FMO DATABASE

FMODB ID: Y19Z2

Calculation Name: 3RKD-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3RKD

Chain ID: A

ChEMBL ID:

UniProt ID: P33426

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	146
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1271343.705919
FMO2-HF: Nuclear repulsion	1218144.299966
FMO2-HF: Total energy	-53199.405953
FMO2-MP2: Total energy	-53359.014139

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:459:SER)

Summations of interaction energy for fragment #1(A:459:SER)

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.
0.85699999999999	2.809	-0.005	-0.698	-1.248	-0.001

Interaction energy analysis for fragmet #1(A:459:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.878 / q_NPA : 0.931

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	461	PRO	0	0.042	0.013	3.877	1.412	2.876	-0.008	-0.569	-0.886	-0.001
47	A	505	THR	0	-0.064	-0.047	3.510	-1.063	-0.875	0.004	-0.058	-0.133	0.000
48	A	506	GLY	0	0.034	0.029	4.093	-7.507	-7.270	0.000	-0.064	-0.173	0.000
49	A	507	ALA	0	-0.051	-0.012	4.446	0.906	0.969	-0.001	-0.007	-0.056	0.000
4	A	462	PHE	0	0.054	0.026	5.964	1.977	1.977	0.000	0.000	0.000	0.000
5	A	463	SER	0	0.029	0.006	8.545	1.214	1.214	0.000	0.000	0.000	0.000
6	A	464	VAL	0	-0.029	0.003	8.352	1.598	1.598	0.000	0.000	0.000	0.000
7	A	465	LEU	0	0.039	0.034	9.365	-2.482	-2.482	0.000	0.000	0.000	0.000
8	A	466	ARG	1	0.931	0.944	8.482	30.004	30.004	0.000	0.000	0.000	0.000
9	A	467	ALA	0	0.049	0.022	13.477	0.181	0.181	0.000	0.000	0.000	0.000
10	A	468	ASN	0	-0.049	-0.033	15.288	-0.149	-0.149	0.000	0.000	0.000	0.000
11	A	469	ASP	-1	-0.710	-0.793	10.380	-27.927	-27.927	0.000	0.000	0.000	0.000
12	A	470	VAL	0	0.007	0.006	12.702	1.377	1.377	0.000	0.000	0.000	0.000
13	A	471	LEU	0	-0.021	-0.011	11.971	-1.844	-1.844	0.000	0.000	0.000	0.000
14	A	472	TRP	0	0.051	0.021	13.767	1.158	1.158	0.000	0.000	0.000	0.000
15	A	473	LEU	0	-0.029	-0.027	15.254	-0.926	-0.926	0.000	0.000	0.000	0.000
16	A	474	SER	0	-0.003	0.000	18.041	0.739	0.739	0.000	0.000	0.000	0.000
17	A	475	LEU	0	-0.002	-0.003	19.870	-0.321	-0.321	0.000	0.000	0.000	0.000
18	A	476	THR	0	0.025	0.001	21.995	0.448	0.448	0.000	0.000	0.000	0.000
19	A	477	ALA	0	-0.014	-0.006	24.381	0.055	0.055	0.000	0.000	0.000	0.000
20	A	478	ALA	0	0.002	0.018	26.529	0.146	0.146	0.000	0.000	0.000	0.000
21	A	479	GLU	-1	-0.861	-0.933	28.430	-8.742	-8.742	0.000	0.000	0.000	0.000
22	A	480	TYR	0	-0.043	-0.039	31.502	-0.282	-0.282	0.000	0.000	0.000	0.000
23	A	481	ASP	-1	-0.729	-0.862	33.384	-8.601	-8.601	0.000	0.000	0.000	0.000
24	A	482	GLN	0	0.015	0.011	34.932	-0.174	-0.174	0.000	0.000	0.000	0.000
25	A	483	SER	0	-0.088	-0.045	37.251	0.275	0.275	0.000	0.000	0.000	0.000
26	A	484	THR	0	-0.031	-0.010	34.625	0.114	0.114	0.000	0.000	0.000	0.000
27	A	485	TYR	0	-0.094	-0.110	29.169	-0.092	-0.092	0.000	0.000	0.000	0.000
28	A	486	GLY	0	0.017	0.023	32.358	-0.262	-0.262	0.000	0.000	0.000	0.000
29	A	487	SER	0	-0.040	-0.026	34.449	0.240	0.240	0.000	0.000	0.000	0.000
30	A	488	SER	0	0.019	-0.009	37.930	-0.116	-0.116	0.000	0.000	0.000	0.000
31	A	489	THR	0	-0.029	-0.010	38.878	0.126	0.126	0.000	0.000	0.000	0.000
32	A	490	GLY	0	0.000	-0.012	35.286	-0.109	-0.109	0.000	0.000	0.000	0.000
33	A	491	PRO	0	-0.043	0.016	34.646	-0.171	-0.171	0.000	0.000	0.000	0.000
34	A	492	VAL	0	-0.022	-0.020	29.731	-0.282	-0.282	0.000	0.000	0.000	0.000
35	A	493	TYR	0	0.001	-0.003	28.576	0.235	0.235	0.000	0.000	0.000	0.000
36	A	494	VAL	0	-0.019	-0.018	27.374	-0.438	-0.438	0.000	0.000	0.000	0.000
37	A	495	SER	0	0.050	0.010	24.745	0.127	0.127	0.000	0.000	0.000	0.000
38	A	496	ASP	-1	-0.777	-0.870	24.129	-11.617	-11.617	0.000	0.000	0.000	0.000
39	A	497	SER	0	-0.065	-0.027	22.488	-0.502	-0.502	0.000	0.000	0.000	0.000
40	A	498	VAL	0	0.000	0.007	18.875	-0.013	-0.013	0.000	0.000	0.000	0.000
41	A	499	THR	0	-0.031	-0.013	15.101	-0.523	-0.523	0.000	0.000	0.000	0.000
42	A	500	LEU	0	0.021	0.009	13.889	0.688	0.688	0.000	0.000	0.000	0.000
43	A	501	VAL	0	0.012	-0.004	9.759	-1.409	-1.409	0.000	0.000	0.000	0.000
44	A	502	ASN	0	-0.025	-0.010	7.625	1.190	1.190	0.000	0.000	0.000	0.000
45	A	503	VAL	0	0.006	-0.011	8.536	-2.159	-2.159	0.000	0.000	0.000	0.000
46	A	504	ALA	0	-0.003	0.013	8.961	-0.081	-0.081	0.000	0.000	0.000	0.000
50	A	508	GLN	0	0.004	-0.014	5.869	3.473	3.473	0.000	0.000	0.000	0.000
51	A	509	ALA	0	0.013	0.014	9.290	-1.251	-1.251	0.000	0.000	0.000	0.000
52	A	510	VAL	0	0.034	0.013	12.134	1.000	1.000	0.000	0.000	0.000	0.000
53	A	511	ALA	0	0.031	0.021	15.746	0.014	0.014	0.000	0.000	0.000	0.000
54	A	512	ARG	1	0.851	0.910	18.200	12.595	12.595	0.000	0.000	0.000	0.000
55	A	513	SER	0	-0.040	-0.020	16.300	0.683	0.683	0.000	0.000	0.000	0.000
56	A	514	LEU	0	0.022	0.021	13.101	-1.144	-1.144	0.000	0.000	0.000	0.000
57	A	515	ASP	-1	-0.806	-0.873	16.168	-15.130	-15.130	0.000	0.000	0.000	0.000
58	A	516	TRP	0	0.009	-0.021	16.958	-1.111	-1.111	0.000	0.000	0.000	0.000
59	A	517	THR	0	-0.073	-0.054	18.700	0.019	0.019	0.000	0.000	0.000	0.000
60	A	518	LYS	1	0.862	0.920	15.275	16.901	16.901	0.000	0.000	0.000	0.000
61	A	519	VAL	0	-0.050	-0.003	14.071	-1.760	-1.760	0.000	0.000	0.000	0.000
62	A	520	THR	0	-0.046	-0.025	13.570	0.905	0.905	0.000	0.000	0.000	0.000
63	A	521	LEU	0	0.018	0.013	14.090	-1.541	-1.541	0.000	0.000	0.000	0.000
64	A	522	ASP	-1	-0.801	-0.913	15.124	-17.258	-17.258	0.000	0.000	0.000	0.000
65	A	523	GLY	0	-0.042	-0.020	15.337	0.767	0.767	0.000	0.000	0.000	0.000
66	A	524	ARG	1	0.914	0.965	16.357	15.845	15.845	0.000	0.000	0.000	0.000
67	A	525	PRO	0	0.027	0.000	18.281	-0.780	-0.780	0.000	0.000	0.000	0.000
68	A	526	LEU	0	-0.009	0.009	17.201	0.398	0.398	0.000	0.000	0.000	0.000
69	A	527	SER	0	0.017	0.018	20.525	0.351	0.351	0.000	0.000	0.000	0.000
70	A	528	THR	0	-0.012	-0.022	24.022	-0.177	-0.177	0.000	0.000	0.000	0.000
71	A	529	ILE	0	0.005	0.011	26.662	0.297	0.297	0.000	0.000	0.000	0.000
72	A	530	GLN	0	-0.032	-0.024	29.876	0.049	0.049	0.000	0.000	0.000	0.000
73	A	531	GLN	0	0.017	-0.001	31.629	0.113	0.113	0.000	0.000	0.000	0.000
74	A	532	HIS	0	0.036	0.026	33.330	0.104	0.104	0.000	0.000	0.000	0.000
75	A	533	SER	0	-0.006	0.001	36.156	0.012	0.012	0.000	0.000	0.000	0.000
76	A	534	LYS	1	0.848	0.950	31.331	9.563	9.563	0.000	0.000	0.000	0.000
77	A	535	THR	0	0.010	-0.002	28.564	0.125	0.125	0.000	0.000	0.000	0.000
78	A	536	PHE	0	-0.010	-0.003	26.389	-0.244	-0.244	0.000	0.000	0.000	0.000
79	A	537	PHE	0	0.013	-0.002	21.737	0.117	0.117	0.000	0.000	0.000	0.000
80	A	538	VAL	0	0.008	-0.001	23.306	0.166	0.166	0.000	0.000	0.000	0.000
81	A	539	LEU	0	-0.005	0.001	16.923	-0.717	-0.717	0.000	0.000	0.000	0.000
82	A	540	PRO	0	0.041	0.013	20.604	0.387	0.387	0.000	0.000	0.000	0.000
83	A	541	LEU	0	-0.007	0.007	19.654	-0.859	-0.859	0.000	0.000	0.000	0.000
84	A	542	ARG	1	0.874	0.930	19.642	14.912	14.912	0.000	0.000	0.000	0.000
85	A	543	GLY	0	0.017	0.014	23.152	-0.203	-0.203	0.000	0.000	0.000	0.000
86	A	544	LYS	1	0.809	0.895	25.935	9.761	9.761	0.000	0.000	0.000	0.000
87	A	545	LEU	0	-0.043	-0.014	21.802	-0.451	-0.451	0.000	0.000	0.000	0.000
88	A	546	SER	0	0.002	0.014	22.803	0.624	0.624	0.000	0.000	0.000	0.000
89	A	547	PHE	0	0.019	-0.011	23.174	-0.590	-0.590	0.000	0.000	0.000	0.000
90	A	548	TRP	0	0.016	0.013	21.072	0.286	0.286	0.000	0.000	0.000	0.000
91	A	549	GLU	-1	-0.833	-0.902	26.403	-9.748	-9.748	0.000	0.000	0.000	0.000
92	A	550	ALA	0	0.002	-0.004	24.354	-0.023	-0.023	0.000	0.000	0.000	0.000
93	A	551	GLY	0	-0.019	-0.006	25.458	0.270	0.270	0.000	0.000	0.000	0.000
94	A	552	THR	0	-0.052	-0.025	27.040	0.427	0.427	0.000	0.000	0.000	0.000
95	A	553	THR	0	0.008	-0.010	28.319	-0.297	-0.297	0.000	0.000	0.000	0.000
96	A	554	LYS	1	0.861	0.943	30.480	9.089	9.089	0.000	0.000	0.000	0.000
97	A	555	ALA	0	0.025	0.000	29.352	-0.254	-0.254	0.000	0.000	0.000	0.000
98	A	556	GLY	0	0.008	0.009	29.413	0.358	0.358	0.000	0.000	0.000	0.000
99	A	557	TYR	0	-0.032	-0.027	30.584	-0.058	-0.058	0.000	0.000	0.000	0.000
100	A	558	PRO	0	0.033	0.021	29.517	0.190	0.190	0.000	0.000	0.000	0.000
101	A	559	TYR	0	0.033	0.006	31.451	0.294	0.294	0.000	0.000	0.000	0.000
102	A	560	ASN	0	-0.013	-0.007	33.117	0.451	0.451	0.000	0.000	0.000	0.000
103	A	561	TYR	0	0.000	0.001	33.316	-0.186	-0.186	0.000	0.000	0.000	0.000
104	A	562	ASN	0	0.009	0.005	34.308	-0.230	-0.230	0.000	0.000	0.000	0.000
105	A	563	THR	0	0.019	0.016	34.269	0.043	0.043	0.000	0.000	0.000	0.000
106	A	564	THR	0	0.029	0.001	33.034	-0.197	-0.197	0.000	0.000	0.000	0.000
107	A	565	ALA	0	-0.009	0.014	31.298	-0.260	-0.260	0.000	0.000	0.000	0.000
108	A	566	SER	0	0.003	0.006	25.675	-0.102	-0.102	0.000	0.000	0.000	0.000
109	A	567	ASP	-1	-0.822	-0.911	25.779	-10.569	-10.569	0.000	0.000	0.000	0.000
110	A	568	GLN	0	-0.033	-0.036	23.759	-0.178	-0.178	0.000	0.000	0.000	0.000
111	A	569	LEU	0	-0.014	0.004	18.830	0.200	0.200	0.000	0.000	0.000	0.000
112	A	570	LEU	0	0.006	0.018	22.951	-0.164	-0.164	0.000	0.000	0.000	0.000
113	A	571	VAL	0	0.022	0.003	20.025	-0.012	-0.012	0.000	0.000	0.000	0.000
114	A	572	GLU	-1	-0.747	-0.834	23.444	-10.433	-10.433	0.000	0.000	0.000	0.000
115	A	573	ASN	0	-0.021	-0.017	24.646	-0.835	-0.835	0.000	0.000	0.000	0.000
116	A	574	ALA	0	0.027	0.016	25.959	0.373	0.373	0.000	0.000	0.000	0.000
117	A	575	ALA	0	0.030	0.012	25.485	-0.515	-0.515	0.000	0.000	0.000	0.000
118	A	576	GLY	0	0.007	-0.005	24.221	0.318	0.318	0.000	0.000	0.000	0.000
119	A	577	HIS	1	0.774	0.885	20.736	13.480	13.480	0.000	0.000	0.000	0.000
120	A	578	ARG	1	0.919	0.960	22.516	10.362	10.362	0.000	0.000	0.000	0.000
121	A	579	VAL	0	-0.003	0.007	20.265	-0.051	-0.051	0.000	0.000	0.000	0.000
122	A	580	ALA	0	0.013	0.003	23.650	0.353	0.353	0.000	0.000	0.000	0.000
123	A	581	ILE	0	-0.010	-0.008	23.612	-0.385	-0.385	0.000	0.000	0.000	0.000
124	A	582	SER	0	0.048	0.026	26.586	0.506	0.506	0.000	0.000	0.000	0.000
125	A	583	THR	0	-0.027	-0.022	29.537	-0.173	-0.173	0.000	0.000	0.000	0.000
126	A	584	TYR	0	0.006	0.002	32.257	0.195	0.195	0.000	0.000	0.000	0.000
127	A	585	THR	0	0.014	0.010	35.495	0.221	0.221	0.000	0.000	0.000	0.000
128	A	586	THR	0	0.034	0.035	35.301	-0.250	-0.250	0.000	0.000	0.000	0.000
129	A	587	SER	0	-0.040	-0.018	33.548	0.035	0.035	0.000	0.000	0.000	0.000
130	A	588	LEU	0	-0.030	-0.025	29.185	0.055	0.055	0.000	0.000	0.000	0.000
131	A	589	GLY	0	0.028	0.022	33.549	-0.020	-0.020	0.000	0.000	0.000	0.000
132	A	590	ALA	0	0.013	-0.006	35.237	-0.163	-0.163	0.000	0.000	0.000	0.000
133	A	591	GLY	0	0.021	0.029	33.092	-0.200	-0.200	0.000	0.000	0.000	0.000
134	A	592	PRO	0	-0.008	0.001	31.294	0.248	0.248	0.000	0.000	0.000	0.000
135	A	593	VAL	0	-0.031	-0.019	29.663	0.043	0.043	0.000	0.000	0.000	0.000
136	A	594	SER	0	-0.011	-0.007	25.197	-0.268	-0.268	0.000	0.000	0.000	0.000
137	A	595	ILE	0	-0.006	0.012	24.693	0.125	0.125	0.000	0.000	0.000	0.000
138	A	596	SER	0	-0.040	-0.008	21.781	-0.685	-0.685	0.000	0.000	0.000	0.000
139	A	597	ALA	0	0.032	0.003	20.676	0.579	0.579	0.000	0.000	0.000	0.000
140	A	598	VAL	0	-0.032	-0.008	17.338	-0.922	-0.922	0.000	0.000	0.000	0.000
141	A	599	ALA	0	0.028	0.017	17.885	0.834	0.834	0.000	0.000	0.000	0.000
142	A	600	VAL	0	0.018	0.005	17.003	-1.088	-1.088	0.000	0.000	0.000	0.000
143	A	601	LEU	0	0.002	0.007	14.421	0.820	0.820	0.000	0.000	0.000	0.000
144	A	602	ALA	0	-0.012	-0.005	17.842	-0.056	-0.056	0.000	0.000	0.000	0.000
145	A	603	PRO	0	-0.024	-0.031	19.175	-0.680	-0.680	0.000	0.000	0.000	0.000
146	A	604	PRO	-1	-0.972	-0.954	19.132	-12.679	-12.679	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:459:SER)