FMO DATABASE

FMODB ID: RM8Z8

Calculation Name: 3KNP-E-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3KNP

Chain ID: E

ChEMBL ID:

UniProt ID: Q8IIS0

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	-1609543.913835
FMO2-HF: Nuclear repulsion	1545242.561265
FMO2-HF: Total energy	-64301.352569
FMO2-MP2: Total energy	-64490.842426

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.
-158.62	-155.693	63.454	-27.578	-38.801	-0.246

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 : 0.696 / q_NPA : 0.857

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	3	VAL	0	0.008	-0.002	3.361	2.406	4.751	0.020	-1.060	-1.305	-0.003
41	A	41	LEU	0	0.026	0.001	2.756	-4.046	-4.001	2.888	-0.468	-2.465	0.003
42	A	42	GLY	0	0.024	0.016	4.119	4.544	4.804	-0.001	-0.053	-0.206	0.000
43	A	43	ILE	0	-0.027	-0.016	2.313	-18.789	-16.057	2.324	-1.884	-3.172	-0.014
44	A	44	HIS	0	0.038	0.016	2.688	3.778	4.892	0.230	-0.262	-1.082	-0.003
45	A	45	LYS	1	0.936	0.957	4.363	28.483	28.615	-0.001	-0.011	-0.120	0.000
47	A	47	ASP	-1	-0.748	-0.845	1.704	-130.195	-134.181	23.830	-10.817	-9.026	-0.126
48	A	48	THR	0	0.002	-0.014	4.512	10.450	10.610	-0.001	-0.057	-0.102	0.000
51	A	51	ASP	-1	-0.798	-0.868	2.114	-78.293	-76.621	2.679	-2.190	-2.161	-0.011
52	A	52	ALA	0	0.011	-0.010	2.102	-7.260	-5.734	4.872	-3.202	-3.196	-0.022
53	A	53	LEU	0	0.047	0.023	3.173	1.246	0.077	0.020	1.547	-0.398	-0.003
55	A	55	ILE	0	0.030	0.003	2.064	4.323	0.859	10.236	-1.929	-4.844	-0.001
56	A	56	ILE	0	0.025	0.037	4.041	3.947	4.200	0.001	-0.031	-0.223	0.000
92	A	92	PHE	0	-0.027	-0.024	2.922	-2.552	-1.951	0.061	-0.162	-0.500	0.000
115	A	115	PHE	0	-0.047	-0.029	2.856	-0.767	-0.555	1.745	-0.508	-1.448	0.002
119	A	119	ILE	0	-0.008	-0.018	2.491	-0.643	-1.257	3.107	-0.418	-2.075	-0.004
156	A	156	ASP	-1	-0.806	-0.904	3.309	-72.972	-72.297	0.011	-0.380	-0.306	-0.003
157	A	157	THR	0	-0.088	-0.062	1.795	-16.262	-17.140	10.916	-5.041	-4.997	-0.055
158	A	158	HIS	0	-0.033	0.003	2.788	32.350	33.661	0.517	-0.652	-1.175	-0.006
4	A	4	VAL	0	-0.003	0.004	5.527	1.366	1.366	0.000	0.000	0.000	0.000
5	A	5	ILE	0	0.019	0.003	8.314	0.998	0.998	0.000	0.000	0.000	0.000
6	A	6	GLN	0	0.008	-0.001	10.626	0.777	0.777	0.000	0.000	0.000	0.000
7	A	7	ARG	1	0.851	0.899	14.220	13.970	13.970	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.023	-0.007	16.464	0.442	0.442	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.846	0.904	18.928	12.154	12.154	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.027	0.015	20.870	0.472	0.472	0.000	0.000	0.000	0.000
11	A	11	ALA	0	-0.063	-0.022	17.488	-0.246	-0.246	0.000	0.000	0.000	0.000
12	A	12	ILE	0	0.060	0.034	19.563	0.084	0.084	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.015	0.010	15.592	-0.503	-0.503	0.000	0.000	0.000	0.000
14	A	14	SER	0	0.019	-0.008	19.563	0.557	0.557	0.000	0.000	0.000	0.000
15	A	15	VAL	0	-0.020	-0.006	20.590	-0.683	-0.683	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.816	0.886	22.844	11.092	11.092	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.823	0.918	25.939	8.677	8.677	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.817	-0.888	29.092	-9.865	-9.865	0.000	0.000	0.000	0.000
19	A	19	ASN	0	-0.049	-0.034	31.708	-0.178	-0.178	0.000	0.000	0.000	0.000
20	A	20	ILE	0	0.027	0.003	32.673	0.211	0.211	0.000	0.000	0.000	0.000
21	A	21	GLY	0	-0.013	0.002	36.088	0.081	0.081	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.848	-0.924	38.714	-7.558	-7.558	0.000	0.000	0.000	0.000
23	A	23	ASN	0	-0.090	-0.039	36.894	-0.066	-0.066	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.837	-0.894	34.940	-8.806	-8.806	0.000	0.000	0.000	0.000
25	A	25	LYS	1	0.746	0.826	30.485	9.027	9.027	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.756	-0.858	30.381	-9.066	-9.066	0.000	0.000	0.000	0.000
27	A	27	LEU	0	-0.016	-0.015	25.961	-0.373	-0.373	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.913	-0.943	25.256	-10.255	-10.255	0.000	0.000	0.000	0.000
29	A	29	ILE	0	-0.004	-0.017	23.018	-0.510	-0.510	0.000	0.000	0.000	0.000
30	A	30	ILE	0	-0.028	-0.011	19.242	0.149	0.149	0.000	0.000	0.000	0.000
31	A	31	SER	0	-0.068	-0.052	17.032	-0.110	-0.110	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.840	-0.907	19.851	-11.126	-11.126	0.000	0.000	0.000	0.000
33	A	33	ILE	0	-0.065	-0.021	15.373	-0.168	-0.168	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.861	0.912	19.441	11.394	11.394	0.000	0.000	0.000	0.000
35	A	35	ASN	0	-0.007	-0.009	20.032	-0.392	-0.392	0.000	0.000	0.000	0.000
36	A	36	GLY	0	0.037	0.011	17.045	0.024	0.024	0.000	0.000	0.000	0.000
37	A	37	LEU	0	-0.064	-0.020	11.847	-0.131	-0.131	0.000	0.000	0.000	0.000
38	A	38	ILE	0	0.025	0.025	12.339	0.217	0.217	0.000	0.000	0.000	0.000
39	A	39	CYS	0	-0.037	-0.021	6.942	-0.462	-0.462	0.000	0.000	0.000	0.000
40	A	40	PHE	0	0.030	0.020	8.149	-0.350	-0.350	0.000	0.000	0.000	0.000
46	A	46	ASN	0	-0.013	-0.015	6.044	6.039	6.039	0.000	0.000	0.000	0.000
49	A	49	TRP	0	0.000	-0.021	5.253	-4.079	-4.079	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.868	-0.934	6.770	-27.752	-27.752	0.000	0.000	0.000	0.000
54	A	54	TYR	0	-0.029	-0.011	5.038	3.514	3.514	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.953	0.976	6.049	27.641	27.641	0.000	0.000	0.000	0.000
58	A	58	LYS	1	0.887	0.951	7.456	27.029	27.029	0.000	0.000	0.000	0.000
59	A	59	CYS	0	-0.019	-0.022	6.218	1.943	1.943	0.000	0.000	0.000	0.000
60	A	60	LEU	0	0.006	0.015	9.170	1.942	1.942	0.000	0.000	0.000	0.000
61	A	61	ASN	0	-0.024	-0.018	11.814	1.589	1.589	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.031	-0.010	10.731	0.769	0.769	0.000	0.000	0.000	0.000
63	A	63	ARG	1	0.847	0.923	14.213	14.221	14.221	0.000	0.000	0.000	0.000
64	A	64	LEU	0	0.025	0.016	13.546	-0.004	-0.004	0.000	0.000	0.000	0.000
65	A	65	TRP	0	-0.002	0.004	16.017	0.149	0.149	0.000	0.000	0.000	0.000
66	A	66	ASN	0	-0.001	-0.010	21.613	-0.361	-0.361	0.000	0.000	0.000	0.000
67	A	67	ASN	0	-0.102	-0.064	25.218	0.165	0.165	0.000	0.000	0.000	0.000
68	A	68	ASP	-1	-0.828	-0.905	27.357	-8.905	-8.905	0.000	0.000	0.000	0.000
69	A	69	ASN	0	-0.005	0.008	31.043	0.125	0.125	0.000	0.000	0.000	0.000
70	A	70	LYS	1	0.890	0.955	27.486	10.300	10.300	0.000	0.000	0.000	0.000
71	A	71	THR	0	0.023	0.003	25.530	-0.126	-0.126	0.000	0.000	0.000	0.000
72	A	72	TRP	0	-0.031	-0.018	18.556	-0.311	-0.311	0.000	0.000	0.000	0.000
73	A	73	ASP	-1	-0.826	-0.904	21.777	-11.934	-11.934	0.000	0.000	0.000	0.000
74	A	74	LYS	1	0.935	0.974	21.378	11.238	11.238	0.000	0.000	0.000	0.000
75	A	75	ASN	0	-0.040	-0.037	15.948	-0.585	-0.585	0.000	0.000	0.000	0.000
76	A	76	VAL	0	0.053	0.024	13.457	0.653	0.653	0.000	0.000	0.000	0.000
77	A	77	LYS	1	0.924	0.973	14.442	17.163	17.163	0.000	0.000	0.000	0.000
78	A	78	ASP	-1	-0.852	-0.920	17.926	-13.175	-13.175	0.000	0.000	0.000	0.000
79	A	79	LEU	0	-0.044	-0.017	20.413	0.616	0.616	0.000	0.000	0.000	0.000
80	A	80	ASN	0	-0.041	-0.015	20.204	-0.016	-0.016	0.000	0.000	0.000	0.000
81	A	81	TYR	0	0.020	0.019	18.035	0.313	0.313	0.000	0.000	0.000	0.000
82	A	82	GLU	-1	-0.782	-0.886	16.165	-13.239	-13.239	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.022	-0.015	10.170	-0.517	-0.517	0.000	0.000	0.000	0.000
84	A	84	LEU	0	0.021	0.031	12.698	0.146	0.146	0.000	0.000	0.000	0.000
85	A	85	ILE	0	0.002	0.007	6.740	-1.469	-1.469	0.000	0.000	0.000	0.000
86	A	86	VAL	0	0.033	0.020	8.929	1.060	1.060	0.000	0.000	0.000	0.000
87	A	87	SER	0	-0.002	0.012	8.138	-2.921	-2.921	0.000	0.000	0.000	0.000
88	A	88	GLN	0	0.007	-0.014	7.677	2.559	2.559	0.000	0.000	0.000	0.000
89	A	89	PHE	0	0.037	0.021	7.774	-3.489	-3.489	0.000	0.000	0.000	0.000
90	A	90	THR	0	0.025	0.005	8.787	-1.525	-1.525	0.000	0.000	0.000	0.000
91	A	91	LEU	0	0.004	0.019	6.652	0.781	0.781	0.000	0.000	0.000	0.000
93	A	93	GLY	0	0.014	0.010	8.664	1.660	1.660	0.000	0.000	0.000	0.000
94	A	94	ASN	0	-0.009	-0.006	12.196	1.963	1.963	0.000	0.000	0.000	0.000
95	A	95	THR	0	0.058	0.013	13.611	1.035	1.035	0.000	0.000	0.000	0.000
96	A	96	LYS	1	0.931	0.973	13.455	21.576	21.576	0.000	0.000	0.000	0.000
97	A	97	LYS	1	0.847	0.926	17.386	17.679	17.679	0.000	0.000	0.000	0.000
98	A	98	GLY	0	0.040	0.020	19.586	0.843	0.843	0.000	0.000	0.000	0.000
99	A	99	ASN	0	0.013	-0.007	20.048	-0.899	-0.899	0.000	0.000	0.000	0.000
100	A	100	LYS	1	0.997	1.026	19.797	14.775	14.775	0.000	0.000	0.000	0.000
101	A	101	PRO	0	-0.014	-0.003	15.640	-0.187	-0.187	0.000	0.000	0.000	0.000
102	A	102	ASP	-1	-0.876	-0.945	15.617	-19.069	-19.069	0.000	0.000	0.000	0.000
103	A	103	PHE	0	0.020	-0.005	12.043	-1.084	-1.084	0.000	0.000	0.000	0.000
104	A	104	HIS	0	0.009	0.008	11.616	-1.141	-1.141	0.000	0.000	0.000	0.000
105	A	105	LEU	0	-0.067	-0.017	7.342	-0.742	-0.742	0.000	0.000	0.000	0.000
106	A	106	ALA	0	0.004	0.003	7.041	-5.553	-5.553	0.000	0.000	0.000	0.000
107	A	107	LYS	1	0.789	0.900	7.005	35.642	35.642	0.000	0.000	0.000	0.000
108	A	108	GLU	-1	-0.791	-0.869	8.808	-17.760	-17.760	0.000	0.000	0.000	0.000
109	A	109	PRO	0	0.039	-0.010	11.231	-0.838	-0.838	0.000	0.000	0.000	0.000
110	A	110	ASN	0	-0.034	-0.026	12.681	0.304	0.304	0.000	0.000	0.000	0.000
111	A	111	GLU	-1	-0.842	-0.912	10.773	-25.885	-25.885	0.000	0.000	0.000	0.000
112	A	112	ALA	0	-0.028	-0.019	8.339	-0.969	-0.969	0.000	0.000	0.000	0.000
113	A	113	LEU	0	0.001	0.014	8.927	-0.507	-0.507	0.000	0.000	0.000	0.000
114	A	114	ILE	0	-0.005	-0.008	11.282	0.233	0.233	0.000	0.000	0.000	0.000
116	A	116	TYR	0	0.005	-0.028	6.908	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	117	ASN	0	0.015	-0.012	7.874	-0.025	-0.025	0.000	0.000	0.000	0.000
118	A	118	LYS	1	0.975	1.010	9.097	20.520	20.520	0.000	0.000	0.000	0.000
120	A	120	ILE	0	-0.008	0.001	6.176	-0.137	-0.137	0.000	0.000	0.000	0.000
121	A	121	ASP	-1	-0.868	-0.927	8.869	-16.273	-16.273	0.000	0.000	0.000	0.000
122	A	122	GLU	-1	-0.851	-0.919	7.418	-19.015	-19.015	0.000	0.000	0.000	0.000
123	A	123	PHE	0	0.022	-0.014	5.043	0.104	0.104	0.000	0.000	0.000	0.000
124	A	124	LYS	1	0.824	0.910	9.289	16.141	16.141	0.000	0.000	0.000	0.000
125	A	125	LYS	1	0.813	0.909	12.345	18.663	18.663	0.000	0.000	0.000	0.000
126	A	126	GLN	0	-0.049	-0.032	9.541	-0.766	-0.766	0.000	0.000	0.000	0.000
127	A	127	TYR	0	-0.081	-0.054	12.772	0.555	0.555	0.000	0.000	0.000	0.000
128	A	128	ASN	0	0.040	0.001	14.458	0.873	0.873	0.000	0.000	0.000	0.000
129	A	129	ASP	-1	-0.812	-0.902	15.757	-14.098	-14.098	0.000	0.000	0.000	0.000
130	A	130	ASP	-1	-0.840	-0.898	16.889	-12.075	-12.075	0.000	0.000	0.000	0.000
131	A	131	LYS	1	0.813	0.902	16.147	12.203	12.203	0.000	0.000	0.000	0.000
132	A	132	ILE	0	-0.036	-0.008	10.911	-0.813	-0.813	0.000	0.000	0.000	0.000
133	A	133	LYS	1	0.890	0.952	13.709	13.863	13.863	0.000	0.000	0.000	0.000
134	A	134	ILE	0	0.030	0.008	11.773	-1.233	-1.233	0.000	0.000	0.000	0.000
135	A	135	GLY	0	0.063	0.043	12.999	0.909	0.909	0.000	0.000	0.000	0.000
136	A	136	LYS	1	0.936	0.963	14.815	13.875	13.875	0.000	0.000	0.000	0.000
137	A	137	PHE	0	0.033	-0.007	9.200	-0.088	-0.088	0.000	0.000	0.000	0.000
138	A	138	GLY	0	-0.035	-0.013	13.684	0.714	0.714	0.000	0.000	0.000	0.000
139	A	139	ASN	0	-0.044	-0.019	15.222	0.954	0.954	0.000	0.000	0.000	0.000
140	A	140	TYR	0	0.035	0.015	17.484	-0.513	-0.513	0.000	0.000	0.000	0.000
141	A	141	MET	0	-0.013	0.002	14.359	0.190	0.190	0.000	0.000	0.000	0.000
142	A	142	ASN	0	-0.016	0.014	19.567	-0.462	-0.462	0.000	0.000	0.000	0.000
143	A	143	ILE	0	-0.024	-0.016	15.452	-0.122	-0.122	0.000	0.000	0.000	0.000
144	A	144	ASP	-1	-0.867	-0.901	19.655	-11.926	-11.926	0.000	0.000	0.000	0.000
145	A	145	VAL	0	-0.023	-0.039	17.383	-0.334	-0.334	0.000	0.000	0.000	0.000
146	A	146	THR	0	-0.007	0.010	20.233	0.395	0.395	0.000	0.000	0.000	0.000
147	A	147	ASN	0	-0.004	-0.019	18.712	-0.811	-0.811	0.000	0.000	0.000	0.000
148	A	148	ASP	-1	-0.810	-0.901	20.125	-12.065	-12.065	0.000	0.000	0.000	0.000
149	A	149	GLY	0	-0.012	0.009	21.227	-0.498	-0.498	0.000	0.000	0.000	0.000
150	A	150	PRO	0	0.031	0.023	20.132	0.465	0.465	0.000	0.000	0.000	0.000
151	A	151	VAL	0	-0.004	-0.009	16.758	0.079	0.079	0.000	0.000	0.000	0.000
152	A	152	THR	0	0.004	0.001	14.003	-0.312	-0.312	0.000	0.000	0.000	0.000
153	A	153	ILE	0	-0.026	-0.010	11.579	0.436	0.436	0.000	0.000	0.000	0.000
154	A	154	TYR	0	-0.004	0.005	7.046	-1.258	-1.258	0.000	0.000	0.000	0.000
155	A	155	ILE	0	-0.025	-0.017	6.457	2.051	2.051	0.000	0.000	0.000	0.000

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