FMO DATABASE

FMODB ID: 3MZ4L

Calculation Name: 2KCD-A-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2KCD

Chain ID: A

ChEMBL ID:

UniProt ID: Q4A134

Base Structure: SolutionNMR

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	120
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1042682.610516
FMO2-HF: Nuclear repulsion	992366.328392
FMO2-HF: Total energy	-50316.282123
FMO2-MP2: Total energy	-50463.345371

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.
-68.394	-66.413	-0.02	-0.711	-1.25	0

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 : 0.839 / q_NPA : 0.904

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].
3	A	3	LEU	0	0.088	0.040	3.783	3.019	4.667	-0.018	-0.656	-0.973
5	A	5	LEU	0	-0.035	-0.010	4.334	0.538	0.711	-0.001	-0.019	-0.153
6	A	6	GLN	0	-0.045	-0.037	4.230	-2.703	-2.543	-0.001	-0.036	-0.124
4	A	4	GLU	-1	-0.797	-0.865	6.719	-25.311	-25.311	0.000	0.000	0.000
7	A	7	LEU	0	0.061	0.048	6.954	2.728	2.728	0.000	0.000	0.000
8	A	8	LYS	1	0.868	0.949	10.198	23.466	23.466	0.000	0.000	0.000
9	A	9	HIS	0	-0.001	-0.007	7.568	2.941	2.941	0.000	0.000	0.000
10	A	10	TYR	0	-0.004	0.013	10.635	1.743	1.743	0.000	0.000	0.000
11	A	11	ILE	0	0.051	0.018	12.315	1.438	1.438	0.000	0.000	0.000
12	A	12	THR	0	-0.059	-0.051	13.491	0.907	0.907	0.000	0.000	0.000
13	A	13	ASN	0	0.000	-0.010	11.834	1.342	1.342	0.000	0.000	0.000
14	A	14	LEU	0	-0.038	0.002	15.689	0.887	0.887	0.000	0.000	0.000
15	A	15	PHE	0	0.028	0.008	17.969	0.881	0.881	0.000	0.000	0.000
16	A	16	ASN	0	-0.088	-0.039	19.055	0.391	0.391	0.000	0.000	0.000
17	A	17	LEU	0	-0.009	0.009	18.666	0.576	0.576	0.000	0.000	0.000
18	A	18	PRO	0	-0.004	-0.015	17.996	-0.889	-0.889	0.000	0.000	0.000
19	A	19	ARG	1	0.876	0.938	12.903	20.860	20.860	0.000	0.000	0.000
20	A	20	ASP	-1	-0.908	-0.963	14.197	-18.075	-18.075	0.000	0.000	0.000
21	A	21	GLU	-1	-0.894	-0.931	16.396	-14.396	-14.396	0.000	0.000	0.000
22	A	22	LYS	1	0.897	0.954	15.160	17.464	17.464	0.000	0.000	0.000
23	A	23	TRP	0	0.018	-0.011	14.971	0.058	0.058	0.000	0.000	0.000
24	A	24	GLU	-1	-0.888	-0.918	17.575	-13.993	-13.993	0.000	0.000	0.000
25	A	25	CYS	0	-0.092	-0.049	15.345	-0.424	-0.424	0.000	0.000	0.000
26	A	26	GLU	-1	-0.881	-0.933	18.800	-12.205	-12.205	0.000	0.000	0.000
27	A	27	SER	0	-0.079	-0.039	19.527	-0.652	-0.652	0.000	0.000	0.000
28	A	28	ILE	0	0.033	0.018	21.497	0.553	0.553	0.000	0.000	0.000
29	A	29	GLU	-1	-0.978	-0.996	23.623	-12.634	-12.634	0.000	0.000	0.000
30	A	30	GLU	-1	-0.849	-0.930	25.498	-10.973	-10.973	0.000	0.000	0.000
31	A	31	VAL	0	-0.035	-0.011	26.463	-0.364	-0.364	0.000	0.000	0.000
32	A	32	ALA	0	-0.014	-0.018	24.981	-0.140	-0.140	0.000	0.000	0.000
33	A	33	ASP	0	-0.075	-0.074	26.327	-0.065	-0.065	0.000	0.000	0.000
34	A	34	ASP	-1	-0.873	-0.920	29.433	-9.996	-9.996	0.000	0.000	0.000
35	A	35	ILE	0	-0.046	-0.008	23.601	-0.074	-0.074	0.000	0.000	0.000
36	A	36	LEU	0	-0.051	-0.028	22.010	-0.178	-0.178	0.000	0.000	0.000
37	A	37	PRO	0	0.078	0.043	25.772	0.405	0.405	0.000	0.000	0.000
38	A	38	ASP	-1	-0.791	-0.892	28.445	-9.932	-9.932	0.000	0.000	0.000
39	A	39	GLN	0	-0.102	-0.057	28.340	-0.109	-0.109	0.000	0.000	0.000
40	A	40	TYR	0	-0.021	-0.011	21.565	-0.151	-0.151	0.000	0.000	0.000
41	A	41	VAL	0	-0.019	-0.004	26.585	-0.107	-0.107	0.000	0.000	0.000
42	A	42	ARG	1	0.948	0.987	28.951	9.598	9.598	0.000	0.000	0.000
43	A	43	LEU	0	-0.031	-0.027	31.079	0.363	0.363	0.000	0.000	0.000
44	A	44	GLY	0	0.034	0.037	28.178	-0.023	-0.023	0.000	0.000	0.000
45	A	45	PRO	0	-0.034	-0.028	25.906	0.225	0.225	0.000	0.000	0.000
46	A	46	LEU	0	0.006	-0.022	22.400	-0.019	-0.019	0.000	0.000	0.000
47	A	47	SER	0	-0.002	0.010	26.846	-0.001	-0.001	0.000	0.000	0.000
48	A	48	ASN	0	0.035	0.021	30.393	-0.120	-0.120	0.000	0.000	0.000
49	A	49	LYS	1	0.857	0.943	26.147	11.992	11.992	0.000	0.000	0.000
50	A	50	ILE	0	0.051	0.034	26.791	-0.156	-0.156	0.000	0.000	0.000
51	A	51	LEU	0	-0.079	-0.047	21.194	-0.345	-0.345	0.000	0.000	0.000
52	A	52	GLN	0	-0.031	-0.006	20.647	-0.390	-0.390	0.000	0.000	0.000
53	A	53	THR	0	0.028	0.009	19.972	-1.181	-1.181	0.000	0.000	0.000
54	A	54	ASN	0	-0.022	0.000	15.020	1.274	1.274	0.000	0.000	0.000
55	A	55	THR	0	0.055	0.018	17.960	-0.683	-0.683	0.000	0.000	0.000
56	A	56	TYR	0	-0.099	-0.084	13.295	0.092	0.092	0.000	0.000	0.000
57	A	57	TYR	0	-0.010	-0.023	19.133	0.392	0.392	0.000	0.000	0.000
58	A	58	SER	0	0.044	0.005	20.375	-0.272	-0.272	0.000	0.000	0.000
59	A	59	ASP	-1	-0.846	-0.917	22.514	-11.883	-11.883	0.000	0.000	0.000
60	A	60	THR	0	-0.025	-0.024	20.466	0.228	0.228	0.000	0.000	0.000
61	A	61	LEU	0	-0.020	0.010	18.513	0.118	0.118	0.000	0.000	0.000
62	A	62	HIS	0	0.041	0.026	22.622	0.149	0.149	0.000	0.000	0.000
63	A	63	LYS	1	0.912	0.954	26.250	11.492	11.492	0.000	0.000	0.000
64	A	64	SER	0	-0.073	-0.057	23.762	0.429	0.429	0.000	0.000	0.000
65	A	65	ASN	0	-0.031	-0.012	25.889	0.071	0.071	0.000	0.000	0.000
66	A	66	ILE	0	-0.008	0.020	20.069	-0.139	-0.139	0.000	0.000	0.000
67	A	67	TYR	0	0.013	0.002	22.436	-0.143	-0.143	0.000	0.000	0.000
68	A	68	PRO	0	-0.021	-0.014	16.842	-0.214	-0.214	0.000	0.000	0.000
69	A	69	PHE	0	0.016	-0.003	18.028	0.013	0.013	0.000	0.000	0.000
70	A	70	ILE	0	-0.042	-0.015	11.948	-1.197	-1.197	0.000	0.000	0.000
71	A	71	LEU	0	0.038	0.029	16.188	0.663	0.663	0.000	0.000	0.000
72	A	72	TYR	0	-0.023	-0.025	15.994	-1.227	-1.227	0.000	0.000	0.000
73	A	73	TYR	0	0.071	0.023	18.044	1.404	1.404	0.000	0.000	0.000
74	A	74	GLN	0	-0.020	-0.013	19.159	-0.542	-0.542	0.000	0.000	0.000
75	A	75	LYS	1	0.929	0.963	15.647	17.621	17.621	0.000	0.000	0.000
76	A	76	GLN	0	0.012	0.023	14.728	-1.082	-1.082	0.000	0.000	0.000
77	A	77	LEU	0	-0.025	-0.016	10.932	0.533	0.533	0.000	0.000	0.000
78	A	78	ILE	0	-0.042	-0.013	14.469	0.431	0.431	0.000	0.000	0.000
79	A	79	ALA	0	0.001	-0.012	16.279	0.227	0.227	0.000	0.000	0.000
80	A	80	ILE	0	-0.021	-0.016	11.119	-0.909	-0.909	0.000	0.000	0.000
81	A	81	GLY	0	0.050	0.019	15.487	0.306	0.306	0.000	0.000	0.000
82	A	82	PHE	0	-0.044	-0.009	17.137	-0.809	-0.809	0.000	0.000	0.000
83	A	83	ILE	0	0.039	0.040	19.914	0.255	0.255	0.000	0.000	0.000
84	A	84	ASP	-1	-0.863	-0.935	23.352	-12.450	-12.450	0.000	0.000	0.000
85	A	85	GLU	-1	-0.937	-0.975	24.759	-9.843	-9.843	0.000	0.000	0.000
86	A	86	ASN	0	-0.045	-0.017	27.951	0.721	0.721	0.000	0.000	0.000
87	A	87	HIS	0	-0.077	-0.042	28.190	0.403	0.403	0.000	0.000	0.000
88	A	88	ASP	-1	-0.891	-0.935	25.468	-11.743	-11.743	0.000	0.000	0.000
89	A	89	MET	0	-0.080	-0.047	23.550	-0.358	-0.358	0.000	0.000	0.000
90	A	90	ASP	-1	-0.835	-0.910	19.370	-14.527	-14.527	0.000	0.000	0.000
91	A	91	PHE	0	-0.071	-0.042	18.612	-0.920	-0.920	0.000	0.000	0.000
92	A	92	LEU	0	-0.028	-0.023	13.422	-0.447	-0.447	0.000	0.000	0.000
93	A	93	TYR	0	-0.058	-0.046	12.184	-1.563	-1.563	0.000	0.000	0.000
94	A	94	LEU	0	0.007	0.022	14.367	0.431	0.431	0.000	0.000	0.000
95	A	95	HIS	0	-0.034	-0.043	14.275	-0.245	-0.245	0.000	0.000	0.000
96	A	96	ASN	0	0.071	0.032	17.340	0.140	0.140	0.000	0.000	0.000
97	A	97	THR	0	0.009	-0.005	20.129	-0.171	-0.171	0.000	0.000	0.000
98	A	98	VAL	0	-0.052	-0.011	21.366	-0.031	-0.031	0.000	0.000	0.000
99	A	99	MET	0	0.006	-0.003	19.741	-0.072	-0.072	0.000	0.000	0.000
100	A	100	PRO	0	-0.011	0.006	16.004	0.292	0.292	0.000	0.000	0.000
101	A	101	LEU	0	-0.042	-0.014	18.603	0.715	0.715	0.000	0.000	0.000
102	A	102	LEU	0	0.013	0.006	18.738	0.388	0.388	0.000	0.000	0.000
103	A	103	ASP	-1	-0.896	-0.947	13.808	-18.963	-18.963	0.000	0.000	0.000
104	A	104	GLN	0	0.019	0.008	13.840	-0.991	-0.991	0.000	0.000	0.000
105	A	105	ARG	1	0.989	0.982	6.240	29.310	29.310	0.000	0.000	0.000
106	A	106	TYR	0	0.012	0.010	11.482	-1.197	-1.197	0.000	0.000	0.000
107	A	107	LEU	0	0.039	0.034	13.831	-0.052	-0.052	0.000	0.000	0.000
108	A	108	LEU	0	0.002	0.001	8.911	-0.659	-0.659	0.000	0.000	0.000
109	A	109	THR	0	-0.100	-0.073	8.428	-1.230	-1.230	0.000	0.000	0.000
110	A	110	GLY	0	0.022	0.033	11.016	0.053	0.053	0.000	0.000	0.000
111	A	111	GLY	0	-0.058	-0.031	14.660	0.099	0.099	0.000	0.000	0.000
112	A	112	GLN	0	-0.015	-0.009	16.328	0.224	0.224	0.000	0.000	0.000
113	A	113	LEU	0	0.020	0.003	19.076	0.161	0.161	0.000	0.000	0.000
114	A	114	GLU	-1	-0.948	-0.971	22.297	-11.840	-11.840	0.000	0.000	0.000
115	A	115	HIS	0	0.035	0.005	18.397	-0.734	-0.734	0.000	0.000	0.000
116	A	116	HIS	0	-0.019	-0.001	21.482	-0.118	-0.118	0.000	0.000	0.000
117	A	117	HIS	0	-0.001	-0.009	24.344	0.124	0.124	0.000	0.000	0.000
118	A	118	HIS	1	0.919	0.966	20.294	13.000	13.000	0.000	0.000	0.000
119	A	119	HIS	0	-0.158	-0.076	24.792	-0.333	-0.333	0.000	0.000	0.000
120	A	120	HIS	-1	-0.828	-0.896	26.375	-9.335	-9.335	0.000	0.000	0.000

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