FMO DATABASE

FMODB ID: 9MZG2

Calculation Name: 1NYH-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

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	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422
Remarks

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	-326519.932586
FMO2-HF: Nuclear repulsion	296340.648636
FMO2-HF: Total energy	-30179.28395
FMO2-MP2: Total energy	-30265.875963

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: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.
-3.021	-1.132	0.009	-0.821	-1.076	0.003

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 : 0.126 / q_NPA : 0.046

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	-0.027	0.072	4.600	0.516	0.653	-0.001	-0.053	-0.083	0.000
5	A	1273	PHE	0	0.126	-0.077	3.842	1.104	2.060	-0.008	-0.575	-0.373	0.003
6	A	1273	PHE	0	-0.055	0.108	6.953	0.015	0.015	0.000	0.000	0.000	0.000
7	A	1274	VAL	0	0.057	-0.136	6.357	0.561	0.561	0.000	0.000	0.000	0.000
8	A	1274	VAL	0	-0.030	0.130	7.682	-0.019	-0.019	0.000	0.000	0.000	0.000
9	A	1275	ASP	0	0.108	-0.100	4.328	0.567	0.623	0.000	0.003	-0.058	0.000
10	A	1275	ASP	-1	-0.977	-0.834	3.683	-4.646	-4.366	0.013	-0.022	-0.271	-0.001
11	A	1276	ILE	0	0.049	-0.100	5.720	0.719	0.812	-0.002	-0.004	-0.087	0.000
12	A	1276	ILE	0	-0.109	0.088	3.746	-0.725	-0.358	0.007	-0.170	-0.204	0.001
13	A	1277	VAL	0	0.088	-0.128	6.539	-0.064	-0.064	0.000	0.000	0.000	0.000
14	A	1277	VAL	0	-0.093	0.113	9.716	-0.025	-0.025	0.000	0.000	0.000	0.000
15	A	1278	LEU	0	0.068	-0.135	9.531	0.078	0.078	0.000	0.000	0.000	0.000
16	A	1278	LEU	0	-0.036	0.147	8.829	-0.013	-0.013	0.000	0.000	0.000	0.000
17	A	1279	SER	0	0.040	-0.082	8.607	-0.226	-0.226	0.000	0.000	0.000	0.000
18	A	1279	SER	0	-0.066	0.092	7.370	0.132	0.132	0.000	0.000	0.000	0.000
19	A	1280	LYS	0	0.086	-0.093	9.840	-0.033	-0.033	0.000	0.000	0.000	0.000
20	A	1280	LYS	1	0.862	1.061	9.994	-0.937	-0.937	0.000	0.000	0.000	0.000
21	A	1281	ALA	0	0.128	-0.078	12.184	-0.033	-0.033	0.000	0.000	0.000	0.000
22	A	1281	ALA	0	-0.105	0.106	13.915	-0.018	-0.018	0.000	0.000	0.000	0.000
23	A	1282	ALA	0	0.111	-0.147	13.186	-0.046	-0.046	0.000	0.000	0.000	0.000
24	A	1282	ALA	0	-0.100	0.139	12.773	-0.004	-0.004	0.000	0.000	0.000	0.000
25	A	1283	SER	0	0.017	-0.087	13.820	-0.070	-0.070	0.000	0.000	0.000	0.000
26	A	1283	SER	0	-0.062	0.081	13.315	0.048	0.048	0.000	0.000	0.000	0.000
27	A	1284	ALA	0	0.185	-0.094	15.297	-0.020	-0.020	0.000	0.000	0.000	0.000
28	A	1284	ALA	0	-0.137	0.105	17.201	-0.005	-0.005	0.000	0.000	0.000	0.000
29	A	1285	LEU	0	0.081	-0.132	17.902	-0.017	-0.017	0.000	0.000	0.000	0.000
30	A	1285	LEU	0	-0.094	0.125	18.382	-0.005	-0.005	0.000	0.000	0.000	0.000
31	A	1286	ASP	0	0.082	-0.104	18.182	-0.036	-0.036	0.000	0.000	0.000	0.000
32	A	1286	ASP	-1	-0.946	-0.831	17.680	0.245	0.245	0.000	0.000	0.000	0.000
33	A	1287	GLU	0	0.140	-0.092	19.307	-0.023	-0.023	0.000	0.000	0.000	0.000
34	A	1287	GLU	-1	-1.083	-0.875	18.373	0.347	0.347	0.000	0.000	0.000	0.000
35	A	1288	LYS	0	0.072	-0.137	21.206	-0.017	-0.017	0.000	0.000	0.000	0.000
36	A	1288	LYS	1	0.808	1.051	22.981	-0.138	-0.138	0.000	0.000	0.000	0.000
37	A	1289	GLU	0	0.114	-0.138	22.898	-0.014	-0.014	0.000	0.000	0.000	0.000
38	A	1289	GLU	-1	-1.007	-0.809	22.732	0.073	0.073	0.000	0.000	0.000	0.000
39	A	1290	LYS	0	0.067	-0.105	24.014	-0.019	-0.019	0.000	0.000	0.000	0.000
40	A	1290	LYS	1	0.781	1.029	20.204	-0.222	-0.222	0.000	0.000	0.000	0.000
41	A	1291	GLN	0	0.050	-0.104	25.640	-0.009	-0.009	0.000	0.000	0.000	0.000
42	A	1291	GLN	0	-0.061	0.103	25.278	0.005	0.005	0.000	0.000	0.000	0.000
43	A	1292	LEU	0	0.117	-0.127	27.482	-0.006	-0.006	0.000	0.000	0.000	0.000
44	A	1292	LEU	0	-0.095	0.150	28.102	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	1293	ALA	0	0.107	-0.127	28.268	-0.012	-0.012	0.000	0.000	0.000	0.000
46	A	1293	ALA	0	-0.088	0.128	28.038	0.001	0.001	0.000	0.000	0.000	0.000
47	A	1294	VAL	0	0.027	-0.104	29.828	-0.008	-0.008	0.000	0.000	0.000	0.000
48	A	1294	VAL	0	-0.073	0.077	29.280	0.001	0.001	0.000	0.000	0.000	0.000
49	A	1295	ALA	0	0.133	-0.116	31.694	-0.005	-0.005	0.000	0.000	0.000	0.000
50	A	1295	ALA	0	-0.110	0.132	32.652	0.000	0.000	0.000	0.000	0.000	0.000
51	A	1296	ASN	0	0.081	-0.086	33.131	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	1296	ASN	0	-0.111	0.074	31.852	-0.005	-0.005	0.000	0.000	0.000	0.000
53	A	1297	GLU	0	0.150	-0.081	34.316	-0.007	-0.007	0.000	0.000	0.000	0.000
54	A	1297	GLU	-1	-0.989	-0.829	34.195	0.061	0.061	0.000	0.000	0.000	0.000
55	A	1298	ILE	0	0.152	-0.082	36.044	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	1298	ILE	0	-0.124	0.099	35.669	0.000	0.000	0.000	0.000	0.000	0.000
57	A	1299	ILE	0	0.087	-0.130	37.654	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	1299	ILE	0	-0.100	0.127	36.329	0.000	0.000	0.000	0.000	0.000	0.000
59	A	1300	ARG	0	0.092	-0.069	38.720	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	1300	ARG	1	0.781	1.016	37.697	-0.047	-0.047	0.000	0.000	0.000	0.000
61	A	1301	SER	0	0.101	-0.061	40.056	-0.004	-0.004	0.000	0.000	0.000	0.000
62	A	1301	SER	0	-0.085	0.043	40.207	0.000	0.000	0.000	0.000	0.000	0.000
63	A	1302	LEU	0	0.030	-0.138	41.941	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	1302	LEU	0	-0.068	0.118	41.789	0.000	0.000	0.000	0.000	0.000	0.000
65	A	1303	SER	0	0.055	-0.071	43.307	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	1303	SER	0	-0.059	0.078	43.249	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	1304	ASP	0	0.138	-0.093	44.725	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	1304	ASP	-1	-1.072	-0.881	44.930	0.036	0.036	0.000	0.000	0.000	0.000
69	A	1305	GLU	0	0.061	-0.114	46.298	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	1305	GLU	-1	-1.002	-0.850	46.935	0.042	0.042	0.000	0.000	0.000	0.000
71	A	1306	VAL	0	0.050	-0.141	47.863	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	1306	VAL	0	-0.091	0.143	48.114	0.000	0.000	0.000	0.000	0.000	0.000
73	A	1307	MET	0	0.171	-0.070	49.258	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	1307	MET	0	-0.097	0.092	48.624	0.000	0.000	0.000	0.000	0.000	0.000
75	A	1308	ARG	0	0.047	-0.117	50.737	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	1308	ARG	1	0.831	1.034	46.949	-0.034	-0.034	0.000	0.000	0.000	0.000
77	A	1309	ASN	0	0.080	-0.105	52.236	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	1309	ASN	0	-0.126	0.084	51.468	0.000	0.000	0.000	0.000	0.000	0.000
79	A	1310	GLU	0	0.103	-0.111	53.860	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	1310	GLU	-1	-0.984	-0.822	53.198	0.022	0.022	0.000	0.000	0.000	0.000
81	A	1311	ILE	0	0.028	-0.106	55.539	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	1311	ILE	0	-0.114	0.086	54.721	0.000	0.000	0.000	0.000	0.000	0.000
83	A	1312	ARG	0	0.194	-0.064	56.820	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	1312	ARG	1	0.863	1.066	56.304	-0.028	-0.028	0.000	0.000	0.000	0.000
85	A	1313	ILE	0	0.017	-0.156	58.131	0.000	0.000	0.000	0.000	0.000	0.000
86	A	1313	ILE	0	-0.093	0.122	57.270	0.000	0.000	0.000	0.000	0.000	0.000
87	A	1314	THR	0	0.078	-0.066	59.937	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	1314	THR	0	-0.031	0.088	59.957	0.000	0.000	0.000	0.000	0.000	0.000
89	A	1315	SER	0	0.002	-0.086	61.407	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	1315	SER	0	-0.048	0.081	61.580	0.000	0.000	0.000	0.000	0.000	0.000
91	A	1316	LEU	0	0.107	-0.094	62.729	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	1316	LEU	0	-0.097	0.109	61.612	0.000	0.000	0.000	0.000	0.000	0.000
93	A	1317	GLN	0	0.082	-0.121	64.188	0.000	0.000	0.000	0.000	0.000	0.000
94	A	1317	GLN	0	-0.090	0.131	63.560	0.000	0.000	0.000	0.000	0.000	0.000
95	A	1318	GLY	0	0.018	-0.089	65.893	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	1319	ASP	0	0.133	-0.025	67.199	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	1319	ASP	-1	-1.016	-0.832	66.456	0.019	0.019	0.000	0.000	0.000	0.000
98	A	1320	LEU	0	0.121	-0.127	68.458	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	1320	LEU	0	-0.156	0.111	68.469	0.000	0.000	0.000	0.000	0.000	0.000
100	A	1321	THR	0	0.016	-0.133	70.103	0.000	0.000	0.000	0.000	0.000	0.000
101	A	1321	THR	0	-0.055	0.064	69.740	0.000	0.000	0.000	0.000	0.000	0.000
102	A	1322	PHE	0	0.069	-0.069	71.875	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	1322	PHE	0	-0.034	0.116	72.717	0.000	0.000	0.000	0.000	0.000	0.000
104	A	1323	THR	0	0.061	-0.106	73.143	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	1323	THR	0	-0.025	0.089	72.424	0.000	0.000	0.000	0.000	0.000	0.000
106	A	1324	LYS	0	0.070	-0.089	74.422	0.000	0.000	0.000	0.000	0.000	0.000
107	A	1324	LYS	1	0.862	1.086	72.207	-0.015	-0.015	0.000	0.000	0.000	0.000
108	A	1325	LYS	0	0.145	-0.084	76.269	0.000	0.000	0.000	0.000	0.000	0.000
109	A	1325	LYS	1	0.859	1.089	77.010	-0.011	-0.011	0.000	0.000	0.000	0.000
110	A	1326	CYS	0	0.096	-0.154	77.718	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	1326	CYS	0	-0.175	0.130	77.301	0.000	0.000	0.000	0.000	0.000	0.000
112	A	1327	LEU	0	0.125	-0.128	78.761	0.000	0.000	0.000	0.000	0.000	0.000
113	A	1327	LEU	0	-0.143	0.125	78.689	0.000	0.000	0.000	0.000	0.000	0.000
114	A	1328	GLU	0	0.068	-0.135	80.283	0.000	0.000	0.000	0.000	0.000	0.000
115	A	1328	GLU	-1	-1.019	-0.856	80.531	0.011	0.011	0.000	0.000	0.000	0.000
116	A	1329	ASN	0	0.116	-0.082	82.244	0.000	0.000	0.000	0.000	0.000	0.000
117	A	1329	ASN	0	-0.137	0.058	82.751	0.000	0.000	0.000	0.000	0.000	0.000
118	A	1330	ALA	0	0.191	-0.088	83.545	0.000	0.000	0.000	0.000	0.000	0.000
119	A	1330	ALA	0	-0.105	0.126	83.665	0.000	0.000	0.000	0.000	0.000	0.000
120	A	1331	ARG	0	-0.006	-0.164	84.514	0.000	0.000	0.000	0.000	0.000	0.000
121	A	1331	ARG	1	0.886	1.076	83.379	-0.012	-0.012	0.000	0.000	0.000	0.000
122	A	1332	SER	0	0.044	-0.048	86.194	0.000	0.000	0.000	0.000	0.000	0.000
123	A	1332	SER	0	-0.039	0.089	86.992	0.000	0.000	0.000	0.000	0.000	0.000
124	A	1333	GLN	0	0.145	-0.074	88.413	0.000	0.000	0.000	0.000	0.000	0.000
125	A	1333	GLN	0	-0.148	0.060	86.650	0.000	0.000	0.000	0.000	0.000	0.000
126	A	1334	ILE	0	0.089	-0.078	89.207	0.000	0.000	0.000	0.000	0.000	0.000
127	A	1334	ILE	0	-0.079	0.102	87.227	0.000	0.000	0.000	0.000	0.000	0.000
128	A	1335	SER	0	0.138	-0.038	90.572	0.000	0.000	0.000	0.000	0.000	0.000
129	A	1335	SER	0	-0.045	0.069	91.069	0.000	0.000	0.000	0.000	0.000	0.000
130	A	1336	GLU	0	0.051	-0.106	92.499	0.000	0.000	0.000	0.000	0.000	0.000
131	A	1336	GLU	-1	-1.089	-0.891	92.487	0.009	0.009	0.000	0.000	0.000	0.000
132	A	1337	LYS	0	-0.008	-0.126	93.851	0.000	0.000	0.000	0.000	0.000	0.000
133	A	1337	LYS	1	0.876	1.052	92.237	-0.010	-0.010	0.000	0.000	0.000	0.000
134	A	1338	ASP	0	0.147	-0.106	94.718	0.000	0.000	0.000	0.000	0.000	0.000
135	A	1338	ASP	-1	-1.019	-0.834	94.256	0.010	0.010	0.000	0.000	0.000	0.000
136	A	1339	ALA	0	0.120	-0.078	96.243	0.000	0.000	0.000	0.000	0.000	0.000
137	A	1339	ALA	0	-0.088	0.098	97.854	0.000	0.000	0.000	0.000	0.000	0.000
138	A	1340	LYS	0	0.026	-0.096	98.620	0.000	0.000	0.000	0.000	0.000	0.000
139	A	1340	LYS	1	0.842	1.030	98.902	-0.008	-0.008	0.000	0.000	0.000	0.000
140	A	1341	ILE	0	0.048	-0.106	99.148	0.000	0.000	0.000	0.000	0.000	0.000
141	A	1341	ILE	0	-0.062	0.106	97.954	0.000	0.000	0.000	0.000	0.000	0.000
142	A	1342	ASN	0	0.115	-0.078	100.272	0.000	0.000	0.000	0.000	0.000	0.000
143	A	1342	ASN	0	-0.109	0.061	99.565	0.000	0.000	0.000	0.000	0.000	0.000
144	A	1343	LYS	0	0.141	-0.042	102.084	0.000	0.000	0.000	0.000	0.000	0.000
145	A	1343	LYS	1	0.791	1.021	103.345	-0.007	-0.007	0.000	0.000	0.000	0.000
146	A	1344	LEU	0	-0.054	-0.093	104.159	0.000	0.000	0.000	0.000	0.000	0.000
147	A	1344	LEU	0	-0.121	0.048	103.829	0.000	0.000	0.000	0.000	0.000	0.000
148	A	1345	MET	0	0.115	-0.100	105.668	0.000	0.000	0.000	0.000	0.000	0.000
149	A	1345	MET	0	-0.065	0.114	102.473	0.000	0.000	0.000	0.000	0.000	0.000
150	A	1346	GLU	0	-0.123	-0.170	106.719	0.000	0.000	0.000	0.000	0.000	0.000
151	A	1346	GLU	-1	-0.877	-0.923	108.027	0.007	0.007	0.000	0.000	0.000	0.000

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