FMO DATABASE

FMODB ID: K8Z63

Calculation Name: 4YKB-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4YKB

Chain ID: A

ChEMBL ID:

UniProt ID: A8I5N5

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	158
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1694661.379779
FMO2-HF: Nuclear repulsion	1630438.245945
FMO2-HF: Total energy	-64223.133833
FMO2-MP2: Total energy	-64412.496934

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:81:SER)

Summations of interaction energy for fragment #1(A:81: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.
-109.082	-99.209	5.032	-7.222	-7.683	-0.06

Interaction energy analysis for fragmet #1(A:81:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.861 / q_NPA : 0.921

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	83	LYS	1	0.956	0.985	3.856	39.131	40.889	-0.012	-0.775	-0.971	0.000
4	A	84	GLU	-1	-0.875	-0.959	2.035	-77.789	-74.458	4.582	-3.837	-4.075	-0.044
5	A	85	ALA	0	0.042	0.027	2.653	4.866	6.444	0.406	-0.774	-1.210	0.001
6	A	86	VAL	0	-0.056	-0.026	4.031	6.556	6.705	0.002	-0.051	-0.100	0.000
8	A	88	GLU	-1	-0.953	-0.973	2.967	-61.909	-58.852	0.054	-1.785	-1.327	-0.017
7	A	87	MET	0	-0.062	-0.032	6.236	4.854	4.854	0.000	0.000	0.000	0.000
9	A	89	VAL	0	-0.060	-0.017	7.487	3.005	3.005	0.000	0.000	0.000	0.000
10	A	90	GLN	0	0.002	0.004	10.068	0.827	0.827	0.000	0.000	0.000	0.000
11	A	91	LEU	0	-0.004	0.002	13.087	0.223	0.223	0.000	0.000	0.000	0.000
12	A	92	SER	0	-0.037	-0.017	16.195	0.930	0.930	0.000	0.000	0.000	0.000
13	A	93	SER	0	-0.011	-0.031	19.360	0.038	0.038	0.000	0.000	0.000	0.000
14	A	94	THR	0	-0.069	-0.045	22.768	0.371	0.371	0.000	0.000	0.000	0.000
15	A	95	ALA	0	-0.016	-0.009	26.079	0.384	0.384	0.000	0.000	0.000	0.000
16	A	96	GLY	0	-0.006	0.002	25.995	0.192	0.192	0.000	0.000	0.000	0.000
17	A	97	ILE	0	-0.046	-0.028	22.079	0.080	0.080	0.000	0.000	0.000	0.000
18	A	98	ASP	-1	-0.824	-0.882	19.978	-15.140	-15.140	0.000	0.000	0.000	0.000
19	A	99	TYR	0	-0.018	-0.056	16.890	-0.065	-0.065	0.000	0.000	0.000	0.000
20	A	100	THR	0	-0.043	-0.046	15.765	-1.092	-1.092	0.000	0.000	0.000	0.000
21	A	101	VAL	0	0.030	0.022	15.615	-0.953	-0.953	0.000	0.000	0.000	0.000
22	A	102	LEU	0	0.007	0.011	15.714	-0.556	-0.556	0.000	0.000	0.000	0.000
23	A	103	ARG	1	0.842	0.893	11.213	20.109	20.109	0.000	0.000	0.000	0.000
24	A	104	ASP	-1	-0.791	-0.879	11.572	-22.531	-22.531	0.000	0.000	0.000	0.000
25	A	105	HIS	0	-0.012	-0.014	12.657	-0.320	-0.320	0.000	0.000	0.000	0.000
26	A	106	LEU	0	-0.028	-0.025	11.330	-0.995	-0.995	0.000	0.000	0.000	0.000
27	A	107	ALA	0	0.005	0.005	8.210	-2.575	-2.575	0.000	0.000	0.000	0.000
28	A	108	ASN	0	-0.097	-0.066	8.731	-4.684	-4.684	0.000	0.000	0.000	0.000
29	A	109	GLY	0	0.002	0.021	11.486	-0.242	-0.242	0.000	0.000	0.000	0.000
30	A	110	GLU	-1	-0.838	-0.881	12.343	-17.641	-17.641	0.000	0.000	0.000	0.000
31	A	111	PHE	0	0.011	-0.026	11.079	0.889	0.889	0.000	0.000	0.000	0.000
32	A	112	ARG	1	0.804	0.882	16.571	13.914	13.914	0.000	0.000	0.000	0.000
33	A	113	GLU	-1	-0.856	-0.936	18.641	-15.406	-15.406	0.000	0.000	0.000	0.000
34	A	114	ALA	0	0.040	0.019	16.026	0.551	0.551	0.000	0.000	0.000	0.000
35	A	115	GLU	-1	-0.764	-0.851	18.101	-12.706	-12.706	0.000	0.000	0.000	0.000
36	A	116	ASP	-1	-0.758	-0.843	20.806	-11.955	-11.955	0.000	0.000	0.000	0.000
37	A	117	GLU	0	-0.012	-0.028	19.748	0.428	0.428	0.000	0.000	0.000	0.000
38	A	118	THR	0	-0.012	-0.002	19.195	0.095	0.095	0.000	0.000	0.000	0.000
39	A	119	ARG	1	0.830	0.898	21.455	12.450	12.450	0.000	0.000	0.000	0.000
40	A	120	ALA	0	0.002	0.002	24.890	0.486	0.486	0.000	0.000	0.000	0.000
41	A	121	LEU	0	0.009	0.002	20.405	0.462	0.462	0.000	0.000	0.000	0.000
42	A	122	LEU	0	-0.007	0.000	24.544	0.429	0.429	0.000	0.000	0.000	0.000
43	A	123	ILE	0	-0.037	-0.025	26.196	0.439	0.439	0.000	0.000	0.000	0.000
44	A	124	LYS	1	0.906	0.963	27.170	10.521	10.521	0.000	0.000	0.000	0.000
45	A	125	LEU	0	-0.006	-0.002	23.556	0.357	0.357	0.000	0.000	0.000	0.000
46	A	126	ALA	0	-0.014	0.007	28.263	0.246	0.246	0.000	0.000	0.000	0.000
47	A	127	GLY	0	0.059	0.042	31.234	0.346	0.346	0.000	0.000	0.000	0.000
48	A	128	PRO	0	-0.003	-0.021	33.596	0.000	0.000	0.000	0.000	0.000	0.000
49	A	129	GLU	-1	-0.777	-0.894	36.446	-7.587	-7.587	0.000	0.000	0.000	0.000
50	A	130	ALA	0	0.008	0.018	33.576	0.094	0.094	0.000	0.000	0.000	0.000
51	A	131	VAL	0	0.003	-0.017	32.414	-0.070	-0.070	0.000	0.000	0.000	0.000
52	A	132	LYS	1	0.781	0.892	34.160	7.484	7.484	0.000	0.000	0.000	0.000
53	A	133	ARG	1	0.765	0.867	36.109	8.717	8.717	0.000	0.000	0.000	0.000
54	A	134	ASN	0	-0.015	-0.007	32.060	-0.178	-0.178	0.000	0.000	0.000	0.000
55	A	135	TRP	0	-0.024	-0.015	32.764	-0.230	-0.230	0.000	0.000	0.000	0.000
56	A	136	VAL	0	0.040	0.043	29.782	0.252	0.252	0.000	0.000	0.000	0.000
57	A	137	TYR	0	0.045	0.013	33.078	0.001	0.001	0.000	0.000	0.000	0.000
58	A	138	PHE	0	0.050	0.009	33.380	-0.195	-0.195	0.000	0.000	0.000	0.000
59	A	139	THR	0	-0.017	-0.009	34.276	-0.147	-0.147	0.000	0.000	0.000	0.000
60	A	140	GLU	-1	-0.714	-0.842	33.711	-8.911	-8.911	0.000	0.000	0.000	0.000
61	A	141	VAL	0	0.006	0.008	28.429	-0.175	-0.175	0.000	0.000	0.000	0.000
62	A	142	LYS	1	0.871	0.929	29.736	8.856	8.856	0.000	0.000	0.000	0.000
63	A	143	ASN	0	-0.037	-0.016	32.088	0.192	0.192	0.000	0.000	0.000	0.000
64	A	144	ILE	0	-0.027	0.014	25.523	-0.084	-0.084	0.000	0.000	0.000	0.000
65	A	145	SER	0	0.008	-0.019	25.051	-0.108	-0.108	0.000	0.000	0.000	0.000
66	A	146	VAL	0	0.057	0.010	22.858	-0.365	-0.365	0.000	0.000	0.000	0.000
67	A	147	THR	0	-0.012	-0.008	21.115	-0.575	-0.575	0.000	0.000	0.000	0.000
68	A	148	ASP	-1	-0.667	-0.750	20.067	-13.225	-13.225	0.000	0.000	0.000	0.000
69	A	149	PHE	0	0.048	0.014	20.288	-0.631	-0.631	0.000	0.000	0.000	0.000
70	A	150	GLN	0	-0.005	-0.003	17.808	-0.511	-0.511	0.000	0.000	0.000	0.000
71	A	151	THR	0	-0.011	0.004	15.852	-1.420	-1.420	0.000	0.000	0.000	0.000
72	A	152	LEU	0	0.010	0.005	15.302	-1.151	-1.151	0.000	0.000	0.000	0.000
73	A	153	ASP	-1	-0.774	-0.846	15.779	-18.644	-18.644	0.000	0.000	0.000	0.000
74	A	154	ASN	0	-0.041	-0.041	11.955	-1.805	-1.805	0.000	0.000	0.000	0.000
75	A	155	LEU	0	0.030	0.030	10.915	-2.172	-2.172	0.000	0.000	0.000	0.000
76	A	156	TRP	0	0.031	-0.001	11.072	-2.225	-2.225	0.000	0.000	0.000	0.000
77	A	157	LYS	1	0.820	0.932	10.988	18.850	18.850	0.000	0.000	0.000	0.000
78	A	158	ALA	0	0.006	0.007	6.789	-1.697	-1.697	0.000	0.000	0.000	0.000
79	A	159	SER	0	-0.040	-0.026	6.823	-3.850	-3.850	0.000	0.000	0.000	0.000
80	A	160	SER	0	0.019	-0.016	9.107	-0.435	-0.435	0.000	0.000	0.000	0.000
81	A	161	ASN	0	-0.055	-0.026	6.704	0.249	0.249	0.000	0.000	0.000	0.000
82	A	162	ASN	0	0.007	-0.011	8.099	3.136	3.136	0.000	0.000	0.000	0.000
83	A	163	LYS	1	0.855	0.950	11.574	22.850	22.850	0.000	0.000	0.000	0.000
84	A	164	PHE	0	0.008	-0.013	13.320	1.588	1.588	0.000	0.000	0.000	0.000
85	A	165	GLY	0	0.032	0.011	14.501	-0.971	-0.971	0.000	0.000	0.000	0.000
86	A	166	TYR	0	0.004	-0.008	17.002	0.377	0.377	0.000	0.000	0.000	0.000
87	A	167	SER	0	-0.058	-0.059	17.323	0.385	0.385	0.000	0.000	0.000	0.000
88	A	168	VAL	0	-0.022	0.002	15.421	0.592	0.592	0.000	0.000	0.000	0.000
89	A	169	GLN	0	-0.024	-0.038	18.780	0.825	0.825	0.000	0.000	0.000	0.000
90	A	170	LYS	1	0.795	0.887	21.984	12.298	12.298	0.000	0.000	0.000	0.000
91	A	171	GLU	-1	-0.794	-0.854	18.990	-15.486	-15.486	0.000	0.000	0.000	0.000
92	A	172	ILE	0	0.011	0.009	21.142	0.609	0.609	0.000	0.000	0.000	0.000
93	A	173	TRP	0	-0.015	-0.013	23.538	0.618	0.618	0.000	0.000	0.000	0.000
94	A	174	VAL	0	-0.002	-0.001	26.270	0.552	0.552	0.000	0.000	0.000	0.000
95	A	175	GLN	0	0.011	0.014	23.296	0.419	0.419	0.000	0.000	0.000	0.000
96	A	176	ASN	0	-0.067	-0.025	27.211	0.247	0.247	0.000	0.000	0.000	0.000
97	A	177	GLN	0	-0.006	-0.005	29.323	0.409	0.409	0.000	0.000	0.000	0.000
98	A	178	LYS	1	0.893	0.948	30.846	9.630	9.630	0.000	0.000	0.000	0.000
99	A	179	ARG	1	0.946	0.977	32.171	8.730	8.730	0.000	0.000	0.000	0.000
100	A	180	TRP	0	0.044	-0.005	29.002	-0.153	-0.153	0.000	0.000	0.000	0.000
101	A	181	PRO	0	0.020	0.019	31.275	-0.268	-0.268	0.000	0.000	0.000	0.000
102	A	182	LYS	1	0.885	0.949	27.921	10.788	10.788	0.000	0.000	0.000	0.000
103	A	183	PHE	0	0.045	0.024	24.470	-0.266	-0.266	0.000	0.000	0.000	0.000
104	A	184	PHE	0	0.028	-0.011	26.911	-0.338	-0.338	0.000	0.000	0.000	0.000
105	A	185	LYS	0	-0.014	0.045	27.800	-0.290	-0.290	0.000	0.000	0.000	0.000
106	A	186	GLN	0	-0.054	-0.038	23.904	0.127	0.127	0.000	0.000	0.000	0.000
107	A	187	ILE	0	-0.015	0.009	22.104	-0.630	-0.630	0.000	0.000	0.000	0.000
108	A	188	ASP	-1	-0.804	-0.900	22.949	-13.141	-13.141	0.000	0.000	0.000	0.000
109	A	189	TRP	0	-0.081	-0.046	22.924	0.248	0.248	0.000	0.000	0.000	0.000
110	A	190	THR	0	0.033	-0.019	27.187	0.214	0.214	0.000	0.000	0.000	0.000
111	A	191	GLN	0	-0.003	0.016	27.715	0.001	0.001	0.000	0.000	0.000	0.000
112	A	192	GLY	0	-0.043	-0.027	28.736	0.038	0.038	0.000	0.000	0.000	0.000
113	A	193	GLU	-1	-0.856	-0.892	31.155	-8.858	-8.858	0.000	0.000	0.000	0.000
114	A	194	ASN	0	-0.062	-0.054	33.917	0.313	0.313	0.000	0.000	0.000	0.000
115	A	195	ASN	0	-0.044	-0.035	37.509	0.068	0.068	0.000	0.000	0.000	0.000
116	A	196	ASN	0	-0.063	-0.028	32.273	-0.185	-0.185	0.000	0.000	0.000	0.000
117	A	197	TYR	0	-0.004	-0.008	31.433	-0.100	-0.100	0.000	0.000	0.000	0.000
118	A	198	ARG	1	0.782	0.883	25.657	11.851	11.851	0.000	0.000	0.000	0.000
119	A	199	LYS	1	0.958	0.971	30.141	9.253	9.253	0.000	0.000	0.000	0.000
120	A	200	TRP	0	-0.074	-0.011	26.095	-0.003	-0.003	0.000	0.000	0.000	0.000
121	A	201	PRO	0	-0.030	-0.029	26.520	0.449	0.449	0.000	0.000	0.000	0.000
122	A	202	MET	0	-0.021	-0.041	26.435	-0.257	-0.257	0.000	0.000	0.000	0.000
123	A	203	GLU	-1	-0.791	-0.867	27.143	-10.542	-10.542	0.000	0.000	0.000	0.000
124	A	204	PHE	0	-0.031	-0.012	23.399	0.008	0.008	0.000	0.000	0.000	0.000
125	A	205	ILE	0	0.004	0.005	18.600	-0.131	-0.131	0.000	0.000	0.000	0.000
126	A	206	TYR	0	-0.058	-0.057	18.603	-0.467	-0.467	0.000	0.000	0.000	0.000
127	A	207	SER	0	0.000	-0.041	14.933	-0.265	-0.265	0.000	0.000	0.000	0.000
128	A	208	MET	0	0.017	0.013	7.972	0.703	0.703	0.000	0.000	0.000	0.000
129	A	209	ASP	-1	-0.852	-0.892	12.742	-20.109	-20.109	0.000	0.000	0.000	0.000
130	A	210	ALA	0	-0.015	0.010	15.600	0.763	0.763	0.000	0.000	0.000	0.000
131	A	211	PRO	0	0.019	0.003	16.659	-1.109	-1.109	0.000	0.000	0.000	0.000
132	A	212	ARG	1	0.763	0.838	15.108	17.588	17.588	0.000	0.000	0.000	0.000
133	A	213	GLY	0	0.040	0.012	17.430	0.934	0.934	0.000	0.000	0.000	0.000
134	A	214	HIS	0	-0.032	-0.003	18.950	0.525	0.525	0.000	0.000	0.000	0.000
135	A	215	LEU	0	0.020	0.025	16.664	0.580	0.580	0.000	0.000	0.000	0.000
136	A	216	PRO	0	0.046	0.027	18.083	-0.591	-0.591	0.000	0.000	0.000	0.000
137	A	217	LEU	0	0.011	0.030	20.200	0.589	0.589	0.000	0.000	0.000	0.000
138	A	218	THR	0	-0.032	-0.045	23.859	-0.057	-0.057	0.000	0.000	0.000	0.000
139	A	219	ASN	0	-0.037	-0.033	26.541	0.456	0.456	0.000	0.000	0.000	0.000
140	A	220	ALA	0	0.060	0.047	29.106	0.355	0.355	0.000	0.000	0.000	0.000
141	A	221	LEU	0	0.012	0.014	30.548	0.201	0.201	0.000	0.000	0.000	0.000
142	A	222	ARG	1	0.815	0.901	31.978	9.794	9.794	0.000	0.000	0.000	0.000
143	A	223	GLY	0	0.088	0.057	34.733	-0.023	-0.023	0.000	0.000	0.000	0.000
144	A	224	THR	0	0.054	0.013	32.814	-0.217	-0.217	0.000	0.000	0.000	0.000
145	A	225	GLN	0	-0.026	-0.017	32.778	-0.193	-0.193	0.000	0.000	0.000	0.000
146	A	226	LEU	0	-0.043	-0.025	30.271	-0.025	-0.025	0.000	0.000	0.000	0.000
147	A	227	PHE	0	0.007	0.003	24.482	-0.029	-0.029	0.000	0.000	0.000	0.000
148	A	228	GLN	0	0.001	-0.004	28.407	-0.152	-0.152	0.000	0.000	0.000	0.000
149	A	229	ALA	0	-0.028	-0.009	29.930	-0.106	-0.106	0.000	0.000	0.000	0.000
150	A	230	ILE	0	-0.020	0.004	24.450	-0.018	-0.018	0.000	0.000	0.000	0.000
151	A	231	MET	0	-0.028	-0.011	25.114	-0.163	-0.163	0.000	0.000	0.000	0.000
152	A	232	GLU	-1	-0.784	-0.890	26.373	-9.589	-9.589	0.000	0.000	0.000	0.000
153	A	233	HIS	0	-0.014	0.016	25.828	0.066	0.066	0.000	0.000	0.000	0.000
154	A	234	PRO	0	0.035	0.004	26.042	-0.353	-0.353	0.000	0.000	0.000	0.000
155	A	235	ALA	0	-0.041	-0.019	22.035	-0.230	-0.230	0.000	0.000	0.000	0.000
156	A	236	PHE	0	-0.069	-0.056	19.675	-0.836	-0.836	0.000	0.000	0.000	0.000
157	A	237	GLU	-1	-0.916	-0.944	22.717	-10.556	-10.556	0.000	0.000	0.000	0.000
158	A	238	LYS	0	0.102	0.078	17.295	3.524	3.524	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:81:SER)