FMO DATABASE

FMODB ID: 9RNV2

Calculation Name: 1IIB-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1IIB

Chain ID: A

ChEMBL ID:

UniProt ID: P69795

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	103
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-737781.494622
FMO2-HF: Nuclear repulsion	699472.724421
FMO2-HF: Total energy	-38308.770201
FMO2-MP2: Total energy	-38421.268228

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:LYS)

Summations of interaction energy for fragment #1(A:3: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.
-206.813	-196.972	11.942	-9.131	-12.651	-0.1

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.768 / q_NPA : 1.878

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	HIS	0	0.063	0.041	3.774	-1.775	-0.112	-0.009	-0.757	-0.897	-0.002
26	A	28	GLU	-1	-0.922	-0.952	4.433	-90.147	-90.015	-0.001	-0.020	-0.111	0.000
31	A	33	PRO	0	0.008	0.009	2.685	-17.031	-15.600	0.678	-0.550	-1.560	-0.004
32	A	34	VAL	0	-0.069	-0.046	2.124	-22.394	-19.597	8.565	-5.572	-5.789	-0.061
33	A	35	ILE	0	-0.006	-0.004	2.528	-23.428	-19.702	2.709	-2.210	-4.224	-0.033
34	A	36	ILE	0	0.007	0.009	4.404	6.823	6.915	0.000	-0.022	-0.070	0.000
4	A	6	ILE	0	0.017	0.010	6.080	6.938	6.938	0.000	0.000	0.000	0.000
5	A	7	TYR	0	-0.035	-0.030	8.199	1.706	1.706	0.000	0.000	0.000	0.000
6	A	8	LEU	0	0.004	0.002	11.610	2.277	2.277	0.000	0.000	0.000	0.000
7	A	9	PHE	0	0.007	0.006	14.581	0.093	0.093	0.000	0.000	0.000	0.000
8	A	10	SER	0	-0.014	-0.028	18.108	1.353	1.353	0.000	0.000	0.000	0.000
9	A	11	SER	0	0.097	0.066	21.427	-0.499	-0.499	0.000	0.000	0.000	0.000
10	A	12	ALA	0	-0.041	-0.008	23.683	0.575	0.575	0.000	0.000	0.000	0.000
11	A	13	GLY	0	0.050	0.029	21.132	-1.126	-1.126	0.000	0.000	0.000	0.000
12	A	14	MET	0	0.029	0.017	20.178	-1.771	-1.771	0.000	0.000	0.000	0.000
13	A	15	SER	0	0.026	-0.002	20.225	-0.778	-0.778	0.000	0.000	0.000	0.000
14	A	16	THR	0	0.013	0.008	16.979	-0.964	-0.964	0.000	0.000	0.000	0.000
15	A	17	SER	0	0.020	-0.001	15.919	-2.562	-2.562	0.000	0.000	0.000	0.000
16	A	18	LEU	0	-0.029	0.000	15.359	-1.972	-1.972	0.000	0.000	0.000	0.000
17	A	19	LEU	0	0.034	0.027	15.748	-1.222	-1.222	0.000	0.000	0.000	0.000
18	A	20	VAL	0	0.041	0.016	10.767	-1.825	-1.825	0.000	0.000	0.000	0.000
19	A	21	SER	0	-0.080	-0.052	11.193	-3.180	-3.180	0.000	0.000	0.000	0.000
20	A	22	LYS	1	0.955	0.976	11.934	29.539	29.539	0.000	0.000	0.000	0.000
21	A	23	MET	0	-0.022	-0.002	10.787	-0.174	-0.174	0.000	0.000	0.000	0.000
22	A	24	ARG	1	0.855	0.925	7.125	51.746	51.746	0.000	0.000	0.000	0.000
23	A	25	ALA	0	0.010	0.013	7.721	-3.648	-3.648	0.000	0.000	0.000	0.000
24	A	26	GLN	0	-0.019	-0.023	10.361	-0.310	-0.310	0.000	0.000	0.000	0.000
25	A	27	ALA	0	-0.001	-0.014	5.820	0.486	0.486	0.000	0.000	0.000	0.000
27	A	29	LYS	1	0.888	0.955	6.949	39.693	39.693	0.000	0.000	0.000	0.000
28	A	30	TYR	0	-0.083	-0.047	9.507	5.279	5.279	0.000	0.000	0.000	0.000
29	A	31	GLU	-1	-0.901	-0.933	6.665	-53.193	-53.193	0.000	0.000	0.000	0.000
30	A	32	VAL	0	-0.008	0.006	6.066	-4.962	-4.962	0.000	0.000	0.000	0.000
35	A	37	GLU	-1	-0.862	-0.929	8.024	-55.206	-55.206	0.000	0.000	0.000	0.000
36	A	38	ALA	0	-0.001	0.000	11.136	1.360	1.360	0.000	0.000	0.000	0.000
37	A	39	PHE	0	-0.007	-0.004	12.478	0.424	0.424	0.000	0.000	0.000	0.000
38	A	40	PRO	0	0.043	0.027	17.472	0.483	0.483	0.000	0.000	0.000	0.000
39	A	41	GLU	-1	-0.799	-0.931	20.334	-25.648	-25.648	0.000	0.000	0.000	0.000
40	A	42	THR	0	-0.016	-0.011	22.225	-0.545	-0.545	0.000	0.000	0.000	0.000
41	A	43	LEU	0	0.007	0.012	18.559	0.002	0.002	0.000	0.000	0.000	0.000
42	A	44	ALA	0	0.010	0.007	18.239	-1.555	-1.555	0.000	0.000	0.000	0.000
43	A	45	GLY	0	0.038	-0.002	18.228	-1.309	-1.309	0.000	0.000	0.000	0.000
44	A	46	GLU	-1	-0.889	-0.923	18.224	-30.383	-30.383	0.000	0.000	0.000	0.000
45	A	47	LYS	1	0.878	0.920	14.142	33.208	33.208	0.000	0.000	0.000	0.000
46	A	48	GLY	0	0.035	0.014	13.653	-3.029	-3.029	0.000	0.000	0.000	0.000
47	A	49	GLN	0	-0.005	-0.007	14.399	-1.842	-1.842	0.000	0.000	0.000	0.000
48	A	50	ASN	0	-0.046	-0.029	10.616	-1.545	-1.545	0.000	0.000	0.000	0.000
49	A	51	ALA	0	-0.021	0.016	9.472	-5.540	-5.540	0.000	0.000	0.000	0.000
50	A	52	ASP	-1	-0.850	-0.930	6.420	-72.730	-72.730	0.000	0.000	0.000	0.000
51	A	53	VAL	0	-0.024	-0.021	9.627	3.318	3.318	0.000	0.000	0.000	0.000
52	A	54	VAL	0	-0.021	0.003	11.721	-1.831	-1.831	0.000	0.000	0.000	0.000
53	A	55	LEU	0	0.000	-0.005	13.036	1.694	1.694	0.000	0.000	0.000	0.000
54	A	56	LEU	0	0.025	0.009	15.984	-0.120	-0.120	0.000	0.000	0.000	0.000
55	A	57	GLY	0	0.021	0.006	19.479	0.105	0.105	0.000	0.000	0.000	0.000
56	A	58	PRO	0	-0.005	-0.010	21.202	0.816	0.816	0.000	0.000	0.000	0.000
57	A	59	GLN	0	0.023	0.007	23.792	0.270	0.270	0.000	0.000	0.000	0.000
58	A	60	ILE	0	0.004	0.001	21.211	0.771	0.771	0.000	0.000	0.000	0.000
59	A	61	ALA	0	0.009	0.010	24.665	-0.196	-0.196	0.000	0.000	0.000	0.000
60	A	62	TYR	0	0.012	-0.002	25.681	-0.134	-0.134	0.000	0.000	0.000	0.000
61	A	63	MET	0	0.017	0.019	24.804	-0.008	-0.008	0.000	0.000	0.000	0.000
62	A	64	LEU	0	-0.015	0.014	22.163	-0.525	-0.525	0.000	0.000	0.000	0.000
63	A	65	PRO	0	0.013	-0.007	24.336	-0.521	-0.521	0.000	0.000	0.000	0.000
64	A	66	GLU	-1	-0.980	-0.985	26.509	-20.872	-20.872	0.000	0.000	0.000	0.000
65	A	67	ILE	0	0.025	-0.008	19.969	-0.436	-0.436	0.000	0.000	0.000	0.000
66	A	68	GLN	0	-0.023	-0.017	21.726	0.023	0.023	0.000	0.000	0.000	0.000
67	A	69	ARG	1	0.931	0.966	22.975	20.781	20.781	0.000	0.000	0.000	0.000
68	A	70	LEU	0	-0.038	0.004	22.188	0.111	0.111	0.000	0.000	0.000	0.000
69	A	71	LEU	0	-0.051	-0.015	16.994	-0.866	-0.866	0.000	0.000	0.000	0.000
70	A	72	PRO	0	0.024	0.014	19.466	-0.997	-0.997	0.000	0.000	0.000	0.000
71	A	73	ASN	0	-0.033	-0.018	16.978	0.179	0.179	0.000	0.000	0.000	0.000
72	A	74	LYS	1	0.826	0.917	12.028	40.874	40.874	0.000	0.000	0.000	0.000
73	A	75	PRO	0	0.018	0.029	13.708	2.048	2.048	0.000	0.000	0.000	0.000
74	A	76	VAL	0	0.006	-0.010	15.616	-1.762	-1.762	0.000	0.000	0.000	0.000
75	A	77	GLU	-1	-0.930	-0.969	17.255	-30.678	-30.678	0.000	0.000	0.000	0.000
76	A	78	VAL	0	-0.012	-0.005	18.908	-0.755	-0.755	0.000	0.000	0.000	0.000
77	A	79	ILE	0	-0.036	-0.016	16.886	-0.235	-0.235	0.000	0.000	0.000	0.000
78	A	80	ASP	-1	-0.793	-0.900	19.894	-23.789	-23.789	0.000	0.000	0.000	0.000
79	A	81	SER	0	0.032	0.000	22.547	-0.678	-0.678	0.000	0.000	0.000	0.000
80	A	82	LEU	0	0.018	0.022	25.130	0.230	0.230	0.000	0.000	0.000	0.000
81	A	83	LEU	0	-0.047	-0.032	19.781	-0.318	-0.318	0.000	0.000	0.000	0.000
82	A	84	TYR	0	-0.002	-0.010	19.952	-0.183	-0.183	0.000	0.000	0.000	0.000
83	A	85	GLY	0	-0.020	-0.007	21.840	-0.185	-0.185	0.000	0.000	0.000	0.000
84	A	86	LYS	1	0.921	0.967	23.040	24.851	24.851	0.000	0.000	0.000	0.000
85	A	87	VAL	0	-0.031	-0.013	18.099	-0.468	-0.468	0.000	0.000	0.000	0.000
86	A	88	ASP	-1	-0.834	-0.916	18.484	-32.137	-32.137	0.000	0.000	0.000	0.000
87	A	89	GLY	0	0.008	-0.018	14.582	-0.914	-0.914	0.000	0.000	0.000	0.000
88	A	90	LEU	0	-0.019	-0.006	13.589	-2.763	-2.763	0.000	0.000	0.000	0.000
89	A	91	GLY	0	0.002	-0.008	15.348	-1.038	-1.038	0.000	0.000	0.000	0.000
90	A	92	VAL	0	0.036	0.003	14.618	-0.365	-0.365	0.000	0.000	0.000	0.000
91	A	93	LEU	0	-0.008	0.016	8.923	-1.377	-1.377	0.000	0.000	0.000	0.000
92	A	94	LYS	1	0.941	0.961	12.251	31.812	31.812	0.000	0.000	0.000	0.000
93	A	95	ALA	0	0.021	0.018	14.633	-0.119	-0.119	0.000	0.000	0.000	0.000
94	A	96	ALA	0	0.029	0.015	10.833	0.028	0.028	0.000	0.000	0.000	0.000
95	A	97	VAL	0	-0.003	-0.007	8.808	-1.512	-1.512	0.000	0.000	0.000	0.000
96	A	98	ALA	0	-0.033	-0.017	11.139	0.451	0.451	0.000	0.000	0.000	0.000
97	A	99	ALA	0	0.039	0.027	14.013	0.986	0.986	0.000	0.000	0.000	0.000
98	A	100	ILE	0	-0.028	-0.024	7.611	-0.609	-0.609	0.000	0.000	0.000	0.000
99	A	101	LYS	1	0.878	0.933	11.549	39.425	39.425	0.000	0.000	0.000	0.000
100	A	102	LYS	1	0.987	0.996	13.196	28.732	28.732	0.000	0.000	0.000	0.000
101	A	103	ALA	0	-0.012	0.000	13.684	1.621	1.621	0.000	0.000	0.000	0.000
102	A	104	ALA	0	-0.082	-0.038	12.393	0.046	0.046	0.000	0.000	0.000	0.000
103	A	105	ALA	-1	-0.949	-0.955	14.525	-29.286	-29.286	0.000	0.000	0.000	0.000

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