FMO DATABASE

FMODB ID: GN8M1

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	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	-1402197.494604
FMO2-HF: Nuclear repulsion	1344083.53224
FMO2-HF: Total energy	-58113.962364
FMO2-MP2: Total energy	-58283.341189

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.
-86.865	-78.583	1.366	-4.579	-5.069	0.035

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 : -0.917 / q_NPA : -0.962

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	0.970	0.996	2.912	-81.190	-74.826	0.442	-3.614	-3.192	0.028
4	A	9	ARG	1	0.867	0.920	5.423	-28.196	-28.196	0.000	0.000	0.000	0.000
5	A	10	THR	0	0.037	0.033	9.065	0.890	0.890	0.000	0.000	0.000	0.000
6	A	11	THR	0	-0.042	-0.005	12.269	-0.913	-0.913	0.000	0.000	0.000	0.000
7	A	12	LEU	0	0.053	0.026	15.917	0.244	0.244	0.000	0.000	0.000	0.000
8	A	13	ASP	-1	-0.896	-0.942	19.042	13.186	13.186	0.000	0.000	0.000	0.000
9	A	14	SER	0	0.003	-0.012	22.683	-0.140	-0.140	0.000	0.000	0.000	0.000
10	A	15	PRO	0	0.018	0.014	24.937	-0.095	-0.095	0.000	0.000	0.000	0.000
11	A	16	LEU	0	0.004	0.004	25.362	-0.261	-0.261	0.000	0.000	0.000	0.000
12	A	17	GLY	0	-0.019	0.005	24.892	-0.022	-0.022	0.000	0.000	0.000	0.000
13	A	18	LYS	1	0.892	0.938	19.814	-13.196	-13.196	0.000	0.000	0.000	0.000
14	A	19	LEU	0	0.042	0.025	18.989	0.132	0.132	0.000	0.000	0.000	0.000
15	A	20	GLU	-1	-0.899	-0.958	13.172	21.587	21.587	0.000	0.000	0.000	0.000
16	A	21	LEU	0	-0.016	-0.017	13.388	-0.012	-0.012	0.000	0.000	0.000	0.000
17	A	22	SER	0	-0.020	-0.010	9.226	1.846	1.846	0.000	0.000	0.000	0.000
18	A	23	GLY	0	0.039	-0.013	7.565	-2.127	-2.127	0.000	0.000	0.000	0.000
19	A	24	CYS	0	-0.024	0.013	2.387	-2.245	-0.907	0.926	-0.932	-1.332	0.007
20	A	25	GLU	-1	-0.912	-0.985	3.866	31.287	31.688	-0.001	-0.029	-0.371	0.000
21	A	26	GLN	0	-0.033	-0.013	4.644	-0.512	-0.333	-0.001	-0.004	-0.174	0.000
22	A	27	GLY	0	0.020	-0.001	7.059	-2.475	-2.475	0.000	0.000	0.000	0.000
23	A	28	LEU	0	-0.060	-0.045	8.234	2.196	2.196	0.000	0.000	0.000	0.000
24	A	29	HIS	0	-0.026	-0.022	8.415	0.132	0.132	0.000	0.000	0.000	0.000
25	A	30	GLU	-1	-0.966	-1.001	10.465	17.430	17.430	0.000	0.000	0.000	0.000
26	A	31	ILE	0	-0.020	0.010	13.607	0.968	0.968	0.000	0.000	0.000	0.000
27	A	32	LYS	1	0.975	0.986	16.322	-17.544	-17.544	0.000	0.000	0.000	0.000
28	A	33	LEU	0	0.020	-0.010	17.863	0.162	0.162	0.000	0.000	0.000	0.000
29	A	34	LEU	0	-0.057	-0.020	16.818	-0.190	-0.190	0.000	0.000	0.000	0.000
30	A	35	GLY	0	-0.016	0.011	20.929	-0.454	-0.454	0.000	0.000	0.000	0.000
31	A	56	PRO	0	0.005	0.001	6.765	-0.310	-0.310	0.000	0.000	0.000	0.000
32	A	57	GLU	-1	-0.859	-0.952	9.185	17.435	17.435	0.000	0.000	0.000	0.000
33	A	58	PRO	0	-0.015	0.007	8.788	-1.459	-1.459	0.000	0.000	0.000	0.000
34	A	59	LEU	0	0.030	0.007	9.203	-1.349	-1.349	0.000	0.000	0.000	0.000
35	A	60	MET	0	0.007	0.017	12.414	-1.547	-1.547	0.000	0.000	0.000	0.000
36	A	61	GLN	0	0.032	0.031	13.988	-1.779	-1.779	0.000	0.000	0.000	0.000
37	A	62	CYS	0	0.009	0.008	14.858	-1.199	-1.199	0.000	0.000	0.000	0.000
38	A	63	THR	0	-0.076	-0.050	15.309	-0.797	-0.797	0.000	0.000	0.000	0.000
39	A	64	ALA	0	0.005	0.007	17.874	-0.538	-0.538	0.000	0.000	0.000	0.000
40	A	65	TRP	0	0.050	0.026	19.661	-0.527	-0.527	0.000	0.000	0.000	0.000
41	A	66	LEU	0	0.005	-0.002	18.694	-0.628	-0.628	0.000	0.000	0.000	0.000
42	A	67	ASN	0	-0.038	-0.027	21.856	-0.179	-0.179	0.000	0.000	0.000	0.000
43	A	68	ALA	0	0.033	0.034	23.790	-0.467	-0.467	0.000	0.000	0.000	0.000
44	A	69	TYR	0	-0.052	-0.077	24.910	-0.452	-0.452	0.000	0.000	0.000	0.000
45	A	70	PHE	0	-0.032	-0.038	23.525	-0.325	-0.325	0.000	0.000	0.000	0.000
46	A	71	HIS	0	-0.039	-0.028	26.100	-0.634	-0.634	0.000	0.000	0.000	0.000
47	A	72	GLN	0	-0.019	0.000	28.895	-0.169	-0.169	0.000	0.000	0.000	0.000
48	A	73	PRO	0	0.001	0.007	29.629	0.152	0.152	0.000	0.000	0.000	0.000
49	A	74	GLU	-1	-0.960	-0.980	30.662	8.428	8.428	0.000	0.000	0.000	0.000
50	A	75	ALA	0	-0.013	0.004	30.699	-0.170	-0.170	0.000	0.000	0.000	0.000
51	A	76	ILE	0	0.006	0.004	24.651	0.317	0.317	0.000	0.000	0.000	0.000
52	A	77	GLU	-1	-0.921	-0.980	26.049	10.442	10.442	0.000	0.000	0.000	0.000
53	A	78	GLU	-1	-0.993	-0.980	26.805	10.414	10.414	0.000	0.000	0.000	0.000
54	A	79	PHE	0	-0.029	-0.010	22.299	0.498	0.498	0.000	0.000	0.000	0.000
55	A	80	PRO	0	-0.011	0.006	19.075	-0.188	-0.188	0.000	0.000	0.000	0.000
56	A	81	VAL	0	-0.004	-0.015	18.621	0.497	0.497	0.000	0.000	0.000	0.000
57	A	82	PRO	0	-0.006	0.000	13.866	0.200	0.200	0.000	0.000	0.000	0.000
58	A	83	ALA	0	0.038	0.033	11.830	-0.533	-0.533	0.000	0.000	0.000	0.000
59	A	84	LEU	0	-0.021	-0.003	12.224	1.170	1.170	0.000	0.000	0.000	0.000
60	A	85	HIS	0	0.021	0.004	6.390	-1.823	-1.823	0.000	0.000	0.000	0.000
61	A	86	HIS	0	0.042	0.022	10.514	-0.321	-0.321	0.000	0.000	0.000	0.000
62	A	87	PRO	0	-0.010	-0.009	10.974	-0.948	-0.948	0.000	0.000	0.000	0.000
63	A	88	VAL	0	-0.030	-0.004	13.428	-1.024	-1.024	0.000	0.000	0.000	0.000
64	A	89	PHE	0	-0.009	-0.024	13.940	-1.128	-1.128	0.000	0.000	0.000	0.000
65	A	90	GLN	0	0.002	0.015	10.205	-1.052	-1.052	0.000	0.000	0.000	0.000
66	A	91	GLN	0	-0.012	-0.011	15.836	-1.199	-1.199	0.000	0.000	0.000	0.000
67	A	92	GLU	-1	-0.855	-0.939	18.862	11.385	11.385	0.000	0.000	0.000	0.000
68	A	93	SER	0	-0.022	-0.016	21.931	-0.239	-0.239	0.000	0.000	0.000	0.000
69	A	94	PHE	0	0.027	0.015	24.372	-0.111	-0.111	0.000	0.000	0.000	0.000
70	A	95	THR	0	0.031	0.008	21.545	-0.247	-0.247	0.000	0.000	0.000	0.000
71	A	96	ARG	1	0.916	0.996	18.983	-12.983	-12.983	0.000	0.000	0.000	0.000
72	A	97	GLN	0	0.066	0.048	22.124	0.243	0.243	0.000	0.000	0.000	0.000
73	A	98	VAL	0	-0.007	-0.019	25.372	-0.138	-0.138	0.000	0.000	0.000	0.000
74	A	99	LEU	0	-0.017	-0.018	20.018	-0.134	-0.134	0.000	0.000	0.000	0.000
75	A	100	TRP	0	0.024	0.022	18.680	-0.179	-0.179	0.000	0.000	0.000	0.000
76	A	101	LYS	1	0.861	0.921	23.581	-9.607	-9.607	0.000	0.000	0.000	0.000
77	A	102	LEU	0	-0.037	-0.019	25.271	-0.365	-0.365	0.000	0.000	0.000	0.000
78	A	103	LEU	0	0.019	0.005	20.750	-0.172	-0.172	0.000	0.000	0.000	0.000
79	A	104	LYS	1	0.903	0.963	24.831	-10.041	-10.041	0.000	0.000	0.000	0.000
80	A	105	VAL	0	-0.080	-0.055	26.751	-0.189	-0.189	0.000	0.000	0.000	0.000
81	A	106	VAL	0	0.017	0.020	28.790	-0.194	-0.194	0.000	0.000	0.000	0.000
82	A	107	LYS	1	0.899	0.947	27.965	-9.471	-9.471	0.000	0.000	0.000	0.000
83	A	108	PHE	0	0.043	0.003	29.361	-0.164	-0.164	0.000	0.000	0.000	0.000
84	A	109	GLY	0	0.063	0.052	31.397	-0.204	-0.204	0.000	0.000	0.000	0.000
85	A	110	GLU	-1	-0.939	-0.953	33.204	8.424	8.424	0.000	0.000	0.000	0.000
86	A	111	VAL	0	-0.030	-0.034	33.593	0.210	0.210	0.000	0.000	0.000	0.000
87	A	112	ILE	0	-0.026	-0.002	31.875	-0.216	-0.216	0.000	0.000	0.000	0.000
88	A	113	SER	0	0.003	-0.010	33.998	0.150	0.150	0.000	0.000	0.000	0.000
89	A	114	TYR	0	0.038	-0.003	31.257	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	115	GLN	0	0.003	-0.017	34.179	0.054	0.054	0.000	0.000	0.000	0.000
91	A	116	GLN	0	0.035	0.038	36.429	0.075	0.075	0.000	0.000	0.000	0.000
92	A	117	LEU	0	0.032	0.023	28.546	0.028	0.028	0.000	0.000	0.000	0.000
93	A	118	ALA	0	-0.034	-0.007	31.893	0.197	0.197	0.000	0.000	0.000	0.000
94	A	119	ALA	0	-0.025	-0.033	33.637	0.052	0.052	0.000	0.000	0.000	0.000
95	A	120	LEU	0	-0.042	0.009	31.674	0.000	0.000	0.000	0.000	0.000	0.000
96	A	121	ALA	0	-0.019	-0.008	28.978	0.080	0.080	0.000	0.000	0.000	0.000
97	A	122	GLY	0	0.048	0.015	30.585	0.131	0.131	0.000	0.000	0.000	0.000
98	A	123	ASN	0	-0.010	-0.004	33.328	-0.430	-0.430	0.000	0.000	0.000	0.000
99	A	124	PRO	0	0.073	0.025	35.118	0.117	0.117	0.000	0.000	0.000	0.000
100	A	125	LYS	1	0.959	0.982	37.495	-7.198	-7.198	0.000	0.000	0.000	0.000
101	A	126	ALA	0	-0.054	-0.010	32.996	-0.038	-0.038	0.000	0.000	0.000	0.000
102	A	127	ALA	0	0.092	0.032	33.084	0.248	0.248	0.000	0.000	0.000	0.000
103	A	128	ARG	1	0.957	0.975	33.159	-7.807	-7.807	0.000	0.000	0.000	0.000
104	A	129	ALA	0	0.010	0.005	30.104	0.161	0.161	0.000	0.000	0.000	0.000
105	A	130	VAL	0	0.038	0.027	28.903	0.367	0.367	0.000	0.000	0.000	0.000
106	A	131	GLY	0	-0.003	0.007	28.420	0.280	0.280	0.000	0.000	0.000	0.000
107	A	132	GLY	0	-0.004	-0.013	27.363	0.256	0.256	0.000	0.000	0.000	0.000
108	A	133	ALA	0	0.026	0.025	24.742	0.448	0.448	0.000	0.000	0.000	0.000
109	A	134	MET	0	0.009	0.003	23.731	0.496	0.496	0.000	0.000	0.000	0.000
110	A	135	ARG	1	0.840	0.929	24.485	-10.753	-10.753	0.000	0.000	0.000	0.000
111	A	136	GLY	0	-0.005	-0.024	21.731	0.281	0.281	0.000	0.000	0.000	0.000
112	A	137	ASN	0	0.023	0.027	19.950	1.051	1.051	0.000	0.000	0.000	0.000
113	A	138	PRO	0	0.037	0.029	15.464	-0.201	-0.201	0.000	0.000	0.000	0.000
114	A	139	VAL	0	-0.007	-0.013	15.628	0.989	0.989	0.000	0.000	0.000	0.000
115	A	140	PRO	0	0.053	0.036	18.320	-0.624	-0.624	0.000	0.000	0.000	0.000
116	A	141	ILE	0	-0.004	0.004	21.150	0.350	0.350	0.000	0.000	0.000	0.000
117	A	142	LEU	0	0.006	-0.007	17.241	-0.308	-0.308	0.000	0.000	0.000	0.000
118	A	143	ILE	0	-0.036	0.003	19.697	-0.475	-0.475	0.000	0.000	0.000	0.000
119	A	144	PRO	0	0.003	-0.010	22.411	0.015	0.015	0.000	0.000	0.000	0.000
120	A	145	SER	0	0.030	-0.004	24.194	-0.246	-0.246	0.000	0.000	0.000	0.000
121	A	146	HIS	0	-0.092	-0.070	26.768	-0.115	-0.115	0.000	0.000	0.000	0.000
122	A	147	ARG	1	0.852	0.910	27.625	-10.426	-10.426	0.000	0.000	0.000	0.000
123	A	148	VAL	0	-0.011	0.011	29.196	-0.292	-0.292	0.000	0.000	0.000	0.000
124	A	149	VAL	0	-0.006	0.004	32.016	0.086	0.086	0.000	0.000	0.000	0.000
125	A	150	CYS	0	-0.080	-0.058	35.288	0.008	0.008	0.000	0.000	0.000	0.000
126	A	151	SER	0	0.070	0.012	38.094	0.008	0.008	0.000	0.000	0.000	0.000
127	A	152	SER	0	-0.071	-0.019	40.486	-0.040	-0.040	0.000	0.000	0.000	0.000
128	A	153	GLY	0	0.054	0.037	41.492	-0.154	-0.154	0.000	0.000	0.000	0.000
129	A	154	ALA	0	-0.023	-0.007	40.787	0.099	0.099	0.000	0.000	0.000	0.000
130	A	155	VAL	0	0.163	0.073	35.531	0.123	0.123	0.000	0.000	0.000	0.000
131	A	156	GLY	0	0.029	0.028	35.499	0.254	0.254	0.000	0.000	0.000	0.000
132	A	157	ASN	0	0.011	0.004	32.888	0.263	0.263	0.000	0.000	0.000	0.000
133	A	158	TYR	0	0.045	-0.009	25.335	0.073	0.073	0.000	0.000	0.000	0.000
134	A	159	SER	0	0.007	0.007	23.858	-0.062	-0.062	0.000	0.000	0.000	0.000
135	A	160	GLY	0	0.011	0.019	25.454	-0.059	-0.059	0.000	0.000	0.000	0.000
136	A	161	GLY	0	0.017	0.007	26.017	-0.040	-0.040	0.000	0.000	0.000	0.000
137	A	162	LEU	0	-0.063	-0.046	29.725	0.106	0.106	0.000	0.000	0.000	0.000
138	A	163	ALA	0	0.056	0.043	31.982	-0.103	-0.103	0.000	0.000	0.000	0.000
139	A	164	VAL	0	0.026	0.017	26.879	-0.099	-0.099	0.000	0.000	0.000	0.000
140	A	165	LYS	1	0.767	0.879	30.240	-9.219	-9.219	0.000	0.000	0.000	0.000
141	A	166	GLU	-1	-0.907	-0.957	31.253	8.113	8.113	0.000	0.000	0.000	0.000
142	A	167	TRP	0	0.032	0.012	29.763	0.000	0.000	0.000	0.000	0.000	0.000
143	A	168	LEU	0	0.000	-0.012	27.061	-0.007	-0.007	0.000	0.000	0.000	0.000
144	A	169	LEU	0	0.003	0.005	31.458	-0.094	-0.094	0.000	0.000	0.000	0.000
145	A	170	ALA	0	-0.025	-0.007	34.197	-0.184	-0.184	0.000	0.000	0.000	0.000
146	A	171	HIS	0	-0.021	-0.009	30.405	-0.303	-0.303	0.000	0.000	0.000	0.000
147	A	172	GLU	-1	-0.799	-0.794	29.822	9.895	9.895	0.000	0.000	0.000	0.000
148	A	173	GLY	0	0.031	0.007	34.279	-0.143	-0.143	0.000	0.000	0.000	0.000
149	A	174	HIS	0	-0.054	-0.011	35.600	-0.402	-0.402	0.000	0.000	0.000	0.000
150	A	175	ARG	1	0.933	0.963	39.080	-6.754	-6.754	0.000	0.000	0.000	0.000
151	A	176	LEU	0	-0.001	-0.001	38.062	-0.042	-0.042	0.000	0.000	0.000	0.000

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