FMO DATABASE

FMODB ID: VRV41

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1409059.636466
FMO2-HF: Nuclear repulsion	1350341.991552
FMO2-HF: Total energy	-58717.644914
FMO2-MP2: Total energy	-58886.776878

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.
-4.825	-18.642	38.36	-12.69	-11.851	0.054

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 : 0.020 / q_NPA : 0.009

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	-0.091	-0.029	3.356	1.275	4.685	0.151	-1.581	-1.980	0.004
4	A	8	LYS	1	0.969	1.003	5.583	1.896	1.896	0.000	0.000	0.000	0.000
5	A	9	ARG	1	0.884	0.902	8.567	0.411	0.411	0.000	0.000	0.000	0.000
6	A	10	THR	0	0.047	0.037	11.918	-0.172	-0.172	0.000	0.000	0.000	0.000
7	A	11	THR	0	-0.025	-0.019	14.061	0.111	0.111	0.000	0.000	0.000	0.000
8	A	12	LEU	0	0.027	0.010	17.463	-0.019	-0.019	0.000	0.000	0.000	0.000
9	A	13	ASP	-1	-0.868	-0.910	20.065	0.090	0.090	0.000	0.000	0.000	0.000
10	A	14	SER	0	0.055	0.030	23.273	0.021	0.021	0.000	0.000	0.000	0.000
11	A	15	PRO	0	0.029	0.019	25.198	-0.015	-0.015	0.000	0.000	0.000	0.000
12	A	16	LEU	0	-0.038	-0.018	25.447	-0.005	-0.005	0.000	0.000	0.000	0.000
13	A	17	GLY	0	-0.002	0.012	26.559	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	18	LYS	1	0.815	0.875	21.971	-0.034	-0.034	0.000	0.000	0.000	0.000
15	A	19	LEU	0	-0.035	-0.021	19.224	0.013	0.013	0.000	0.000	0.000	0.000
16	A	20	GLU	-1	-0.855	-0.909	14.094	0.194	0.194	0.000	0.000	0.000	0.000
17	A	21	LEU	0	0.027	0.018	13.207	0.078	0.078	0.000	0.000	0.000	0.000
18	A	22	SER	0	-0.020	0.010	10.053	0.054	0.054	0.000	0.000	0.000	0.000
19	A	23	GLY	0	0.065	0.002	7.125	0.328	0.328	0.000	0.000	0.000	0.000
20	A	24	CYS	0	-0.128	-0.038	1.819	1.724	-18.495	37.204	-9.877	-7.107	0.054
21	A	25	GLU	-1	-0.835	-0.923	2.455	-1.246	-0.108	0.488	-0.647	-0.978	-0.002
22	A	26	GLN	0	0.047	0.010	2.761	-0.729	0.320	0.146	-0.341	-0.854	-0.001
23	A	27	GLY	0	-0.006	-0.053	4.662	-1.139	-1.101	-0.001	-0.012	-0.024	0.000
24	A	28	LEU	0	-0.025	-0.014	6.583	0.515	0.515	0.000	0.000	0.000	0.000
25	A	29	HIS	0	0.005	-0.021	6.901	0.882	0.882	0.000	0.000	0.000	0.000
26	A	30	GLU	-1	-0.968	-1.005	9.037	0.430	0.430	0.000	0.000	0.000	0.000
27	A	31	ILE	0	0.024	0.002	12.561	0.016	0.016	0.000	0.000	0.000	0.000
28	A	32	LYS	1	0.955	1.003	15.800	-0.295	-0.295	0.000	0.000	0.000	0.000
29	A	33	LEU	0	0.028	0.011	18.421	-0.042	-0.042	0.000	0.000	0.000	0.000
30	A	34	LEU	0	-0.116	-0.050	19.935	-0.020	-0.020	0.000	0.000	0.000	0.000
31	A	35	GLY	0	0.061	0.037	22.876	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	56	PRO	0	0.000	0.004	7.191	-0.152	-0.152	0.000	0.000	0.000	0.000
33	A	57	GLU	-1	-0.903	-0.957	8.225	1.039	1.039	0.000	0.000	0.000	0.000
34	A	58	PRO	0	0.025	0.011	6.693	-0.097	-0.097	0.000	0.000	0.000	0.000
35	A	59	LEU	0	0.019	0.026	7.860	-0.135	-0.135	0.000	0.000	0.000	0.000
36	A	60	MET	0	0.006	0.015	10.865	-0.129	-0.129	0.000	0.000	0.000	0.000
37	A	61	GLN	0	0.002	0.004	12.613	0.090	0.090	0.000	0.000	0.000	0.000
38	A	62	CYS	0	-0.036	-0.022	13.110	-0.020	-0.020	0.000	0.000	0.000	0.000
39	A	63	THR	0	-0.054	-0.045	14.581	-0.091	-0.091	0.000	0.000	0.000	0.000
40	A	64	ALA	0	0.009	0.016	16.780	-0.049	-0.049	0.000	0.000	0.000	0.000
41	A	65	TRP	0	0.059	0.035	18.248	-0.022	-0.022	0.000	0.000	0.000	0.000
42	A	66	LEU	0	-0.002	0.000	17.184	-0.032	-0.032	0.000	0.000	0.000	0.000
43	A	67	ASN	0	-0.051	-0.040	20.456	-0.054	-0.054	0.000	0.000	0.000	0.000
44	A	68	ALA	0	0.029	0.031	22.531	-0.027	-0.027	0.000	0.000	0.000	0.000
45	A	69	TYR	0	-0.066	-0.070	23.491	-0.019	-0.019	0.000	0.000	0.000	0.000
46	A	70	PHE	0	-0.038	-0.042	22.768	-0.017	-0.017	0.000	0.000	0.000	0.000
47	A	71	HIS	0	-0.033	-0.025	25.565	-0.016	-0.016	0.000	0.000	0.000	0.000
48	A	72	GLN	0	-0.045	-0.024	27.239	-0.025	-0.025	0.000	0.000	0.000	0.000
49	A	73	PRO	0	0.006	0.017	28.015	0.018	0.018	0.000	0.000	0.000	0.000
50	A	74	GLU	-1	-0.932	-0.964	29.034	0.189	0.189	0.000	0.000	0.000	0.000
51	A	75	ALA	0	0.032	0.016	28.993	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	76	ILE	0	0.004	0.008	22.945	0.014	0.014	0.000	0.000	0.000	0.000
53	A	77	GLU	-1	-0.984	-0.997	23.944	0.377	0.377	0.000	0.000	0.000	0.000
54	A	78	GLU	-1	-1.005	-0.986	24.710	0.246	0.246	0.000	0.000	0.000	0.000
55	A	79	PHE	0	-0.042	-0.022	20.769	0.001	0.001	0.000	0.000	0.000	0.000
56	A	80	PRO	0	-0.027	-0.003	17.436	0.029	0.029	0.000	0.000	0.000	0.000
57	A	81	VAL	0	-0.018	-0.015	16.162	0.013	0.013	0.000	0.000	0.000	0.000
58	A	82	PRO	0	0.019	0.012	11.719	0.047	0.047	0.000	0.000	0.000	0.000
59	A	83	ALA	0	0.018	0.017	9.286	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	84	LEU	0	0.013	0.014	10.148	0.239	0.239	0.000	0.000	0.000	0.000
61	A	85	HIS	1	0.847	0.947	3.928	-8.382	-7.615	0.372	-0.232	-0.908	-0.001
62	A	86	HIS	0	0.116	0.042	7.533	0.212	0.212	0.000	0.000	0.000	0.000
63	A	87	PRO	0	-0.017	-0.016	8.382	-0.178	-0.178	0.000	0.000	0.000	0.000
64	A	88	VAL	0	-0.044	-0.012	10.863	-0.190	-0.190	0.000	0.000	0.000	0.000
65	A	89	PHE	0	0.009	-0.017	11.829	-0.214	-0.214	0.000	0.000	0.000	0.000
66	A	90	GLN	0	-0.060	-0.017	7.143	0.736	0.736	0.000	0.000	0.000	0.000
67	A	91	GLN	0	0.029	0.034	11.996	-0.109	-0.109	0.000	0.000	0.000	0.000
68	A	92	GLU	-1	-0.814	-0.880	15.277	0.726	0.726	0.000	0.000	0.000	0.000
69	A	93	SER	0	0.013	-0.011	18.851	-0.075	-0.075	0.000	0.000	0.000	0.000
70	A	94	PHE	0	0.042	0.018	20.918	0.004	0.004	0.000	0.000	0.000	0.000
71	A	95	THR	0	0.017	-0.013	19.126	-0.018	-0.018	0.000	0.000	0.000	0.000
72	A	96	ARG	1	0.873	0.945	16.442	-0.943	-0.943	0.000	0.000	0.000	0.000
73	A	97	GLN	0	0.007	0.000	19.421	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	98	VAL	0	0.005	0.001	22.461	-0.006	-0.006	0.000	0.000	0.000	0.000
75	A	99	LEU	0	-0.004	0.008	17.560	-0.026	-0.026	0.000	0.000	0.000	0.000
76	A	100	TRP	0	0.030	-0.003	14.622	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	101	LYS	1	0.890	0.936	20.623	-0.460	-0.460	0.000	0.000	0.000	0.000
78	A	102	LEU	0	-0.006	-0.008	23.080	-0.039	-0.039	0.000	0.000	0.000	0.000
79	A	103	LEU	0	0.011	0.008	18.809	-0.023	-0.023	0.000	0.000	0.000	0.000
80	A	104	LYS	1	0.902	0.965	19.532	-0.687	-0.687	0.000	0.000	0.000	0.000
81	A	105	VAL	0	-0.045	-0.021	24.681	-0.028	-0.028	0.000	0.000	0.000	0.000
82	A	106	VAL	0	-0.046	-0.007	27.144	-0.031	-0.031	0.000	0.000	0.000	0.000
83	A	107	LYS	1	0.889	0.926	27.145	-0.280	-0.280	0.000	0.000	0.000	0.000
84	A	108	PHE	0	0.026	-0.006	27.700	0.000	0.000	0.000	0.000	0.000	0.000
85	A	109	GLY	0	0.065	0.042	29.303	-0.016	-0.016	0.000	0.000	0.000	0.000
86	A	110	GLU	-1	-0.863	-0.914	31.482	0.283	0.283	0.000	0.000	0.000	0.000
87	A	111	VAL	0	0.017	0.002	31.812	0.012	0.012	0.000	0.000	0.000	0.000
88	A	112	ILE	0	-0.027	-0.013	29.631	-0.004	-0.004	0.000	0.000	0.000	0.000
89	A	113	SER	0	0.019	0.021	32.224	0.003	0.003	0.000	0.000	0.000	0.000
90	A	114	TYR	0	0.035	0.003	29.003	0.009	0.009	0.000	0.000	0.000	0.000
91	A	115	GLN	0	-0.004	-0.022	31.187	0.022	0.022	0.000	0.000	0.000	0.000
92	A	116	GLN	0	0.098	0.043	33.050	0.011	0.011	0.000	0.000	0.000	0.000
93	A	117	LEU	0	0.002	0.019	25.881	0.003	0.003	0.000	0.000	0.000	0.000
94	A	118	ALA	0	0.016	-0.003	29.427	0.017	0.017	0.000	0.000	0.000	0.000
95	A	119	ALA	0	-0.036	-0.007	30.435	0.000	0.000	0.000	0.000	0.000	0.000
96	A	120	LEU	0	0.006	0.018	29.054	0.008	0.008	0.000	0.000	0.000	0.000
97	A	121	ALA	0	-0.072	-0.033	26.303	0.017	0.017	0.000	0.000	0.000	0.000
98	A	122	GLY	0	0.008	0.004	27.756	0.012	0.012	0.000	0.000	0.000	0.000
99	A	123	ASN	0	-0.006	-0.021	30.240	-0.034	-0.034	0.000	0.000	0.000	0.000
100	A	124	PRO	0	0.098	0.057	31.716	0.007	0.007	0.000	0.000	0.000	0.000
101	A	125	LYS	1	0.895	0.948	34.306	-0.201	-0.201	0.000	0.000	0.000	0.000
102	A	126	ALA	0	-0.017	-0.011	30.690	-0.008	-0.008	0.000	0.000	0.000	0.000
103	A	127	ALA	0	0.092	0.048	30.633	0.019	0.019	0.000	0.000	0.000	0.000
104	A	128	ARG	1	0.980	0.979	30.446	-0.192	-0.192	0.000	0.000	0.000	0.000
105	A	129	ALA	0	0.001	0.006	27.539	0.005	0.005	0.000	0.000	0.000	0.000
106	A	130	VAL	0	0.059	0.025	26.408	0.029	0.029	0.000	0.000	0.000	0.000
107	A	131	GLY	0	0.019	0.021	26.378	0.015	0.015	0.000	0.000	0.000	0.000
108	A	132	GLY	0	-0.054	-0.034	25.360	0.016	0.016	0.000	0.000	0.000	0.000
109	A	133	ALA	0	-0.024	-0.011	22.349	0.034	0.034	0.000	0.000	0.000	0.000
110	A	134	MET	0	0.028	0.023	21.544	0.050	0.050	0.000	0.000	0.000	0.000
111	A	135	ARG	1	0.909	0.962	22.283	-0.317	-0.317	0.000	0.000	0.000	0.000
112	A	136	GLY	0	-0.037	-0.011	19.434	0.008	0.008	0.000	0.000	0.000	0.000
113	A	137	ASN	0	0.001	-0.033	17.644	0.166	0.166	0.000	0.000	0.000	0.000
114	A	138	PRO	0	-0.040	0.003	13.730	-0.066	-0.066	0.000	0.000	0.000	0.000
115	A	139	VAL	0	0.030	-0.007	13.822	-0.012	-0.012	0.000	0.000	0.000	0.000
116	A	140	PRO	0	0.056	0.034	16.666	-0.040	-0.040	0.000	0.000	0.000	0.000
117	A	141	ILE	0	-0.023	0.003	19.851	0.017	0.017	0.000	0.000	0.000	0.000
118	A	142	LEU	0	-0.003	-0.007	15.672	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	143	ILE	0	-0.026	0.001	17.159	-0.014	-0.014	0.000	0.000	0.000	0.000
120	A	144	PRO	0	0.013	0.003	20.808	-0.011	-0.011	0.000	0.000	0.000	0.000
121	A	145	CYS	0	-0.067	-0.025	23.143	-0.025	-0.025	0.000	0.000	0.000	0.000
122	A	146	HIS	0	-0.026	-0.044	24.943	-0.005	-0.005	0.000	0.000	0.000	0.000
123	A	147	ARG	1	0.864	0.925	26.180	-0.371	-0.371	0.000	0.000	0.000	0.000
124	A	148	VAL	0	-0.016	-0.001	27.074	-0.017	-0.017	0.000	0.000	0.000	0.000
125	A	149	VAL	0	0.023	0.010	30.101	-0.011	-0.011	0.000	0.000	0.000	0.000
126	A	150	CYS	0	-0.036	-0.020	33.468	0.006	0.006	0.000	0.000	0.000	0.000
127	A	151	SER	0	0.019	-0.011	35.768	-0.003	-0.003	0.000	0.000	0.000	0.000
128	A	152	SER	0	-0.066	-0.029	38.350	-0.003	-0.003	0.000	0.000	0.000	0.000
129	A	153	GLY	0	0.044	0.035	39.573	-0.010	-0.010	0.000	0.000	0.000	0.000
130	A	154	ALA	0	0.001	0.007	38.819	0.001	0.001	0.000	0.000	0.000	0.000
131	A	155	VAL	0	0.090	0.038	33.739	0.013	0.013	0.000	0.000	0.000	0.000
132	A	156	GLY	0	-0.059	-0.053	33.432	0.006	0.006	0.000	0.000	0.000	0.000
133	A	157	ASN	0	0.005	0.006	30.897	-0.009	-0.009	0.000	0.000	0.000	0.000
134	A	158	TYR	0	0.058	0.008	24.638	0.017	0.017	0.000	0.000	0.000	0.000
135	A	159	SER	0	-0.013	-0.010	23.151	-0.026	-0.026	0.000	0.000	0.000	0.000
136	A	160	GLY	0	0.003	0.019	25.254	-0.019	-0.019	0.000	0.000	0.000	0.000
137	A	161	GLY	0	0.038	0.019	25.864	-0.015	-0.015	0.000	0.000	0.000	0.000
138	A	162	LEU	0	-0.007	-0.015	29.662	0.011	0.011	0.000	0.000	0.000	0.000
139	A	163	ALA	0	0.035	0.012	31.979	0.003	0.003	0.000	0.000	0.000	0.000
140	A	164	VAL	0	0.044	0.020	26.370	-0.003	-0.003	0.000	0.000	0.000	0.000
141	A	165	LYS	1	0.818	0.933	29.697	-0.253	-0.253	0.000	0.000	0.000	0.000
142	A	166	GLU	-1	-0.918	-0.955	30.514	0.172	0.172	0.000	0.000	0.000	0.000
143	A	167	TRP	0	0.039	0.021	28.856	0.005	0.005	0.000	0.000	0.000	0.000
144	A	168	LEU	0	0.003	0.010	26.211	0.000	0.000	0.000	0.000	0.000	0.000
145	A	169	LEU	0	0.000	-0.007	30.241	0.001	0.001	0.000	0.000	0.000	0.000
146	A	170	ALA	0	-0.016	-0.017	32.927	-0.004	-0.004	0.000	0.000	0.000	0.000
147	A	171	HIS	0	-0.031	-0.007	29.022	-0.017	-0.017	0.000	0.000	0.000	0.000
148	A	172	GLU	-1	-0.721	-0.794	28.354	0.314	0.314	0.000	0.000	0.000	0.000
149	A	173	GLY	0	-0.044	-0.009	32.832	-0.003	-0.003	0.000	0.000	0.000	0.000
150	A	174	HIS	0	-0.071	-0.036	34.827	-0.009	-0.009	0.000	0.000	0.000	0.000
151	A	175	ARG	1	0.943	0.975	38.214	-0.128	-0.128	0.000	0.000	0.000	0.000

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