FMO DATABASE

FMODB ID: 7KJGK

Calculation Name: 1KF3-A-Xray547

Preferred Name: Ribonuclease pancreatic

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1KF3

Chain ID: A

ChEMBL ID: CHEMBL6091

UniProt ID: P61823

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	120
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1021515.157241
FMO2-HF: Nuclear repulsion	970682.672796
FMO2-HF: Total energy	-50832.484444
FMO2-MP2: Total energy	-50971.384858

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:1:LYS)

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

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.
149.912	151.964	0.122	-1.038	-1.136	-0.005

Interaction energy analysis for fragmet #1(A:1:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.824 / q_NPA : 1.899

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	3	THR	0	0.035	0.016	3.216	-11.715	-9.663	0.122	-1.038	-1.136	-0.005
4	A	4	ALA	0	0.044	0.012	5.840	3.552	3.552	0.000	0.000	0.000	0.000
5	A	5	ALA	0	0.101	0.063	8.374	3.346	3.346	0.000	0.000	0.000	0.000
6	A	6	ALA	0	0.032	0.017	7.948	2.609	2.609	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.934	0.975	7.141	66.413	66.413	0.000	0.000	0.000	0.000
8	A	8	PHE	0	0.023	0.013	9.258	3.804	3.804	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.877	-0.954	12.677	-37.179	-37.179	0.000	0.000	0.000	0.000
10	A	10	ARG	1	0.758	0.837	8.068	57.905	57.905	0.000	0.000	0.000	0.000
11	A	11	GLN	0	-0.073	-0.053	11.626	-0.239	-0.239	0.000	0.000	0.000	0.000
12	A	12	HIS	0	-0.012	0.001	14.555	0.254	0.254	0.000	0.000	0.000	0.000
13	A	13	MET	0	0.015	0.041	16.870	1.847	1.847	0.000	0.000	0.000	0.000
14	A	14	ASP	-1	-0.765	-0.839	18.784	-26.866	-26.866	0.000	0.000	0.000	0.000
15	A	15	SER	0	0.005	-0.016	21.590	0.685	0.685	0.000	0.000	0.000	0.000
16	A	16	SER	0	-0.092	-0.049	23.075	0.842	0.842	0.000	0.000	0.000	0.000
17	A	17	THR	0	-0.019	-0.023	24.919	1.153	1.153	0.000	0.000	0.000	0.000
18	A	18	SER	0	0.077	0.034	26.986	-0.363	-0.363	0.000	0.000	0.000	0.000
19	A	19	ALA	0	-0.011	0.000	29.366	0.219	0.219	0.000	0.000	0.000	0.000
20	A	20	ALA	0	-0.030	-0.001	27.886	-0.188	-0.188	0.000	0.000	0.000	0.000
21	A	21	SER	0	0.016	0.006	29.329	0.455	0.455	0.000	0.000	0.000	0.000
22	A	22	SER	0	0.016	0.004	30.932	0.533	0.533	0.000	0.000	0.000	0.000
23	A	23	SER	0	0.050	0.015	30.752	-0.673	-0.673	0.000	0.000	0.000	0.000
24	A	24	ASN	0	0.048	0.042	29.174	-0.750	-0.750	0.000	0.000	0.000	0.000
25	A	25	TYR	0	-0.024	-0.030	23.643	-0.789	-0.789	0.000	0.000	0.000	0.000
26	A	26	CYS	0	0.005	0.005	22.575	-0.153	-0.153	0.000	0.000	0.000	0.000
27	A	27	ASN	0	0.035	0.017	23.182	-1.628	-1.628	0.000	0.000	0.000	0.000
28	A	28	GLN	0	0.000	0.000	23.627	-0.152	-0.152	0.000	0.000	0.000	0.000
29	A	29	MET	0	-0.007	0.024	20.031	-1.196	-1.196	0.000	0.000	0.000	0.000
30	A	30	MET	0	-0.013	0.000	18.755	-2.154	-2.154	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.966	0.990	17.873	24.592	24.592	0.000	0.000	0.000	0.000
32	A	32	SER	0	-0.015	-0.024	17.565	-1.831	-1.831	0.000	0.000	0.000	0.000
33	A	33	ARG	1	0.836	0.908	15.159	32.160	32.160	0.000	0.000	0.000	0.000
34	A	34	ASN	0	-0.043	-0.018	12.412	-2.254	-2.254	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.034	-0.024	13.035	-3.183	-3.183	0.000	0.000	0.000	0.000
36	A	36	THR	0	-0.018	-0.012	15.099	-0.006	-0.006	0.000	0.000	0.000	0.000
37	A	37	LYS	1	0.871	0.934	10.880	48.876	48.876	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.810	-0.891	11.253	-45.538	-45.538	0.000	0.000	0.000	0.000
39	A	39	ARG	1	0.947	0.976	14.139	37.370	37.370	0.000	0.000	0.000	0.000
40	A	40	CYS	0	-0.012	0.020	16.948	-0.549	-0.549	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.879	0.950	14.568	37.334	37.334	0.000	0.000	0.000	0.000
42	A	42	PRO	0	0.047	0.029	18.121	0.623	0.623	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.009	-0.010	20.083	1.519	1.519	0.000	0.000	0.000	0.000
44	A	44	ASN	0	-0.017	-0.019	17.442	-3.569	-3.569	0.000	0.000	0.000	0.000
45	A	45	THR	0	0.012	0.013	19.820	1.514	1.514	0.000	0.000	0.000	0.000
46	A	46	PHE	0	0.021	0.013	17.881	-1.483	-1.483	0.000	0.000	0.000	0.000
47	A	47	VAL	0	0.044	0.012	21.271	1.439	1.439	0.000	0.000	0.000	0.000
48	A	48	HIS	1	0.749	0.879	22.752	22.755	22.755	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.730	-0.857	24.406	-20.843	-20.843	0.000	0.000	0.000	0.000
50	A	50	SER	0	-0.028	-0.034	23.925	-1.384	-1.384	0.000	0.000	0.000	0.000
51	A	51	LEU	0	0.010	-0.007	17.199	-0.023	-0.023	0.000	0.000	0.000	0.000
52	A	52	ALA	0	0.030	0.020	21.107	-0.728	-0.728	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.815	-0.877	23.320	-22.730	-22.730	0.000	0.000	0.000	0.000
54	A	54	VAL	0	-0.027	-0.027	19.806	0.003	0.003	0.000	0.000	0.000	0.000
55	A	55	GLN	0	-0.017	-0.020	16.846	0.502	0.502	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.034	0.029	20.683	-0.093	-0.093	0.000	0.000	0.000	0.000
57	A	57	VAL	0	-0.014	0.001	22.762	0.996	0.996	0.000	0.000	0.000	0.000
58	A	58	CYS	0	-0.090	-0.026	16.668	-1.551	-1.551	0.000	0.000	0.000	0.000
59	A	59	SER	0	-0.059	-0.035	22.460	0.312	0.312	0.000	0.000	0.000	0.000
60	A	60	GLN	0	0.023	0.018	25.889	1.460	1.460	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.950	0.982	28.131	19.725	19.725	0.000	0.000	0.000	0.000
62	A	62	ASN	0	-0.027	-0.012	24.656	0.232	0.232	0.000	0.000	0.000	0.000
63	A	63	VAL	0	-0.062	-0.037	25.224	1.171	1.171	0.000	0.000	0.000	0.000
64	A	64	ALA	0	0.007	0.006	24.510	-0.850	-0.850	0.000	0.000	0.000	0.000
65	A	65	CYS	0	-0.017	0.002	20.094	-1.656	-1.656	0.000	0.000	0.000	0.000
66	A	66	LYS	1	0.880	0.923	21.999	26.214	26.214	0.000	0.000	0.000	0.000
67	A	67	ASN	0	-0.060	-0.040	17.204	1.476	1.476	0.000	0.000	0.000	0.000
68	A	68	GLY	0	0.022	0.016	21.383	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	69	GLN	0	-0.026	-0.002	15.649	-0.116	-0.116	0.000	0.000	0.000	0.000
70	A	70	THR	0	0.047	0.015	20.844	0.063	0.063	0.000	0.000	0.000	0.000
71	A	71	ASN	0	-0.010	0.012	16.260	1.468	1.468	0.000	0.000	0.000	0.000
72	A	73	TYR	0	0.017	0.001	21.360	1.534	1.534	0.000	0.000	0.000	0.000
73	A	74	GLN	0	-0.019	-0.009	23.867	-0.754	-0.754	0.000	0.000	0.000	0.000
74	A	75	SER	0	0.002	-0.006	26.432	0.122	0.122	0.000	0.000	0.000	0.000
75	A	76	TYR	0	0.019	0.001	27.958	0.453	0.453	0.000	0.000	0.000	0.000
76	A	77	SER	0	0.002	0.013	30.933	0.838	0.838	0.000	0.000	0.000	0.000
77	A	78	THR	0	-0.036	-0.015	30.379	-0.555	-0.555	0.000	0.000	0.000	0.000
78	A	79	MET	0	-0.001	0.002	25.410	-0.432	-0.432	0.000	0.000	0.000	0.000
79	A	80	SER	0	-0.020	-0.022	29.014	0.232	0.232	0.000	0.000	0.000	0.000
80	A	81	ILE	0	-0.003	-0.011	25.247	-1.082	-1.082	0.000	0.000	0.000	0.000
81	A	82	THR	0	-0.036	-0.018	25.212	0.950	0.950	0.000	0.000	0.000	0.000
82	A	83	ASP	-1	-0.833	-0.889	24.368	-24.585	-24.585	0.000	0.000	0.000	0.000
83	A	85	ARG	1	0.884	0.925	23.499	21.733	21.733	0.000	0.000	0.000	0.000
84	A	86	GLU	-1	-0.839	-0.894	23.176	-25.402	-25.402	0.000	0.000	0.000	0.000
85	A	87	THR	0	-0.051	-0.028	25.847	0.922	0.922	0.000	0.000	0.000	0.000
86	A	88	GLY	0	0.023	0.002	28.674	-0.402	-0.402	0.000	0.000	0.000	0.000
87	A	89	SER	0	-0.013	-0.007	30.993	0.391	0.391	0.000	0.000	0.000	0.000
88	A	90	SER	0	-0.092	-0.054	24.530	-0.146	-0.146	0.000	0.000	0.000	0.000
89	A	91	LYS	1	0.984	0.980	25.861	21.119	21.119	0.000	0.000	0.000	0.000
90	A	92	TYR	0	-0.022	-0.007	17.249	0.707	0.707	0.000	0.000	0.000	0.000
91	A	93	PRO	0	0.001	-0.009	21.433	0.728	0.728	0.000	0.000	0.000	0.000
92	A	94	ASN	0	-0.041	-0.023	22.432	-1.006	-1.006	0.000	0.000	0.000	0.000
93	A	96	ALA	0	0.027	0.017	23.751	0.012	0.012	0.000	0.000	0.000	0.000
94	A	97	TYR	0	-0.016	-0.037	20.628	-0.078	-0.078	0.000	0.000	0.000	0.000
95	A	98	LYS	1	0.910	0.960	26.830	19.768	19.768	0.000	0.000	0.000	0.000
96	A	99	THR	0	-0.004	-0.038	27.992	-0.916	-0.916	0.000	0.000	0.000	0.000
97	A	100	THR	0	-0.024	-0.020	28.493	1.224	1.224	0.000	0.000	0.000	0.000
98	A	101	GLN	0	0.038	0.031	29.055	-1.209	-1.209	0.000	0.000	0.000	0.000
99	A	102	ALA	0	-0.010	-0.007	30.043	0.652	0.652	0.000	0.000	0.000	0.000
100	A	103	ASN	0	0.001	-0.003	30.624	-0.368	-0.368	0.000	0.000	0.000	0.000
101	A	104	LYS	1	0.862	0.931	28.896	19.860	19.860	0.000	0.000	0.000	0.000
102	A	105	HIS	0	0.002	0.011	29.247	0.070	0.070	0.000	0.000	0.000	0.000
103	A	106	ILE	0	-0.012	-0.013	22.252	-0.360	-0.360	0.000	0.000	0.000	0.000
104	A	107	ILE	0	0.010	0.003	22.854	0.379	0.379	0.000	0.000	0.000	0.000
105	A	108	VAL	0	0.008	-0.001	18.859	-1.064	-1.064	0.000	0.000	0.000	0.000
106	A	109	ALA	0	0.045	0.018	16.432	1.020	1.020	0.000	0.000	0.000	0.000
107	A	111	GLU	-1	-0.910	-0.964	12.250	-44.958	-44.958	0.000	0.000	0.000	0.000
108	A	112	GLY	0	0.002	0.001	13.770	-0.385	-0.385	0.000	0.000	0.000	0.000
109	A	113	ASN	0	0.018	0.003	14.465	3.354	3.354	0.000	0.000	0.000	0.000
110	A	114	PRO	0	0.025	0.004	14.960	-1.394	-1.394	0.000	0.000	0.000	0.000
111	A	115	TYR	0	-0.046	0.002	15.989	-1.660	-1.660	0.000	0.000	0.000	0.000
112	A	116	VAL	0	0.018	0.005	13.882	1.340	1.340	0.000	0.000	0.000	0.000
113	A	117	PRO	0	0.034	0.003	15.843	-1.141	-1.141	0.000	0.000	0.000	0.000
114	A	118	VAL	0	-0.062	-0.026	11.574	-2.919	-2.919	0.000	0.000	0.000	0.000
115	A	119	HIS	0	-0.078	-0.052	12.360	-4.160	-4.160	0.000	0.000	0.000	0.000
116	A	120	PHE	0	0.008	0.004	14.956	1.870	1.870	0.000	0.000	0.000	0.000
117	A	121	ASP	-1	-0.795	-0.874	18.215	-28.684	-28.684	0.000	0.000	0.000	0.000
118	A	122	ALA	0	-0.038	-0.042	20.426	0.966	0.966	0.000	0.000	0.000	0.000
119	A	123	SER	0	-0.013	0.001	23.885	-0.159	-0.159	0.000	0.000	0.000	0.000
120	A	124	VAL	-1	-0.798	-0.879	26.547	-19.499	-19.499	0.000	0.000	0.000	0.000

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