FMO DATABASE

FMODB ID: ZYMRN

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	OptHSide
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	-451826.909393
FMO2-HF: Nuclear repulsion	414154.415597
FMO2-HF: Total energy	-37672.493796
FMO2-MP2: Total energy	-37781.811663

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.
-18.313	-18.699	16.345	-8.143	-7.815	-0.057

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 : -0.018 / q_NPA : -0.012

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	0.059	0.029	2.099	-3.239	-1.725	2.868	-1.894	-2.487	0.005
4	A	1192	ASP	-1	-0.855	-0.926	1.857	-18.621	-21.150	13.476	-5.959	-4.988	-0.063
5	A	1193	ARG	1	0.720	0.797	3.945	1.554	2.183	0.001	-0.290	-0.340	0.001
6	A	1194	GLU	-1	-0.789	-0.869	5.831	1.431	1.431	0.000	0.000	0.000	0.000
7	A	1195	TYR	0	-0.011	0.003	7.306	0.342	0.342	0.000	0.000	0.000	0.000
8	A	1196	GLU	-1	-0.867	-0.910	8.078	-0.884	-0.884	0.000	0.000	0.000	0.000
9	A	1197	GLU	-1	-0.786	-0.877	9.817	0.084	0.084	0.000	0.000	0.000	0.000
10	A	1198	GLU	-1	-0.944	-0.970	11.667	-0.121	-0.121	0.000	0.000	0.000	0.000
11	A	1199	ILE	0	-0.027	-0.014	12.453	0.074	0.074	0.000	0.000	0.000	0.000
12	A	1200	HIS	0	-0.040	-0.014	13.884	0.049	0.049	0.000	0.000	0.000	0.000
13	A	1201	SER	0	0.029	0.015	15.741	0.071	0.071	0.000	0.000	0.000	0.000
14	A	1202	LEU	0	0.006	-0.002	16.767	0.043	0.043	0.000	0.000	0.000	0.000
15	A	1203	LYS	1	0.928	0.969	15.496	0.660	0.660	0.000	0.000	0.000	0.000
16	A	1204	GLU	-1	-0.830	-0.892	19.973	-0.091	-0.091	0.000	0.000	0.000	0.000
17	A	1205	ARG	1	0.791	0.871	20.363	0.157	0.157	0.000	0.000	0.000	0.000
18	A	1206	LEU	0	0.020	0.014	23.283	0.019	0.019	0.000	0.000	0.000	0.000
19	A	1207	HIS	0	0.027	0.024	24.757	0.015	0.015	0.000	0.000	0.000	0.000
20	A	1208	MET	0	0.010	-0.004	25.674	0.019	0.019	0.000	0.000	0.000	0.000
21	A	1209	SER	0	-0.049	-0.018	27.911	0.013	0.013	0.000	0.000	0.000	0.000
22	A	1210	ASN	0	0.044	0.015	28.456	0.015	0.015	0.000	0.000	0.000	0.000
23	A	1211	ARG	1	0.932	0.968	30.215	0.115	0.115	0.000	0.000	0.000	0.000
24	A	1212	LYS	1	0.827	0.900	32.327	0.060	0.060	0.000	0.000	0.000	0.000
25	A	1213	LEU	0	0.038	0.020	33.858	0.008	0.008	0.000	0.000	0.000	0.000
26	A	1214	GLU	-1	-0.793	-0.875	35.060	-0.085	-0.085	0.000	0.000	0.000	0.000
27	A	1215	GLU	-1	-0.844	-0.913	36.871	-0.044	-0.044	0.000	0.000	0.000	0.000
28	A	1216	TYR	0	-0.056	-0.045	35.748	0.009	0.009	0.000	0.000	0.000	0.000
29	A	1217	GLU	-1	-0.884	-0.920	39.557	-0.087	-0.087	0.000	0.000	0.000	0.000
30	A	1218	ARG	1	0.842	0.909	38.153	0.075	0.075	0.000	0.000	0.000	0.000
31	A	1219	ARG	1	0.864	0.914	39.952	0.046	0.046	0.000	0.000	0.000	0.000
32	A	1220	LEU	0	-0.024	0.001	44.063	0.004	0.004	0.000	0.000	0.000	0.000
33	A	1221	LEU	0	0.055	0.027	45.855	0.003	0.003	0.000	0.000	0.000	0.000
34	A	1222	SER	0	-0.028	-0.008	47.236	0.004	0.004	0.000	0.000	0.000	0.000
35	A	1223	GLN	0	-0.022	-0.027	48.805	0.003	0.003	0.000	0.000	0.000	0.000
36	A	1224	GLU	-1	-0.914	-0.941	50.384	-0.046	-0.046	0.000	0.000	0.000	0.000
37	A	1225	GLU	-1	-0.912	-0.945	51.412	-0.044	-0.044	0.000	0.000	0.000	0.000
38	A	1226	GLN	0	-0.058	-0.035	51.643	0.004	0.004	0.000	0.000	0.000	0.000
39	A	1227	THR	0	-0.008	-0.027	53.912	0.003	0.003	0.000	0.000	0.000	0.000
40	A	1228	SER	0	0.015	0.018	56.507	0.002	0.002	0.000	0.000	0.000	0.000
41	A	1229	LYS	1	0.924	0.963	57.744	0.028	0.028	0.000	0.000	0.000	0.000
42	A	1230	ILE	0	-0.037	-0.028	57.429	0.002	0.002	0.000	0.000	0.000	0.000
43	A	1231	LEU	0	0.032	0.021	59.888	0.002	0.002	0.000	0.000	0.000	0.000
44	A	1232	MET	0	0.061	0.040	62.618	0.002	0.002	0.000	0.000	0.000	0.000
45	A	1233	GLN	0	-0.014	-0.009	62.068	0.000	0.000	0.000	0.000	0.000	0.000
46	A	1234	TYR	0	-0.034	-0.040	61.872	0.002	0.002	0.000	0.000	0.000	0.000
47	A	1235	GLN	0	-0.014	0.001	66.528	0.001	0.001	0.000	0.000	0.000	0.000
48	A	1236	ALA	0	0.018	0.004	68.364	0.001	0.001	0.000	0.000	0.000	0.000
49	A	1237	ARG	1	0.907	0.944	68.441	0.015	0.015	0.000	0.000	0.000	0.000
50	A	1238	LEU	0	0.062	0.053	69.667	0.001	0.001	0.000	0.000	0.000	0.000
51	A	1239	GLU	-1	-0.819	-0.880	72.540	-0.019	-0.019	0.000	0.000	0.000	0.000
52	A	1240	GLN	0	-0.098	-0.045	74.302	0.001	0.001	0.000	0.000	0.000	0.000
53	A	1241	SER	0	-0.046	-0.045	74.481	0.001	0.001	0.000	0.000	0.000	0.000
54	A	1242	GLU	-1	-0.833	-0.932	76.901	-0.014	-0.014	0.000	0.000	0.000	0.000
55	A	1243	LYS	1	0.943	0.972	78.831	0.017	0.017	0.000	0.000	0.000	0.000
56	A	1244	ARG	1	0.877	0.930	77.819	0.013	0.013	0.000	0.000	0.000	0.000
57	A	1245	LEU	0	0.026	0.021	80.394	0.001	0.001	0.000	0.000	0.000	0.000
58	A	1246	ARG	1	0.914	0.954	82.568	0.014	0.014	0.000	0.000	0.000	0.000
59	A	1247	GLN	0	-0.017	0.015	84.708	0.000	0.000	0.000	0.000	0.000	0.000
60	A	1248	GLN	0	-0.010	-0.023	86.033	0.001	0.001	0.000	0.000	0.000	0.000
61	A	1249	GLN	0	-0.001	0.006	87.068	0.000	0.000	0.000	0.000	0.000	0.000
62	A	1250	VAL	0	0.033	0.024	88.932	0.000	0.000	0.000	0.000	0.000	0.000
63	A	1251	GLU	-1	-0.830	-0.894	90.897	-0.008	-0.008	0.000	0.000	0.000	0.000
64	A	1252	LYS	1	0.835	0.878	90.601	0.008	0.008	0.000	0.000	0.000	0.000
65	A	1253	ASP	-1	-0.824	-0.896	91.986	-0.009	-0.009	0.000	0.000	0.000	0.000
66	A	1254	SER	0	-0.107	-0.047	94.506	0.000	0.000	0.000	0.000	0.000	0.000
67	A	1255	GLN	0	-0.038	-0.048	94.547	0.000	0.000	0.000	0.000	0.000	0.000
68	A	1256	ILE	0	0.054	0.029	94.508	0.000	0.000	0.000	0.000	0.000	0.000
69	A	1257	LYS	1	0.996	1.007	98.498	0.009	0.009	0.000	0.000	0.000	0.000
70	A	1258	SER	0	-0.074	-0.032	100.848	0.000	0.000	0.000	0.000	0.000	0.000
71	A	1259	ILE	0	0.000	-0.001	99.704	0.000	0.000	0.000	0.000	0.000	0.000
72	A	1260	ILE	0	0.057	0.029	100.736	0.000	0.000	0.000	0.000	0.000	0.000
73	A	1261	GLY	0	-0.002	0.004	104.219	0.000	0.000	0.000	0.000	0.000	0.000
74	A	1262	ARG	1	0.910	0.943	105.138	0.006	0.006	0.000	0.000	0.000	0.000
75	A	1263	LEU	0	-0.003	0.003	104.354	0.000	0.000	0.000	0.000	0.000	0.000
76	A	1264	MET	0	0.022	0.015	106.704	0.000	0.000	0.000	0.000	0.000	0.000
77	A	1265	LEU	0	-0.048	-0.010	109.947	0.000	0.000	0.000	0.000	0.000	0.000
78	A	1266	VAL	0	0.008	0.002	111.457	0.000	0.000	0.000	0.000	0.000	0.000
79	A	1267	GLU	-1	-0.907	-0.965	108.396	-0.005	-0.005	0.000	0.000	0.000	0.000
80	A	1268	GLU	-1	-0.812	-0.871	113.120	-0.005	-0.005	0.000	0.000	0.000	0.000
81	A	1269	GLU	-1	-0.885	-0.946	115.732	-0.005	-0.005	0.000	0.000	0.000	0.000
82	A	1270	LEU	0	0.016	0.009	114.508	0.000	0.000	0.000	0.000	0.000	0.000
83	A	1271	ARG	1	0.774	0.864	116.757	0.005	0.005	0.000	0.000	0.000	0.000
84	A	1272	ARG	1	0.740	0.855	117.533	0.005	0.005	0.000	0.000	0.000	0.000
85	A	1273	ASP	-1	-0.932	-0.943	121.486	-0.003	-0.003	0.000	0.000	0.000	0.000
86	A	1274	HIS	0	-0.093	-0.042	119.273	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)