FMO DATABASE

FMODB ID: YY922

Calculation Name: 1T39-A-Xray372

Preferred Name: 6-O-methylguanine-DNA methyltransferase

Target Type: SINGLE PROTEIN

Ligand Name: phosphoric acid mono-[5-(1-ethyl-2,6-dioxo-1,2,3,6-tetrahydro-purin-9-yl)-3-hydroxy-tetrahydro-furan-2-ylmethyl]ester

ligand 3-letter code: E1X

PDB ID: 1T39

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	OptH
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
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1408041.817789
FMO2-HF: Nuclear repulsion	1349325.384527
FMO2-HF: Total energy	-58716.433262
FMO2-MP2: Total energy	-58885.685123

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:5:CYS)

Summations of interaction energy for fragment #1(A:5:CYS)

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.
-4.078	-30.785	61.213	-18.5	-16.004	0.065

Interaction energy analysis for fragmet #1(A:5:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.036 / 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	7	MET	0	-0.095	-0.041	2.878	2.501	3.102	4.419	-1.415	-3.605	0.006
4	A	8	LYS	1	0.969	1.002	5.546	-0.478	-0.478	0.000	0.000	0.000	0.000
5	A	9	ARG	1	0.940	0.953	8.621	-0.004	-0.004	0.000	0.000	0.000	0.000
6	A	10	THR	0	0.037	0.039	11.971	-0.155	-0.155	0.000	0.000	0.000	0.000
7	A	11	THR	0	-0.012	-0.014	14.115	0.051	0.051	0.000	0.000	0.000	0.000
8	A	12	LEU	0	0.023	0.004	17.515	0.004	0.004	0.000	0.000	0.000	0.000
9	A	13	ASP	-1	-0.938	-0.967	20.115	0.241	0.241	0.000	0.000	0.000	0.000
10	A	14	SER	0	0.068	0.047	23.335	0.015	0.015	0.000	0.000	0.000	0.000
11	A	15	PRO	0	0.028	0.013	25.242	-0.016	-0.016	0.000	0.000	0.000	0.000
12	A	16	LEU	0	-0.030	-0.017	25.323	-0.015	-0.015	0.000	0.000	0.000	0.000
13	A	17	GLY	0	-0.010	0.010	26.605	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	18	LYS	1	0.888	0.927	22.043	-0.225	-0.225	0.000	0.000	0.000	0.000
15	A	19	LEU	0	-0.031	-0.026	19.482	-0.001	-0.001	0.000	0.000	0.000	0.000
16	A	20	GLU	-1	-0.939	-0.971	14.845	0.498	0.498	0.000	0.000	0.000	0.000
17	A	21	LEU	0	0.022	0.015	13.468	0.042	0.042	0.000	0.000	0.000	0.000
18	A	22	SER	0	-0.006	0.007	9.713	0.104	0.104	0.000	0.000	0.000	0.000
19	A	23	GLY	0	0.054	0.001	7.041	0.110	0.110	0.000	0.000	0.000	0.000
20	A	24	CYS	0	-0.145	-0.014	1.728	4.248	-26.709	55.115	-15.244	-8.913	0.060
21	A	25	GLU	-1	-0.893	-0.949	2.506	-0.266	1.306	0.454	-0.935	-1.090	-0.001
22	A	26	GLN	0	0.053	0.004	2.643	-1.786	-0.440	0.212	-0.548	-1.010	0.000
23	A	27	GLY	0	0.003	-0.055	4.646	-1.016	-0.974	-0.001	-0.015	-0.026	0.000
24	A	28	LEU	0	-0.039	-0.020	6.603	0.834	0.834	0.000	0.000	0.000	0.000
25	A	29	HIS	0	-0.007	-0.023	6.495	0.784	0.784	0.000	0.000	0.000	0.000
26	A	30	GLU	-1	-0.969	-1.000	8.938	0.487	0.487	0.000	0.000	0.000	0.000
27	A	31	ILE	0	0.014	0.004	12.457	0.072	0.072	0.000	0.000	0.000	0.000
28	A	32	LYS	1	0.974	1.012	15.719	-0.458	-0.458	0.000	0.000	0.000	0.000
29	A	33	LEU	0	0.034	0.009	18.314	-0.023	-0.023	0.000	0.000	0.000	0.000
30	A	34	LEU	0	-0.134	-0.049	19.959	-0.035	-0.035	0.000	0.000	0.000	0.000
31	A	35	GLY	0	0.064	0.039	22.751	-0.006	-0.006	0.000	0.000	0.000	0.000
32	A	56	PRO	0	0.029	-0.001	7.285	0.061	0.061	0.000	0.000	0.000	0.000
33	A	57	GLU	-1	-0.935	-0.969	8.316	0.975	0.975	0.000	0.000	0.000	0.000
34	A	58	PRO	0	0.032	0.020	6.753	-0.186	-0.186	0.000	0.000	0.000	0.000
35	A	59	LEU	0	0.027	0.029	7.864	-0.239	-0.239	0.000	0.000	0.000	0.000
36	A	60	MET	0	0.003	0.023	10.907	-0.212	-0.212	0.000	0.000	0.000	0.000
37	A	61	GLN	0	0.049	0.035	12.651	0.042	0.042	0.000	0.000	0.000	0.000
38	A	62	CYS	0	-0.062	-0.034	13.307	-0.138	-0.138	0.000	0.000	0.000	0.000
39	A	63	THR	0	-0.030	-0.050	14.585	-0.120	-0.120	0.000	0.000	0.000	0.000
40	A	64	ALA	0	-0.010	0.005	16.821	-0.076	-0.076	0.000	0.000	0.000	0.000
41	A	65	TRP	0	0.067	0.044	18.278	-0.037	-0.037	0.000	0.000	0.000	0.000
42	A	66	LEU	0	0.005	0.000	17.678	-0.054	-0.054	0.000	0.000	0.000	0.000
43	A	67	ASN	0	-0.007	-0.015	20.785	-0.065	-0.065	0.000	0.000	0.000	0.000
44	A	68	ALA	0	0.014	0.023	22.565	-0.038	-0.038	0.000	0.000	0.000	0.000
45	A	69	TYR	0	-0.055	-0.054	23.522	-0.028	-0.028	0.000	0.000	0.000	0.000
46	A	70	PHE	0	-0.044	-0.043	22.918	-0.027	-0.027	0.000	0.000	0.000	0.000
47	A	71	HIS	0	-0.032	-0.022	26.134	-0.031	-0.031	0.000	0.000	0.000	0.000
48	A	72	GLN	0	-0.011	0.004	27.218	-0.017	-0.017	0.000	0.000	0.000	0.000
49	A	73	PRO	0	0.000	0.012	28.044	0.014	0.014	0.000	0.000	0.000	0.000
50	A	74	GLU	-1	-0.971	-0.996	29.062	0.235	0.235	0.000	0.000	0.000	0.000
51	A	75	ALA	0	0.026	0.017	28.968	-0.011	-0.011	0.000	0.000	0.000	0.000
52	A	76	ILE	0	0.009	0.013	22.985	0.018	0.018	0.000	0.000	0.000	0.000
53	A	77	GLU	-1	-0.989	-1.003	23.963	0.374	0.374	0.000	0.000	0.000	0.000
54	A	78	GLU	-1	-1.007	-0.989	24.722	0.283	0.283	0.000	0.000	0.000	0.000
55	A	79	PHE	0	-0.049	-0.023	20.780	0.018	0.018	0.000	0.000	0.000	0.000
56	A	80	PRO	0	-0.040	-0.005	17.468	0.017	0.017	0.000	0.000	0.000	0.000
57	A	81	VAL	0	0.009	-0.008	16.383	0.039	0.039	0.000	0.000	0.000	0.000
58	A	82	PRO	0	0.002	0.008	11.777	0.016	0.016	0.000	0.000	0.000	0.000
59	A	83	ALA	0	0.014	0.018	9.267	-0.065	-0.065	0.000	0.000	0.000	0.000
60	A	84	LEU	0	0.019	0.013	10.154	0.329	0.329	0.000	0.000	0.000	0.000
61	A	85	HIS	1	0.833	0.949	3.348	-8.838	-8.149	1.014	-0.343	-1.360	0.000
62	A	86	HIS	0	0.137	0.061	7.458	0.317	0.317	0.000	0.000	0.000	0.000
63	A	87	PRO	0	-0.018	-0.021	8.378	-0.225	-0.225	0.000	0.000	0.000	0.000
64	A	88	VAL	0	-0.037	-0.017	10.848	-0.199	-0.199	0.000	0.000	0.000	0.000
65	A	89	PHE	0	0.004	-0.010	11.722	-0.192	-0.192	0.000	0.000	0.000	0.000
66	A	90	GLN	0	-0.061	-0.023	7.160	0.556	0.556	0.000	0.000	0.000	0.000
67	A	91	GLN	0	0.025	0.034	12.002	-0.135	-0.135	0.000	0.000	0.000	0.000
68	A	92	GLU	-1	-0.880	-0.947	15.293	0.477	0.477	0.000	0.000	0.000	0.000
69	A	93	SER	0	0.011	-0.007	18.860	-0.053	-0.053	0.000	0.000	0.000	0.000
70	A	94	PHE	0	0.055	0.015	20.914	0.005	0.005	0.000	0.000	0.000	0.000
71	A	95	THR	0	0.009	-0.020	19.028	-0.013	-0.013	0.000	0.000	0.000	0.000
72	A	96	ARG	1	0.906	0.984	15.593	-0.666	-0.666	0.000	0.000	0.000	0.000
73	A	97	GLN	0	0.059	0.036	19.394	0.058	0.058	0.000	0.000	0.000	0.000
74	A	98	VAL	0	-0.006	-0.002	22.431	0.005	0.005	0.000	0.000	0.000	0.000
75	A	99	LEU	0	0.019	0.017	17.580	-0.013	-0.013	0.000	0.000	0.000	0.000
76	A	100	TRP	0	0.029	-0.001	14.670	0.006	0.006	0.000	0.000	0.000	0.000
77	A	101	LYS	1	0.886	0.934	20.575	-0.366	-0.366	0.000	0.000	0.000	0.000
78	A	102	LEU	0	-0.005	-0.017	23.167	-0.030	-0.030	0.000	0.000	0.000	0.000
79	A	103	LEU	0	0.033	0.024	18.819	-0.016	-0.016	0.000	0.000	0.000	0.000
80	A	104	LYS	1	0.894	0.962	19.544	-0.587	-0.587	0.000	0.000	0.000	0.000
81	A	105	VAL	0	-0.078	-0.043	24.643	-0.029	-0.029	0.000	0.000	0.000	0.000
82	A	106	VAL	0	-0.014	0.016	27.080	-0.026	-0.026	0.000	0.000	0.000	0.000
83	A	107	LYS	1	0.984	0.997	27.112	-0.259	-0.259	0.000	0.000	0.000	0.000
84	A	108	PHE	0	0.012	-0.018	28.068	0.003	0.003	0.000	0.000	0.000	0.000
85	A	109	GLY	0	0.061	0.046	29.319	-0.017	-0.017	0.000	0.000	0.000	0.000
86	A	110	GLU	-1	-0.933	-0.968	31.464	0.258	0.258	0.000	0.000	0.000	0.000
87	A	111	VAL	0	0.018	0.002	31.727	0.015	0.015	0.000	0.000	0.000	0.000
88	A	112	ILE	0	-0.030	-0.013	29.616	-0.009	-0.009	0.000	0.000	0.000	0.000
89	A	113	SER	0	0.019	0.018	32.152	0.010	0.010	0.000	0.000	0.000	0.000
90	A	114	TYR	0	0.012	-0.006	29.604	0.008	0.008	0.000	0.000	0.000	0.000
91	A	115	GLN	0	-0.016	-0.024	31.133	0.015	0.015	0.000	0.000	0.000	0.000
92	A	116	GLN	0	0.073	0.026	33.002	0.000	0.000	0.000	0.000	0.000	0.000
93	A	117	LEU	0	0.001	0.009	25.636	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	118	ALA	0	0.005	-0.009	29.387	0.010	0.010	0.000	0.000	0.000	0.000
95	A	119	ALA	0	-0.028	-0.001	30.394	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	120	LEU	0	0.006	0.017	28.754	0.002	0.002	0.000	0.000	0.000	0.000
97	A	121	ALA	0	-0.098	-0.043	26.289	0.009	0.009	0.000	0.000	0.000	0.000
98	A	122	GLY	0	0.006	0.003	27.725	0.004	0.004	0.000	0.000	0.000	0.000
99	A	123	ASN	0	-0.001	-0.017	30.211	-0.024	-0.024	0.000	0.000	0.000	0.000
100	A	124	PRO	0	0.095	0.053	31.687	0.009	0.009	0.000	0.000	0.000	0.000
101	A	125	LYS	1	0.901	0.954	34.274	-0.144	-0.144	0.000	0.000	0.000	0.000
102	A	126	ALA	0	-0.018	-0.011	30.607	-0.006	-0.006	0.000	0.000	0.000	0.000
103	A	127	ALA	0	0.099	0.048	30.596	0.017	0.017	0.000	0.000	0.000	0.000
104	A	128	ARG	1	0.973	0.978	30.398	-0.157	-0.157	0.000	0.000	0.000	0.000
105	A	129	ALA	0	-0.002	0.006	27.440	0.007	0.007	0.000	0.000	0.000	0.000
106	A	130	VAL	0	0.050	0.023	26.366	0.025	0.025	0.000	0.000	0.000	0.000
107	A	131	GLY	0	0.041	0.025	26.322	0.019	0.019	0.000	0.000	0.000	0.000
108	A	132	GLY	0	-0.067	-0.043	25.311	0.020	0.020	0.000	0.000	0.000	0.000
109	A	133	ALA	0	-0.021	-0.007	22.308	0.030	0.030	0.000	0.000	0.000	0.000
110	A	134	MET	0	0.010	0.005	21.486	0.051	0.051	0.000	0.000	0.000	0.000
111	A	135	ARG	1	0.919	0.974	22.211	-0.272	-0.272	0.000	0.000	0.000	0.000
112	A	136	GLY	0	-0.036	-0.013	19.375	0.017	0.017	0.000	0.000	0.000	0.000
113	A	137	ASN	0	-0.005	-0.025	17.581	0.152	0.152	0.000	0.000	0.000	0.000
114	A	138	PRO	0	-0.027	0.009	13.647	-0.049	-0.049	0.000	0.000	0.000	0.000
115	A	139	VAL	0	0.038	-0.011	13.904	0.031	0.031	0.000	0.000	0.000	0.000
116	A	140	PRO	0	0.043	0.034	16.572	-0.058	-0.058	0.000	0.000	0.000	0.000
117	A	141	ILE	0	-0.014	0.004	19.792	0.031	0.031	0.000	0.000	0.000	0.000
118	A	142	LEU	0	-0.004	-0.009	15.647	-0.008	-0.008	0.000	0.000	0.000	0.000
119	A	143	ILE	0	-0.045	-0.010	17.469	-0.035	-0.035	0.000	0.000	0.000	0.000
120	A	144	PRO	0	0.026	0.009	20.723	-0.003	-0.003	0.000	0.000	0.000	0.000
121	A	145	CYS	0	-0.054	-0.026	23.241	-0.023	-0.023	0.000	0.000	0.000	0.000
122	A	146	HIS	0	-0.052	-0.068	24.860	-0.012	-0.012	0.000	0.000	0.000	0.000
123	A	147	ARG	1	0.853	0.927	26.492	-0.380	-0.380	0.000	0.000	0.000	0.000
124	A	148	VAL	0	-0.014	0.003	27.176	-0.022	-0.022	0.000	0.000	0.000	0.000
125	A	149	VAL	0	0.005	-0.005	30.024	-0.006	-0.006	0.000	0.000	0.000	0.000
126	A	150	CYS	0	-0.055	-0.034	33.391	0.000	0.000	0.000	0.000	0.000	0.000
127	A	151	SER	0	0.064	0.018	35.696	0.002	0.002	0.000	0.000	0.000	0.000
128	A	152	SER	0	-0.054	-0.018	38.283	-0.002	-0.002	0.000	0.000	0.000	0.000
129	A	153	GLY	0	0.049	0.037	39.504	-0.008	-0.008	0.000	0.000	0.000	0.000
130	A	154	ALA	0	0.008	0.012	38.705	0.003	0.003	0.000	0.000	0.000	0.000
131	A	155	VAL	0	0.077	0.036	33.480	0.009	0.009	0.000	0.000	0.000	0.000
132	A	156	GLY	0	-0.075	-0.055	33.355	0.009	0.009	0.000	0.000	0.000	0.000
133	A	157	ASN	0	0.034	0.024	30.530	-0.010	-0.010	0.000	0.000	0.000	0.000
134	A	158	TYR	0	0.043	-0.003	24.502	0.019	0.019	0.000	0.000	0.000	0.000
135	A	159	SER	0	-0.013	-0.006	23.093	-0.028	-0.028	0.000	0.000	0.000	0.000
136	A	160	GLY	0	-0.001	0.016	25.122	-0.015	-0.015	0.000	0.000	0.000	0.000
137	A	161	GLY	0	0.042	0.021	25.766	-0.010	-0.010	0.000	0.000	0.000	0.000
138	A	162	LEU	0	-0.022	-0.017	29.564	0.013	0.013	0.000	0.000	0.000	0.000
139	A	163	ALA	0	0.035	0.014	31.882	0.002	0.002	0.000	0.000	0.000	0.000
140	A	164	VAL	0	0.043	0.018	26.354	-0.003	-0.003	0.000	0.000	0.000	0.000
141	A	165	LYS	1	0.838	0.949	29.512	-0.267	-0.267	0.000	0.000	0.000	0.000
142	A	166	GLU	-1	-0.910	-0.957	30.415	0.193	0.193	0.000	0.000	0.000	0.000
143	A	167	TRP	0	0.068	0.031	28.734	0.004	0.004	0.000	0.000	0.000	0.000
144	A	168	LEU	0	0.011	0.011	26.091	0.000	0.000	0.000	0.000	0.000	0.000
145	A	169	LEU	0	-0.030	-0.020	30.270	-0.002	-0.002	0.000	0.000	0.000	0.000
146	A	170	ALA	0	-0.017	-0.023	32.931	-0.006	-0.006	0.000	0.000	0.000	0.000
147	A	171	HIS	0	-0.027	-0.003	29.332	-0.020	-0.020	0.000	0.000	0.000	0.000
148	A	172	GLU	-1	-0.721	-0.822	28.566	0.337	0.337	0.000	0.000	0.000	0.000
149	A	173	GLY	0	-0.047	-0.007	32.857	-0.007	-0.007	0.000	0.000	0.000	0.000
150	A	174	HIS	0	-0.033	-0.008	34.533	-0.014	-0.014	0.000	0.000	0.000	0.000
151	A	175	ARG	1	0.939	0.969	38.238	-0.145	-0.145	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:CYS)