	A	1301	SER	0	0.050	-0.086	38.901	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	1301	SER	0	-0.023	0.079	39.205	0.002	0.002	0.000	0.000	0.000	0.000
63	A	1302	LEU	0	0.041	-0.110	40.691	0.001	0.001	0.000	0.000	0.000	0.000
64	A	1302	LEU	0	-0.083	0.105	40.100	0.000	0.000	0.000	0.000	0.000	0.000
65	A	1303	SER	0	0.070	-0.082	42.146	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	1303	SER	0	-0.072	0.042	41.672	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	1304	ASP	0	0.068	-0.070	43.528	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	1304	ASP	-1	-0.940	-0.794	43.755	0.021	0.021	0.000	0.000	0.000	0.000
69	A	1305	GLU	0	0.098	-0.133	44.979	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	1305	GLU	-1	-1.001	-0.839	45.142	0.022	0.022	0.000	0.000	0.000	0.000
71	A	1306	VAL	0	0.013	-0.124	46.604	0.001	0.001	0.000	0.000	0.000	0.000
72	A	1306	VAL	0	-0.063	0.123	46.663	0.000	0.000	0.000	0.000	0.000	0.000
73	A	1307	MET	0	0.192	-0.055	48.159	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	1307	MET	0	-0.091	0.093	47.558	0.000	0.000	0.000	0.000	0.000	0.000
75	A	1308	ARG	0	0.046	-0.119	49.560	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	1308	ARG	1	0.728	0.967	46.574	-0.020	-0.020	0.000	0.000	0.000	0.000
77	A	1309	ASN	0	0.075	-0.079	51.067	0.000	0.000	0.000	0.000	0.000	0.000
78	A	1309	ASN	0	-0.155	0.049	49.909	0.000	0.000	0.000	0.000	0.000	0.000
79	A	1310	GLU	0	0.118	-0.126	52.637	0.000	0.000	0.000	0.000	0.000	0.000
80	A	1310	GLU	-1	-0.997	-0.821	52.010	0.002	0.002	0.000	0.000	0.000	0.000
81	A	1311	ILE	0	0.052	-0.086	54.230	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	1311	ILE	0	-0.096	0.100	53.608	0.000	0.000	0.000	0.000	0.000	0.000
83	A	1312	ARG	0	0.155	-0.066	55.515	0.000	0.000	0.000	0.000	0.000	0.000
84	A	1312	ARG	1	0.864	1.052	55.025	-0.017	-0.017	0.000	0.000	0.000	0.000
85	A	1313	ILE	0	0.018	-0.133	56.988	0.001	0.001	0.000	0.000	0.000	0.000
86	A	1313	ILE	0	-0.080	0.105	56.555	0.000	0.000	0.000	0.000	0.000	0.000
87	A	1314	THR	0	0.063	-0.086	58.610	0.000	0.000	0.000	0.000	0.000	0.000
88	A	1314	THR	0	-0.056	0.054	58.193	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	1315	SER	0	0.022	-0.081	60.204	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	1315	SER	0	-0.083	0.053	60.763	0.000	0.000	0.000	0.000	0.000	0.000
91	A	1316	LEU	0	0.086	-0.077	61.557	0.000	0.000	0.000	0.000	0.000	0.000
92	A	1316	LEU	0	-0.095	0.095	60.014	0.000	0.000	0.000	0.000	0.000	0.000
93	A	1317	GLN	0	0.042	-0.131	63.055	0.000	0.000	0.000	0.000	0.000	0.000
94	A	1317	GLN	0	-0.074	0.119	62.005	0.000	0.000	0.000	0.000	0.000	0.000
95	A	1318	GLY	0	0.034	-0.066	64.812	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	1319	ASP	0	0.086	-0.008	66.052	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	1319	ASP	-1	-0.914	-0.805	64.603	0.011	0.011	0.000	0.000	0.000	0.000
98	A	1320	LEU	0	0.126	-0.085	67.288	0.000	0.000	0.000	0.000	0.000	0.000
99	A	1320	LEU	0	-0.102	0.102	67.475	0.000	0.000	0.000	0.000	0.000	0.000
100	A	1321	THR	0	0.008	-0.113	68.977	0.000	0.000	0.000	0.000	0.000	0.000
101	A	1321	THR	0	-0.062	0.055	68.575	0.000	0.000	0.000	0.000	0.000	0.000
102	A	1322	PHE	0	0.086	-0.090	70.688	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	1322	PHE	0	-0.040	0.116	71.241	0.000	0.000	0.000	0.000	0.000	0.000
104	A	1323	THR	0	0.038	-0.086	71.815	0.000	0.000	0.000	0.000	0.000	0.000
105	A	1323	THR	0	-0.060	0.056	71.007	0.000	0.000	0.000	0.000	0.000	0.000
106	A	1324	LYS	0	0.049	-0.098	73.166	0.000	0.000	0.000	0.000	0.000	0.000
107	A	1324	LYS	1	0.861	1.065	70.504	-0.004	-0.004	0.000	0.000	0.000	0.000
108	A	1325	LYS	0	0.119	-0.077	75.012	0.000	0.000	0.000	0.000	0.000	0.000
109	A	1325	LYS	1	0.761	1.003	75.565	-0.003	-0.003	0.000	0.000	0.000	0.000
110	A	1326	CYS	0	0.076	-0.141	76.513	0.000	0.000	0.000	0.000	0.000	0.000
111	A	1326	CYS	0	-0.157	0.099	75.897	0.000	0.000	0.000	0.000	0.000	0.000
112	A	1327	LEU	0	0.108	-0.078	77.615	0.000	0.000	0.000	0.000	0.000	0.000
113	A	1327	LEU	0	-0.100	0.095	77.412	0.000	0.000	0.000	0.000	0.000	0.000
114	A	1328	GLU	0	0.103	-0.116	79.156	0.000	0.000	0.000	0.000	0.000	0.000
115	A	1328	GLU	-1	-0.896	-0.771	79.387	0.003	0.003	0.000	0.000	0.000	0.000
116	A	1329	ASN	0	0.104	-0.045	81.089	0.000	0.000	0.000	0.000	0.000	0.000
117	A	1329	ASN	0	-0.084	0.077	81.982	0.000	0.000	0.000	0.000	0.000	0.000
118	A	1330	ALA	0	0.156	-0.081	82.261	0.000	0.000	0.000	0.000	0.000	0.000
119	A	1330	ALA	0	-0.091	0.102	82.174	0.000	0.000	0.000	0.000	0.000	0.000
120	A	1331	ARG	0	-0.027	-0.150	83.326	0.000	0.000	0.000	0.000	0.000	0.000
121	A	1331	ARG	1	0.889	1.071	82.236	-0.005	-0.005	0.000	0.000	0.000	0.000
122	A	1332	SER	0	0.055	-0.062	85.038	0.000	0.000	0.000	0.000	0.000	0.000
123	A	1332	SER	0	-0.053	0.060	84.972	0.000	0.000	0.000	0.000	0.000	0.000
124	A	1333	GLN	0	0.139	-0.069	86.960	0.000	0.000	0.000	0.000	0.000	0.000
125	A	1333	GLN	0	-0.104	0.087	85.756	0.000	0.000	0.000	0.000	0.000	0.000
126	A	1334	ILE	0	0.070	-0.065	87.784	0.000	0.000	0.000	0.000	0.000	0.000
127	A	1334	ILE	0	-0.093	0.078	85.648	0.000	0.000	0.000	0.000	0.000	0.000
128	A	1335	SER	0	0.123	-0.059	89.319	0.000	0.000	0.000	0.000	0.000	0.000
129	A	1335	SER	0	-0.029	0.073	89.795	0.000	0.000	0.000	0.000	0.000	0.000
130	A	1336	GLU	0	0.008	-0.128	91.264	0.000	0.000	0.000	0.000	0.000	0.000
131	A	1336	GLU	-1	-0.994	-0.864	89.941	0.004	0.004	0.000	0.000	0.000	0.000
132	A	1337	LYS	0	-0.010	-0.109	92.500	0.000	0.000	0.000	0.000	0.000	0.000
133	A	1337	LYS	1	0.792	1.011	90.288	-0.005	-0.005	0.000	0.000	0.000	0.000
134	A	1338	ASP	0	0.141	-0.084	93.448	0.000	0.000	0.000	0.000	0.000	0.000
135	A	1338	ASP	-1	-0.983	-0.837	92.150	0.005	0.005	0.000	0.000	0.000	0.000
136	A	1339	ALA	0	0.134	-0.070	95.127	0.000	0.000	0.000	0.000	0.000	0.000
137	A	1339	ALA	0	-0.078	0.105	96.268	0.000	0.000	0.000	0.000	0.000	0.000
138	A	1340	LYS	0	-0.006	-0.111	97.072	0.000	0.000	0.000	0.000	0.000	0.000
139	A	1340	LYS	1	0.826	1.033	97.216	-0.004	-0.004	0.000	0.000	0.000	0.000
140	A	1341	ILE	0	0.109	-0.089	97.978	0.000	0.000	0.000	0.000	0.000	0.000
141	A	1341	ILE	0	-0.083	0.101	96.846	0.000	0.000	0.000	0.000	0.000	0.000
142	A	1342	ASN	0	0.125	-0.059	99.177	0.000	0.000	0.000	0.000	0.000	0.000
143	A	1342	ASN	0	-0.155	0.030	97.713	0.000	0.000	0.000	0.000	0.000	0.000
144	A	1343	LYS	0	0.153	-0.047	101.006	0.000	0.000	0.000	0.000	0.000	0.000
145	A	1343	LYS	1	0.848	1.038	102.500	-0.003	-0.003	0.000	0.000	0.000	0.000
146	A	1344	LEU	0	-0.030	-0.106	102.907	0.000	0.000	0.000	0.000	0.000	0.000
147	A	1344	LEU	0	-0.115	0.061	102.153	0.000	0.000	0.000	0.000	0.000	0.000
148	A	1345	MET	0	0.090	-0.107	104.233	0.000	0.000	0.000	0.000	0.000	0.000
149	A	1345	MET	0	-0.106	0.093	102.417	0.000	0.000	0.000	0.000	0.000	0.000
150	A	1346	GLU	0	-0.144	-0.167	105.332	0.000	0.000	0.000	0.000	0.000	0.000
151	A	1346	GLU	-1	-0.878	-0.924	106.446	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:1271:LEU)