FMO DATABASE

FMODB ID: 82G1Y

Calculation Name: 1T38-A-Xray372

Preferred Name: 6-O-methylguanine-DNA methyltransferase

Target Type: SINGLE PROTEIN

Ligand Name: 6-o-methyl guanosine-5'-monophosphate

ligand 3-letter code: 6OG

PDB ID: 1T38

Chain ID: A

ChEMBL ID: CHEMBL2864

UniProt ID: P16455

Base Structure: X-ray

Registration Date: 2023-03-13

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	151
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1403164.824759
FMO2-HF: Nuclear repulsion	1345049.950293
FMO2-HF: Total energy	-58114.874465
FMO2-MP2: Total energy	-58284.213031

3D Structure

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:6:GLU)

Summations of interaction energy for fragment #1(A:6: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.
-145.954	-148.594	28.084	-13.875	-11.569	0.157

Interaction energy analysis for fragmet #1(A:6:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.815 / q_NPA : -0.900

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	8	LYS	1	0.861	0.928	1.771	-139.003	-143.181	27.134	-13.036	-9.920	0.152
4	A	9	ARG	1	0.744	0.839	6.119	-30.532	-30.532	0.000	0.000	0.000	0.000
5	A	10	THR	0	0.050	0.037	9.668	1.037	1.037	0.000	0.000	0.000	0.000
6	A	11	THR	0	-0.029	0.002	12.692	-0.933	-0.933	0.000	0.000	0.000	0.000
7	A	12	LEU	0	0.017	0.014	16.294	0.285	0.285	0.000	0.000	0.000	0.000
8	A	13	ASP	-1	-0.817	-0.888	19.500	13.640	13.640	0.000	0.000	0.000	0.000
9	A	14	SER	0	0.016	0.001	23.099	-0.157	-0.157	0.000	0.000	0.000	0.000
10	A	15	PRO	0	0.030	0.020	25.568	-0.084	-0.084	0.000	0.000	0.000	0.000
11	A	16	LEU	0	-0.012	0.001	25.472	-0.274	-0.274	0.000	0.000	0.000	0.000
12	A	17	GLY	0	-0.011	0.005	25.411	-0.020	-0.020	0.000	0.000	0.000	0.000
13	A	18	LYS	1	0.802	0.866	20.175	-13.884	-13.884	0.000	0.000	0.000	0.000
14	A	19	LEU	0	0.036	0.027	19.441	0.153	0.153	0.000	0.000	0.000	0.000
15	A	20	GLU	-1	-0.788	-0.882	13.284	22.922	22.922	0.000	0.000	0.000	0.000
16	A	21	LEU	0	-0.015	-0.010	13.521	-0.134	-0.134	0.000	0.000	0.000	0.000
17	A	22	SER	0	0.011	0.000	9.268	2.089	2.089	0.000	0.000	0.000	0.000
18	A	23	GLY	0	0.024	-0.018	7.562	-2.543	-2.543	0.000	0.000	0.000	0.000
19	A	24	CYS	0	-0.026	0.017	2.321	-1.155	-0.023	0.951	-0.809	-1.274	0.005
20	A	25	GLU	-1	-0.903	-0.979	3.853	32.103	32.509	-0.001	-0.030	-0.375	0.000
21	A	26	GLN	0	-0.029	-0.016	4.889	-0.274	-0.274	0.000	0.000	0.000	0.000
22	A	27	GLY	0	0.019	-0.005	7.047	-2.563	-2.563	0.000	0.000	0.000	0.000
23	A	28	LEU	0	-0.059	-0.046	8.219	2.372	2.372	0.000	0.000	0.000	0.000
24	A	29	HIS	0	-0.005	-0.015	8.386	-0.251	-0.251	0.000	0.000	0.000	0.000
25	A	30	GLU	-1	-0.883	-0.956	10.465	19.493	19.493	0.000	0.000	0.000	0.000
26	A	31	ILE	0	-0.029	0.003	13.607	1.072	1.072	0.000	0.000	0.000	0.000
27	A	32	LYS	1	0.900	0.943	15.295	-20.163	-20.163	0.000	0.000	0.000	0.000
28	A	33	LEU	0	0.012	-0.006	17.883	0.198	0.198	0.000	0.000	0.000	0.000
29	A	34	LEU	0	-0.041	-0.012	17.058	-0.141	-0.141	0.000	0.000	0.000	0.000
30	A	35	GLY	0	-0.033	-0.006	21.228	-0.648	-0.648	0.000	0.000	0.000	0.000
31	A	56	PRO	0	0.010	0.003	6.603	-0.420	-0.420	0.000	0.000	0.000	0.000
32	A	57	GLU	-1	-0.837	-0.943	9.195	17.607	17.607	0.000	0.000	0.000	0.000
33	A	58	PRO	0	0.007	0.024	8.777	-1.431	-1.431	0.000	0.000	0.000	0.000
34	A	59	LEU	0	0.030	0.012	9.159	-1.481	-1.481	0.000	0.000	0.000	0.000
35	A	60	MET	0	0.000	0.024	12.404	-1.592	-1.592	0.000	0.000	0.000	0.000
36	A	61	GLN	0	-0.006	0.010	14.104	-1.926	-1.926	0.000	0.000	0.000	0.000
37	A	62	CYS	0	0.011	0.005	14.849	-1.293	-1.293	0.000	0.000	0.000	0.000
38	A	63	THR	0	-0.096	-0.068	15.302	-0.784	-0.784	0.000	0.000	0.000	0.000
39	A	64	ALA	0	-0.007	-0.001	17.864	-0.573	-0.573	0.000	0.000	0.000	0.000
40	A	65	TRP	0	0.050	0.027	19.648	-0.571	-0.571	0.000	0.000	0.000	0.000
41	A	66	LEU	0	0.007	0.000	18.874	-0.659	-0.659	0.000	0.000	0.000	0.000
42	A	67	ASN	0	-0.037	-0.022	21.846	-0.301	-0.301	0.000	0.000	0.000	0.000
43	A	68	ALA	0	0.034	0.033	23.781	-0.482	-0.482	0.000	0.000	0.000	0.000
44	A	69	TYR	0	-0.052	-0.065	24.871	-0.447	-0.447	0.000	0.000	0.000	0.000
45	A	70	PHE	0	-0.032	-0.035	23.451	-0.361	-0.361	0.000	0.000	0.000	0.000
46	A	71	HIS	0	-0.022	-0.023	26.287	-0.699	-0.699	0.000	0.000	0.000	0.000
47	A	72	GLN	0	-0.021	0.000	28.954	-0.196	-0.196	0.000	0.000	0.000	0.000
48	A	73	PRO	0	-0.002	0.010	29.613	0.168	0.168	0.000	0.000	0.000	0.000
49	A	74	GLU	-1	-0.952	-0.978	30.649	8.765	8.765	0.000	0.000	0.000	0.000
50	A	75	ALA	0	-0.016	0.000	30.810	-0.177	-0.177	0.000	0.000	0.000	0.000
51	A	76	ILE	0	0.013	0.003	24.537	0.336	0.336	0.000	0.000	0.000	0.000
52	A	77	GLU	-1	-0.860	-0.924	26.035	10.639	10.639	0.000	0.000	0.000	0.000
53	A	78	GLU	-1	-0.978	-0.972	26.792	10.509	10.509	0.000	0.000	0.000	0.000
54	A	79	PHE	0	-0.025	-0.007	22.323	0.482	0.482	0.000	0.000	0.000	0.000
55	A	80	PRO	0	-0.004	0.006	19.068	-0.212	-0.212	0.000	0.000	0.000	0.000
56	A	81	VAL	0	-0.011	-0.015	18.606	0.543	0.543	0.000	0.000	0.000	0.000
57	A	82	PRO	0	0.001	0.000	13.786	0.185	0.185	0.000	0.000	0.000	0.000
58	A	83	ALA	0	0.037	0.034	11.841	-0.577	-0.577	0.000	0.000	0.000	0.000
59	A	84	LEU	0	-0.007	0.003	12.209	1.294	1.294	0.000	0.000	0.000	0.000
60	A	85	HIS	0	0.012	0.006	5.999	-2.258	-2.258	0.000	0.000	0.000	0.000
61	A	86	HIS	0	0.046	0.025	10.499	-0.555	-0.555	0.000	0.000	0.000	0.000
62	A	87	PRO	0	0.006	-0.001	10.956	-0.983	-0.983	0.000	0.000	0.000	0.000
63	A	88	VAL	0	-0.020	-0.004	13.428	-1.083	-1.083	0.000	0.000	0.000	0.000
64	A	89	PHE	0	0.003	-0.014	14.134	-1.130	-1.130	0.000	0.000	0.000	0.000
65	A	90	GLN	0	-0.041	-0.002	10.204	-1.123	-1.123	0.000	0.000	0.000	0.000
66	A	91	GLN	0	-0.019	-0.008	15.836	-1.051	-1.051	0.000	0.000	0.000	0.000
67	A	92	GLU	-1	-0.791	-0.875	18.862	11.628	11.628	0.000	0.000	0.000	0.000
68	A	93	SER	0	-0.022	-0.018	21.865	-0.249	-0.249	0.000	0.000	0.000	0.000
69	A	94	PHE	0	0.017	0.008	24.372	-0.106	-0.106	0.000	0.000	0.000	0.000
70	A	95	THR	0	0.034	0.008	21.808	-0.241	-0.241	0.000	0.000	0.000	0.000
71	A	96	ARG	1	0.849	0.924	18.621	-13.086	-13.086	0.000	0.000	0.000	0.000
72	A	97	GLN	0	0.026	0.022	22.124	-0.109	-0.109	0.000	0.000	0.000	0.000
73	A	98	VAL	0	-0.002	-0.013	25.372	-0.128	-0.128	0.000	0.000	0.000	0.000
74	A	99	LEU	0	0.010	-0.004	19.929	-0.118	-0.118	0.000	0.000	0.000	0.000
75	A	100	TRP	0	0.009	0.011	18.410	-0.138	-0.138	0.000	0.000	0.000	0.000
76	A	101	LYS	1	0.869	0.924	23.566	-9.592	-9.592	0.000	0.000	0.000	0.000
77	A	102	LEU	0	-0.036	-0.017	25.043	-0.369	-0.369	0.000	0.000	0.000	0.000
78	A	103	LEU	0	0.019	0.004	20.573	-0.157	-0.157	0.000	0.000	0.000	0.000
79	A	104	LYS	1	0.904	0.966	24.816	-10.130	-10.130	0.000	0.000	0.000	0.000
80	A	105	VAL	0	-0.066	-0.045	26.736	-0.187	-0.187	0.000	0.000	0.000	0.000
81	A	106	VAL	0	-0.002	0.018	28.701	-0.181	-0.181	0.000	0.000	0.000	0.000
82	A	107	LYS	1	0.849	0.884	27.438	-9.846	-9.846	0.000	0.000	0.000	0.000
83	A	108	PHE	0	0.017	-0.008	29.373	-0.182	-0.182	0.000	0.000	0.000	0.000
84	A	109	GLY	0	0.072	0.046	31.382	-0.221	-0.221	0.000	0.000	0.000	0.000
85	A	110	GLU	-1	-0.909	-0.928	33.255	8.526	8.526	0.000	0.000	0.000	0.000
86	A	111	VAL	0	-0.024	-0.032	33.577	0.223	0.223	0.000	0.000	0.000	0.000
87	A	112	ILE	0	-0.042	-0.010	31.710	-0.236	-0.236	0.000	0.000	0.000	0.000
88	A	113	SER	0	0.009	-0.013	33.983	0.158	0.158	0.000	0.000	0.000	0.000
89	A	114	TYR	0	0.044	-0.001	31.128	0.000	0.000	0.000	0.000	0.000	0.000
90	A	115	GLN	0	0.001	-0.016	34.179	0.064	0.064	0.000	0.000	0.000	0.000
91	A	116	GLN	0	0.030	0.038	36.554	0.066	0.066	0.000	0.000	0.000	0.000
92	A	117	LEU	0	0.033	0.027	28.714	0.027	0.027	0.000	0.000	0.000	0.000
93	A	118	ALA	0	-0.034	-0.007	31.893	0.196	0.196	0.000	0.000	0.000	0.000
94	A	119	ALA	0	-0.021	-0.030	33.637	0.045	0.045	0.000	0.000	0.000	0.000
95	A	120	LEU	0	-0.029	0.015	31.722	-0.015	-0.015	0.000	0.000	0.000	0.000
96	A	121	ALA	0	-0.009	-0.003	29.007	0.071	0.071	0.000	0.000	0.000	0.000
97	A	122	GLY	0	0.045	0.012	30.585	0.121	0.121	0.000	0.000	0.000	0.000
98	A	123	ASN	0	0.003	0.007	33.328	-0.424	-0.424	0.000	0.000	0.000	0.000
99	A	124	PRO	0	0.076	0.027	35.118	0.125	0.125	0.000	0.000	0.000	0.000
100	A	125	LYS	1	0.948	0.973	37.495	-7.196	-7.196	0.000	0.000	0.000	0.000
101	A	126	ALA	0	-0.063	-0.013	33.021	-0.030	-0.030	0.000	0.000	0.000	0.000
102	A	127	ALA	0	0.092	0.032	33.084	0.257	0.257	0.000	0.000	0.000	0.000
103	A	128	ARG	1	0.959	0.975	33.159	-7.914	-7.914	0.000	0.000	0.000	0.000
104	A	129	ALA	0	0.007	0.005	30.166	0.172	0.172	0.000	0.000	0.000	0.000
105	A	130	VAL	0	0.051	0.030	28.846	0.378	0.378	0.000	0.000	0.000	0.000
106	A	131	GLY	0	-0.011	0.005	28.420	0.295	0.295	0.000	0.000	0.000	0.000
107	A	132	GLY	0	-0.004	-0.010	27.308	0.274	0.274	0.000	0.000	0.000	0.000
108	A	133	ALA	0	0.014	0.022	24.727	0.472	0.472	0.000	0.000	0.000	0.000
109	A	134	MET	0	0.020	0.006	23.731	0.535	0.535	0.000	0.000	0.000	0.000
110	A	135	ARG	1	0.836	0.922	24.464	-11.000	-11.000	0.000	0.000	0.000	0.000
111	A	136	GLY	0	0.001	-0.021	21.706	0.317	0.317	0.000	0.000	0.000	0.000
112	A	137	ASN	0	0.011	0.009	19.922	1.248	1.248	0.000	0.000	0.000	0.000
113	A	138	PRO	0	0.010	0.023	15.437	-0.148	-0.148	0.000	0.000	0.000	0.000
114	A	139	VAL	0	0.010	-0.006	15.537	1.056	1.056	0.000	0.000	0.000	0.000
115	A	140	PRO	0	0.021	0.023	18.304	-0.654	-0.654	0.000	0.000	0.000	0.000
116	A	141	ILE	0	-0.014	0.002	21.135	0.410	0.410	0.000	0.000	0.000	0.000
117	A	142	LEU	0	0.024	0.001	17.337	-0.328	-0.328	0.000	0.000	0.000	0.000
118	A	143	ILE	0	-0.022	0.009	19.250	-0.529	-0.529	0.000	0.000	0.000	0.000
119	A	144	PRO	0	-0.012	-0.008	22.395	0.046	0.046	0.000	0.000	0.000	0.000
120	A	145	SER	0	0.032	-0.009	24.296	-0.216	-0.216	0.000	0.000	0.000	0.000
121	A	146	HIS	0	-0.097	-0.061	26.593	-0.109	-0.109	0.000	0.000	0.000	0.000
122	A	147	ARG	1	0.857	0.915	27.436	-10.680	-10.680	0.000	0.000	0.000	0.000
123	A	148	VAL	0	-0.011	0.013	29.280	-0.309	-0.309	0.000	0.000	0.000	0.000
124	A	149	VAL	0	-0.007	0.010	32.016	0.095	0.095	0.000	0.000	0.000	0.000
125	A	150	CYS	0	-0.069	-0.039	35.288	0.013	0.013	0.000	0.000	0.000	0.000
126	A	151	SER	0	0.072	0.012	38.094	0.003	0.003	0.000	0.000	0.000	0.000
127	A	152	SER	0	-0.069	-0.020	40.486	-0.043	-0.043	0.000	0.000	0.000	0.000
128	A	153	GLY	0	0.047	0.034	41.484	-0.158	-0.158	0.000	0.000	0.000	0.000
129	A	154	ALA	0	-0.029	-0.011	40.802	0.106	0.106	0.000	0.000	0.000	0.000
130	A	155	VAL	0	0.147	0.067	35.526	0.123	0.123	0.000	0.000	0.000	0.000
131	A	156	GLY	0	0.047	0.015	35.499	0.255	0.255	0.000	0.000	0.000	0.000
132	A	157	ASN	0	0.001	-0.006	33.121	0.228	0.228	0.000	0.000	0.000	0.000
133	A	158	TYR	0	0.039	-0.001	25.478	0.081	0.081	0.000	0.000	0.000	0.000
134	A	159	SER	0	0.006	-0.001	24.156	-0.089	-0.089	0.000	0.000	0.000	0.000
135	A	160	GLY	0	0.000	0.016	25.445	-0.045	-0.045	0.000	0.000	0.000	0.000
136	A	161	GLY	0	0.015	0.009	26.007	-0.028	-0.028	0.000	0.000	0.000	0.000
137	A	162	LEU	0	-0.046	-0.040	29.716	0.108	0.108	0.000	0.000	0.000	0.000
138	A	163	ALA	0	0.068	0.047	32.191	-0.101	-0.101	0.000	0.000	0.000	0.000
139	A	164	VAL	0	0.031	0.017	26.792	-0.095	-0.095	0.000	0.000	0.000	0.000
140	A	165	LYS	1	0.774	0.890	30.240	-9.457	-9.457	0.000	0.000	0.000	0.000
141	A	166	GLU	-1	-0.936	-0.966	31.253	8.307	8.307	0.000	0.000	0.000	0.000
142	A	167	TRP	0	0.022	0.005	29.774	0.017	0.017	0.000	0.000	0.000	0.000
143	A	168	LEU	0	-0.005	-0.014	27.134	0.000	0.000	0.000	0.000	0.000	0.000
144	A	169	LEU	0	0.025	0.016	31.443	-0.092	-0.092	0.000	0.000	0.000	0.000
145	A	170	ALA	0	-0.031	-0.007	34.183	-0.195	-0.195	0.000	0.000	0.000	0.000
146	A	171	HIS	0	-0.027	-0.013	30.117	-0.315	-0.315	0.000	0.000	0.000	0.000
147	A	172	GLU	-1	-0.770	-0.799	29.756	10.138	10.138	0.000	0.000	0.000	0.000
148	A	173	GLY	0	0.033	0.003	34.265	-0.159	-0.159	0.000	0.000	0.000	0.000
149	A	174	HIS	0	-0.083	-0.030	36.099	-0.396	-0.396	0.000	0.000	0.000	0.000
150	A	175	ARG	1	0.926	0.958	39.065	-6.859	-6.859	0.000	0.000	0.000	0.000
151	A	176	LEU	0	0.002	0.002	37.990	-0.046	-0.046	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:6:GLU)