FMO DATABASE

FMODB ID: R53N8

Calculation Name: 5JXC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5JXC

Chain ID: A

ChEMBL ID:

UniProt ID: F6SEU4

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	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	86
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-452397.775145
FMO2-HF: Nuclear repulsion	414724.974189
FMO2-HF: Total energy	-37672.800957
FMO2-MP2: Total energy	-37782.04797

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:1189:SER)

Summations of interaction energy for fragment #1(A:1189:SER)

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.
-17.724	-18.159	13.593	-6.572	-6.586	-0.059

Interaction energy analysis for fragmet #1(A:1189:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.020 / q_NPA : -0.017

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	1191	LEU	0	0.054	0.020	2.201	-2.553	-0.790	1.280	-1.232	-1.811	0.003
4	A	1192	ASP	-1	-0.858	-0.919	1.843	-18.633	-21.159	12.314	-5.230	-4.558	-0.062
5	A	1193	ARG	1	0.765	0.824	4.077	2.123	2.451	-0.001	-0.110	-0.217	0.000
6	A	1194	GLU	-1	-0.784	-0.855	6.038	0.976	0.976	0.000	0.000	0.000	0.000
7	A	1195	TYR	0	0.006	0.003	7.660	0.401	0.401	0.000	0.000	0.000	0.000
8	A	1196	GLU	-1	-0.874	-0.909	7.987	-1.093	-1.093	0.000	0.000	0.000	0.000
9	A	1197	GLU	-1	-0.791	-0.878	9.850	-0.046	-0.046	0.000	0.000	0.000	0.000
10	A	1198	GLU	-1	-0.957	-0.972	11.902	-0.275	-0.275	0.000	0.000	0.000	0.000
11	A	1199	ILE	0	-0.030	-0.024	12.486	0.126	0.126	0.000	0.000	0.000	0.000
12	A	1200	HIS	0	-0.037	-0.015	13.989	0.038	0.038	0.000	0.000	0.000	0.000
13	A	1201	SER	0	0.028	0.014	15.767	0.093	0.093	0.000	0.000	0.000	0.000
14	A	1202	LEU	0	0.011	-0.007	16.894	0.057	0.057	0.000	0.000	0.000	0.000
15	A	1203	LYS	1	0.918	0.976	15.423	0.741	0.741	0.000	0.000	0.000	0.000
16	A	1204	GLU	-1	-0.827	-0.891	20.079	-0.156	-0.156	0.000	0.000	0.000	0.000
17	A	1205	ARG	1	0.805	0.875	20.229	0.236	0.236	0.000	0.000	0.000	0.000
18	A	1206	LEU	0	0.025	0.026	23.433	0.024	0.024	0.000	0.000	0.000	0.000
19	A	1207	HIS	0	0.014	0.016	24.780	0.023	0.023	0.000	0.000	0.000	0.000
20	A	1208	MET	0	0.009	-0.007	26.036	0.024	0.024	0.000	0.000	0.000	0.000
21	A	1209	SER	0	-0.060	-0.032	27.891	0.016	0.016	0.000	0.000	0.000	0.000
22	A	1210	ASN	0	0.041	0.013	28.498	0.019	0.019	0.000	0.000	0.000	0.000
23	A	1211	ARG	1	0.832	0.901	29.912	0.139	0.139	0.000	0.000	0.000	0.000
24	A	1212	LYS	1	0.836	0.905	32.356	0.088	0.088	0.000	0.000	0.000	0.000
25	A	1213	LEU	0	0.026	0.028	33.891	0.009	0.009	0.000	0.000	0.000	0.000
26	A	1214	GLU	-1	-0.730	-0.840	34.877	-0.104	-0.104	0.000	0.000	0.000	0.000
27	A	1215	GLU	-1	-0.831	-0.896	36.857	-0.065	-0.065	0.000	0.000	0.000	0.000
28	A	1216	TYR	0	-0.040	-0.034	35.572	0.010	0.010	0.000	0.000	0.000	0.000
29	A	1217	GLU	-1	-0.895	-0.941	39.493	-0.104	-0.104	0.000	0.000	0.000	0.000
30	A	1218	ARG	1	0.845	0.907	37.936	0.093	0.093	0.000	0.000	0.000	0.000
31	A	1219	ARG	1	0.845	0.905	39.774	0.068	0.068	0.000	0.000	0.000	0.000
32	A	1220	LEU	0	-0.013	0.005	44.234	0.005	0.005	0.000	0.000	0.000	0.000
33	A	1221	LEU	0	0.062	0.036	46.103	0.003	0.003	0.000	0.000	0.000	0.000
34	A	1222	SER	0	0.002	0.015	47.458	0.004	0.004	0.000	0.000	0.000	0.000
35	A	1223	GLN	0	0.005	-0.007	48.790	0.004	0.004	0.000	0.000	0.000	0.000
36	A	1224	GLU	-1	-0.922	-0.940	50.420	-0.057	-0.057	0.000	0.000	0.000	0.000
37	A	1225	GLU	-1	-0.905	-0.962	51.231	-0.054	-0.054	0.000	0.000	0.000	0.000
38	A	1226	GLN	0	-0.063	-0.041	51.754	0.005	0.005	0.000	0.000	0.000	0.000
39	A	1227	THR	0	-0.022	-0.033	53.948	0.003	0.003	0.000	0.000	0.000	0.000
40	A	1228	SER	0	0.003	0.012	56.456	0.003	0.003	0.000	0.000	0.000	0.000
41	A	1229	LYS	1	0.924	0.966	57.613	0.037	0.037	0.000	0.000	0.000	0.000
42	A	1230	ILE	0	-0.032	-0.020	57.348	0.002	0.002	0.000	0.000	0.000	0.000
43	A	1231	LEU	0	0.029	0.013	59.634	0.002	0.002	0.000	0.000	0.000	0.000
44	A	1232	MET	0	0.032	0.026	62.486	0.002	0.002	0.000	0.000	0.000	0.000
45	A	1233	GLN	0	-0.017	-0.015	61.906	0.000	0.000	0.000	0.000	0.000	0.000
46	A	1234	TYR	0	-0.040	-0.036	61.954	0.002	0.002	0.000	0.000	0.000	0.000
47	A	1235	GLN	0	0.010	-0.002	66.578	0.001	0.001	0.000	0.000	0.000	0.000
48	A	1236	ALA	0	0.024	0.011	68.509	0.001	0.001	0.000	0.000	0.000	0.000
49	A	1237	ARG	1	0.905	0.944	68.484	0.022	0.022	0.000	0.000	0.000	0.000
50	A	1238	LEU	0	0.036	0.048	69.746	0.001	0.001	0.000	0.000	0.000	0.000
51	A	1239	GLU	-1	-0.790	-0.879	72.439	-0.025	-0.025	0.000	0.000	0.000	0.000
52	A	1240	GLN	0	-0.111	-0.055	74.118	0.001	0.001	0.000	0.000	0.000	0.000
53	A	1241	SER	0	-0.045	-0.043	74.629	0.001	0.001	0.000	0.000	0.000	0.000
54	A	1242	GLU	-1	-0.827	-0.928	77.206	-0.019	-0.019	0.000	0.000	0.000	0.000
55	A	1243	LYS	1	0.972	0.992	79.104	0.022	0.022	0.000	0.000	0.000	0.000
56	A	1244	ARG	1	0.870	0.932	77.856	0.018	0.018	0.000	0.000	0.000	0.000
57	A	1245	LEU	0	0.022	0.026	80.510	0.001	0.001	0.000	0.000	0.000	0.000
58	A	1246	ARG	1	0.900	0.937	82.589	0.019	0.019	0.000	0.000	0.000	0.000
59	A	1247	GLN	0	-0.028	0.007	85.014	0.000	0.000	0.000	0.000	0.000	0.000
60	A	1248	GLN	0	-0.009	-0.020	86.230	0.001	0.001	0.000	0.000	0.000	0.000
61	A	1249	GLN	0	0.018	0.018	87.215	0.000	0.000	0.000	0.000	0.000	0.000
62	A	1250	VAL	0	0.016	0.009	88.988	0.000	0.000	0.000	0.000	0.000	0.000
63	A	1251	GLU	-1	-0.821	-0.880	90.856	-0.012	-0.012	0.000	0.000	0.000	0.000
64	A	1252	LYS	1	0.834	0.878	90.561	0.013	0.013	0.000	0.000	0.000	0.000
65	A	1253	ASP	-1	-0.815	-0.888	92.013	-0.013	-0.013	0.000	0.000	0.000	0.000
66	A	1254	SER	0	-0.066	-0.038	94.744	0.000	0.000	0.000	0.000	0.000	0.000
67	A	1255	GLN	0	0.002	-0.016	94.566	0.000	0.000	0.000	0.000	0.000	0.000
68	A	1256	ILE	0	0.049	0.023	94.505	0.000	0.000	0.000	0.000	0.000	0.000
69	A	1257	LYS	1	0.891	0.949	98.639	0.013	0.013	0.000	0.000	0.000	0.000
70	A	1258	SER	0	-0.054	-0.014	101.086	0.000	0.000	0.000	0.000	0.000	0.000
71	A	1259	ILE	0	-0.008	-0.011	99.549	0.000	0.000	0.000	0.000	0.000	0.000
72	A	1260	ILE	0	0.053	0.019	100.923	0.000	0.000	0.000	0.000	0.000	0.000
73	A	1261	GLY	0	0.010	0.011	104.188	0.000	0.000	0.000	0.000	0.000	0.000
74	A	1262	ARG	1	0.910	0.943	105.188	0.009	0.009	0.000	0.000	0.000	0.000
75	A	1263	LEU	0	-0.017	0.004	104.436	0.000	0.000	0.000	0.000	0.000	0.000
76	A	1264	MET	0	0.045	0.021	106.525	0.000	0.000	0.000	0.000	0.000	0.000
77	A	1265	LEU	0	-0.044	-0.014	110.031	0.000	0.000	0.000	0.000	0.000	0.000
78	A	1266	VAL	0	-0.002	0.001	111.698	0.000	0.000	0.000	0.000	0.000	0.000
79	A	1267	GLU	-1	-0.913	-0.966	108.632	-0.008	-0.008	0.000	0.000	0.000	0.000
80	A	1268	GLU	-1	-0.815	-0.881	113.363	-0.008	-0.008	0.000	0.000	0.000	0.000
81	A	1269	GLU	-1	-0.884	-0.930	115.789	-0.007	-0.007	0.000	0.000	0.000	0.000
82	A	1270	LEU	0	0.037	0.021	114.612	0.000	0.000	0.000	0.000	0.000	0.000
83	A	1271	ARG	1	0.748	0.849	116.905	0.008	0.008	0.000	0.000	0.000	0.000
84	A	1272	ARG	1	0.730	0.843	117.814	0.007	0.007	0.000	0.000	0.000	0.000
85	A	1273	ASP	-1	-0.899	-0.932	121.464	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	1274	HIS	0	-0.101	-0.040	119.670	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1189:SER)