FMO DATABASE

FMODB ID: RL118

Calculation Name: 1K5A-A-Xray547

Preferred Name: Angiogenin

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1K5A

Chain ID: A

ChEMBL ID: CHEMBL5829

UniProt ID: P03950

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	115
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-981535.241287
FMO2-HF: Nuclear repulsion	933574.44052
FMO2-HF: Total energy	-47960.800767
FMO2-MP2: Total energy	-48097.339442

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:3:ASN)

Summations of interaction energy for fragment #1(A:3: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.
162.823	167	0.074	-1.435	-2.815	-0.005

Interaction energy analysis for fragmet #1(A:3:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.934 / q_NPA : 0.954

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	5	ARG	1	1.039	1.024	3.761	35.573	37.386	-0.005	-0.718	-1.090	0.000
4	A	6	TYR	0	0.041	0.028	2.847	5.685	6.629	0.049	-0.294	-0.699	-0.002
5	A	7	THR	0	-0.016	-0.012	3.554	6.799	7.192	-0.001	-0.107	-0.285	0.000
103	A	108	GLU	-1	-0.850	-0.927	4.695	-41.607	-41.494	-0.001	-0.008	-0.103	0.000
104	A	109	ASN	0	-0.010	-0.014	3.273	-1.309	-0.977	0.002	-0.102	-0.231	-0.001
106	A	111	LEU	0	-0.081	-0.044	3.273	-1.867	-1.285	0.030	-0.206	-0.407	-0.002
6	A	8	HIS	0	0.044	0.034	5.993	4.561	4.561	0.000	0.000	0.000	0.000
7	A	9	PHE	0	0.014	0.008	8.028	3.251	3.251	0.000	0.000	0.000	0.000
8	A	10	LEU	0	-0.042	-0.030	6.966	3.666	3.666	0.000	0.000	0.000	0.000
9	A	11	THR	0	0.019	-0.007	9.666	3.154	3.154	0.000	0.000	0.000	0.000
10	A	12	GLN	0	0.026	0.018	11.979	3.021	3.021	0.000	0.000	0.000	0.000
11	A	13	HIS	0	-0.016	0.002	12.744	0.834	0.834	0.000	0.000	0.000	0.000
12	A	14	TYR	0	-0.055	-0.044	12.480	0.101	0.101	0.000	0.000	0.000	0.000
13	A	15	ASP	-1	-0.804	-0.877	14.423	-16.258	-16.258	0.000	0.000	0.000	0.000
14	A	16	ALA	0	-0.001	0.016	16.858	0.772	0.772	0.000	0.000	0.000	0.000
15	A	17	LYS	1	0.979	0.973	18.273	12.763	12.763	0.000	0.000	0.000	0.000
16	A	18	PRO	0	0.012	0.036	21.678	0.205	0.205	0.000	0.000	0.000	0.000
17	A	19	GLN	0	-0.014	-0.018	23.817	0.248	0.248	0.000	0.000	0.000	0.000
18	A	20	GLY	0	0.025	0.023	27.261	0.280	0.280	0.000	0.000	0.000	0.000
19	A	21	ARG	1	0.804	0.875	24.595	11.647	11.647	0.000	0.000	0.000	0.000
20	A	22	ASP	-1	-0.766	-0.873	27.708	-10.117	-10.117	0.000	0.000	0.000	0.000
21	A	23	ASP	-1	-0.762	-0.892	28.752	-10.297	-10.297	0.000	0.000	0.000	0.000
22	A	24	ARG	1	0.934	0.961	29.405	9.367	9.367	0.000	0.000	0.000	0.000
23	A	25	TYR	0	-0.069	-0.063	21.155	-0.419	-0.419	0.000	0.000	0.000	0.000
24	A	26	CYS	0	-0.048	-0.024	23.789	-0.140	-0.140	0.000	0.000	0.000	0.000
25	A	27	GLU	-1	-0.839	-0.913	24.947	-10.652	-10.652	0.000	0.000	0.000	0.000
26	A	28	SER	0	-0.034	-0.011	25.646	-0.462	-0.462	0.000	0.000	0.000	0.000
27	A	29	ILE	0	-0.065	-0.038	18.855	-0.473	-0.473	0.000	0.000	0.000	0.000
28	A	30	MET	0	0.009	0.013	20.923	-1.145	-1.145	0.000	0.000	0.000	0.000
29	A	31	ARG	1	0.952	0.988	21.824	10.815	10.815	0.000	0.000	0.000	0.000
30	A	32	ARG	1	0.871	0.930	20.399	13.851	13.851	0.000	0.000	0.000	0.000
31	A	33	ARG	1	0.768	0.867	14.224	19.224	19.224	0.000	0.000	0.000	0.000
32	A	34	GLY	0	0.025	0.030	17.083	-0.934	-0.934	0.000	0.000	0.000	0.000
33	A	35	LEU	0	-0.055	-0.026	16.953	-0.152	-0.152	0.000	0.000	0.000	0.000
34	A	36	THR	0	0.008	-0.014	20.799	0.632	0.632	0.000	0.000	0.000	0.000
35	A	37	SER	0	-0.025	-0.003	23.283	0.757	0.757	0.000	0.000	0.000	0.000
36	A	38	PRO	0	0.034	0.023	22.986	-0.390	-0.390	0.000	0.000	0.000	0.000
37	A	39	CYS	0	-0.121	-0.034	23.918	-0.383	-0.383	0.000	0.000	0.000	0.000
38	A	40	LYS	1	0.857	0.939	16.879	17.530	17.530	0.000	0.000	0.000	0.000
39	A	41	ASP	-1	-0.825	-0.915	23.183	-11.374	-11.374	0.000	0.000	0.000	0.000
40	A	42	ILE	0	0.018	0.013	22.648	0.193	0.193	0.000	0.000	0.000	0.000
41	A	43	ASN	0	-0.012	-0.020	17.666	-1.249	-1.249	0.000	0.000	0.000	0.000
42	A	44	THR	0	-0.016	0.002	19.438	0.975	0.975	0.000	0.000	0.000	0.000
43	A	45	PHE	0	0.002	0.009	17.222	-1.189	-1.189	0.000	0.000	0.000	0.000
44	A	46	ILE	0	0.012	0.001	14.956	0.836	0.836	0.000	0.000	0.000	0.000
45	A	47	HIS	0	-0.010	0.011	17.205	-0.193	-0.193	0.000	0.000	0.000	0.000
46	A	48	GLY	0	0.034	0.025	19.010	-0.041	-0.041	0.000	0.000	0.000	0.000
47	A	49	ASN	0	-0.013	-0.006	17.119	-1.199	-1.199	0.000	0.000	0.000	0.000
48	A	50	LYS	1	1.026	1.016	9.507	28.482	28.482	0.000	0.000	0.000	0.000
49	A	51	ARG	1	0.939	0.968	12.258	16.060	16.060	0.000	0.000	0.000	0.000
50	A	52	SER	0	0.036	0.005	13.891	-0.261	-0.261	0.000	0.000	0.000	0.000
51	A	53	ILE	0	0.039	0.038	11.829	0.168	0.168	0.000	0.000	0.000	0.000
52	A	54	LYS	1	0.943	0.971	8.002	32.775	32.775	0.000	0.000	0.000	0.000
53	A	55	ALA	0	0.015	0.007	11.312	-0.283	-0.283	0.000	0.000	0.000	0.000
54	A	56	ILE	0	-0.013	0.012	14.172	1.247	1.247	0.000	0.000	0.000	0.000
55	A	57	CYS	0	-0.075	-0.042	9.118	-1.419	-1.419	0.000	0.000	0.000	0.000
56	A	58	GLU	-1	-0.863	-0.911	13.119	-20.846	-20.846	0.000	0.000	0.000	0.000
57	A	59	ASN	0	0.030	-0.005	15.695	0.252	0.252	0.000	0.000	0.000	0.000
58	A	60	LYS	1	0.954	0.997	17.161	17.737	17.737	0.000	0.000	0.000	0.000
59	A	61	ASN	0	-0.008	0.002	17.435	1.605	1.605	0.000	0.000	0.000	0.000
60	A	62	GLY	0	0.030	0.031	18.109	0.003	0.003	0.000	0.000	0.000	0.000
61	A	63	ASN	0	-0.008	-0.003	19.127	0.310	0.310	0.000	0.000	0.000	0.000
62	A	64	PRO	0	0.038	0.011	18.968	-0.745	-0.745	0.000	0.000	0.000	0.000
63	A	65	HIS	0	0.019	-0.002	19.342	0.368	0.368	0.000	0.000	0.000	0.000
64	A	66	ARG	1	0.914	0.951	19.826	12.009	12.009	0.000	0.000	0.000	0.000
65	A	67	GLU	-1	-0.874	-0.907	19.851	-12.715	-12.715	0.000	0.000	0.000	0.000
66	A	68	ASN	0	0.011	-0.009	15.083	-0.391	-0.391	0.000	0.000	0.000	0.000
67	A	69	LEU	0	-0.014	0.002	14.925	-1.500	-1.500	0.000	0.000	0.000	0.000
68	A	70	ARG	1	0.813	0.905	14.160	18.964	18.964	0.000	0.000	0.000	0.000
69	A	71	ILE	0	0.017	0.014	16.914	-0.259	-0.259	0.000	0.000	0.000	0.000
70	A	72	SER	0	-0.020	-0.025	18.649	-0.083	-0.083	0.000	0.000	0.000	0.000
71	A	73	LYS	1	0.847	0.929	20.062	14.968	14.968	0.000	0.000	0.000	0.000
72	A	74	SER	0	-0.010	-0.023	20.979	0.467	0.467	0.000	0.000	0.000	0.000
73	A	75	SER	0	0.009	0.018	22.268	-0.312	-0.312	0.000	0.000	0.000	0.000
74	A	76	PHE	0	-0.014	-0.023	17.387	-0.276	-0.276	0.000	0.000	0.000	0.000
75	A	77	GLN	0	0.051	0.036	21.891	0.503	0.503	0.000	0.000	0.000	0.000
76	A	78	VAL	0	-0.030	-0.026	20.196	-0.861	-0.861	0.000	0.000	0.000	0.000
77	A	79	THR	0	0.019	-0.023	21.827	0.981	0.981	0.000	0.000	0.000	0.000
78	A	80	THR	0	-0.032	-0.014	22.305	-0.655	-0.655	0.000	0.000	0.000	0.000
79	A	82	LYS	1	0.928	0.950	25.233	11.071	11.071	0.000	0.000	0.000	0.000
80	A	83	LEU	0	0.008	0.022	27.504	0.248	0.248	0.000	0.000	0.000	0.000
81	A	84	HIS	0	-0.010	-0.002	29.142	0.134	0.134	0.000	0.000	0.000	0.000
82	A	85	GLY	0	0.004	0.012	32.965	0.034	0.034	0.000	0.000	0.000	0.000
83	A	86	GLY	0	0.043	0.006	33.333	-0.107	-0.107	0.000	0.000	0.000	0.000
84	A	87	SER	0	-0.034	-0.012	33.102	-0.013	-0.013	0.000	0.000	0.000	0.000
85	A	88	PRO	0	0.040	0.010	29.087	-0.267	-0.267	0.000	0.000	0.000	0.000
86	A	89	TRP	0	0.033	0.015	26.619	-0.622	-0.622	0.000	0.000	0.000	0.000
87	A	90	PRO	0	0.025	0.009	28.371	0.233	0.233	0.000	0.000	0.000	0.000
88	A	91	PRO	0	0.009	0.007	30.999	0.201	0.201	0.000	0.000	0.000	0.000
89	A	93	GLN	0	0.018	0.011	29.204	-0.013	-0.013	0.000	0.000	0.000	0.000
90	A	94	TYR	0	-0.073	-0.073	25.041	-0.186	-0.186	0.000	0.000	0.000	0.000
91	A	95	ARG	1	0.909	0.957	29.630	9.809	9.809	0.000	0.000	0.000	0.000
92	A	96	ALA	0	0.007	-0.002	28.036	-0.456	-0.456	0.000	0.000	0.000	0.000
93	A	97	THR	0	-0.037	-0.022	27.556	0.429	0.429	0.000	0.000	0.000	0.000
94	A	98	ALA	0	-0.014	-0.002	26.778	-0.565	-0.565	0.000	0.000	0.000	0.000
95	A	99	GLY	0	0.039	0.030	26.211	0.366	0.366	0.000	0.000	0.000	0.000
96	A	100	PHE	0	-0.025	-0.039	25.249	-0.441	-0.441	0.000	0.000	0.000	0.000
97	A	101	ARG	1	0.937	0.976	22.691	13.803	13.803	0.000	0.000	0.000	0.000
98	A	102	ASN	0	-0.014	-0.007	22.486	-0.222	-0.222	0.000	0.000	0.000	0.000
99	A	103	VAL	0	-0.027	-0.011	17.008	0.078	0.078	0.000	0.000	0.000	0.000
100	A	104	VAL	0	0.043	0.020	17.963	-0.112	-0.112	0.000	0.000	0.000	0.000
101	A	105	VAL	0	-0.005	-0.003	12.612	-0.460	-0.460	0.000	0.000	0.000	0.000
102	A	106	ALA	0	0.071	0.045	11.686	0.950	0.950	0.000	0.000	0.000	0.000
105	A	110	GLY	0	0.047	0.032	6.393	-1.977	-1.977	0.000	0.000	0.000	0.000
107	A	112	PRO	0	0.011	0.007	7.074	0.459	0.459	0.000	0.000	0.000	0.000
108	A	113	VAL	0	-0.042	-0.044	5.035	-4.484	-4.484	0.000	0.000	0.000	0.000
109	A	114	HIS	0	0.008	0.014	7.691	0.110	0.110	0.000	0.000	0.000	0.000
110	A	115	LEU	0	-0.033	-0.015	11.457	-0.093	-0.093	0.000	0.000	0.000	0.000
111	A	116	ASP	-1	-0.840	-0.910	14.602	-15.093	-15.093	0.000	0.000	0.000	0.000
112	A	117	GLN	0	-0.001	-0.006	17.567	-0.054	-0.054	0.000	0.000	0.000	0.000
113	A	118	SER	0	-0.008	-0.009	20.093	0.756	0.756	0.000	0.000	0.000	0.000
114	A	119	ALA	0	0.003	0.008	22.464	0.621	0.621	0.000	0.000	0.000	0.000
115	A	120	ALA	-1	-0.837	-0.924	22.417	-12.497	-12.497	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:ASN)