FMO DATABASE

FMODB ID: KZ2K3

Calculation Name: 4PRO-C-Xray549

Preferred Name: Alpha-lytic protease

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4PRO

Chain ID: C

ChEMBL ID: CHEMBL3085615

UniProt ID: P00778

Base Structure: X-ray

Registration Date: 2025-10-12

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	161
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1336787.182555
FMO2-HF: Nuclear repulsion	1276724.944191
FMO2-HF: Total energy	-60062.238365
FMO2-MP2: Total energy	-60239.799602

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(C:6:PRO)

Summations of interaction energy for fragment #1(C:6:PRO)

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.
71.761	76.93	0.494	-2.041	-3.622	-0.01

Interaction energy analysis for fragmet #1(C:6:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.846 / q_NPA : 0.893

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	C	8	LEU	0	0.040	0.012	2.409	4.727	8.063	0.291	-1.490	-2.137	-0.008
4	C	9	LYS	1	0.955	0.983	2.908	60.291	61.964	0.204	-0.534	-1.343	-0.002
5	C	10	PHE	0	0.039	0.028	5.025	6.069	6.229	-0.001	-0.017	-0.142	0.000
6	C	11	ALA	0	0.040	0.020	7.298	3.436	3.436	0.000	0.000	0.000	0.000
7	C	12	MET	0	0.012	0.007	6.510	3.049	3.049	0.000	0.000	0.000	0.000
8	C	13	GLN	0	-0.001	0.002	9.025	1.979	1.979	0.000	0.000	0.000	0.000
9	C	14	ARG	1	0.788	0.890	11.058	26.505	26.505	0.000	0.000	0.000	0.000
10	C	15	ASP	-1	-0.807	-0.896	12.331	-21.714	-21.714	0.000	0.000	0.000	0.000
11	C	16	LEU	0	-0.005	-0.003	11.588	1.177	1.177	0.000	0.000	0.000	0.000
12	C	17	GLY	0	0.041	0.036	13.974	1.000	1.000	0.000	0.000	0.000	0.000
13	C	18	ILE	0	-0.060	-0.025	10.657	0.872	0.872	0.000	0.000	0.000	0.000
14	C	19	PHE	0	0.049	0.019	10.486	-2.763	-2.763	0.000	0.000	0.000	0.000
15	C	20	PRO	0	-0.036	-0.039	8.126	-0.506	-0.506	0.000	0.000	0.000	0.000
16	C	21	THR	0	0.011	0.001	9.630	-0.854	-0.854	0.000	0.000	0.000	0.000
17	C	22	GLN	0	0.088	0.046	12.830	-0.031	-0.031	0.000	0.000	0.000	0.000
18	C	23	LEU	0	-0.009	-0.001	5.998	-0.479	-0.479	0.000	0.000	0.000	0.000
19	C	24	PRO	0	0.011	0.002	10.448	0.029	0.029	0.000	0.000	0.000	0.000
20	C	25	GLN	0	0.050	0.029	12.176	0.453	0.453	0.000	0.000	0.000	0.000
21	C	26	TYR	0	-0.016	-0.005	10.813	1.133	1.133	0.000	0.000	0.000	0.000
22	C	27	LEU	0	0.002	-0.011	8.177	0.455	0.455	0.000	0.000	0.000	0.000
23	C	28	GLN	0	-0.046	-0.019	12.556	0.748	0.748	0.000	0.000	0.000	0.000
24	C	29	THR	0	0.006	-0.003	16.033	1.286	1.286	0.000	0.000	0.000	0.000
25	C	30	GLU	-1	-0.847	-0.907	12.658	-22.575	-22.575	0.000	0.000	0.000	0.000
26	C	31	LYS	1	0.921	0.959	15.772	17.828	17.828	0.000	0.000	0.000	0.000
27	C	32	LEU	0	0.006	0.022	17.360	0.729	0.729	0.000	0.000	0.000	0.000
28	C	33	ALA	0	0.038	0.008	19.384	0.653	0.653	0.000	0.000	0.000	0.000
29	C	34	ARG	1	0.887	0.943	14.340	19.841	19.841	0.000	0.000	0.000	0.000
30	C	35	THR	0	-0.101	-0.064	20.227	0.575	0.575	0.000	0.000	0.000	0.000
31	C	36	GLN	0	0.030	0.010	22.683	0.959	0.959	0.000	0.000	0.000	0.000
32	C	37	ALA	0	0.017	0.032	24.541	0.531	0.531	0.000	0.000	0.000	0.000
33	C	38	ALA	0	0.074	0.029	26.328	0.405	0.405	0.000	0.000	0.000	0.000
34	C	39	ALA	0	-0.056	-0.023	28.666	0.437	0.437	0.000	0.000	0.000	0.000
35	C	40	ILE	0	0.030	0.000	26.744	0.321	0.321	0.000	0.000	0.000	0.000
36	C	41	GLU	-1	-0.958	-0.964	30.445	-9.800	-9.800	0.000	0.000	0.000	0.000
37	C	42	ARG	1	0.926	0.939	32.285	9.214	9.214	0.000	0.000	0.000	0.000
38	C	43	GLU	-1	-0.808	-0.838	33.519	-9.037	-9.037	0.000	0.000	0.000	0.000
39	C	44	PHE	0	-0.005	-0.013	32.106	0.255	0.255	0.000	0.000	0.000	0.000
40	C	45	GLY	0	0.032	0.028	36.607	0.262	0.262	0.000	0.000	0.000	0.000
41	C	46	ALA	0	0.023	-0.007	37.556	-0.129	-0.129	0.000	0.000	0.000	0.000
42	C	47	GLN	0	-0.014	-0.001	39.285	-0.004	-0.004	0.000	0.000	0.000	0.000
43	C	48	PHE	0	0.043	0.039	29.378	-0.092	-0.092	0.000	0.000	0.000	0.000
44	C	49	ALA	0	0.032	0.003	34.011	0.151	0.151	0.000	0.000	0.000	0.000
45	C	50	GLY	0	0.044	0.037	30.230	-0.142	-0.142	0.000	0.000	0.000	0.000
46	C	51	SER	0	-0.020	-0.024	26.129	0.218	0.218	0.000	0.000	0.000	0.000
47	C	52	TRP	0	-0.063	-0.032	23.388	-0.228	-0.228	0.000	0.000	0.000	0.000
48	C	53	ILE	0	0.020	0.015	17.023	0.052	0.052	0.000	0.000	0.000	0.000
49	C	54	GLU	-1	-0.787	-0.867	20.884	-11.691	-11.691	0.000	0.000	0.000	0.000
50	C	55	ARG	1	0.762	0.875	15.586	17.792	17.792	0.000	0.000	0.000	0.000
51	C	56	ASN	0	0.016	0.011	20.854	0.994	0.994	0.000	0.000	0.000	0.000
52	C	57	GLU	-1	-0.894	-0.956	22.134	-11.616	-11.616	0.000	0.000	0.000	0.000
53	C	58	ASP	-1	-0.824	-0.877	22.699	-13.724	-13.724	0.000	0.000	0.000	0.000
54	C	59	GLY	0	-0.029	-0.011	19.112	-0.593	-0.593	0.000	0.000	0.000	0.000
55	C	60	SER	0	-0.079	-0.054	17.795	-1.192	-1.192	0.000	0.000	0.000	0.000
56	C	61	PHE	0	0.006	-0.026	14.761	0.036	0.036	0.000	0.000	0.000	0.000
57	C	62	LYS	1	0.838	0.923	19.206	12.152	12.152	0.000	0.000	0.000	0.000
58	C	63	LEU	0	0.009	0.008	21.720	-0.411	-0.411	0.000	0.000	0.000	0.000
59	C	64	VAL	0	-0.009	0.009	23.293	0.419	0.419	0.000	0.000	0.000	0.000
60	C	65	ALA	0	0.021	-0.004	26.447	-0.219	-0.219	0.000	0.000	0.000	0.000
61	C	66	ALA	0	0.014	0.028	29.273	0.252	0.252	0.000	0.000	0.000	0.000
62	C	67	THR	0	-0.007	-0.011	32.501	0.093	0.093	0.000	0.000	0.000	0.000
63	C	68	SER	0	0.056	0.033	36.140	-0.021	-0.021	0.000	0.000	0.000	0.000
64	C	69	GLY	0	-0.012	0.006	39.346	0.252	0.252	0.000	0.000	0.000	0.000
65	C	70	ALA	0	-0.018	-0.016	40.344	-0.098	-0.098	0.000	0.000	0.000	0.000
66	C	71	ARG	0	0.035	0.009	31.286	-0.292	-0.292	0.000	0.000	0.000	0.000
67	C	72	LYS	1	0.952	0.976	37.943	7.811	7.811	0.000	0.000	0.000	0.000
68	C	73	SER	0	-0.040	-0.042	34.640	-0.207	-0.207	0.000	0.000	0.000	0.000
69	C	74	SER	0	-0.027	-0.012	31.503	0.048	0.048	0.000	0.000	0.000	0.000
70	C	75	THR	0	-0.054	-0.058	33.599	0.139	0.139	0.000	0.000	0.000	0.000
71	C	76	LEU	0	-0.056	-0.023	28.628	-0.095	-0.095	0.000	0.000	0.000	0.000
72	C	77	GLY	0	0.007	0.003	28.789	0.014	0.014	0.000	0.000	0.000	0.000
73	C	78	GLY	0	-0.029	-0.025	25.366	-0.397	-0.397	0.000	0.000	0.000	0.000
74	C	79	VAL	0	-0.012	-0.009	25.137	-0.532	-0.532	0.000	0.000	0.000	0.000
75	C	80	GLU	-1	-0.779	-0.866	27.101	-10.616	-10.616	0.000	0.000	0.000	0.000
76	C	81	VAL	0	0.002	0.005	28.999	-0.110	-0.110	0.000	0.000	0.000	0.000
77	C	82	ARG	1	0.744	0.828	27.634	10.968	10.968	0.000	0.000	0.000	0.000
78	C	83	ASN	0	-0.051	-0.027	33.642	-0.068	-0.068	0.000	0.000	0.000	0.000
79	C	84	VAL	0	-0.026	-0.010	34.068	-0.073	-0.073	0.000	0.000	0.000	0.000
80	C	85	ARG	1	0.930	0.972	37.428	7.304	7.304	0.000	0.000	0.000	0.000
81	C	86	TYR	0	0.026	0.009	38.505	0.233	0.233	0.000	0.000	0.000	0.000
82	C	87	SER	0	0.017	0.011	37.463	-0.264	-0.264	0.000	0.000	0.000	0.000
83	C	88	LEU	0	0.009	-0.016	31.819	0.045	0.045	0.000	0.000	0.000	0.000
84	C	89	LYS	0	-0.017	-0.014	35.827	-0.038	-0.038	0.000	0.000	0.000	0.000
85	C	90	GLN	0	-0.009	0.017	38.815	0.053	0.053	0.000	0.000	0.000	0.000
86	C	91	LEU	0	0.027	0.020	35.021	0.077	0.077	0.000	0.000	0.000	0.000
87	C	92	GLN	0	-0.049	-0.030	35.050	-0.243	-0.243	0.000	0.000	0.000	0.000
88	C	93	SER	0	-0.019	-0.019	37.580	0.120	0.120	0.000	0.000	0.000	0.000
89	C	94	ALA	0	0.006	0.007	39.916	0.107	0.107	0.000	0.000	0.000	0.000
90	C	95	MET	0	-0.045	-0.005	33.759	-0.022	-0.022	0.000	0.000	0.000	0.000
91	C	96	GLU	-1	-0.868	-0.931	38.136	-8.027	-8.027	0.000	0.000	0.000	0.000
92	C	97	GLN	0	-0.007	-0.005	40.331	0.099	0.099	0.000	0.000	0.000	0.000
93	C	98	LEU	0	0.012	0.015	38.722	0.112	0.112	0.000	0.000	0.000	0.000
94	C	99	ASP	-1	-0.846	-0.910	37.107	-8.704	-8.704	0.000	0.000	0.000	0.000
95	C	100	ALA	0	-0.037	-0.020	40.016	0.095	0.095	0.000	0.000	0.000	0.000
96	C	101	GLY	0	0.026	0.016	43.755	0.146	0.146	0.000	0.000	0.000	0.000
97	C	102	ALA	0	-0.023	-0.016	40.493	0.102	0.102	0.000	0.000	0.000	0.000
98	C	103	ASN	0	-0.061	-0.026	42.169	0.183	0.183	0.000	0.000	0.000	0.000
99	C	104	ALA	0	0.020	0.014	43.516	0.095	0.095	0.000	0.000	0.000	0.000
100	C	105	ARG	1	0.834	0.917	44.216	7.009	7.009	0.000	0.000	0.000	0.000
101	C	106	VAL	0	0.004	0.004	43.706	0.092	0.092	0.000	0.000	0.000	0.000
102	C	107	LYS	1	0.821	0.903	43.125	7.007	7.007	0.000	0.000	0.000	0.000
103	C	108	GLY	0	0.040	0.025	39.289	-0.127	-0.127	0.000	0.000	0.000	0.000
104	C	109	VAL	0	0.025	-0.008	35.414	0.187	0.187	0.000	0.000	0.000	0.000
105	C	110	SER	0	0.068	0.023	37.729	0.011	0.011	0.000	0.000	0.000	0.000
106	C	111	LYS	1	0.872	0.928	40.383	7.248	7.248	0.000	0.000	0.000	0.000
107	C	112	PRO	0	-0.038	0.003	40.876	0.227	0.227	0.000	0.000	0.000	0.000
108	C	113	LEU	0	0.047	0.015	41.182	0.225	0.225	0.000	0.000	0.000	0.000
109	C	114	ASP	-1	-0.792	-0.858	40.165	-8.169	-8.169	0.000	0.000	0.000	0.000
110	C	115	GLY	0	0.051	0.031	40.177	0.203	0.203	0.000	0.000	0.000	0.000
111	C	116	VAL	0	-0.024	-0.007	37.544	-0.163	-0.163	0.000	0.000	0.000	0.000
112	C	117	GLN	0	-0.060	-0.027	32.296	-0.360	-0.360	0.000	0.000	0.000	0.000
113	C	118	SER	0	-0.038	-0.027	31.584	-0.262	-0.262	0.000	0.000	0.000	0.000
114	C	119	TRP	0	-0.021	-0.037	33.716	0.146	0.146	0.000	0.000	0.000	0.000
115	C	120	TYR	0	0.008	-0.002	28.992	-0.233	-0.233	0.000	0.000	0.000	0.000
116	C	121	VAL	0	0.046	0.025	32.005	0.154	0.154	0.000	0.000	0.000	0.000
117	C	122	ASP	-1	-0.824	-0.900	28.963	-11.208	-11.208	0.000	0.000	0.000	0.000
118	C	123	PRO	0	-0.006	-0.018	28.465	0.222	0.222	0.000	0.000	0.000	0.000
119	C	124	ARG	1	0.837	0.942	23.904	12.439	12.439	0.000	0.000	0.000	0.000
120	C	125	SER	0	-0.060	-0.062	28.987	0.225	0.225	0.000	0.000	0.000	0.000
121	C	126	ASN	0	-0.056	-0.037	32.403	0.557	0.557	0.000	0.000	0.000	0.000
122	C	127	ALA	0	0.066	0.036	33.944	0.321	0.321	0.000	0.000	0.000	0.000
123	C	128	VAL	0	0.004	0.005	34.215	-0.314	-0.314	0.000	0.000	0.000	0.000
124	C	129	VAL	0	-0.021	-0.004	31.545	0.208	0.208	0.000	0.000	0.000	0.000
125	C	130	VAL	0	0.031	0.001	34.404	-0.038	-0.038	0.000	0.000	0.000	0.000
126	C	131	LYS	1	0.911	0.970	28.133	11.005	11.005	0.000	0.000	0.000	0.000
127	C	132	VAL	0	0.014	0.005	34.554	0.105	0.105	0.000	0.000	0.000	0.000
128	C	133	ASP	-1	-0.758	-0.868	35.742	-8.956	-8.956	0.000	0.000	0.000	0.000
129	C	134	ASP	-1	-0.835	-0.907	35.495	-8.882	-8.882	0.000	0.000	0.000	0.000
130	C	135	GLY	0	-0.053	-0.024	38.121	0.144	0.144	0.000	0.000	0.000	0.000
131	C	136	ALA	0	-0.028	0.000	40.335	0.223	0.223	0.000	0.000	0.000	0.000
132	C	137	THR	0	0.022	-0.001	41.391	-0.063	-0.063	0.000	0.000	0.000	0.000
133	C	138	ASP	-1	-0.896	-0.942	42.277	-6.849	-6.849	0.000	0.000	0.000	0.000
134	C	139	ALA	0	0.010	0.010	43.022	0.073	0.073	0.000	0.000	0.000	0.000
135	C	140	GLY	0	0.021	0.007	41.456	-0.050	-0.050	0.000	0.000	0.000	0.000
136	C	141	VAL	0	-0.026	-0.019	42.145	0.001	0.001	0.000	0.000	0.000	0.000
137	C	142	ASP	-1	-0.890	-0.943	45.139	-6.487	-6.487	0.000	0.000	0.000	0.000
138	C	143	PHE	0	-0.050	-0.023	39.025	0.072	0.072	0.000	0.000	0.000	0.000
139	C	144	VAL	0	0.013	0.007	41.717	-0.001	-0.001	0.000	0.000	0.000	0.000
140	C	145	ALA	0	-0.010	-0.005	44.307	0.073	0.073	0.000	0.000	0.000	0.000
141	C	146	LEU	0	-0.058	-0.036	47.824	0.131	0.131	0.000	0.000	0.000	0.000
142	C	147	SER	0	-0.035	-0.030	44.394	0.023	0.023	0.000	0.000	0.000	0.000
143	C	148	GLY	0	-0.069	-0.021	46.428	-0.014	-0.014	0.000	0.000	0.000	0.000
144	C	149	ALA	0	0.012	0.013	43.157	0.016	0.016	0.000	0.000	0.000	0.000
145	C	150	ASP	-1	-0.859	-0.934	44.339	-6.964	-6.964	0.000	0.000	0.000	0.000
146	C	151	SER	0	0.049	0.008	43.401	-0.140	-0.140	0.000	0.000	0.000	0.000
147	C	152	ALA	0	-0.092	-0.034	43.449	-0.077	-0.077	0.000	0.000	0.000	0.000
148	C	153	GLN	0	-0.091	-0.048	40.242	-0.264	-0.264	0.000	0.000	0.000	0.000
149	C	154	VAL	0	-0.005	0.006	38.761	-0.262	-0.262	0.000	0.000	0.000	0.000
150	C	155	ARG	1	0.796	0.892	31.618	9.724	9.724	0.000	0.000	0.000	0.000
151	C	156	ILE	0	0.016	0.011	36.529	-0.235	-0.235	0.000	0.000	0.000	0.000
152	C	157	GLU	-1	-0.890	-0.937	30.787	-10.274	-10.274	0.000	0.000	0.000	0.000
153	C	158	SER	0	-0.022	-0.037	35.401	0.109	0.109	0.000	0.000	0.000	0.000
154	C	159	SER	0	-0.057	-0.039	31.248	-0.435	-0.435	0.000	0.000	0.000	0.000
155	C	160	PRO	0	0.027	0.011	30.406	0.139	0.139	0.000	0.000	0.000	0.000
156	C	161	GLY	0	-0.048	-0.012	31.353	-0.272	-0.272	0.000	0.000	0.000	0.000
157	C	162	LYS	1	0.806	0.864	32.050	8.723	8.723	0.000	0.000	0.000	0.000
158	C	163	LEU	0	-0.006	0.017	29.235	-0.348	-0.348	0.000	0.000	0.000	0.000
159	C	164	GLN	0	-0.038	-0.031	30.383	0.594	0.594	0.000	0.000	0.000	0.000
160	C	165	THR	0	-0.017	-0.012	28.795	-0.245	-0.245	0.000	0.000	0.000	0.000
161	C	166	THR	-1	-0.955	-0.967	24.847	-11.957	-11.957	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:6:PRO)