FMO DATABASE

FMODB ID: 37LQL

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	OptHSide
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	-326520.696186
FMO2-HF: Nuclear repulsion	296338.729021
FMO2-HF: Total energy	-30181.967166
FMO2-MP2: Total energy	-30268.533687

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.
-5.312	-2.552	0.132	-1.301	-1.59	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 : 0.185 / q_NPA : 0.068

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	-0.036	0.072	4.864	0.523	0.713	-0.001	-0.079	-0.110	0.000
5	A	1273	PHE	0	0.104	-0.074	3.842	-2.161	-0.106	-0.011	-1.302	-0.742	0.007
6	A	1273	PHE	0	-0.058	0.100	7.041	0.110	0.110	0.000	0.000	0.000	0.000
7	A	1274	VAL	0	0.047	-0.115	6.192	0.494	0.494	0.000	0.000	0.000	0.000
8	A	1274	VAL	0	-0.038	0.117	7.892	0.034	0.034	0.000	0.000	0.000	0.000
9	A	1275	ASP	0	0.080	-0.118	4.424	1.195	1.255	-0.001	0.000	-0.058	0.000
10	A	1275	ASP	-1	-0.868	-0.807	3.647	-7.468	-7.477	0.021	0.270	-0.282	-0.002
11	A	1276	ILE	0	0.034	-0.073	5.231	0.539	0.539	0.000	0.000	0.000	0.000
12	A	1276	ILE	0	-0.097	0.086	2.793	-0.306	0.158	0.124	-0.190	-0.398	0.001
13	A	1277	VAL	0	0.091	-0.098	5.576	0.469	0.469	0.000	0.000	0.000	0.000
14	A	1277	VAL	0	-0.089	0.099	9.301	0.028	0.028	0.000	0.000	0.000	0.000
15	A	1278	LEU	0	0.078	-0.103	9.027	0.304	0.304	0.000	0.000	0.000	0.000
16	A	1278	LEU	0	-0.037	0.114	8.847	0.007	0.007	0.000	0.000	0.000	0.000
17	A	1279	SER	0	0.037	-0.096	7.639	0.171	0.171	0.000	0.000	0.000	0.000
18	A	1279	SER	0	-0.073	0.066	6.410	0.189	0.189	0.000	0.000	0.000	0.000
19	A	1280	LYS	0	0.060	-0.093	8.920	0.222	0.222	0.000	0.000	0.000	0.000
20	A	1280	LYS	1	0.861	1.055	9.217	0.007	0.007	0.000	0.000	0.000	0.000
21	A	1281	ALA	0	0.132	-0.063	11.179	0.125	0.125	0.000	0.000	0.000	0.000
22	A	1281	ALA	0	-0.099	0.095	13.231	-0.011	-0.011	0.000	0.000	0.000	0.000
23	A	1282	ALA	0	0.080	-0.099	12.490	0.075	0.075	0.000	0.000	0.000	0.000
24	A	1282	ALA	0	-0.079	0.096	12.134	-0.012	-0.012	0.000	0.000	0.000	0.000
25	A	1283	SER	0	0.040	-0.092	12.850	0.041	0.041	0.000	0.000	0.000	0.000
26	A	1283	SER	0	-0.074	0.048	12.450	0.035	0.035	0.000	0.000	0.000	0.000
27	A	1284	ALA	0	0.117	-0.048	14.330	0.048	0.048	0.000	0.000	0.000	0.000
28	A	1284	ALA	0	-0.121	0.076	16.143	-0.006	-0.006	0.000	0.000	0.000	0.000
29	A	1285	LEU	0	0.084	-0.117	16.914	0.041	0.041	0.000	0.000	0.000	0.000
30	A	1285	LEU	0	-0.087	0.110	17.694	-0.010	-0.010	0.000	0.000	0.000	0.000
31	A	1286	ASP	0	0.081	-0.082	17.261	0.011	0.011	0.000	0.000	0.000	0.000
32	A	1286	ASP	-1	-0.911	-0.815	16.728	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	1287	GLU	0	0.164	-0.091	18.350	0.020	0.020	0.000	0.000	0.000	0.000
34	A	1287	GLU	-1	-1.010	-0.844	16.373	-0.014	-0.014	0.000	0.000	0.000	0.000
35	A	1288	LYS	0	0.025	-0.129	20.256	0.019	0.019	0.000	0.000	0.000	0.000
36	A	1288	LYS	1	0.805	1.039	21.875	0.077	0.077	0.000	0.000	0.000	0.000
37	A	1289	GLU	0	0.104	-0.110	21.931	0.011	0.011	0.000	0.000	0.000	0.000
38	A	1289	GLU	-1	-0.982	-0.838	22.076	-0.115	-0.115	0.000	0.000	0.000	0.000
39	A	1290	LYS	0	0.088	-0.105	23.090	0.003	0.003	0.000	0.000	0.000	0.000
40	A	1290	LYS	1	0.731	0.994	19.287	-0.021	-0.021	0.000	0.000	0.000	0.000
41	A	1291	GLN	0	0.049	-0.084	24.692	0.010	0.010	0.000	0.000	0.000	0.000
42	A	1291	GLN	0	-0.064	0.087	24.449	-0.012	-0.012	0.000	0.000	0.000	0.000
43	A	1292	LEU	0	0.100	-0.114	26.520	0.010	0.010	0.000	0.000	0.000	0.000
44	A	1292	LEU	0	-0.090	0.132	27.125	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	1293	ALA	0	0.118	-0.093	27.338	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	1293	ALA	0	-0.081	0.110	27.223	0.001	0.001	0.000	0.000	0.000	0.000
47	A	1294	VAL	0	0.042	-0.101	28.914	0.002	0.002	0.000	0.000	0.000	0.000
48	A	1294	VAL	0	-0.097	0.080	28.415	0.002	0.002	0.000	0.000	0.000	0.000
49	A	1295	ALA	0	0.114	-0.085	30.758	0.006	0.006	0.000	0.000	0.000	0.000
50	A	1295	ALA	0	-0.088	0.098	31.691	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	1296	ASN	0	0.081	-0.079	32.190	0.003	0.003	0.000	0.000	0.000	0.000
52	A	1296	ASN	0	-0.124	0.044	31.236	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	1297	GLU	0	0.154	-0.072	33.410	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	1297	GLU	-1	-0.957	-0.796	33.450	0.001	0.001	0.000	0.000	0.000	0.000
55	A	1298	ILE	0	0.116	-0.078	35.152	0.002	0.002	0.000	0.000	0.000	0.000
56	A	1298	ILE	0	-0.111	0.081	34.637	0.000	0.000	0.000	0.000	0.000	0.000
57	A	1299	ILE	0	0.094	-0.092	36.720	0.003	0.003	0.000	0.000	0.000	0.000
58	A	1299	ILE	0	-0.095	0.100	35.788	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	1300	ARG	0	0.134	-0.047	37.804	0.000	0.000	0.000	0.000	0.000	0.000
60	A	1300	ARG	1	0.754	0.993	36.899	0.002	0.002	0.000	0.000	0.000	0.000
61	A	1301	SER	0	0.059	-0.088	39.163	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	1301	SER	0	-0.047	0.065	39.412	0.002	0.002	0.000	0.000	0.000	0.000
63	A	1302	LEU	0	0.016	-0.120	41.053	0.002	0.002	0.000	0.000	0.000	0.000
64	A	1302	LEU	0	-0.073	0.099	40.850	0.000	0.000	0.000	0.000	0.000	0.000
65	A	1303	SER	0	0.079	-0.082	42.384	0.001	0.001	0.000	0.000	0.000	0.000
66	A	1303	SER	0	-0.064	0.046	41.842	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	1304	ASP	0	0.085	-0.067	43.835	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	1304	ASP	-1	-0.965	-0.809	43.871	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	1305	GLU	0	0.124	-0.116	45.403	0.000	0.000	0.000	0.000	0.000	0.000
70	A	1305	GLU	-1	-1.018	-0.850	45.826	0.001	0.001	0.000	0.000	0.000	0.000
71	A	1306	VAL	0	0.002	-0.143	46.944	0.001	0.001	0.000	0.000	0.000	0.000
72	A	1306	VAL	0	-0.078	0.117	46.788	0.000	0.000	0.000	0.000	0.000	0.000
73	A	1307	MET	0	0.184	-0.044	48.348	0.000	0.000	0.000	0.000	0.000	0.000
74	A	1307	MET	0	-0.091	0.084	47.679	0.000	0.000	0.000	0.000	0.000	0.000
75	A	1308	ARG	0	0.074	-0.100	49.842	0.000	0.000	0.000	0.000	0.000	0.000
76	A	1308	ARG	1	0.698	0.956	46.812	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	1309	ASN	0	0.078	-0.077	51.333	0.001	0.001	0.000	0.000	0.000	0.000
78	A	1309	ASN	0	-0.139	0.062	50.202	0.001	0.001	0.000	0.000	0.000	0.000
79	A	1310	GLU	0	0.127	-0.129	52.941	0.001	0.001	0.000	0.000	0.000	0.000
80	A	1310	GLU	-1	-0.994	-0.815	52.675	-0.015	-0.015	0.000	0.000	0.000	0.000
81	A	1311	ILE	0	0.042	-0.094	54.637	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	1311	ILE	0	-0.113	0.086	53.745	0.000	0.000	0.000	0.000	0.000	0.000
83	A	1312	ARG	0	0.192	-0.056	55.929	0.000	0.000	0.000	0.000	0.000	0.000
84	A	1312	ARG	1	0.857	1.057	55.294	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	1313	ILE	0	0.000	-0.138	57.215	0.001	0.001	0.000	0.000	0.000	0.000
86	A	1313	ILE	0	-0.091	0.096	56.560	0.000	0.000	0.000	0.000	0.000	0.000
87	A	1314	THR	0	0.072	-0.075	59.023	0.000	0.000	0.000	0.000	0.000	0.000
88	A	1314	THR	0	-0.041	0.067	58.768	0.000	0.000	0.000	0.000	0.000	0.000
89	A	1315	SER	0	0.051	-0.070	60.510	0.000	0.000	0.000	0.000	0.000	0.000
90	A	1315	SER	0	-0.067	0.068	60.901	0.000	0.000	0.000	0.000	0.000	0.000
91	A	1316	LEU	0	0.081	-0.057	61.832	0.000	0.000	0.000	0.000	0.000	0.000
92	A	1316	LEU	0	-0.107	0.088	60.402	0.000	0.000	0.000	0.000	0.000	0.000
93	A	1317	GLN	0	0.076	-0.114	63.273	0.001	0.001	0.000	0.000	0.000	0.000
94	A	1317	GLN	0	-0.083	0.108	62.663	0.000	0.000	0.000	0.000	0.000	0.000
95	A	1318	GLY	0	0.007	-0.083	64.987	0.000	0.000	0.000	0.000	0.000	0.000
96	A	1319	ASP	0	0.090	-0.011	66.305	0.000	0.000	0.000	0.000	0.000	0.000
97	A	1319	ASP	-1	-0.951	-0.833	65.170	0.000	0.000	0.000	0.000	0.000	0.000
98	A	1320	LEU	0	0.117	-0.100	67.553	0.000	0.000	0.000	0.000	0.000	0.000
99	A	1320	LEU	0	-0.127	0.089	67.684	0.000	0.000	0.000	0.000	0.000	0.000
100	A	1321	THR	0	0.004	-0.119	69.188	0.000	0.000	0.000	0.000	0.000	0.000
101	A	1321	THR	0	-0.066	0.056	68.781	0.000	0.000	0.000	0.000	0.000	0.000
102	A	1322	PHE	0	0.113	-0.079	70.973	0.000	0.000	0.000	0.000	0.000	0.000
103	A	1322	PHE	0	-0.052	0.110	71.751	0.000	0.000	0.000	0.000	0.000	0.000
104	A	1323	THR	0	0.026	-0.085	72.247	0.000	0.000	0.000	0.000	0.000	0.000
105	A	1323	THR	0	-0.037	0.068	71.436	0.000	0.000	0.000	0.000	0.000	0.000
106	A	1324	LYS	0	0.097	-0.081	73.509	0.000	0.000	0.000	0.000	0.000	0.000
107	A	1324	LYS	1	0.869	1.072	71.118	0.005	0.005	0.000	0.000	0.000	0.000
108	A	1325	LYS	0	0.113	-0.074	75.351	0.000	0.000	0.000	0.000	0.000	0.000
109	A	1325	LYS	1	0.757	1.006	76.020	0.005	0.005	0.000	0.000	0.000	0.000
110	A	1326	CYS	0	0.055	-0.145	76.819	0.000	0.000	0.000	0.000	0.000	0.000
111	A	1326	CYS	0	-0.159	0.098	76.247	0.000	0.000	0.000	0.000	0.000	0.000
112	A	1327	LEU	0	0.117	-0.084	77.856	0.000	0.000	0.000	0.000	0.000	0.000
113	A	1327	LEU	0	-0.119	0.091	77.873	0.000	0.000	0.000	0.000	0.000	0.000
114	A	1328	GLU	0	0.084	-0.111	79.369	0.000	0.000	0.000	0.000	0.000	0.000
115	A	1328	GLU	-1	-0.919	-0.797	79.707	-0.005	-0.005	0.000	0.000	0.000	0.000
116	A	1329	ASN	0	0.093	-0.046	81.325	0.000	0.000	0.000	0.000	0.000	0.000
117	A	1329	ASN	0	-0.111	0.052	82.170	0.000	0.000	0.000	0.000	0.000	0.000
118	A	1330	ALA	0	0.163	-0.083	82.649	0.000	0.000	0.000	0.000	0.000	0.000
119	A	1330	ALA	0	-0.093	0.096	82.699	0.000	0.000	0.000	0.000	0.000	0.000
120	A	1331	ARG	0	-0.016	-0.137	83.608	0.000	0.000	0.000	0.000	0.000	0.000
121	A	1331	ARG	1	0.885	1.065	82.409	0.002	0.002	0.000	0.000	0.000	0.000
122	A	1332	SER	0	0.053	-0.049	85.278	0.000	0.000	0.000	0.000	0.000	0.000
123	A	1332	SER	0	-0.030	0.073	86.330	0.000	0.000	0.000	0.000	0.000	0.000
124	A	1333	GLN	0	0.189	-0.037	87.516	0.000	0.000	0.000	0.000	0.000	0.000
125	A	1333	GLN	0	-0.125	0.063	86.043	0.000	0.000	0.000	0.000	0.000	0.000
126	A	1334	ILE	0	0.078	-0.066	88.304	0.000	0.000	0.000	0.000	0.000	0.000
127	A	1334	ILE	0	-0.085	0.082	86.169	0.000	0.000	0.000	0.000	0.000	0.000
128	A	1335	SER	0	0.150	-0.038	89.648	0.000	0.000	0.000	0.000	0.000	0.000
129	A	1335	SER	0	-0.040	0.064	90.000	0.000	0.000	0.000	0.000	0.000	0.000
130	A	1336	GLU	0	0.031	-0.103	91.578	0.000	0.000	0.000	0.000	0.000	0.000
131	A	1336	GLU	-1	-1.056	-0.893	90.739	-0.002	-0.002	0.000	0.000	0.000	0.000
132	A	1337	LYS	0	-0.039	-0.128	92.956	0.000	0.000	0.000	0.000	0.000	0.000
133	A	1337	LYS	1	0.840	1.016	90.664	0.000	0.000	0.000	0.000	0.000	0.000
134	A	1338	ASP	0	0.128	-0.098	93.808	0.000	0.000	0.000	0.000	0.000	0.000
135	A	1338	ASP	-1	-0.973	-0.825	92.749	-0.001	-0.001	0.000	0.000	0.000	0.000
136	A	1339	ALA	0	0.124	-0.066	95.333	0.000	0.000	0.000	0.000	0.000	0.000
137	A	1339	ALA	0	-0.087	0.097	96.856	0.000	0.000	0.000	0.000	0.000	0.000
138	A	1340	LYS	0	0.008	-0.109	97.719	0.000	0.000	0.000	0.000	0.000	0.000
139	A	1340	LYS	1	0.860	1.028	97.892	0.001	0.001	0.000	0.000	0.000	0.000
140	A	1341	ILE	0	0.062	-0.082	98.242	0.000	0.000	0.000	0.000	0.000	0.000
141	A	1341	ILE	0	-0.067	0.108	96.943	0.000	0.000	0.000	0.000	0.000	0.000
142	A	1342	ASN	0	0.079	-0.076	99.387	0.000	0.000	0.000	0.000	0.000	0.000
143	A	1342	ASN	0	-0.148	0.030	97.887	0.000	0.000	0.000	0.000	0.000	0.000
144	A	1343	LYS	0	0.173	-0.031	101.168	0.000	0.000	0.000	0.000	0.000	0.000
145	A	1343	LYS	1	0.813	1.019	102.646	0.002	0.002	0.000	0.000	0.000	0.000
146	A	1344	LEU	0	-0.055	-0.100	103.260	0.000	0.000	0.000	0.000	0.000	0.000
147	A	1344	LEU	0	-0.108	0.051	102.876	0.000	0.000	0.000	0.000	0.000	0.000
148	A	1345	MET	0	0.123	-0.095	104.715	0.000	0.000	0.000	0.000	0.000	0.000
149	A	1345	MET	0	-0.085	0.106	102.087	0.000	0.000	0.000	0.000	0.000	0.000
150	A	1346	GLU	0	-0.160	-0.185	105.815	0.000	0.000	0.000	0.000	0.000	0.000
151	A	1346	GLU	-1	-0.850	-0.911	107.040	-0.001	-0.001	0.000	0.000	0.000	0.000

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