FMO DATABASE

FMODB ID: 145QZ

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	OptAll
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	-1408658.532909
FMO2-HF: Nuclear repulsion	1349939.632982
FMO2-HF: Total energy	-58718.899927
FMO2-MP2: Total energy	-58887.827654

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.
-2.611	-13.736	32.392	-11.397	-9.867	0.053

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 : 0.049 / q_NPA : 0.036

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	-0.080	-0.027	3.266	0.361	3.755	0.035	-1.599	-1.829	0.002
4	A	8	LYS	1	0.936	0.975	5.117	3.667	3.809	-0.001	-0.010	-0.130	0.000
5	A	9	ARG	1	0.832	0.883	8.383	0.812	0.812	0.000	0.000	0.000	0.000
6	A	10	THR	0	0.003	0.012	11.739	-0.097	-0.097	0.000	0.000	0.000	0.000
7	A	11	THR	0	-0.048	-0.034	14.349	0.067	0.067	0.000	0.000	0.000	0.000
8	A	12	LEU	0	0.015	0.018	17.877	-0.015	-0.015	0.000	0.000	0.000	0.000
9	A	13	ASP	-1	-0.865	-0.923	20.625	-0.048	-0.048	0.000	0.000	0.000	0.000
10	A	14	SER	0	0.031	0.005	24.175	0.026	0.026	0.000	0.000	0.000	0.000
11	A	15	PRO	0	0.026	0.010	26.153	-0.013	-0.013	0.000	0.000	0.000	0.000
12	A	16	LEU	0	-0.037	-0.005	25.339	0.000	0.000	0.000	0.000	0.000	0.000
13	A	17	GLY	0	0.007	0.017	27.109	-0.006	-0.006	0.000	0.000	0.000	0.000
14	A	18	LYS	1	0.841	0.907	22.447	0.098	0.098	0.000	0.000	0.000	0.000
15	A	19	LEU	0	0.013	-0.001	19.620	0.022	0.022	0.000	0.000	0.000	0.000
16	A	20	GLU	-1	-0.873	-0.916	13.774	-0.309	-0.309	0.000	0.000	0.000	0.000
17	A	21	LEU	0	0.005	-0.001	13.436	0.077	0.077	0.000	0.000	0.000	0.000
18	A	22	SER	0	-0.005	-0.006	9.563	-0.092	-0.092	0.000	0.000	0.000	0.000
19	A	23	GLY	0	0.048	0.002	6.488	0.487	0.487	0.000	0.000	0.000	0.000
20	A	24	CYS	0	-0.135	-0.077	2.011	-0.062	-15.626	30.217	-9.059	-5.593	0.053
21	A	25	GLU	-1	-0.781	-0.899	3.514	0.399	0.773	0.004	-0.117	-0.261	0.000
22	A	26	GLN	0	0.020	0.012	3.697	0.247	0.628	0.008	-0.091	-0.298	0.000
23	A	27	GLY	0	-0.010	-0.028	5.564	-0.637	-0.637	0.000	0.000	0.000	0.000
24	A	28	LEU	0	0.004	0.011	6.914	0.385	0.385	0.000	0.000	0.000	0.000
25	A	29	HIS	0	-0.001	-0.019	6.883	0.750	0.750	0.000	0.000	0.000	0.000
26	A	30	GLU	-1	-0.867	-0.931	9.028	-0.155	-0.155	0.000	0.000	0.000	0.000
27	A	31	ILE	0	0.010	0.011	12.227	-0.025	-0.025	0.000	0.000	0.000	0.000
28	A	32	LYS	1	0.906	0.964	15.563	0.020	0.020	0.000	0.000	0.000	0.000
29	A	33	LEU	0	0.061	0.031	17.724	-0.043	-0.043	0.000	0.000	0.000	0.000
30	A	34	LEU	0	-0.083	-0.046	19.923	-0.012	-0.012	0.000	0.000	0.000	0.000
31	A	35	GLY	0	0.055	0.041	22.913	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	56	PRO	0	0.035	0.018	7.783	-0.150	-0.150	0.000	0.000	0.000	0.000
33	A	57	GLU	-1	-0.879	-0.945	8.754	0.796	0.796	0.000	0.000	0.000	0.000
34	A	58	PRO	0	-0.004	0.000	7.596	-0.109	-0.109	0.000	0.000	0.000	0.000
35	A	59	LEU	0	-0.001	0.012	8.274	-0.048	-0.048	0.000	0.000	0.000	0.000
36	A	60	MET	0	-0.012	0.012	11.394	-0.097	-0.097	0.000	0.000	0.000	0.000
37	A	61	GLN	0	-0.002	-0.005	13.302	0.096	0.096	0.000	0.000	0.000	0.000
38	A	62	CYS	0	-0.013	-0.005	13.709	-0.023	-0.023	0.000	0.000	0.000	0.000
39	A	63	THR	0	-0.032	-0.034	15.161	-0.064	-0.064	0.000	0.000	0.000	0.000
40	A	64	ALA	0	0.012	0.015	17.410	-0.031	-0.031	0.000	0.000	0.000	0.000
41	A	65	TRP	0	0.038	0.022	18.664	-0.016	-0.016	0.000	0.000	0.000	0.000
42	A	66	LEU	0	-0.015	-0.018	17.545	-0.018	-0.018	0.000	0.000	0.000	0.000
43	A	67	ASN	0	-0.045	-0.042	21.035	-0.037	-0.037	0.000	0.000	0.000	0.000
44	A	68	ALA	0	0.031	0.033	23.178	-0.016	-0.016	0.000	0.000	0.000	0.000
45	A	69	TYR	0	-0.062	-0.065	23.915	-0.013	-0.013	0.000	0.000	0.000	0.000
46	A	70	PHE	0	-0.041	-0.035	22.987	-0.009	-0.009	0.000	0.000	0.000	0.000
47	A	71	HIS	0	-0.022	-0.021	25.730	-0.009	-0.009	0.000	0.000	0.000	0.000
48	A	72	GLN	0	-0.078	-0.030	28.066	-0.017	-0.017	0.000	0.000	0.000	0.000
49	A	73	PRO	0	0.027	0.018	28.629	0.017	0.017	0.000	0.000	0.000	0.000
50	A	74	GLU	-1	-0.892	-0.947	29.680	0.130	0.130	0.000	0.000	0.000	0.000
51	A	75	ALA	0	0.038	0.025	29.433	0.002	0.002	0.000	0.000	0.000	0.000
52	A	76	ILE	0	-0.039	-0.010	23.637	0.018	0.018	0.000	0.000	0.000	0.000
53	A	77	GLU	-1	-0.975	-1.002	24.649	0.299	0.299	0.000	0.000	0.000	0.000
54	A	78	GLU	-1	-0.961	-0.973	25.411	0.204	0.204	0.000	0.000	0.000	0.000
55	A	79	PHE	0	-0.043	-0.014	21.511	0.005	0.005	0.000	0.000	0.000	0.000
56	A	80	PRO	0	-0.028	-0.011	17.826	0.026	0.026	0.000	0.000	0.000	0.000
57	A	81	VAL	0	-0.012	-0.018	16.746	0.006	0.006	0.000	0.000	0.000	0.000
58	A	82	PRO	0	-0.002	0.010	12.312	0.048	0.048	0.000	0.000	0.000	0.000
59	A	83	ALA	0	0.025	0.016	10.038	0.030	0.030	0.000	0.000	0.000	0.000
60	A	84	LEU	0	-0.005	-0.004	10.688	0.080	0.080	0.000	0.000	0.000	0.000
61	A	85	HIS	1	0.806	0.910	3.319	-7.843	-7.695	2.129	-0.521	-1.756	-0.002
62	A	86	HIS	0	0.137	0.058	7.282	-0.021	-0.021	0.000	0.000	0.000	0.000
63	A	87	PRO	0	0.004	-0.007	8.435	-0.035	-0.035	0.000	0.000	0.000	0.000
64	A	88	VAL	0	-0.046	-0.016	10.913	-0.092	-0.092	0.000	0.000	0.000	0.000
65	A	89	PHE	0	0.000	-0.030	11.459	-0.168	-0.168	0.000	0.000	0.000	0.000
66	A	90	GLN	0	-0.038	-0.009	6.838	0.592	0.592	0.000	0.000	0.000	0.000
67	A	91	GLN	0	0.024	0.031	11.415	-0.065	-0.065	0.000	0.000	0.000	0.000
68	A	92	GLU	-1	-0.798	-0.880	14.886	0.667	0.667	0.000	0.000	0.000	0.000
69	A	93	SER	0	-0.004	-0.017	18.575	-0.059	-0.059	0.000	0.000	0.000	0.000
70	A	94	PHE	0	0.038	0.020	20.979	0.011	0.011	0.000	0.000	0.000	0.000
71	A	95	THR	0	0.013	-0.003	19.208	-0.017	-0.017	0.000	0.000	0.000	0.000
72	A	96	ARG	1	0.882	0.959	15.815	-0.874	-0.874	0.000	0.000	0.000	0.000
73	A	97	GLN	0	-0.033	-0.035	18.860	-0.022	-0.022	0.000	0.000	0.000	0.000
74	A	98	VAL	0	-0.005	-0.010	22.035	-0.015	-0.015	0.000	0.000	0.000	0.000
75	A	99	LEU	0	-0.027	-0.009	17.637	-0.023	-0.023	0.000	0.000	0.000	0.000
76	A	100	TRP	0	0.046	0.009	14.546	0.003	0.003	0.000	0.000	0.000	0.000
77	A	101	LYS	1	0.882	0.925	20.184	-0.390	-0.390	0.000	0.000	0.000	0.000
78	A	102	LEU	0	0.011	0.000	22.973	-0.029	-0.029	0.000	0.000	0.000	0.000
79	A	103	LEU	0	0.014	0.012	18.376	-0.025	-0.025	0.000	0.000	0.000	0.000
80	A	104	LYS	1	0.894	0.952	20.017	-0.555	-0.555	0.000	0.000	0.000	0.000
81	A	105	VAL	0	-0.048	-0.014	24.743	-0.019	-0.019	0.000	0.000	0.000	0.000
82	A	106	VAL	0	-0.038	-0.006	27.194	-0.023	-0.023	0.000	0.000	0.000	0.000
83	A	107	LYS	1	0.883	0.927	27.375	-0.230	-0.230	0.000	0.000	0.000	0.000
84	A	108	PHE	0	0.056	0.014	28.257	-0.005	-0.005	0.000	0.000	0.000	0.000
85	A	109	GLY	0	0.050	0.032	30.025	-0.007	-0.007	0.000	0.000	0.000	0.000
86	A	110	GLU	-1	-0.862	-0.894	31.517	0.218	0.218	0.000	0.000	0.000	0.000
87	A	111	VAL	0	-0.005	-0.011	31.991	0.004	0.004	0.000	0.000	0.000	0.000
88	A	112	ILE	0	-0.027	-0.004	29.565	0.001	0.001	0.000	0.000	0.000	0.000
89	A	113	SER	0	0.015	0.014	32.597	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	114	TYR	0	0.031	-0.007	28.676	0.011	0.011	0.000	0.000	0.000	0.000
91	A	115	GLN	0	0.018	-0.006	31.097	0.017	0.017	0.000	0.000	0.000	0.000
92	A	116	GLN	0	0.067	0.043	33.437	0.008	0.008	0.000	0.000	0.000	0.000
93	A	117	LEU	0	0.038	0.021	25.836	0.007	0.007	0.000	0.000	0.000	0.000
94	A	118	ALA	0	-0.005	-0.010	28.866	0.020	0.020	0.000	0.000	0.000	0.000
95	A	119	ALA	0	-0.017	-0.017	30.287	0.008	0.008	0.000	0.000	0.000	0.000
96	A	120	LEU	0	-0.001	0.018	28.810	0.008	0.008	0.000	0.000	0.000	0.000
97	A	121	ALA	0	-0.027	0.002	26.123	0.024	0.024	0.000	0.000	0.000	0.000
98	A	122	GLY	0	0.018	0.014	27.571	0.012	0.012	0.000	0.000	0.000	0.000
99	A	123	ASN	0	-0.011	-0.011	30.280	-0.030	-0.030	0.000	0.000	0.000	0.000
100	A	124	PRO	0	0.060	0.021	31.870	0.000	0.000	0.000	0.000	0.000	0.000
101	A	125	LYS	1	0.952	0.974	34.358	-0.169	-0.169	0.000	0.000	0.000	0.000
102	A	126	ALA	0	-0.020	0.004	29.889	-0.009	-0.009	0.000	0.000	0.000	0.000
103	A	127	ALA	0	0.066	0.026	30.198	0.013	0.013	0.000	0.000	0.000	0.000
104	A	128	ARG	1	0.963	0.975	30.664	-0.136	-0.136	0.000	0.000	0.000	0.000
105	A	129	ALA	0	0.002	0.003	27.070	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	130	VAL	0	0.033	0.031	26.102	0.021	0.021	0.000	0.000	0.000	0.000
107	A	131	GLY	0	0.027	0.020	26.008	0.012	0.012	0.000	0.000	0.000	0.000
108	A	132	GLY	0	-0.063	-0.039	25.655	0.000	0.000	0.000	0.000	0.000	0.000
109	A	133	ALA	0	0.008	-0.002	22.014	0.012	0.012	0.000	0.000	0.000	0.000
110	A	134	MET	0	-0.014	-0.001	21.485	0.026	0.026	0.000	0.000	0.000	0.000
111	A	135	ARG	1	0.909	0.954	22.401	-0.204	-0.204	0.000	0.000	0.000	0.000
112	A	136	GLY	0	-0.014	0.000	19.242	-0.018	-0.018	0.000	0.000	0.000	0.000
113	A	137	ASN	0	0.019	-0.004	17.517	0.129	0.129	0.000	0.000	0.000	0.000
114	A	138	PRO	0	-0.027	0.004	13.231	-0.070	-0.070	0.000	0.000	0.000	0.000
115	A	139	VAL	0	0.017	-0.010	13.399	-0.022	-0.022	0.000	0.000	0.000	0.000
116	A	140	PRO	0	0.027	0.011	16.361	-0.004	-0.004	0.000	0.000	0.000	0.000
117	A	141	ILE	0	-0.012	0.006	19.839	0.002	0.002	0.000	0.000	0.000	0.000
118	A	142	LEU	0	0.027	0.012	15.874	0.005	0.005	0.000	0.000	0.000	0.000
119	A	143	ILE	0	-0.033	-0.003	16.758	0.016	0.016	0.000	0.000	0.000	0.000
120	A	144	PRO	0	0.001	0.013	20.387	-0.027	-0.027	0.000	0.000	0.000	0.000
121	A	145	CYS	0	-0.040	-0.034	22.985	-0.023	-0.023	0.000	0.000	0.000	0.000
122	A	146	HIS	0	-0.027	-0.025	24.928	-0.008	-0.008	0.000	0.000	0.000	0.000
123	A	147	ARG	1	0.843	0.903	26.405	-0.264	-0.264	0.000	0.000	0.000	0.000
124	A	148	VAL	0	-0.023	-0.002	27.101	-0.006	-0.006	0.000	0.000	0.000	0.000
125	A	149	VAL	0	0.026	0.027	30.081	-0.010	-0.010	0.000	0.000	0.000	0.000
126	A	150	CYS	0	-0.040	-0.029	33.483	0.009	0.009	0.000	0.000	0.000	0.000
127	A	151	SER	0	-0.010	-0.024	35.900	-0.003	-0.003	0.000	0.000	0.000	0.000
128	A	152	SER	0	-0.038	-0.013	38.324	-0.001	-0.001	0.000	0.000	0.000	0.000
129	A	153	GLY	0	0.035	0.023	39.546	-0.007	-0.007	0.000	0.000	0.000	0.000
130	A	154	ALA	0	-0.012	0.002	38.746	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	155	VAL	0	0.113	0.046	33.740	0.009	0.009	0.000	0.000	0.000	0.000
132	A	156	GLY	0	0.038	0.019	33.552	0.012	0.012	0.000	0.000	0.000	0.000
133	A	157	ASN	0	-0.027	-0.026	30.403	0.000	0.000	0.000	0.000	0.000	0.000
134	A	158	TYR	0	0.072	0.022	24.469	0.011	0.011	0.000	0.000	0.000	0.000
135	A	159	SER	0	-0.004	-0.008	22.899	-0.017	-0.017	0.000	0.000	0.000	0.000
136	A	160	GLY	0	-0.016	0.011	24.934	-0.016	-0.016	0.000	0.000	0.000	0.000
137	A	161	GLY	0	0.044	0.028	25.442	-0.015	-0.015	0.000	0.000	0.000	0.000
138	A	162	LEU	0	-0.009	-0.017	29.242	0.007	0.007	0.000	0.000	0.000	0.000
139	A	163	ALA	0	0.038	0.011	31.842	0.006	0.006	0.000	0.000	0.000	0.000
140	A	164	VAL	0	0.037	0.024	26.263	0.000	0.000	0.000	0.000	0.000	0.000
141	A	165	LYS	1	0.760	0.887	29.615	-0.155	-0.155	0.000	0.000	0.000	0.000
142	A	166	GLU	-1	-0.906	-0.961	30.388	0.101	0.101	0.000	0.000	0.000	0.000
143	A	167	TRP	0	0.020	0.012	29.160	0.003	0.003	0.000	0.000	0.000	0.000
144	A	168	LEU	0	-0.007	-0.009	26.117	0.002	0.002	0.000	0.000	0.000	0.000
145	A	169	LEU	0	-0.016	-0.014	30.346	0.006	0.006	0.000	0.000	0.000	0.000
146	A	170	ALA	0	-0.013	-0.005	33.045	0.000	0.000	0.000	0.000	0.000	0.000
147	A	171	HIS	0	-0.053	-0.024	29.170	-0.012	-0.012	0.000	0.000	0.000	0.000
148	A	172	GLU	-1	-0.722	-0.794	28.654	0.213	0.213	0.000	0.000	0.000	0.000
149	A	173	GLY	0	0.006	0.012	33.285	0.004	0.004	0.000	0.000	0.000	0.000
150	A	174	HIS	0	-0.116	-0.056	35.023	-0.012	-0.012	0.000	0.000	0.000	0.000
151	A	175	ARG	1	0.952	0.971	38.160	-0.082	-0.082	0.000	0.000	0.000	0.000

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