FMO DATABASE

FMODB ID: 9LKL2

Calculation Name: 1KHC-A-Xray547

Preferred Name: DNA (cytosine-5)-methyltransferase 3B

Target Type: SINGLE PROTEIN

Ligand Name: unknown atom or ion

Ligand 3-letter code: UNX

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1KHC

Chain ID: A

ChEMBL ID: CHEMBL2189115

UniProt ID: O88509

Base Structure: X-ray

Registration Date: 2025-10-03

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	135
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1229505.369599
FMO2-HF: Nuclear repulsion	1175954.758644
FMO2-HF: Total energy	-53550.610955
FMO2-MP2: Total energy	-53707.346115

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:223:GLU)

Summations of interaction energy for fragment #1(A:223:GLU)

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.
-152.24	-156.473	38.601	-15.426	-18.94	0.183

Interaction energy analysis for fragmet #1(A:223:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / q_NPA : 0.019

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	225	GLN	0	-0.031	-0.002	2.392	0.901	4.177	0.788	-1.615	-2.449	-0.011
4	A	226	ASP	-1	-0.760	-0.869	4.551	-8.940	-8.769	-0.001	-0.014	-0.156	0.000
10	A	232	ILE	0	-0.065	-0.055	2.723	2.461	3.801	1.087	-0.711	-1.716	0.006
30	A	252	SER	0	0.007	-0.009	1.717	-15.811	-22.813	21.681	-9.077	-5.602	0.091
31	A	253	TRP	0	0.061	0.014	1.994	-20.646	-23.780	7.919	-0.039	-4.745	0.045
32	A	254	LYS	1	0.854	0.948	2.088	-76.101	-75.317	7.129	-3.950	-3.962	0.052
39	A	261	ALA	0	-0.007	0.005	4.302	-2.370	-2.215	-0.001	-0.010	-0.144	0.000
45	A	267	TRP	0	-0.004	-0.004	4.574	-2.736	-2.559	-0.001	-0.010	-0.166	0.000
5	A	227	ASP	-1	-0.919	-0.943	7.635	-3.598	-3.598	0.000	0.000	0.000	0.000
6	A	228	LYS	0	-0.039	-0.001	9.731	1.045	1.045	0.000	0.000	0.000	0.000
7	A	229	GLU	-1	-0.902	-0.951	9.903	-4.120	-4.120	0.000	0.000	0.000	0.000
8	A	230	PHE	0	-0.057	-0.037	9.271	0.404	0.404	0.000	0.000	0.000	0.000
9	A	231	GLY	0	0.063	0.032	6.126	-2.019	-2.019	0.000	0.000	0.000	0.000
11	A	233	GLY	0	0.018	0.018	6.328	-1.508	-1.508	0.000	0.000	0.000	0.000
12	A	234	ASP	-1	-0.754	-0.869	9.497	-0.939	-0.939	0.000	0.000	0.000	0.000
13	A	235	LEU	0	-0.022	-0.011	11.504	0.946	0.946	0.000	0.000	0.000	0.000
14	A	236	VAL	0	-0.003	0.004	12.335	-0.556	-0.556	0.000	0.000	0.000	0.000
15	A	237	TRP	0	-0.046	-0.015	15.175	0.356	0.356	0.000	0.000	0.000	0.000
16	A	238	GLY	0	0.072	0.025	16.372	-0.117	-0.117	0.000	0.000	0.000	0.000
17	A	239	LYS	1	0.883	0.948	17.221	-0.703	-0.703	0.000	0.000	0.000	0.000
18	A	240	ILE	0	0.039	0.024	18.111	0.102	0.102	0.000	0.000	0.000	0.000
19	A	241	LYS	1	0.853	0.923	20.575	-2.422	-2.422	0.000	0.000	0.000	0.000
20	A	242	GLY	0	0.047	0.044	23.688	-0.116	-0.116	0.000	0.000	0.000	0.000
21	A	243	PHE	0	-0.001	-0.016	24.047	0.063	0.063	0.000	0.000	0.000	0.000
22	A	244	SER	0	-0.018	0.003	24.046	-0.083	-0.083	0.000	0.000	0.000	0.000
23	A	245	TRP	0	0.032	0.003	18.391	0.135	0.135	0.000	0.000	0.000	0.000
24	A	246	TRP	0	-0.029	-0.021	19.615	0.006	0.006	0.000	0.000	0.000	0.000
25	A	247	PRO	0	0.039	0.027	18.474	0.042	0.042	0.000	0.000	0.000	0.000
26	A	248	ALA	0	-0.010	-0.018	13.437	0.208	0.208	0.000	0.000	0.000	0.000
27	A	249	MET	0	-0.008	0.009	10.194	-0.884	-0.884	0.000	0.000	0.000	0.000
28	A	250	VAL	0	0.026	0.022	6.310	1.339	1.339	0.000	0.000	0.000	0.000
29	A	251	VAL	0	-0.013	-0.006	6.298	-0.250	-0.250	0.000	0.000	0.000	0.000
33	A	255	ALA	0	0.012	0.016	6.060	-4.667	-4.667	0.000	0.000	0.000	0.000
34	A	256	THR	0	-0.069	-0.055	6.619	-3.572	-3.572	0.000	0.000	0.000	0.000
35	A	257	SER	0	-0.011	-0.002	9.167	-2.024	-2.024	0.000	0.000	0.000	0.000
36	A	258	LYS	1	0.903	0.961	8.955	-7.277	-7.277	0.000	0.000	0.000	0.000
37	A	259	ARG	1	0.816	0.879	8.771	-4.371	-4.371	0.000	0.000	0.000	0.000
38	A	260	GLN	0	0.053	0.007	4.916	3.801	3.801	0.000	0.000	0.000	0.000
40	A	262	MET	0	-0.009	-0.008	6.026	-2.642	-2.642	0.000	0.000	0.000	0.000
41	A	263	PRO	0	0.019	-0.004	7.597	-0.372	-0.372	0.000	0.000	0.000	0.000
42	A	264	GLY	0	0.087	0.060	8.124	1.208	1.208	0.000	0.000	0.000	0.000
43	A	265	MET	0	-0.135	-0.054	8.410	1.268	1.268	0.000	0.000	0.000	0.000
44	A	266	ARG	1	0.736	0.828	5.685	4.531	4.531	0.000	0.000	0.000	0.000
46	A	268	VAL	0	0.009	0.002	7.034	0.622	0.622	0.000	0.000	0.000	0.000
47	A	269	GLN	0	-0.050	-0.039	9.733	0.802	0.802	0.000	0.000	0.000	0.000
48	A	270	TRP	0	-0.025	-0.016	11.921	-0.676	-0.676	0.000	0.000	0.000	0.000
49	A	271	PHE	0	0.036	0.019	15.613	0.203	0.203	0.000	0.000	0.000	0.000
50	A	272	GLY	0	0.006	0.003	18.007	-0.211	-0.211	0.000	0.000	0.000	0.000
51	A	273	ASP	-1	-0.919	-0.961	18.424	2.991	2.991	0.000	0.000	0.000	0.000
52	A	274	GLY	0	0.036	0.035	16.036	0.021	0.021	0.000	0.000	0.000	0.000
53	A	275	LYS	1	0.956	0.981	14.893	-2.357	-2.357	0.000	0.000	0.000	0.000
54	A	276	PHE	0	0.059	0.030	9.888	0.222	0.222	0.000	0.000	0.000	0.000
55	A	277	SER	0	-0.063	-0.034	11.159	-1.273	-1.273	0.000	0.000	0.000	0.000
56	A	278	GLU	-1	-0.703	-0.805	9.094	5.508	5.508	0.000	0.000	0.000	0.000
57	A	279	ILE	0	-0.042	-0.028	10.458	-0.961	-0.961	0.000	0.000	0.000	0.000
58	A	280	SER	0	0.046	0.018	10.487	0.272	0.272	0.000	0.000	0.000	0.000
59	A	281	ALA	0	0.077	0.040	9.988	0.481	0.481	0.000	0.000	0.000	0.000
60	A	282	ASP	-1	-0.811	-0.900	11.789	-1.407	-1.407	0.000	0.000	0.000	0.000
61	A	283	LYS	1	0.795	0.892	14.572	-0.090	-0.090	0.000	0.000	0.000	0.000
62	A	284	LEU	0	-0.044	-0.010	10.851	0.440	0.440	0.000	0.000	0.000	0.000
63	A	285	VAL	0	0.003	0.001	14.980	-0.398	-0.398	0.000	0.000	0.000	0.000
64	A	286	ALA	0	0.093	0.042	15.939	0.337	0.337	0.000	0.000	0.000	0.000
65	A	287	LEU	0	-0.021	-0.025	16.854	-0.033	-0.033	0.000	0.000	0.000	0.000
66	A	288	GLY	0	0.055	0.005	18.831	-0.036	-0.036	0.000	0.000	0.000	0.000
67	A	289	LEU	0	-0.030	0.006	20.569	-0.079	-0.079	0.000	0.000	0.000	0.000
68	A	290	PHE	0	0.061	0.028	22.739	0.107	0.107	0.000	0.000	0.000	0.000
69	A	291	SER	0	0.051	-0.016	24.280	0.054	0.054	0.000	0.000	0.000	0.000
70	A	292	GLN	0	-0.004	0.006	25.018	0.065	0.065	0.000	0.000	0.000	0.000
71	A	293	HIS	1	0.806	0.896	22.454	-0.473	-0.473	0.000	0.000	0.000	0.000
72	A	294	PHE	0	0.049	0.026	24.736	0.100	0.100	0.000	0.000	0.000	0.000
73	A	295	ASN	0	0.026	0.020	26.424	-0.083	-0.083	0.000	0.000	0.000	0.000
74	A	296	LEU	0	0.073	0.033	29.012	0.065	0.065	0.000	0.000	0.000	0.000
75	A	297	ALA	0	0.040	0.023	32.140	0.022	0.022	0.000	0.000	0.000	0.000
76	A	298	THR	0	-0.061	-0.054	27.251	0.031	0.031	0.000	0.000	0.000	0.000
77	A	299	PHE	0	0.033	0.011	28.208	0.073	0.073	0.000	0.000	0.000	0.000
78	A	300	ASN	0	0.033	0.010	30.295	0.054	0.054	0.000	0.000	0.000	0.000
79	A	301	LYS	1	0.941	0.984	31.275	-0.884	-0.884	0.000	0.000	0.000	0.000
80	A	302	LEU	0	-0.042	-0.017	27.752	0.027	0.027	0.000	0.000	0.000	0.000
81	A	303	VAL	0	0.108	0.048	29.294	0.045	0.045	0.000	0.000	0.000	0.000
82	A	304	SER	0	0.004	-0.001	25.121	0.036	0.036	0.000	0.000	0.000	0.000
83	A	305	TYR	0	0.022	0.017	24.338	0.125	0.125	0.000	0.000	0.000	0.000
84	A	306	ARG	1	0.817	0.900	25.293	-0.948	-0.948	0.000	0.000	0.000	0.000
85	A	307	LYS	1	0.925	0.956	22.733	-2.237	-2.237	0.000	0.000	0.000	0.000
86	A	308	ALA	0	-0.016	-0.018	21.067	0.118	0.118	0.000	0.000	0.000	0.000
87	A	309	MET	0	-0.010	0.022	21.685	0.100	0.100	0.000	0.000	0.000	0.000
88	A	310	TYR	0	0.034	0.022	23.839	0.050	0.050	0.000	0.000	0.000	0.000
89	A	311	HIS	0	-0.005	-0.018	20.191	0.022	0.022	0.000	0.000	0.000	0.000
90	A	312	THR	0	-0.033	-0.028	18.950	0.195	0.195	0.000	0.000	0.000	0.000
91	A	313	LEU	0	-0.008	-0.011	20.295	-0.043	-0.043	0.000	0.000	0.000	0.000
92	A	314	GLU	-1	-0.774	-0.840	22.620	1.327	1.327	0.000	0.000	0.000	0.000
93	A	315	LYS	1	0.925	0.967	14.267	-3.943	-3.943	0.000	0.000	0.000	0.000
94	A	316	ALA	0	0.020	0.000	19.772	-0.104	-0.104	0.000	0.000	0.000	0.000
95	A	317	ARG	1	0.801	0.869	21.078	-1.395	-1.395	0.000	0.000	0.000	0.000
96	A	318	VAL	0	-0.049	-0.024	20.902	-0.111	-0.111	0.000	0.000	0.000	0.000
97	A	319	ARG	1	0.781	0.896	13.091	-2.246	-2.246	0.000	0.000	0.000	0.000
98	A	320	ALA	0	-0.008	0.000	20.775	-0.171	-0.171	0.000	0.000	0.000	0.000
99	A	321	GLY	0	0.017	0.020	23.655	-0.115	-0.115	0.000	0.000	0.000	0.000
100	A	322	LYS	1	0.812	0.932	26.107	-0.634	-0.634	0.000	0.000	0.000	0.000
101	A	323	THR	0	0.023	0.000	28.140	0.104	0.104	0.000	0.000	0.000	0.000
102	A	324	PHE	0	-0.027	-0.030	27.940	-0.065	-0.065	0.000	0.000	0.000	0.000
103	A	325	SER	0	-0.013	-0.006	31.968	0.019	0.019	0.000	0.000	0.000	0.000
104	A	326	SER	0	-0.003	0.012	31.906	-0.003	-0.003	0.000	0.000	0.000	0.000
105	A	327	SER	0	-0.020	-0.017	34.771	-0.012	-0.012	0.000	0.000	0.000	0.000
106	A	328	PRO	0	-0.007	-0.028	35.442	0.052	0.052	0.000	0.000	0.000	0.000
107	A	329	GLY	0	0.000	0.006	35.159	-0.039	-0.039	0.000	0.000	0.000	0.000
108	A	330	GLU	-1	-0.841	-0.893	34.759	0.771	0.771	0.000	0.000	0.000	0.000
109	A	331	SER	0	-0.017	-0.021	34.171	0.083	0.083	0.000	0.000	0.000	0.000
110	A	332	LEU	0	0.002	-0.011	28.075	0.035	0.035	0.000	0.000	0.000	0.000
111	A	333	GLU	-1	-0.838	-0.924	31.319	1.034	1.034	0.000	0.000	0.000	0.000
112	A	334	ASP	-1	-0.834	-0.891	33.500	0.692	0.692	0.000	0.000	0.000	0.000
113	A	335	GLN	0	0.038	0.005	30.814	0.014	0.014	0.000	0.000	0.000	0.000
114	A	336	LEU	0	-0.049	-0.037	27.040	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	337	LYS	1	0.877	0.951	30.734	-0.541	-0.541	0.000	0.000	0.000	0.000
116	A	338	PRO	0	0.055	0.028	32.806	-0.033	-0.033	0.000	0.000	0.000	0.000
117	A	339	MET	0	-0.032	-0.013	26.183	-0.017	-0.017	0.000	0.000	0.000	0.000
118	A	340	LEU	0	-0.013	-0.016	27.865	-0.006	-0.006	0.000	0.000	0.000	0.000
119	A	341	GLU	-1	-0.870	-0.919	30.074	0.445	0.445	0.000	0.000	0.000	0.000
120	A	342	TRP	0	-0.048	-0.020	24.128	-0.023	-0.023	0.000	0.000	0.000	0.000
121	A	343	ALA	0	-0.009	-0.008	25.925	-0.058	-0.058	0.000	0.000	0.000	0.000
122	A	344	HIS	0	-0.007	0.003	27.475	-0.105	-0.105	0.000	0.000	0.000	0.000
123	A	345	GLY	0	0.015	0.031	29.862	-0.065	-0.065	0.000	0.000	0.000	0.000
124	A	346	GLY	0	-0.016	-0.016	27.384	-0.072	-0.072	0.000	0.000	0.000	0.000
125	A	347	PHE	0	-0.006	-0.019	23.528	-0.061	-0.061	0.000	0.000	0.000	0.000
126	A	348	LYS	1	0.915	1.000	26.996	-0.067	-0.067	0.000	0.000	0.000	0.000
127	A	349	PRO	0	0.022	-0.010	29.553	0.075	0.075	0.000	0.000	0.000	0.000
128	A	350	THR	0	0.007	0.001	24.477	-0.038	-0.038	0.000	0.000	0.000	0.000
129	A	351	GLY	0	0.013	0.020	25.190	-0.107	-0.107	0.000	0.000	0.000	0.000
130	A	352	ILE	0	-0.005	-0.018	20.415	0.133	0.133	0.000	0.000	0.000	0.000
131	A	353	GLU	-1	-0.816	-0.906	19.888	-0.454	-0.454	0.000	0.000	0.000	0.000
132	A	354	GLY	0	0.013	0.012	19.698	0.015	0.015	0.000	0.000	0.000	0.000
133	A	355	LEU	0	-0.051	-0.029	18.074	0.207	0.207	0.000	0.000	0.000	0.000
134	A	356	LYS	1	0.821	0.916	15.235	1.180	1.180	0.000	0.000	0.000	0.000
135	A	357	PRO	-1	-0.907	-0.945	11.114	1.089	1.089	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:223:GLU)