FMO DATABASE

FMODB ID: N1ZRQ

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	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
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1405974.362492
FMO2-HF: Nuclear repulsion	1347858.599453
FMO2-HF: Total energy	-58115.763039
FMO2-MP2: Total energy	-58284.999567

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.
-151.973	-157.905	32.193	-15.178	-11.082	0.168

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 : -0.810 / q_NPA : -0.892

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	0.850	0.912	1.726	-145.844	-153.181	31.861	-14.574	-9.949	0.164
4	A	9	ARG	1	0.739	0.801	5.603	-32.383	-32.367	-0.001	-0.004	-0.011	0.000
5	A	10	THR	0	0.010	0.017	8.950	0.773	0.773	0.000	0.000	0.000	0.000
6	A	11	THR	0	-0.015	-0.010	11.967	-0.843	-0.843	0.000	0.000	0.000	0.000
7	A	12	LEU	0	0.012	0.013	15.770	0.071	0.071	0.000	0.000	0.000	0.000
8	A	13	ASP	-1	-0.811	-0.883	19.106	13.889	13.889	0.000	0.000	0.000	0.000
9	A	14	SER	0	-0.008	-0.011	22.653	-0.180	-0.180	0.000	0.000	0.000	0.000
10	A	15	PRO	0	0.031	0.011	25.238	-0.123	-0.123	0.000	0.000	0.000	0.000
11	A	16	LEU	0	-0.046	-0.006	25.250	-0.314	-0.314	0.000	0.000	0.000	0.000
12	A	17	GLY	0	0.014	0.015	25.318	0.141	0.141	0.000	0.000	0.000	0.000
13	A	18	LYS	1	0.810	0.885	19.832	-14.226	-14.226	0.000	0.000	0.000	0.000
14	A	19	LEU	0	0.031	0.021	19.478	0.020	0.020	0.000	0.000	0.000	0.000
15	A	20	GLU	-1	-0.767	-0.863	12.885	23.498	23.498	0.000	0.000	0.000	0.000
16	A	21	LEU	0	-0.001	0.009	13.585	-0.573	-0.573	0.000	0.000	0.000	0.000
17	A	22	SER	0	0.001	-0.016	9.188	2.177	2.177	0.000	0.000	0.000	0.000
18	A	23	GLY	0	0.031	0.005	7.377	-3.135	-3.135	0.000	0.000	0.000	0.000
19	A	24	CYS	0	-0.036	0.006	2.715	0.925	2.030	0.334	-0.587	-0.852	0.004
20	A	25	GLU	-1	-0.889	-0.963	4.493	32.659	32.943	-0.001	-0.013	-0.270	0.000
21	A	26	GLN	0	-0.016	-0.009	5.311	0.196	0.196	0.000	0.000	0.000	0.000
22	A	27	GLY	0	0.002	-0.007	7.318	-2.565	-2.565	0.000	0.000	0.000	0.000
23	A	28	LEU	0	-0.019	-0.014	8.054	2.907	2.907	0.000	0.000	0.000	0.000
24	A	29	HIS	0	-0.035	-0.029	8.331	-0.616	-0.616	0.000	0.000	0.000	0.000
25	A	30	GLU	-1	-0.834	-0.927	10.391	20.557	20.557	0.000	0.000	0.000	0.000
26	A	31	ILE	0	-0.030	0.003	13.276	1.349	1.349	0.000	0.000	0.000	0.000
27	A	32	LYS	1	0.885	0.932	14.997	-20.734	-20.734	0.000	0.000	0.000	0.000
28	A	33	LEU	0	0.006	0.000	17.725	0.143	0.143	0.000	0.000	0.000	0.000
29	A	34	LEU	0	-0.032	-0.010	16.393	0.089	0.089	0.000	0.000	0.000	0.000
30	A	35	GLY	0	-0.034	-0.006	20.933	-0.692	-0.692	0.000	0.000	0.000	0.000
31	A	56	PRO	0	0.056	0.012	6.418	-0.157	-0.157	0.000	0.000	0.000	0.000
32	A	57	GLU	-1	-0.859	-0.927	9.529	17.914	17.914	0.000	0.000	0.000	0.000
33	A	58	PRO	0	0.017	0.023	9.173	-1.421	-1.421	0.000	0.000	0.000	0.000
34	A	59	LEU	0	0.018	0.011	9.055	-1.192	-1.192	0.000	0.000	0.000	0.000
35	A	60	MET	0	-0.010	0.017	12.360	-1.561	-1.561	0.000	0.000	0.000	0.000
36	A	61	GLN	0	-0.031	-0.019	14.319	-2.027	-2.027	0.000	0.000	0.000	0.000
37	A	62	CYS	0	-0.037	-0.007	14.835	-1.254	-1.254	0.000	0.000	0.000	0.000
38	A	63	THR	0	-0.006	-0.029	15.647	-0.741	-0.741	0.000	0.000	0.000	0.000
39	A	64	ALA	0	-0.006	0.001	18.087	-0.852	-0.852	0.000	0.000	0.000	0.000
40	A	65	TRP	0	0.039	0.022	19.891	-0.596	-0.596	0.000	0.000	0.000	0.000
41	A	66	LEU	0	0.015	-0.007	18.615	-0.656	-0.656	0.000	0.000	0.000	0.000
42	A	67	ASN	0	-0.022	-0.016	22.034	-0.454	-0.454	0.000	0.000	0.000	0.000
43	A	68	ALA	0	0.016	0.014	24.035	-0.547	-0.547	0.000	0.000	0.000	0.000
44	A	69	TYR	0	-0.051	-0.053	24.896	-0.463	-0.463	0.000	0.000	0.000	0.000
45	A	70	PHE	0	-0.023	-0.027	23.629	-0.428	-0.428	0.000	0.000	0.000	0.000
46	A	71	HIS	0	-0.017	-0.011	25.818	-0.732	-0.732	0.000	0.000	0.000	0.000
47	A	72	GLN	0	-0.043	-0.017	29.203	-0.080	-0.080	0.000	0.000	0.000	0.000
48	A	73	PRO	0	0.030	0.022	29.709	0.101	0.101	0.000	0.000	0.000	0.000
49	A	74	GLU	-1	-0.935	-0.972	30.761	9.014	9.014	0.000	0.000	0.000	0.000
50	A	75	ALA	0	0.023	0.019	30.614	-0.200	-0.200	0.000	0.000	0.000	0.000
51	A	76	ILE	0	-0.036	-0.016	24.745	0.323	0.323	0.000	0.000	0.000	0.000
52	A	77	GLU	-1	-0.847	-0.912	26.214	10.832	10.832	0.000	0.000	0.000	0.000
53	A	78	GLU	-1	-0.980	-0.972	27.268	10.485	10.485	0.000	0.000	0.000	0.000
54	A	79	PHE	0	-0.036	-0.012	22.672	0.524	0.524	0.000	0.000	0.000	0.000
55	A	80	PRO	0	-0.007	0.002	19.350	-0.113	-0.113	0.000	0.000	0.000	0.000
56	A	81	VAL	0	0.001	-0.012	18.482	0.505	0.505	0.000	0.000	0.000	0.000
57	A	82	PRO	0	-0.025	0.000	13.811	0.113	0.113	0.000	0.000	0.000	0.000
58	A	83	ALA	0	0.054	0.025	12.090	-0.432	-0.432	0.000	0.000	0.000	0.000
59	A	84	LEU	0	-0.010	-0.009	12.518	1.168	1.168	0.000	0.000	0.000	0.000
60	A	85	HIS	0	0.012	-0.003	5.842	-2.706	-2.706	0.000	0.000	0.000	0.000
61	A	86	HIS	0	0.059	0.045	10.365	-0.056	-0.056	0.000	0.000	0.000	0.000
62	A	87	PRO	0	0.035	0.006	11.036	-1.093	-1.093	0.000	0.000	0.000	0.000
63	A	88	VAL	0	-0.021	-0.006	13.584	-1.113	-1.113	0.000	0.000	0.000	0.000
64	A	89	PHE	0	-0.001	-0.014	14.185	-1.054	-1.054	0.000	0.000	0.000	0.000
65	A	90	GLN	0	-0.047	-0.012	9.800	-1.389	-1.389	0.000	0.000	0.000	0.000
66	A	91	GLN	0	-0.041	-0.016	15.328	-0.980	-0.980	0.000	0.000	0.000	0.000
67	A	92	GLU	-1	-0.793	-0.881	18.546	11.676	11.676	0.000	0.000	0.000	0.000
68	A	93	SER	0	-0.005	-0.007	21.508	-0.212	-0.212	0.000	0.000	0.000	0.000
69	A	94	PHE	0	0.000	-0.004	24.104	-0.034	-0.034	0.000	0.000	0.000	0.000
70	A	95	THR	0	0.023	0.002	21.842	-0.273	-0.273	0.000	0.000	0.000	0.000
71	A	96	ARG	1	0.860	0.929	18.498	-13.222	-13.222	0.000	0.000	0.000	0.000
72	A	97	GLN	0	0.047	0.033	22.004	-0.237	-0.237	0.000	0.000	0.000	0.000
73	A	98	VAL	0	0.012	-0.007	25.329	-0.209	-0.209	0.000	0.000	0.000	0.000
74	A	99	LEU	0	-0.015	-0.006	20.029	-0.155	-0.155	0.000	0.000	0.000	0.000
75	A	100	TRP	0	0.014	0.001	18.188	-0.133	-0.133	0.000	0.000	0.000	0.000
76	A	101	LYS	1	0.857	0.918	23.568	-9.962	-9.962	0.000	0.000	0.000	0.000
77	A	102	LEU	0	-0.033	-0.024	25.019	-0.247	-0.247	0.000	0.000	0.000	0.000
78	A	103	LEU	0	0.006	0.006	20.413	-0.144	-0.144	0.000	0.000	0.000	0.000
79	A	104	LYS	1	0.905	0.967	24.637	-10.187	-10.187	0.000	0.000	0.000	0.000
80	A	105	VAL	0	-0.064	-0.036	26.821	-0.249	-0.249	0.000	0.000	0.000	0.000
81	A	106	VAL	0	-0.003	0.021	29.254	-0.117	-0.117	0.000	0.000	0.000	0.000
82	A	107	LYS	1	0.847	0.888	27.524	-9.975	-9.975	0.000	0.000	0.000	0.000
83	A	108	PHE	0	0.008	-0.004	29.466	-0.091	-0.091	0.000	0.000	0.000	0.000
84	A	109	GLY	0	0.069	0.041	31.585	-0.242	-0.242	0.000	0.000	0.000	0.000
85	A	110	GLU	-1	-0.914	-0.936	33.299	8.636	8.636	0.000	0.000	0.000	0.000
86	A	111	VAL	0	-0.022	-0.022	33.667	0.219	0.219	0.000	0.000	0.000	0.000
87	A	112	ILE	0	-0.024	-0.007	31.909	-0.212	-0.212	0.000	0.000	0.000	0.000
88	A	113	SER	0	-0.003	-0.011	34.338	0.127	0.127	0.000	0.000	0.000	0.000
89	A	114	TYR	0	0.034	-0.007	31.018	0.000	0.000	0.000	0.000	0.000	0.000
90	A	115	GLN	0	-0.010	-0.013	33.930	0.077	0.077	0.000	0.000	0.000	0.000
91	A	116	GLN	0	0.042	0.051	36.337	0.078	0.078	0.000	0.000	0.000	0.000
92	A	117	LEU	0	0.060	0.036	28.515	0.002	0.002	0.000	0.000	0.000	0.000
93	A	118	ALA	0	0.001	-0.002	31.799	0.179	0.179	0.000	0.000	0.000	0.000
94	A	119	ALA	0	-0.042	-0.031	33.204	0.007	0.007	0.000	0.000	0.000	0.000
95	A	120	LEU	0	0.002	0.010	32.050	-0.008	-0.008	0.000	0.000	0.000	0.000
96	A	121	ALA	0	-0.029	-0.010	29.206	0.114	0.114	0.000	0.000	0.000	0.000
97	A	122	GLY	0	0.035	0.024	30.668	0.145	0.145	0.000	0.000	0.000	0.000
98	A	123	ASN	0	-0.010	-0.012	33.495	-0.414	-0.414	0.000	0.000	0.000	0.000
99	A	124	PRO	0	0.053	0.017	35.287	0.104	0.104	0.000	0.000	0.000	0.000
100	A	125	LYS	1	0.960	0.983	37.511	-7.254	-7.254	0.000	0.000	0.000	0.000
101	A	126	ALA	0	-0.042	-0.006	32.605	-0.013	-0.013	0.000	0.000	0.000	0.000
102	A	127	ALA	0	0.065	0.026	32.924	0.280	0.280	0.000	0.000	0.000	0.000
103	A	128	ARG	1	0.959	0.970	33.241	-8.061	-8.061	0.000	0.000	0.000	0.000
104	A	129	ALA	0	0.011	0.009	29.894	0.186	0.186	0.000	0.000	0.000	0.000
105	A	130	VAL	0	0.024	0.024	28.751	0.391	0.391	0.000	0.000	0.000	0.000
106	A	131	GLY	0	0.010	0.012	28.500	0.292	0.292	0.000	0.000	0.000	0.000
107	A	132	GLY	0	-0.018	-0.008	27.547	0.251	0.251	0.000	0.000	0.000	0.000
108	A	133	ALA	0	0.006	-0.006	24.435	0.446	0.446	0.000	0.000	0.000	0.000
109	A	134	MET	0	0.005	0.043	23.785	0.515	0.515	0.000	0.000	0.000	0.000
110	A	135	ARG	1	0.842	0.921	24.849	-11.239	-11.239	0.000	0.000	0.000	0.000
111	A	136	GLY	0	0.032	0.019	21.464	0.296	0.296	0.000	0.000	0.000	0.000
112	A	137	ASN	0	0.006	0.001	19.883	1.147	1.147	0.000	0.000	0.000	0.000
113	A	138	PRO	0	0.003	0.017	15.097	-0.093	-0.093	0.000	0.000	0.000	0.000
114	A	139	VAL	0	0.026	0.003	15.101	0.977	0.977	0.000	0.000	0.000	0.000
115	A	140	PRO	0	0.019	0.015	17.959	-0.692	-0.692	0.000	0.000	0.000	0.000
116	A	141	ILE	0	-0.010	0.006	20.967	0.443	0.443	0.000	0.000	0.000	0.000
117	A	142	LEU	0	0.013	0.001	17.370	-0.356	-0.356	0.000	0.000	0.000	0.000
118	A	143	ILE	0	-0.007	0.006	19.148	-0.499	-0.499	0.000	0.000	0.000	0.000
119	A	144	PRO	0	0.012	0.014	22.288	0.061	0.061	0.000	0.000	0.000	0.000
120	A	145	SER	0	-0.002	-0.072	24.800	-0.265	-0.265	0.000	0.000	0.000	0.000
121	A	146	HIS	0	-0.088	-0.041	26.534	-0.084	-0.084	0.000	0.000	0.000	0.000
122	A	147	ARG	1	0.837	0.887	27.544	-10.824	-10.824	0.000	0.000	0.000	0.000
123	A	148	VAL	0	-0.014	0.001	29.008	-0.320	-0.320	0.000	0.000	0.000	0.000
124	A	149	VAL	0	0.010	0.021	31.827	0.076	0.076	0.000	0.000	0.000	0.000
125	A	150	CYS	0	-0.054	-0.033	35.213	0.031	0.031	0.000	0.000	0.000	0.000
126	A	151	SER	0	0.028	-0.011	38.144	-0.026	-0.026	0.000	0.000	0.000	0.000
127	A	152	SER	0	-0.043	-0.012	40.503	-0.070	-0.070	0.000	0.000	0.000	0.000
128	A	153	GLY	0	0.039	0.025	41.122	-0.148	-0.148	0.000	0.000	0.000	0.000
129	A	154	ALA	0	-0.013	0.003	40.734	0.089	0.089	0.000	0.000	0.000	0.000
130	A	155	VAL	0	0.101	0.049	35.254	0.118	0.118	0.000	0.000	0.000	0.000
131	A	156	GLY	0	0.061	0.021	35.448	0.223	0.223	0.000	0.000	0.000	0.000
132	A	157	ASN	0	0.014	-0.003	32.723	0.278	0.278	0.000	0.000	0.000	0.000
133	A	158	TYR	0	0.048	0.013	25.320	0.050	0.050	0.000	0.000	0.000	0.000
134	A	159	SER	0	-0.034	-0.014	24.079	-0.160	-0.160	0.000	0.000	0.000	0.000
135	A	160	GLY	0	0.011	0.009	25.447	0.147	0.147	0.000	0.000	0.000	0.000
136	A	161	GLY	0	0.024	0.019	26.046	-0.033	-0.033	0.000	0.000	0.000	0.000
137	A	162	LEU	0	-0.033	-0.024	29.847	0.149	0.149	0.000	0.000	0.000	0.000
138	A	163	ALA	0	0.078	0.035	32.753	0.017	0.017	0.000	0.000	0.000	0.000
139	A	164	VAL	0	0.008	0.014	26.650	-0.031	-0.031	0.000	0.000	0.000	0.000
140	A	165	LYS	1	0.751	0.879	30.133	-9.475	-9.475	0.000	0.000	0.000	0.000
141	A	166	GLU	-1	-0.903	-0.968	31.227	8.478	8.478	0.000	0.000	0.000	0.000
142	A	167	TRP	0	0.024	0.011	29.828	-0.043	-0.043	0.000	0.000	0.000	0.000
143	A	168	LEU	0	-0.002	-0.009	26.979	-0.044	-0.044	0.000	0.000	0.000	0.000
144	A	169	LEU	0	-0.001	-0.005	31.250	-0.090	-0.090	0.000	0.000	0.000	0.000
145	A	170	ALA	0	-0.017	-0.003	34.203	-0.199	-0.199	0.000	0.000	0.000	0.000
146	A	171	HIS	0	-0.055	-0.023	30.015	-0.374	-0.374	0.000	0.000	0.000	0.000
147	A	172	GLU	-1	-0.733	-0.794	29.822	10.278	10.278	0.000	0.000	0.000	0.000
148	A	173	GLY	0	0.040	0.014	34.291	-0.171	-0.171	0.000	0.000	0.000	0.000
149	A	174	HIS	0	-0.096	-0.051	36.348	-0.408	-0.408	0.000	0.000	0.000	0.000
150	A	175	ARG	1	0.928	0.962	39.261	-6.907	-6.907	0.000	0.000	0.000	0.000
151	A	176	LEU	0	-0.014	-0.002	37.521	-0.202	-0.202	0.000	0.000	0.000	0.000

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