FMO DATABASE

FMODB ID: JVY39

Calculation Name: 2I9A-A-Xray547

Preferred Name: Urokinase-type plasminogen activator

Target Type: SINGLE PROTEIN

Ligand Name: phosphate ion

Ligand 3-letter code: PO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2I9A

Chain ID: A

ChEMBL ID: CHEMBL3286

UniProt ID: P00749

Base Structure: X-ray

Registration Date: 2025-10-05

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	117
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1020269.49365
FMO2-HF: Nuclear repulsion	968203.604112
FMO2-HF: Total energy	-52065.889538
FMO2-MP2: Total energy	-52207.362789

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:10:ASN)

Summations of interaction energy for fragment #1(A:10:ASN)

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.
41.467	44.716	32.567	-16.99	-18.823	-0.168

Interaction energy analysis for fragmet #1(A:10:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.696 / q_NPA : 0.830

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].
3	A	12	ASP	-1	-0.834	-0.916	1.884	-60.080	-59.186	8.113	-4.616	-4.390	-0.058
4	A	13	CYS	0	-0.053	-0.002	3.323	-5.555	-4.252	0.865	-0.643	-1.525	-0.001
18	A	28	ILE	0	-0.019	0.016	4.441	-6.119	-5.994	-0.001	-0.006	-0.118	0.000
19	A	29	HIS	0	0.038	0.008	3.145	5.244	6.158	0.007	-0.352	-0.569	-0.002
20	A	30	TRP	0	-0.048	-0.025	1.797	-42.287	-43.808	11.979	-6.297	-4.161	-0.077
21	A	32	ASN	0	0.029	0.022	4.978	3.619	3.719	-0.001	-0.005	-0.093	0.000
22	A	33	CYS	0	-0.032	0.016	3.907	2.726	2.877	0.001	-0.041	-0.111	0.000
29	A	40	GLN	0	-0.021	-0.014	2.358	-4.620	-3.074	2.778	-1.384	-2.940	0.010
30	A	41	HIS	1	0.859	0.910	1.888	31.793	31.530	8.826	-3.646	-4.916	-0.040
5	A	14	LEU	0	0.076	0.035	5.491	4.226	4.226	0.000	0.000	0.000	0.000
6	A	15	ASN	0	-0.051	-0.039	8.634	0.525	0.525	0.000	0.000	0.000	0.000
7	A	16	GLY	0	0.057	0.028	11.751	0.896	0.896	0.000	0.000	0.000	0.000
8	A	17	GLY	0	-0.044	-0.032	8.154	0.532	0.532	0.000	0.000	0.000	0.000
9	A	18	THR	0	-0.006	0.005	9.059	0.115	0.115	0.000	0.000	0.000	0.000
10	A	20	VAL	0	0.010	0.013	6.763	5.187	5.187	0.000	0.000	0.000	0.000
11	A	21	SER	0	0.091	0.039	6.204	-6.666	-6.666	0.000	0.000	0.000	0.000
12	A	22	ASN	0	-0.028	-0.021	6.762	4.300	4.300	0.000	0.000	0.000	0.000
13	A	23	LYS	1	0.953	0.985	8.373	19.550	19.550	0.000	0.000	0.000	0.000
14	A	24	TYR	0	0.004	-0.009	11.474	1.989	1.989	0.000	0.000	0.000	0.000
15	A	25	PHE	0	0.012	0.016	9.328	0.771	0.771	0.000	0.000	0.000	0.000
16	A	26	SER	0	0.068	0.033	9.682	-2.247	-2.247	0.000	0.000	0.000	0.000
17	A	27	ASN	0	-0.009	-0.019	8.487	-1.074	-1.074	0.000	0.000	0.000	0.000
23	A	34	PRO	0	0.069	0.052	9.618	1.709	1.709	0.000	0.000	0.000	0.000
24	A	35	LYS	1	1.013	0.980	12.974	15.761	15.761	0.000	0.000	0.000	0.000
25	A	36	LYS	1	0.965	0.992	14.910	14.079	14.079	0.000	0.000	0.000	0.000
26	A	37	PHE	0	0.022	0.018	10.633	0.501	0.501	0.000	0.000	0.000	0.000
27	A	38	GLY	0	-0.029	-0.023	9.387	0.216	0.216	0.000	0.000	0.000	0.000
28	A	39	GLY	0	0.027	0.025	7.536	0.495	0.495	0.000	0.000	0.000	0.000
31	A	43	GLU	-1	-0.735	-0.875	6.284	-30.678	-30.678	0.000	0.000	0.000	0.000
32	A	44	ILE	0	-0.062	-0.022	8.932	2.278	2.278	0.000	0.000	0.000	0.000
33	A	45	ASP	-1	-0.788	-0.901	11.883	-16.556	-16.556	0.000	0.000	0.000	0.000
34	A	46	LYS	1	0.839	0.892	12.963	19.421	19.421	0.000	0.000	0.000	0.000
35	A	47	SER	0	-0.083	-0.044	16.460	0.826	0.826	0.000	0.000	0.000	0.000
36	A	48	LYS	1	0.850	0.926	18.842	13.657	13.657	0.000	0.000	0.000	0.000
37	A	49	THR	0	0.004	-0.005	20.710	-0.237	-0.237	0.000	0.000	0.000	0.000
38	A	50	CYS	0	-0.126	-0.044	23.811	0.145	0.145	0.000	0.000	0.000	0.000
39	A	51	TYR	0	-0.029	-0.028	23.108	-0.775	-0.775	0.000	0.000	0.000	0.000
40	A	52	GLU	-1	-0.766	-0.885	23.597	-12.121	-12.121	0.000	0.000	0.000	0.000
41	A	53	GLY	0	0.035	0.022	24.870	-0.374	-0.374	0.000	0.000	0.000	0.000
42	A	54	ASN	0	0.011	-0.003	24.727	-0.210	-0.210	0.000	0.000	0.000	0.000
43	A	55	GLY	0	0.019	0.005	22.767	-0.132	-0.132	0.000	0.000	0.000	0.000
44	A	56	HIS	1	0.816	0.926	20.620	13.160	13.160	0.000	0.000	0.000	0.000
45	A	57	PHE	0	0.036	0.001	16.704	-0.664	-0.664	0.000	0.000	0.000	0.000
46	A	58	TYR	0	0.006	0.027	17.507	-0.665	-0.665	0.000	0.000	0.000	0.000
47	A	59	ARG	1	0.836	0.900	13.150	17.774	17.774	0.000	0.000	0.000	0.000
48	A	60	GLY	0	0.028	0.030	15.061	-0.748	-0.748	0.000	0.000	0.000	0.000
49	A	61	LYS	1	0.949	0.970	16.078	14.848	14.848	0.000	0.000	0.000	0.000
50	A	62	ALA	0	0.031	0.039	18.738	0.319	0.319	0.000	0.000	0.000	0.000
51	A	63	SER	0	0.032	0.007	21.208	-0.224	-0.224	0.000	0.000	0.000	0.000
52	A	64	THR	0	0.006	0.006	23.093	0.213	0.213	0.000	0.000	0.000	0.000
53	A	65	ASP	-1	-0.703	-0.829	26.914	-9.507	-9.507	0.000	0.000	0.000	0.000
54	A	66	THR	0	-0.020	-0.027	29.312	0.083	0.083	0.000	0.000	0.000	0.000
55	A	67	MET	0	-0.032	-0.003	32.380	0.264	0.264	0.000	0.000	0.000	0.000
56	A	68	GLY	0	0.009	0.011	32.006	0.181	0.181	0.000	0.000	0.000	0.000
57	A	69	ARG	1	0.808	0.883	31.255	8.910	8.910	0.000	0.000	0.000	0.000
58	A	70	PRO	0	0.014	0.006	26.733	-0.263	-0.263	0.000	0.000	0.000	0.000
59	A	71	CYS	0	-0.019	-0.016	23.083	-0.425	-0.425	0.000	0.000	0.000	0.000
60	A	72	LEU	0	0.007	0.007	24.299	-0.171	-0.171	0.000	0.000	0.000	0.000
61	A	73	PRO	0	-0.013	-0.022	19.505	-0.378	-0.378	0.000	0.000	0.000	0.000
62	A	74	TRP	0	-0.024	-0.009	17.076	0.465	0.465	0.000	0.000	0.000	0.000
63	A	75	ASN	0	0.023	0.002	16.244	-0.262	-0.262	0.000	0.000	0.000	0.000
64	A	76	SER	0	-0.036	-0.018	18.371	0.311	0.311	0.000	0.000	0.000	0.000
65	A	77	ALA	0	0.052	0.016	22.096	-0.028	-0.028	0.000	0.000	0.000	0.000
66	A	78	THR	0	0.062	0.031	24.281	0.024	0.024	0.000	0.000	0.000	0.000
67	A	79	VAL	0	0.011	0.003	21.445	0.217	0.217	0.000	0.000	0.000	0.000
68	A	80	LEU	0	-0.033	-0.024	18.321	-0.153	-0.153	0.000	0.000	0.000	0.000
69	A	81	GLN	0	-0.047	-0.011	22.256	-0.101	-0.101	0.000	0.000	0.000	0.000
70	A	82	GLN	0	-0.056	-0.013	24.604	0.595	0.595	0.000	0.000	0.000	0.000
71	A	83	THR	0	0.002	0.003	23.906	-0.286	-0.286	0.000	0.000	0.000	0.000
72	A	84	TYR	0	-0.005	-0.010	19.874	-0.386	-0.386	0.000	0.000	0.000	0.000
73	A	85	HIS	0	0.077	0.034	18.837	-0.423	-0.423	0.000	0.000	0.000	0.000
74	A	86	ALA	0	-0.052	-0.032	14.400	-0.646	-0.646	0.000	0.000	0.000	0.000
75	A	87	HIS	0	0.022	0.012	13.861	-1.839	-1.839	0.000	0.000	0.000	0.000
76	A	88	ARG	1	0.774	0.855	15.611	15.565	15.565	0.000	0.000	0.000	0.000
77	A	89	SER	0	0.028	0.005	13.151	-1.035	-1.035	0.000	0.000	0.000	0.000
78	A	90	ASP	-1	-0.743	-0.833	12.365	-18.278	-18.278	0.000	0.000	0.000	0.000
79	A	91	ALA	0	-0.007	0.010	12.586	-0.021	-0.021	0.000	0.000	0.000	0.000
80	A	92	LEU	0	0.004	0.000	5.713	0.255	0.255	0.000	0.000	0.000	0.000
81	A	93	GLN	0	0.031	0.014	8.758	1.793	1.793	0.000	0.000	0.000	0.000
82	A	94	LEU	0	-0.023	-0.001	11.818	1.269	1.269	0.000	0.000	0.000	0.000
83	A	95	GLY	0	0.002	0.006	12.261	1.015	1.015	0.000	0.000	0.000	0.000
84	A	96	LEU	0	-0.039	-0.007	13.315	0.683	0.683	0.000	0.000	0.000	0.000
85	A	97	GLY	0	0.057	0.005	12.222	-1.539	-1.539	0.000	0.000	0.000	0.000
86	A	98	LYS	1	0.897	0.950	10.066	24.692	24.692	0.000	0.000	0.000	0.000
87	A	99	HIS	0	0.009	0.012	12.936	0.626	0.626	0.000	0.000	0.000	0.000
88	A	100	ASN	0	0.007	-0.006	16.353	-0.279	-0.279	0.000	0.000	0.000	0.000
89	A	101	TYR	0	0.025	0.011	14.466	0.786	0.786	0.000	0.000	0.000	0.000
90	A	102	CYS	0	-0.053	-0.022	18.830	-0.195	-0.195	0.000	0.000	0.000	0.000
91	A	103	ARG	1	0.784	0.884	13.961	16.295	16.295	0.000	0.000	0.000	0.000
92	A	104	ASN	0	0.052	0.009	19.964	0.670	0.670	0.000	0.000	0.000	0.000
93	A	105	PRO	0	0.001	0.022	19.044	-0.070	-0.070	0.000	0.000	0.000	0.000
94	A	106	ASP	-1	-0.779	-0.880	20.631	-11.582	-11.582	0.000	0.000	0.000	0.000
95	A	107	ASN	0	-0.028	-0.004	23.596	0.021	0.021	0.000	0.000	0.000	0.000
96	A	108	ARG	1	0.912	0.942	25.019	10.962	10.962	0.000	0.000	0.000	0.000
97	A	109	ARG	1	0.886	0.890	27.412	8.675	8.675	0.000	0.000	0.000	0.000
98	A	110	ARG	1	0.856	0.940	26.901	9.961	9.961	0.000	0.000	0.000	0.000
99	A	111	PRO	0	-0.042	-0.013	22.701	-0.136	-0.136	0.000	0.000	0.000	0.000
100	A	112	TRP	0	-0.018	-0.007	23.820	0.398	0.398	0.000	0.000	0.000	0.000
101	A	114	TYR	0	0.043	0.021	23.236	0.336	0.336	0.000	0.000	0.000	0.000
102	A	115	VAL	0	0.033	0.008	25.862	-0.250	-0.250	0.000	0.000	0.000	0.000
103	A	116	GLN	0	-0.016	-0.010	28.694	-0.191	-0.191	0.000	0.000	0.000	0.000
104	A	117	VAL	0	-0.019	-0.013	31.012	0.203	0.203	0.000	0.000	0.000	0.000
105	A	118	GLY	0	0.036	0.020	34.557	0.136	0.136	0.000	0.000	0.000	0.000
106	A	119	LEU	0	0.040	0.009	35.299	-0.206	-0.206	0.000	0.000	0.000	0.000
107	A	120	LYS	1	0.950	0.986	32.976	8.120	8.120	0.000	0.000	0.000	0.000
108	A	121	PRO	0	0.017	0.027	28.141	0.074	0.074	0.000	0.000	0.000	0.000
109	A	122	LEU	0	-0.020	-0.020	30.147	0.178	0.178	0.000	0.000	0.000	0.000
110	A	123	VAL	0	-0.005	0.005	27.092	-0.215	-0.215	0.000	0.000	0.000	0.000
111	A	124	GLN	0	-0.011	-0.002	28.248	0.618	0.618	0.000	0.000	0.000	0.000
112	A	125	GLU	-1	-0.757	-0.858	27.853	-9.869	-9.869	0.000	0.000	0.000	0.000
113	A	127	MET	0	0.000	0.005	27.440	0.137	0.137	0.000	0.000	0.000	0.000
114	A	128	VAL	0	-0.025	-0.005	23.715	0.104	0.104	0.000	0.000	0.000	0.000
115	A	129	HIS	0	0.043	0.028	27.095	0.201	0.201	0.000	0.000	0.000	0.000
116	A	130	ASP	-1	-0.869	-0.946	27.379	-10.580	-10.580	0.000	0.000	0.000	0.000
117	A	132	ALA	-1	-0.892	-0.920	28.559	-8.885	-8.885	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:10:ASN)