FMO DATABASE

FMODB ID: 4KJNN

Calculation Name: 3RKC-A-Xray549

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3RKC

Chain ID: A

ChEMBL ID:

UniProt ID: D3VV84

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	147
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230712

Total energy (hartree)

FMO2-HF: Electronic energy	-1334433.221718
FMO2-HF: Nuclear repulsion	1279287.766733
FMO2-HF: Total energy	-55145.454984
FMO2-MP2: Total energy	-55308.82058

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:460:ARG)

Summations of interaction energy for fragment #1(A:460:ARG)

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.
-132.961	-139.963	56.843	-24.442	-25.4	-0.281

Interaction energy analysis for fragmet #1(A:460:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.576 / q_NPA : 1.734

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	462	PHE	0	0.085	0.033	2.811	-13.320	-10.872	0.361	-1.231	-1.579	-0.009
4	A	463	SER	0	0.035	0.007	5.161	-3.887	-3.746	-0.001	-0.003	-0.136	0.000
5	A	464	VAL	0	-0.019	0.013	2.974	5.220	7.279	0.118	-0.913	-1.264	-0.004
6	A	465	LEU	0	0.043	0.043	1.796	-55.829	-60.945	20.011	-8.381	-6.515	-0.101
7	A	466	ARG	1	0.923	0.936	2.468	101.533	103.209	2.092	0.023	-3.791	-0.003
8	A	467	ALA	0	0.070	0.035	3.767	-1.936	-1.821	0.003	-0.007	-0.112	0.000
10	A	469	ASP	-1	-0.715	-0.798	1.697	-180.432	-191.134	31.895	-12.617	-8.575	-0.156
11	A	470	VAL	0	0.015	0.009	4.652	8.864	8.946	-0.001	-0.031	-0.050	0.000
43	A	502	ASN	0	-0.036	-0.016	2.453	7.199	8.294	0.435	-0.514	-1.016	0.000
45	A	504	ALA	0	-0.005	0.010	4.491	3.160	3.238	-0.001	-0.004	-0.073	0.000
46	A	505	THR	0	-0.052	-0.040	2.171	-0.444	0.525	1.933	-0.737	-2.166	-0.008
47	A	506	GLY	0	0.049	0.040	5.237	-0.676	-0.645	-0.001	-0.003	-0.027	0.000
48	A	507	ALA	0	-0.055	-0.019	4.499	4.364	4.486	-0.001	-0.024	-0.096	0.000
9	A	468	ASN	0	-0.034	-0.027	6.064	0.936	0.936	0.000	0.000	0.000	0.000
12	A	471	LEU	0	-0.024	-0.009	5.699	-6.098	-6.098	0.000	0.000	0.000	0.000
13	A	472	TRP	0	0.034	0.004	8.925	4.300	4.300	0.000	0.000	0.000	0.000
14	A	473	LEU	0	-0.035	-0.027	12.116	-2.573	-2.573	0.000	0.000	0.000	0.000
15	A	474	SER	0	0.037	0.020	14.669	1.778	1.778	0.000	0.000	0.000	0.000
16	A	475	LEU	0	-0.008	-0.008	17.763	-0.703	-0.703	0.000	0.000	0.000	0.000
17	A	476	THR	0	0.023	0.004	20.024	1.167	1.167	0.000	0.000	0.000	0.000
18	A	477	ALA	0	-0.018	-0.001	23.347	-0.040	-0.040	0.000	0.000	0.000	0.000
19	A	478	ALA	0	0.010	0.017	23.294	0.256	0.256	0.000	0.000	0.000	0.000
20	A	479	GLU	-1	-0.894	-0.950	25.314	-19.646	-19.646	0.000	0.000	0.000	0.000
21	A	480	TYR	0	-0.027	-0.028	26.983	-0.794	-0.794	0.000	0.000	0.000	0.000
22	A	481	ASP	-1	-0.733	-0.862	27.861	-19.536	-19.536	0.000	0.000	0.000	0.000
23	A	482	GLN	0	-0.005	-0.005	28.777	-0.507	-0.507	0.000	0.000	0.000	0.000
24	A	483	THR	0	-0.094	-0.051	31.222	0.673	0.673	0.000	0.000	0.000	0.000
25	A	484	THR	0	-0.041	-0.015	29.418	0.309	0.309	0.000	0.000	0.000	0.000
26	A	485	TYR	0	-0.102	-0.116	24.128	-0.159	-0.159	0.000	0.000	0.000	0.000
27	A	486	GLY	0	0.049	0.035	25.672	-0.826	-0.826	0.000	0.000	0.000	0.000
28	A	487	SER	0	-0.053	-0.028	27.717	0.781	0.781	0.000	0.000	0.000	0.000
29	A	488	SER	0	0.012	-0.011	30.791	-0.341	-0.341	0.000	0.000	0.000	0.000
30	A	489	THR	0	-0.032	-0.012	31.770	0.079	0.079	0.000	0.000	0.000	0.000
31	A	490	ASN	0	-0.037	-0.012	24.323	-0.480	-0.480	0.000	0.000	0.000	0.000
32	A	491	PRO	0	0.028	0.043	27.579	-0.397	-0.397	0.000	0.000	0.000	0.000
33	A	492	MET	0	-0.018	0.004	22.470	-1.032	-1.032	0.000	0.000	0.000	0.000
34	A	493	TYR	0	-0.001	-0.009	23.214	0.644	0.644	0.000	0.000	0.000	0.000
35	A	494	VAL	0	-0.003	-0.009	22.511	-1.345	-1.345	0.000	0.000	0.000	0.000
36	A	495	SER	0	0.045	0.005	21.366	0.343	0.343	0.000	0.000	0.000	0.000
37	A	496	ASP	-1	-0.826	-0.895	21.325	-26.057	-26.057	0.000	0.000	0.000	0.000
38	A	497	THR	0	-0.041	-0.019	21.390	-0.828	-0.828	0.000	0.000	0.000	0.000
39	A	498	VAL	0	0.013	0.013	15.896	0.110	0.110	0.000	0.000	0.000	0.000
40	A	499	THR	0	-0.025	-0.010	13.809	-1.117	-1.117	0.000	0.000	0.000	0.000
41	A	500	PHE	0	0.023	0.008	10.308	0.905	0.905	0.000	0.000	0.000	0.000
42	A	501	VAL	0	0.021	-0.001	9.811	-1.739	-1.739	0.000	0.000	0.000	0.000
44	A	503	VAL	0	0.014	-0.011	6.772	-0.883	-0.883	0.000	0.000	0.000	0.000
49	A	508	GLN	0	0.027	-0.001	6.564	3.475	3.475	0.000	0.000	0.000	0.000
50	A	509	GLY	0	0.013	0.001	9.151	-3.188	-3.188	0.000	0.000	0.000	0.000
51	A	510	VAL	0	0.021	0.025	11.059	1.932	1.932	0.000	0.000	0.000	0.000
52	A	511	SER	0	0.032	0.005	14.903	-0.307	-0.307	0.000	0.000	0.000	0.000
53	A	512	ARG	1	0.829	0.888	16.039	26.677	26.677	0.000	0.000	0.000	0.000
54	A	513	SER	0	-0.059	-0.034	15.707	0.718	0.718	0.000	0.000	0.000	0.000
55	A	514	LEU	0	-0.008	0.016	10.816	-1.595	-1.595	0.000	0.000	0.000	0.000
56	A	515	ASP	-1	-0.766	-0.850	14.240	-34.041	-34.041	0.000	0.000	0.000	0.000
57	A	516	TRP	0	0.020	-0.017	10.665	-3.593	-3.593	0.000	0.000	0.000	0.000
58	A	517	SER	0	-0.079	-0.050	13.183	-0.775	-0.775	0.000	0.000	0.000	0.000
59	A	518	LYS	1	0.840	0.902	12.212	36.643	36.643	0.000	0.000	0.000	0.000
60	A	519	VAL	0	-0.047	-0.001	7.639	-5.097	-5.097	0.000	0.000	0.000	0.000
61	A	520	THR	0	-0.047	-0.025	6.816	2.009	2.009	0.000	0.000	0.000	0.000
62	A	521	LEU	0	0.003	0.008	5.831	-8.733	-8.733	0.000	0.000	0.000	0.000
63	A	522	ASP	-1	-0.792	-0.900	5.808	-51.478	-51.478	0.000	0.000	0.000	0.000
64	A	523	GLY	0	-0.042	-0.023	6.600	4.785	4.785	0.000	0.000	0.000	0.000
65	A	524	ARG	1	0.927	0.983	8.397	43.953	43.953	0.000	0.000	0.000	0.000
66	A	525	PRO	0	0.040	0.011	9.959	-3.309	-3.309	0.000	0.000	0.000	0.000
67	A	526	LEU	0	0.002	0.014	8.688	1.328	1.328	0.000	0.000	0.000	0.000
68	A	527	THR	0	0.031	0.021	12.159	2.202	2.202	0.000	0.000	0.000	0.000
69	A	528	THR	0	-0.019	-0.015	15.191	-0.569	-0.569	0.000	0.000	0.000	0.000
70	A	529	ILE	0	-0.018	-0.005	18.076	1.052	1.052	0.000	0.000	0.000	0.000
71	A	530	GLN	0	0.050	0.044	21.245	-0.926	-0.926	0.000	0.000	0.000	0.000
72	A	531	GLN	0	-0.002	-0.007	23.540	0.145	0.145	0.000	0.000	0.000	0.000
73	A	532	TYR	0	0.032	0.005	26.116	0.190	0.190	0.000	0.000	0.000	0.000
74	A	533	SER	0	-0.020	-0.006	29.196	0.072	0.072	0.000	0.000	0.000	0.000
75	A	534	LYS	1	0.845	0.943	24.959	22.032	22.032	0.000	0.000	0.000	0.000
76	A	535	THR	0	-0.021	-0.037	20.960	0.265	0.265	0.000	0.000	0.000	0.000
77	A	536	PHE	0	-0.012	-0.015	19.117	-0.424	-0.424	0.000	0.000	0.000	0.000
78	A	537	PHE	0	0.010	0.008	14.075	0.141	0.141	0.000	0.000	0.000	0.000
79	A	538	VAL	0	0.011	-0.004	14.421	0.389	0.389	0.000	0.000	0.000	0.000
80	A	539	LEU	0	-0.012	-0.004	8.427	-3.162	-3.162	0.000	0.000	0.000	0.000
81	A	540	PRO	0	0.040	0.030	10.747	1.921	1.921	0.000	0.000	0.000	0.000
82	A	541	LEU	0	0.002	-0.004	11.000	-3.816	-3.816	0.000	0.000	0.000	0.000
83	A	542	ARG	1	0.849	0.917	10.693	42.959	42.959	0.000	0.000	0.000	0.000
84	A	543	GLY	0	0.029	0.016	14.026	-0.232	-0.232	0.000	0.000	0.000	0.000
85	A	544	LYS	1	0.812	0.897	17.146	23.948	23.948	0.000	0.000	0.000	0.000
86	A	545	LEU	0	-0.037	-0.014	14.862	-1.471	-1.471	0.000	0.000	0.000	0.000
87	A	546	SER	0	-0.011	0.010	16.803	2.203	2.203	0.000	0.000	0.000	0.000
88	A	547	PHE	0	0.026	-0.010	17.837	-1.605	-1.605	0.000	0.000	0.000	0.000
89	A	548	TRP	0	0.005	0.007	17.410	0.633	0.633	0.000	0.000	0.000	0.000
90	A	549	GLU	-1	-0.897	-0.935	22.961	-21.596	-21.596	0.000	0.000	0.000	0.000
91	A	550	ALA	0	-0.011	-0.011	23.072	-0.029	-0.029	0.000	0.000	0.000	0.000
92	A	551	GLY	0	-0.017	-0.007	23.733	0.754	0.754	0.000	0.000	0.000	0.000
93	A	552	THR	0	-0.040	-0.017	25.614	1.057	1.057	0.000	0.000	0.000	0.000
94	A	553	THR	0	0.005	-0.010	25.486	-0.730	-0.730	0.000	0.000	0.000	0.000
95	A	554	LYS	1	0.949	0.978	27.312	19.230	19.230	0.000	0.000	0.000	0.000
96	A	555	ALA	0	0.029	0.005	24.927	-0.671	-0.671	0.000	0.000	0.000	0.000
97	A	556	GLY	0	0.008	0.012	24.367	0.980	0.980	0.000	0.000	0.000	0.000
98	A	557	TYR	0	-0.033	-0.031	24.274	-0.266	-0.266	0.000	0.000	0.000	0.000
99	A	558	PRO	0	0.041	0.022	22.036	0.607	0.607	0.000	0.000	0.000	0.000
100	A	559	TYR	0	0.035	0.008	24.140	0.836	0.836	0.000	0.000	0.000	0.000
101	A	560	ASN	0	-0.019	-0.009	24.437	1.279	1.279	0.000	0.000	0.000	0.000
102	A	561	TYR	0	0.002	0.000	25.251	-0.617	-0.617	0.000	0.000	0.000	0.000
103	A	562	ASN	0	0.007	0.005	26.374	-0.656	-0.656	0.000	0.000	0.000	0.000
104	A	563	THR	0	0.016	0.016	25.229	0.061	0.061	0.000	0.000	0.000	0.000
105	A	564	THR	0	0.031	0.003	23.953	-0.572	-0.572	0.000	0.000	0.000	0.000
106	A	565	ALA	0	-0.004	0.016	21.765	-0.851	-0.851	0.000	0.000	0.000	0.000
107	A	566	SER	0	-0.006	0.001	16.477	-0.225	-0.225	0.000	0.000	0.000	0.000
108	A	567	ASP	-1	-0.828	-0.915	17.493	-26.397	-26.397	0.000	0.000	0.000	0.000
109	A	568	GLN	0	-0.022	-0.026	14.993	-2.115	-2.115	0.000	0.000	0.000	0.000
110	A	569	ILE	0	-0.022	-0.003	11.883	1.184	1.184	0.000	0.000	0.000	0.000
111	A	570	LEU	0	-0.001	0.011	14.983	-1.028	-1.028	0.000	0.000	0.000	0.000
112	A	571	ILE	0	0.010	-0.002	13.190	0.030	0.030	0.000	0.000	0.000	0.000
113	A	572	GLU	-1	-0.739	-0.835	17.173	-24.032	-24.032	0.000	0.000	0.000	0.000
114	A	573	ASN	0	-0.028	-0.022	19.568	-1.788	-1.788	0.000	0.000	0.000	0.000
115	A	574	ALA	0	0.031	0.024	20.545	1.084	1.084	0.000	0.000	0.000	0.000
116	A	575	PRO	0	0.025	-0.002	22.235	-1.201	-1.201	0.000	0.000	0.000	0.000
117	A	576	GLY	0	0.002	0.000	22.718	0.696	0.696	0.000	0.000	0.000	0.000
118	A	577	HIS	1	0.788	0.905	17.686	31.191	31.191	0.000	0.000	0.000	0.000
119	A	578	ARG	1	0.994	1.013	18.813	22.526	22.526	0.000	0.000	0.000	0.000
120	A	579	VAL	0	-0.009	0.011	16.133	-0.474	-0.474	0.000	0.000	0.000	0.000
121	A	580	CYS	0	-0.031	-0.016	18.659	1.765	1.765	0.000	0.000	0.000	0.000
122	A	581	ILE	0	0.019	0.008	17.418	-1.502	-1.502	0.000	0.000	0.000	0.000
123	A	582	SER	0	0.041	0.017	20.018	1.667	1.667	0.000	0.000	0.000	0.000
124	A	583	THR	0	-0.005	-0.008	22.446	-0.439	-0.439	0.000	0.000	0.000	0.000
125	A	584	TYR	0	0.002	-0.002	25.520	0.497	0.497	0.000	0.000	0.000	0.000
126	A	585	THR	0	0.012	0.007	28.863	0.629	0.629	0.000	0.000	0.000	0.000
127	A	586	THR	0	0.018	0.033	29.455	-0.727	-0.727	0.000	0.000	0.000	0.000
128	A	587	ASN	0	-0.051	-0.034	27.203	0.008	0.008	0.000	0.000	0.000	0.000
129	A	588	LEU	0	-0.019	-0.003	24.638	0.072	0.072	0.000	0.000	0.000	0.000
130	A	589	GLY	0	0.037	0.023	29.225	0.019	0.019	0.000	0.000	0.000	0.000
131	A	590	SER	0	-0.004	-0.023	30.770	-0.515	-0.515	0.000	0.000	0.000	0.000
132	A	591	GLY	0	0.021	0.035	29.787	-0.442	-0.442	0.000	0.000	0.000	0.000
133	A	592	PRO	0	-0.004	-0.012	29.343	0.658	0.658	0.000	0.000	0.000	0.000
134	A	593	VAL	0	-0.025	-0.003	26.580	0.292	0.292	0.000	0.000	0.000	0.000
135	A	594	SER	0	-0.015	-0.008	24.312	-0.806	-0.806	0.000	0.000	0.000	0.000
136	A	595	ILE	0	-0.002	0.012	20.577	0.419	0.419	0.000	0.000	0.000	0.000
137	A	596	SER	0	-0.036	-0.008	19.064	-0.900	-0.900	0.000	0.000	0.000	0.000
138	A	597	ALA	0	0.033	0.007	16.370	1.297	1.297	0.000	0.000	0.000	0.000
139	A	598	VAL	0	-0.023	-0.010	12.186	-2.342	-2.342	0.000	0.000	0.000	0.000
140	A	599	GLY	0	0.037	0.024	12.061	2.901	2.901	0.000	0.000	0.000	0.000
141	A	600	VAL	0	-0.010	-0.001	8.806	-3.848	-3.848	0.000	0.000	0.000	0.000
142	A	601	LEU	0	-0.004	0.004	4.909	3.329	3.329	0.000	0.000	0.000	0.000
143	A	602	ALA	0	-0.013	-0.006	8.420	-0.230	-0.230	0.000	0.000	0.000	0.000
144	A	603	PRO	0	0.006	-0.027	9.161	-3.643	-3.643	0.000	0.000	0.000	0.000
145	A	604	HIS	0	-0.073	-0.032	9.900	2.488	2.488	0.000	0.000	0.000	0.000
146	A	605	SER	0	-0.066	-0.048	11.516	2.667	2.667	0.000	0.000	0.000	0.000
147	A	606	ALA	-1	-0.920	-0.941	14.285	-30.889	-30.889	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:460:ARG)