FMO DATABASE

FMODB ID: 1YN9Z

Calculation Name: 3IKK-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3IKK

Chain ID: A

ChEMBL ID:

UniProt ID: O95292

Base Structure: X-ray

Registration Date: 2025-10-04

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	125
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1040709.538931
FMO2-HF: Nuclear repulsion	989532.09437
FMO2-HF: Total energy	-51177.444562
FMO2-MP2: Total energy	-51321.576335

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:MET)

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

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.
-52.154	-59.161	7.544	5.588	-6.125	-0.08

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.745 / q_NPA : 0.886

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	3	LYS	1	0.841	0.914	2.005	46.905	38.980	7.457	5.535	-5.067	-0.066
4	A	4	VAL	0	0.053	0.039	2.715	-8.836	-7.840	0.088	0.082	-1.166	-0.014
112	A	112	GLU	-1	-0.868	-0.950	4.941	-66.326	-66.404	-0.001	-0.029	0.108	0.000
5	A	5	GLU	-1	-0.934	-0.971	5.583	-30.754	-30.754	0.000	0.000	0.000	0.000
6	A	6	GLN	0	-0.035	-0.015	7.750	2.680	2.680	0.000	0.000	0.000	0.000
7	A	7	VAL	0	0.071	0.034	10.900	1.352	1.352	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.060	-0.022	13.517	1.616	1.616	0.000	0.000	0.000	0.000
9	A	9	SER	0	-0.022	-0.011	16.019	-0.318	-0.318	0.000	0.000	0.000	0.000
10	A	10	LEU	0	-0.044	-0.029	16.189	0.452	0.452	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.888	-0.941	19.582	-13.518	-13.518	0.000	0.000	0.000	0.000
12	A	12	PRO	0	0.015	0.004	23.039	0.371	0.371	0.000	0.000	0.000	0.000
13	A	13	GLN	0	0.022	0.013	16.581	-1.260	-1.260	0.000	0.000	0.000	0.000
14	A	14	HIS	0	0.052	0.023	15.678	-0.842	-0.842	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.896	-0.961	19.320	-13.005	-13.005	0.000	0.000	0.000	0.000
16	A	16	LEU	0	0.000	0.017	22.261	0.229	0.229	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.923	0.955	25.054	11.419	11.419	0.000	0.000	0.000	0.000
18	A	18	PHE	0	-0.009	-0.014	26.523	-0.019	-0.019	0.000	0.000	0.000	0.000
19	A	19	ARG	1	0.848	0.909	31.371	9.098	9.098	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.049	0.053	34.985	0.050	0.050	0.000	0.000	0.000	0.000
21	A	21	PRO	0	0.023	-0.005	37.812	0.069	0.069	0.000	0.000	0.000	0.000
22	A	22	PHE	0	-0.020	-0.027	33.558	-0.072	-0.072	0.000	0.000	0.000	0.000
23	A	23	THR	0	0.013	-0.001	38.315	-0.087	-0.087	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.845	-0.909	40.191	-7.651	-7.651	0.000	0.000	0.000	0.000
25	A	25	VAL	0	-0.072	-0.050	35.164	-0.262	-0.262	0.000	0.000	0.000	0.000
26	A	26	VAL	0	0.015	0.034	33.355	-0.024	-0.024	0.000	0.000	0.000	0.000
27	A	27	THR	0	-0.031	-0.033	32.062	-0.375	-0.375	0.000	0.000	0.000	0.000
28	A	28	THR	0	-0.036	-0.014	27.626	0.134	0.134	0.000	0.000	0.000	0.000
29	A	29	ASN	0	0.007	-0.008	28.171	-0.166	-0.166	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.006	0.005	20.145	-0.203	-0.203	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.913	0.955	24.329	12.567	12.567	0.000	0.000	0.000	0.000
32	A	32	LEU	0	-0.005	0.002	18.809	-0.702	-0.702	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.012	-0.008	20.364	0.891	0.891	0.000	0.000	0.000	0.000
34	A	34	ASN	0	-0.015	-0.007	19.012	-1.680	-1.680	0.000	0.000	0.000	0.000
35	A	35	PRO	0	-0.020	0.003	17.775	0.776	0.776	0.000	0.000	0.000	0.000
36	A	36	THR	0	-0.042	-0.031	16.430	-0.076	-0.076	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.856	-0.939	19.893	-14.707	-14.707	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.896	0.943	16.139	18.166	18.166	0.000	0.000	0.000	0.000
39	A	39	ASN	0	0.021	0.014	20.003	-0.287	-0.287	0.000	0.000	0.000	0.000
40	A	40	VAL	0	-0.009	0.001	15.647	-0.813	-0.813	0.000	0.000	0.000	0.000
41	A	41	CYS	0	-0.017	0.022	17.277	1.085	1.085	0.000	0.000	0.000	0.000
42	A	42	PHE	0	0.027	-0.002	16.659	-1.294	-1.294	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.903	0.942	17.312	16.224	16.224	0.000	0.000	0.000	0.000
44	A	44	VAL	0	0.000	0.016	17.643	-1.022	-1.022	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.870	0.936	15.770	19.704	19.704	0.000	0.000	0.000	0.000
46	A	46	THR	0	0.034	0.007	20.243	-0.251	-0.251	0.000	0.000	0.000	0.000
47	A	47	THR	0	-0.014	-0.004	20.761	-0.083	-0.083	0.000	0.000	0.000	0.000
48	A	48	ALA	0	0.016	0.015	22.425	0.241	0.241	0.000	0.000	0.000	0.000
49	A	49	PRO	0	0.029	0.003	24.602	0.393	0.393	0.000	0.000	0.000	0.000
50	A	50	ARG	1	0.958	0.982	27.144	9.814	9.814	0.000	0.000	0.000	0.000
51	A	51	ARG	1	0.895	0.970	29.087	10.168	10.168	0.000	0.000	0.000	0.000
52	A	52	TYR	0	0.036	0.000	27.075	0.090	0.090	0.000	0.000	0.000	0.000
53	A	53	CYS	0	-0.064	-0.016	28.972	-0.126	-0.126	0.000	0.000	0.000	0.000
54	A	54	VAL	0	0.020	0.008	24.066	-0.077	-0.077	0.000	0.000	0.000	0.000
55	A	55	ARG	1	0.897	0.962	27.370	10.608	10.608	0.000	0.000	0.000	0.000
56	A	56	PRO	0	0.119	0.055	25.309	0.157	0.157	0.000	0.000	0.000	0.000
57	A	57	ASN	0	0.002	-0.007	24.211	-0.484	-0.484	0.000	0.000	0.000	0.000
58	A	58	SER	0	-0.056	-0.029	21.726	-0.760	-0.760	0.000	0.000	0.000	0.000
59	A	59	GLY	0	0.042	0.029	21.759	0.750	0.750	0.000	0.000	0.000	0.000
60	A	60	ILE	0	0.035	0.004	21.292	-0.848	-0.848	0.000	0.000	0.000	0.000
61	A	61	ILE	0	-0.055	-0.013	19.870	0.648	0.648	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.802	-0.907	21.718	-12.557	-12.557	0.000	0.000	0.000	0.000
63	A	63	ALA	0	0.010	0.006	22.357	-0.381	-0.381	0.000	0.000	0.000	0.000
64	A	64	GLY	0	0.007	0.014	22.725	0.619	0.619	0.000	0.000	0.000	0.000
65	A	65	ALA	0	-0.015	0.016	24.215	0.405	0.405	0.000	0.000	0.000	0.000
66	A	66	SER	0	-0.033	-0.051	23.779	-0.638	-0.638	0.000	0.000	0.000	0.000
67	A	67	ILE	0	-0.009	0.012	23.228	0.522	0.522	0.000	0.000	0.000	0.000
68	A	68	ASN	0	-0.002	-0.007	25.371	-0.602	-0.602	0.000	0.000	0.000	0.000
69	A	69	VAL	0	-0.008	0.001	22.851	0.172	0.172	0.000	0.000	0.000	0.000
70	A	70	SER	0	0.012	0.011	26.195	0.075	0.075	0.000	0.000	0.000	0.000
71	A	71	VAL	0	-0.038	-0.028	24.715	-0.169	-0.169	0.000	0.000	0.000	0.000
72	A	72	MET	0	-0.011	-0.006	28.002	0.341	0.341	0.000	0.000	0.000	0.000
73	A	73	LEU	0	-0.031	-0.019	30.329	-0.356	-0.356	0.000	0.000	0.000	0.000
74	A	74	GLN	0	-0.007	-0.015	31.877	0.468	0.468	0.000	0.000	0.000	0.000
75	A	75	PRO	0	0.019	0.016	34.765	-0.161	-0.161	0.000	0.000	0.000	0.000
76	A	76	PHE	0	-0.078	-0.051	33.572	-0.193	-0.193	0.000	0.000	0.000	0.000
77	A	77	ASP	-1	-0.883	-0.926	37.810	-7.668	-7.668	0.000	0.000	0.000	0.000
78	A	78	TYR	0	-0.088	-0.039	33.854	-0.325	-0.325	0.000	0.000	0.000	0.000
79	A	79	ASP	-1	-0.893	-0.950	36.304	-8.192	-8.192	0.000	0.000	0.000	0.000
80	A	80	PRO	0	0.020	0.004	36.794	-0.173	-0.173	0.000	0.000	0.000	0.000
81	A	81	ASN	0	-0.013	0.010	35.720	-0.042	-0.042	0.000	0.000	0.000	0.000
82	A	82	GLU	-1	-0.868	-0.953	32.608	-9.917	-9.917	0.000	0.000	0.000	0.000
83	A	83	LYS	1	0.899	0.935	28.085	9.954	9.954	0.000	0.000	0.000	0.000
84	A	84	SER	0	0.064	0.044	27.490	-0.264	-0.264	0.000	0.000	0.000	0.000
85	A	85	LYS	1	0.937	0.957	24.404	11.591	11.591	0.000	0.000	0.000	0.000
86	A	86	HIS	0	0.037	0.044	23.069	-0.727	-0.727	0.000	0.000	0.000	0.000
87	A	87	LYS	1	0.829	0.907	18.377	14.584	14.584	0.000	0.000	0.000	0.000
88	A	88	PHE	0	0.054	0.025	19.870	0.361	0.361	0.000	0.000	0.000	0.000
89	A	89	MET	0	-0.048	-0.025	13.831	-0.489	-0.489	0.000	0.000	0.000	0.000
90	A	90	VAL	0	0.060	0.037	15.377	0.967	0.967	0.000	0.000	0.000	0.000
91	A	91	GLN	0	-0.051	-0.033	11.370	0.542	0.542	0.000	0.000	0.000	0.000
92	A	92	SER	0	-0.003	-0.032	12.552	1.539	1.539	0.000	0.000	0.000	0.000
93	A	93	MET	0	0.027	0.016	12.068	-1.957	-1.957	0.000	0.000	0.000	0.000
94	A	94	PHE	0	0.046	0.016	12.133	1.386	1.386	0.000	0.000	0.000	0.000
95	A	95	ALA	0	0.053	0.012	15.408	-0.242	-0.242	0.000	0.000	0.000	0.000
96	A	96	PRO	0	-0.028	-0.006	16.804	0.246	0.246	0.000	0.000	0.000	0.000
97	A	97	THR	0	-0.024	-0.017	18.686	0.267	0.267	0.000	0.000	0.000	0.000
98	A	98	ASP	-1	-0.863	-0.905	21.178	-13.559	-13.559	0.000	0.000	0.000	0.000
99	A	99	THR	0	-0.098	-0.070	20.868	0.328	0.328	0.000	0.000	0.000	0.000
100	A	100	SER	0	-0.024	0.003	23.458	0.374	0.374	0.000	0.000	0.000	0.000
101	A	101	ASP	-1	-0.817	-0.928	24.839	-11.824	-11.824	0.000	0.000	0.000	0.000
102	A	102	MET	0	-0.085	-0.033	20.720	-0.936	-0.936	0.000	0.000	0.000	0.000
103	A	103	GLU	-1	-0.858	-0.925	23.137	-12.577	-12.577	0.000	0.000	0.000	0.000
104	A	104	ALA	0	-0.077	-0.029	22.779	-0.621	-0.621	0.000	0.000	0.000	0.000
105	A	105	VAL	0	0.042	0.008	17.600	-0.732	-0.732	0.000	0.000	0.000	0.000
106	A	106	TRP	0	-0.044	-0.053	14.898	-1.461	-1.461	0.000	0.000	0.000	0.000
107	A	107	LYS	1	0.807	0.905	16.670	13.487	13.487	0.000	0.000	0.000	0.000
108	A	108	GLU	-1	-0.855	-0.916	16.929	-15.510	-15.510	0.000	0.000	0.000	0.000
109	A	109	ALA	0	-0.009	0.014	13.057	-0.607	-0.607	0.000	0.000	0.000	0.000
110	A	110	LYS	1	0.866	0.915	9.986	23.652	23.652	0.000	0.000	0.000	0.000
111	A	111	PRO	0	-0.025	-0.029	6.561	-0.266	-0.266	0.000	0.000	0.000	0.000
113	A	113	ASP	-1	-0.806	-0.887	6.604	-26.807	-26.807	0.000	0.000	0.000	0.000
114	A	114	LEU	0	-0.062	-0.015	8.366	2.552	2.552	0.000	0.000	0.000	0.000
115	A	115	MET	0	0.022	0.026	7.332	-4.969	-4.969	0.000	0.000	0.000	0.000
116	A	116	ASP	-1	-0.824	-0.898	8.335	-29.341	-29.341	0.000	0.000	0.000	0.000
117	A	117	SER	0	0.007	-0.002	9.895	-0.830	-0.830	0.000	0.000	0.000	0.000
118	A	118	LYS	1	0.905	0.957	12.552	21.803	21.803	0.000	0.000	0.000	0.000
119	A	119	LEU	0	0.031	0.040	15.054	-0.052	-0.052	0.000	0.000	0.000	0.000
120	A	120	ARG	1	0.789	0.871	18.627	14.938	14.938	0.000	0.000	0.000	0.000
121	A	121	CYS	0	-0.048	0.006	21.250	0.172	0.172	0.000	0.000	0.000	0.000
122	A	122	VAL	0	-0.003	0.002	24.758	-0.033	-0.033	0.000	0.000	0.000	0.000
123	A	123	PHE	0	-0.006	-0.006	27.854	-0.080	-0.080	0.000	0.000	0.000	0.000
124	A	124	GLU	-1	-0.848	-0.922	31.514	-9.667	-9.667	0.000	0.000	0.000	0.000
125	A	125	LEU	-1	-0.836	-0.916	34.426	-8.303	-8.303	0.000	0.000	0.000	0.000

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