FMO DATABASE

FMODB ID: R1J88

Calculation Name: 3Q0B-X-Xray308

Preferred Name:

Target Type:

Ligand Name: 5-methyl-2'-deoxy-cytidine-5'-monophosphate

ligand 3-letter code: 5CM

PDB ID: 3Q0B

Chain ID: X

ChEMBL ID:

UniProt ID: O82175

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	156
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1487262.319725
FMO2-HF: Nuclear repulsion	1427947.152762
FMO2-HF: Total energy	-59315.166963
FMO2-MP2: Total energy	-59491.364132

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(X:362:GLN )

Summations of interaction energy for fragment #1(X:362:GLN )

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.
-22.787	-11.66	12.216	-8.031	-15.315	-0.042

Interaction energy analysis for fragmet #1(X:362:GLN )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.065 / q_NPA : -0.057

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	X	364	ILE	0	0.024	0.024	3.808	1.240	3.099	-0.018	-0.756	-1.086	0.001
4	X	365	GLY	0	0.000	0.009	6.214	-0.362	-0.362	0.000	0.000	0.000	0.000
5	X	366	THR	0	0.031	0.000	8.341	0.665	0.665	0.000	0.000	0.000	0.000
6	X	367	VAL	0	0.014	0.020	6.764	0.347	0.347	0.000	0.000	0.000	0.000
7	X	368	PRO	0	-0.031	-0.028	9.232	-0.429	-0.429	0.000	0.000	0.000	0.000
8	X	369	GLY	0	0.022	0.015	12.142	0.190	0.190	0.000	0.000	0.000	0.000
9	X	370	VAL	0	-0.041	-0.006	11.024	0.000	0.000	0.000	0.000	0.000	0.000
10	X	371	GLU	-1	-0.895	-0.951	13.992	1.104	1.104	0.000	0.000	0.000	0.000
11	X	372	VAL	0	-0.077	-0.055	16.425	0.004	0.004	0.000	0.000	0.000	0.000
12	X	373	GLY	0	-0.013	-0.012	17.532	-0.059	-0.059	0.000	0.000	0.000	0.000
13	X	374	ASP	-1	-0.847	-0.887	16.369	1.024	1.024	0.000	0.000	0.000	0.000
14	X	375	GLU	-1	-0.959	-0.987	17.472	0.492	0.492	0.000	0.000	0.000	0.000
15	X	376	PHE	0	0.021	-0.018	14.354	0.056	0.056	0.000	0.000	0.000	0.000
16	X	377	GLN	0	-0.041	-0.015	17.982	-0.146	-0.146	0.000	0.000	0.000	0.000
17	X	378	TYR	0	0.016	-0.001	17.599	-0.113	-0.113	0.000	0.000	0.000	0.000
18	X	379	ARG	1	0.896	0.931	10.637	0.079	0.079	0.000	0.000	0.000	0.000
19	X	380	MET	0	-0.014	-0.019	12.049	0.121	0.121	0.000	0.000	0.000	0.000
20	X	381	GLU	-1	-0.817	-0.915	12.885	1.048	1.048	0.000	0.000	0.000	0.000
21	X	382	LEU	0	0.013	0.013	10.129	0.262	0.262	0.000	0.000	0.000	0.000
22	X	383	ASN	0	-0.100	-0.047	8.292	1.019	1.019	0.000	0.000	0.000	0.000
23	X	384	LEU	0	0.011	0.004	8.145	0.795	0.795	0.000	0.000	0.000	0.000
24	X	385	LEU	0	-0.010	-0.003	9.680	0.260	0.260	0.000	0.000	0.000	0.000
25	X	386	GLY	0	-0.010	0.003	5.410	0.548	0.548	0.000	0.000	0.000	0.000
26	X	387	ILE	0	-0.025	0.008	5.214	1.926	1.926	0.000	0.000	0.000	0.000
27	X	388	HIS	0	-0.006	0.008	5.884	0.111	0.111	0.000	0.000	0.000	0.000
28	X	389	ARG	1	0.873	0.936	2.454	0.747	1.988	5.357	-1.596	-5.002	0.001
29	X	390	PRO	0	-0.017	0.014	5.649	-0.120	-0.120	0.000	0.000	0.000	0.000
30	X	391	SER	0	0.049	0.022	8.879	0.267	0.267	0.000	0.000	0.000	0.000
31	X	392	GLN	0	-0.015	-0.018	12.494	0.030	0.030	0.000	0.000	0.000	0.000
32	X	393	SER	0	0.007	0.012	9.519	0.137	0.137	0.000	0.000	0.000	0.000
33	X	394	GLY	0	0.069	0.044	10.336	0.108	0.108	0.000	0.000	0.000	0.000
34	X	395	ILE	0	0.022	0.030	7.165	0.126	0.126	0.000	0.000	0.000	0.000
35	X	396	ASP	-1	-0.795	-0.893	3.297	-5.804	-4.490	0.293	-0.621	-0.986	-0.003
36	X	397	TYR	0	0.016	0.008	3.541	0.516	1.186	0.027	-0.183	-0.515	0.000
37	X	398	MET	0	-0.038	-0.011	2.257	-12.479	-9.330	4.285	-2.859	-4.576	-0.024
38	X	399	LYS	1	0.926	0.956	3.598	3.643	3.924	0.023	-0.097	-0.207	0.000
39	X	400	ASP	-1	-0.846	-0.925	6.334	-1.706	-1.706	0.000	0.000	0.000	0.000
40	X	401	ASP	-1	-0.917	-0.957	8.638	-0.813	-0.813	0.000	0.000	0.000	0.000
41	X	402	GLY	0	0.032	0.015	11.553	0.160	0.160	0.000	0.000	0.000	0.000
42	X	403	GLY	0	-0.089	-0.050	11.805	-0.184	-0.184	0.000	0.000	0.000	0.000
43	X	404	GLU	-1	-0.932	-0.957	11.898	-1.293	-1.293	0.000	0.000	0.000	0.000
44	X	405	LEU	0	-0.046	-0.022	7.338	-0.349	-0.349	0.000	0.000	0.000	0.000
45	X	406	VAL	0	0.078	0.033	6.509	0.581	0.581	0.000	0.000	0.000	0.000
46	X	407	ALA	0	0.000	-0.010	5.554	-1.661	-1.661	0.000	0.000	0.000	0.000
47	X	408	THR	0	0.024	-0.001	2.215	-8.878	-6.809	2.243	-1.741	-2.571	-0.018
48	X	409	SER	0	-0.017	-0.043	4.505	1.708	1.788	0.000	-0.011	-0.069	0.000
49	X	410	ILE	0	-0.006	0.004	6.545	-0.933	-0.933	0.000	0.000	0.000	0.000
50	X	411	VAL	0	-0.026	-0.009	9.450	0.352	0.352	0.000	0.000	0.000	0.000
51	X	412	SER	0	-0.040	-0.012	12.256	-0.127	-0.127	0.000	0.000	0.000	0.000
52	X	413	SER	0	0.075	0.018	15.817	0.075	0.075	0.000	0.000	0.000	0.000
53	X	414	GLY	0	0.018	0.013	18.268	0.010	0.010	0.000	0.000	0.000	0.000
54	X	415	GLY	0	-0.076	-0.056	19.056	-0.016	-0.016	0.000	0.000	0.000	0.000
55	X	416	TYR	0	0.026	0.000	17.295	-0.023	-0.023	0.000	0.000	0.000	0.000
56	X	417	ASN	0	-0.015	0.025	20.873	-0.003	-0.003	0.000	0.000	0.000	0.000
57	X	418	ASP	-1	-0.792	-0.873	17.799	-0.267	-0.267	0.000	0.000	0.000	0.000
58	X	419	VAL	0	-0.040	-0.027	20.655	0.031	0.031	0.000	0.000	0.000	0.000
59	X	420	LEU	0	0.004	-0.010	18.104	-0.001	-0.001	0.000	0.000	0.000	0.000
60	X	421	ASP	-1	-0.852	-0.891	22.330	0.029	0.029	0.000	0.000	0.000	0.000
61	X	422	ASN	0	-0.035	-0.036	23.822	0.019	0.019	0.000	0.000	0.000	0.000
62	X	423	SER	0	-0.034	-0.029	24.771	0.012	0.012	0.000	0.000	0.000	0.000
63	X	424	ASP	-1	-0.845	-0.917	21.894	0.084	0.084	0.000	0.000	0.000	0.000
64	X	425	VAL	0	-0.032	-0.018	20.610	-0.015	-0.015	0.000	0.000	0.000	0.000
65	X	426	LEU	0	0.026	0.032	15.967	0.003	0.003	0.000	0.000	0.000	0.000
66	X	427	ILE	0	-0.025	-0.016	18.914	-0.054	-0.054	0.000	0.000	0.000	0.000
67	X	428	TYR	0	-0.010	-0.023	12.524	-0.051	-0.051	0.000	0.000	0.000	0.000
68	X	429	THR	0	-0.011	-0.017	17.178	-0.048	-0.048	0.000	0.000	0.000	0.000
69	X	430	GLY	0	0.032	0.027	15.420	-0.070	-0.070	0.000	0.000	0.000	0.000
70	X	431	GLN	0	-0.033	0.000	11.518	-0.096	-0.096	0.000	0.000	0.000	0.000
71	X	432	GLY	0	0.023	-0.002	15.838	-0.035	-0.035	0.000	0.000	0.000	0.000
72	X	433	GLY	0	0.075	0.008	18.475	0.051	0.051	0.000	0.000	0.000	0.000
73	X	434	ASN	0	-0.115	-0.079	21.449	0.020	0.020	0.000	0.000	0.000	0.000
74	X	435	VAL	0	0.041	0.036	21.285	0.047	0.047	0.000	0.000	0.000	0.000
75	X	436	GLY	0	0.017	0.020	22.037	-0.008	-0.008	0.000	0.000	0.000	0.000
76	X	437	LYS	1	0.882	0.952	18.532	0.085	0.085	0.000	0.000	0.000	0.000
77	X	438	LYS	1	0.810	0.895	18.965	0.338	0.338	0.000	0.000	0.000	0.000
78	X	439	LYS	1	0.874	0.925	21.257	0.326	0.326	0.000	0.000	0.000	0.000
79	X	440	ASN	0	0.024	0.016	24.181	-0.028	-0.028	0.000	0.000	0.000	0.000
80	X	441	ASN	0	0.019	-0.004	27.068	0.009	0.009	0.000	0.000	0.000	0.000
81	X	442	GLU	-1	-0.819	-0.882	24.570	-0.360	-0.360	0.000	0.000	0.000	0.000
82	X	443	PRO	0	0.052	0.027	28.182	0.007	0.007	0.000	0.000	0.000	0.000
83	X	444	PRO	0	0.032	0.030	26.799	-0.031	-0.031	0.000	0.000	0.000	0.000
84	X	445	LYS	1	0.883	0.949	22.135	0.506	0.506	0.000	0.000	0.000	0.000
85	X	446	ASP	-1	-0.777	-0.889	24.138	-0.394	-0.394	0.000	0.000	0.000	0.000
86	X	447	GLN	0	-0.109	-0.066	18.841	-0.056	-0.056	0.000	0.000	0.000	0.000
87	X	448	GLN	0	0.040	0.010	18.343	0.041	0.041	0.000	0.000	0.000	0.000
88	X	449	LEU	0	0.017	0.020	15.929	-0.102	-0.102	0.000	0.000	0.000	0.000
89	X	450	VAL	0	0.020	0.000	14.157	-0.025	-0.025	0.000	0.000	0.000	0.000
90	X	451	THR	0	-0.016	-0.012	9.354	0.000	0.000	0.000	0.000	0.000	0.000
91	X	452	GLY	0	0.087	0.037	8.757	-0.152	-0.152	0.000	0.000	0.000	0.000
92	X	453	ASN	0	0.021	0.015	9.740	0.062	0.062	0.000	0.000	0.000	0.000
93	X	454	LEU	0	-0.029	-0.006	12.445	0.114	0.114	0.000	0.000	0.000	0.000
94	X	455	ALA	0	-0.003	0.003	7.708	0.055	0.055	0.000	0.000	0.000	0.000
95	X	456	LEU	0	0.016	0.002	9.803	0.141	0.141	0.000	0.000	0.000	0.000
96	X	457	LYS	1	0.920	0.970	11.062	0.916	0.916	0.000	0.000	0.000	0.000
97	X	458	ASN	0	-0.007	-0.010	11.592	0.313	0.313	0.000	0.000	0.000	0.000
98	X	459	SER	0	-0.027	-0.031	9.526	-0.056	-0.056	0.000	0.000	0.000	0.000
99	X	460	ILE	0	-0.061	0.004	11.887	0.184	0.184	0.000	0.000	0.000	0.000
100	X	461	ASN	0	-0.043	-0.028	15.548	0.123	0.123	0.000	0.000	0.000	0.000
101	X	462	LYS	1	0.891	0.956	11.792	0.943	0.943	0.000	0.000	0.000	0.000
102	X	463	LYS	1	0.930	0.981	14.278	0.374	0.374	0.000	0.000	0.000	0.000
103	X	464	ASN	0	-0.005	0.016	8.053	-0.042	-0.042	0.000	0.000	0.000	0.000
104	X	465	PRO	0	0.024	-0.005	10.580	-0.046	-0.046	0.000	0.000	0.000	0.000
105	X	466	VAL	0	-0.036	0.001	7.974	-0.012	-0.012	0.000	0.000	0.000	0.000
106	X	467	ARG	1	0.778	0.864	3.452	-8.490	-8.026	0.006	-0.167	-0.303	0.001
107	X	468	VAL	0	0.040	0.028	9.442	-0.338	-0.338	0.000	0.000	0.000	0.000
108	X	469	ILE	0	-0.007	0.003	9.770	0.171	0.171	0.000	0.000	0.000	0.000
109	X	470	ARG	1	0.912	0.966	13.304	-0.483	-0.483	0.000	0.000	0.000	0.000
110	X	471	GLY	0	-0.061	-0.058	16.714	0.062	0.062	0.000	0.000	0.000	0.000
111	X	472	ILE	0	-0.049	-0.022	18.620	-0.049	-0.049	0.000	0.000	0.000	0.000
112	X	473	LYS	1	0.937	0.953	22.095	-0.084	-0.084	0.000	0.000	0.000	0.000
113	X	474	NME	0	0.056	0.046	25.217	0.015	0.015	0.000	0.000	0.000	0.000
114	X	483	ACE	0	0.026	0.008	20.609	0.017	0.017	0.000	0.000	0.000	0.000
115	X	484	LYS	1	0.898	0.936	21.125	-0.439	-0.439	0.000	0.000	0.000	0.000
116	X	485	ASN	0	-0.030	-0.001	19.979	-0.074	-0.074	0.000	0.000	0.000	0.000
117	X	486	TYR	0	-0.076	-0.037	15.738	-0.107	-0.107	0.000	0.000	0.000	0.000
118	X	487	VAL	0	0.087	0.057	17.434	0.054	0.054	0.000	0.000	0.000	0.000
119	X	488	TYR	0	-0.017	-0.005	11.443	0.046	0.046	0.000	0.000	0.000	0.000
120	X	489	ASP	-1	-0.761	-0.883	14.652	0.312	0.312	0.000	0.000	0.000	0.000
121	X	490	GLY	0	0.039	0.038	14.362	-0.089	-0.089	0.000	0.000	0.000	0.000
122	X	491	LEU	0	-0.083	-0.051	10.714	0.020	0.020	0.000	0.000	0.000	0.000
123	X	492	TYR	0	0.001	-0.024	12.671	-0.127	-0.127	0.000	0.000	0.000	0.000
124	X	493	LEU	0	0.004	0.010	12.811	-0.004	-0.004	0.000	0.000	0.000	0.000
125	X	494	VAL	0	-0.001	-0.004	12.120	0.012	0.012	0.000	0.000	0.000	0.000
126	X	495	GLU	-1	-0.886	-0.958	15.025	-0.114	-0.114	0.000	0.000	0.000	0.000
127	X	496	GLU	-1	-0.906	-0.968	18.439	-0.268	-0.268	0.000	0.000	0.000	0.000
128	X	497	TYR	0	0.007	-0.011	17.564	-0.048	-0.048	0.000	0.000	0.000	0.000
129	X	498	TRP	0	-0.051	-0.030	19.563	0.018	0.018	0.000	0.000	0.000	0.000
130	X	499	GLU	-1	-0.898	-0.965	21.697	-0.488	-0.488	0.000	0.000	0.000	0.000
131	X	500	GLU	-1	-0.840	-0.911	23.958	-0.218	-0.218	0.000	0.000	0.000	0.000
132	X	501	THR	0	-0.020	-0.013	26.117	-0.022	-0.022	0.000	0.000	0.000	0.000
133	X	502	GLY	0	0.043	0.024	27.814	0.021	0.021	0.000	0.000	0.000	0.000
134	X	503	SER	0	0.016	0.003	28.857	0.000	0.000	0.000	0.000	0.000	0.000
135	X	504	HIS	0	-0.034	-0.014	26.696	0.015	0.015	0.000	0.000	0.000	0.000
136	X	505	GLY	0	-0.023	-0.012	31.590	-0.003	-0.003	0.000	0.000	0.000	0.000
137	X	506	LYS	1	0.880	0.950	26.669	0.282	0.282	0.000	0.000	0.000	0.000
138	X	507	LEU	0	0.015	0.018	23.033	0.013	0.013	0.000	0.000	0.000	0.000
139	X	508	VAL	0	-0.047	-0.029	21.478	-0.027	-0.027	0.000	0.000	0.000	0.000
140	X	509	PHE	0	0.014	0.006	17.980	-0.002	-0.002	0.000	0.000	0.000	0.000
141	X	510	LYS	1	0.856	0.943	19.288	0.298	0.298	0.000	0.000	0.000	0.000
142	X	511	PHE	0	0.004	-0.013	15.179	-0.048	-0.048	0.000	0.000	0.000	0.000
143	X	512	LYS	1	0.949	0.993	17.436	0.216	0.216	0.000	0.000	0.000	0.000
144	X	513	LEU	0	-0.028	-0.022	12.437	-0.043	-0.043	0.000	0.000	0.000	0.000
145	X	514	ARG	1	0.873	0.937	16.987	0.057	0.057	0.000	0.000	0.000	0.000
146	X	515	ARG	1	0.794	0.884	17.308	-0.405	-0.405	0.000	0.000	0.000	0.000
147	X	516	ILE	0	-0.034	-0.017	15.053	-0.035	-0.035	0.000	0.000	0.000	0.000
148	X	517	PRO	0	0.033	0.007	18.854	0.051	0.051	0.000	0.000	0.000	0.000
149	X	518	GLY	0	0.018	0.004	21.243	0.027	0.027	0.000	0.000	0.000	0.000
150	X	519	GLN	0	-0.060	-0.016	16.412	0.166	0.166	0.000	0.000	0.000	0.000
151	X	520	PRO	0	0.055	0.023	19.736	-0.054	-0.054	0.000	0.000	0.000	0.000
152	X	521	GLU	-1	-0.904	-0.938	21.658	0.274	0.274	0.000	0.000	0.000	0.000
153	X	522	LEU	0	-0.029	-0.017	19.302	0.031	0.031	0.000	0.000	0.000	0.000
154	X	523	PRO	0	0.016	0.014	23.736	-0.041	-0.041	0.000	0.000	0.000	0.000
155	X	524	TRP	0	-0.009	-0.026	23.216	0.008	0.008	0.000	0.000	0.000	0.000
156	X	1	NME	0	-0.014	0.018	27.432	-0.010	-0.010	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(X:362:GLN )