FMO DATABASE

FMODB ID: M3LYZ

Calculation Name: 3Q0B-X-Xray372

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: 2023-03-14

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	153
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1476922.258572
FMO2-HF: Nuclear repulsion	1417796.488105
FMO2-HF: Total energy	-59125.770467
FMO2-MP2: Total energy	-59301.263515

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.
-26.986	-17.297	17.695	-9.873	-17.51	-0.035

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 : -0.030 / q_NPA : -0.032

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	0.028	0.019	3.761	1.499	4.302	-0.016	-1.273	-1.514	0.004
4	X	365	GLY	0	0.008	0.014	5.864	-0.625	-0.625	0.000	0.000	0.000	0.000
5	X	366	THR	0	0.028	-0.005	8.064	0.539	0.539	0.000	0.000	0.000	0.000
6	X	367	VAL	0	-0.001	0.013	6.753	0.150	0.150	0.000	0.000	0.000	0.000
7	X	368	PRO	0	-0.017	-0.024	8.522	-0.195	-0.195	0.000	0.000	0.000	0.000
8	X	369	GLY	0	0.015	0.013	11.414	0.099	0.099	0.000	0.000	0.000	0.000
9	X	370	VAL	0	-0.038	-0.004	11.080	0.030	0.030	0.000	0.000	0.000	0.000
10	X	371	GLU	-1	-0.912	-0.953	13.979	0.620	0.620	0.000	0.000	0.000	0.000
11	X	372	VAL	0	-0.060	-0.048	16.083	0.015	0.015	0.000	0.000	0.000	0.000
12	X	373	GLY	0	-0.006	-0.011	17.355	-0.039	-0.039	0.000	0.000	0.000	0.000
13	X	374	ASP	-1	-0.858	-0.902	16.286	0.618	0.618	0.000	0.000	0.000	0.000
14	X	375	GLU	-1	-0.945	-0.997	17.412	0.304	0.304	0.000	0.000	0.000	0.000
15	X	376	PHE	0	-0.011	-0.014	14.663	0.060	0.060	0.000	0.000	0.000	0.000
16	X	377	GLN	0	-0.025	-0.012	18.040	-0.102	-0.102	0.000	0.000	0.000	0.000
17	X	378	TYR	0	0.002	-0.006	17.615	-0.081	-0.081	0.000	0.000	0.000	0.000
18	X	379	ARG	1	0.868	0.909	10.664	0.053	0.053	0.000	0.000	0.000	0.000
19	X	380	MET	0	-0.010	-0.018	12.132	0.097	0.097	0.000	0.000	0.000	0.000
20	X	381	GLU	-1	-0.773	-0.885	12.886	0.741	0.741	0.000	0.000	0.000	0.000
21	X	382	LEU	0	0.025	0.013	10.254	0.151	0.151	0.000	0.000	0.000	0.000
22	X	383	ASN	0	-0.105	-0.054	8.269	0.659	0.659	0.000	0.000	0.000	0.000
23	X	384	LEU	0	-0.002	0.002	8.145	0.620	0.620	0.000	0.000	0.000	0.000
24	X	385	LEU	0	-0.001	0.000	9.179	0.087	0.087	0.000	0.000	0.000	0.000
25	X	386	GLY	0	-0.007	0.003	5.409	0.067	0.067	0.000	0.000	0.000	0.000
26	X	387	ILE	0	-0.026	0.008	5.209	1.664	1.664	0.000	0.000	0.000	0.000
27	X	388	HIS	0	-0.009	-0.006	5.770	0.188	0.188	0.000	0.000	0.000	0.000
28	X	389	ARG	1	0.874	0.923	2.236	-0.383	1.080	5.004	-1.594	-4.872	0.000
29	X	390	PRO	0	-0.033	0.005	5.699	0.003	0.003	0.000	0.000	0.000	0.000
30	X	391	SER	0	0.058	0.034	8.818	0.149	0.149	0.000	0.000	0.000	0.000
31	X	392	GLN	0	0.004	-0.010	12.416	-0.021	-0.021	0.000	0.000	0.000	0.000
32	X	393	SER	0	-0.010	0.011	9.357	0.094	0.094	0.000	0.000	0.000	0.000
33	X	394	GLY	0	0.073	0.041	10.365	0.069	0.069	0.000	0.000	0.000	0.000
34	X	395	ILE	0	0.018	0.028	7.186	0.071	0.071	0.000	0.000	0.000	0.000
35	X	396	ASP	-1	-0.798	-0.876	3.062	-6.374	-4.917	0.400	-0.714	-1.142	-0.004
36	X	397	TYR	0	0.021	0.008	3.397	0.084	0.815	0.035	-0.174	-0.592	0.000
37	X	398	MET	0	-0.023	-0.006	2.359	-10.450	-6.889	4.025	-2.865	-4.721	-0.021
38	X	399	LYS	1	0.923	0.959	3.792	2.272	2.537	0.011	-0.096	-0.181	0.000
39	X	400	ASP	-1	-0.822	-0.898	6.314	-1.176	-1.176	0.000	0.000	0.000	0.000
40	X	401	ASP	-1	-0.862	-0.926	8.630	-0.615	-0.615	0.000	0.000	0.000	0.000
41	X	402	GLY	0	0.048	0.026	11.534	0.100	0.100	0.000	0.000	0.000	0.000
42	X	403	GLY	0	-0.095	-0.057	11.777	-0.107	-0.107	0.000	0.000	0.000	0.000
43	X	404	GLU	-1	-0.922	-0.954	12.020	-0.972	-0.972	0.000	0.000	0.000	0.000
44	X	405	LEU	0	-0.049	-0.020	7.803	-0.243	-0.243	0.000	0.000	0.000	0.000
45	X	406	VAL	0	0.076	0.034	6.327	0.433	0.433	0.000	0.000	0.000	0.000
46	X	407	ALA	0	0.002	-0.010	5.456	-1.434	-1.434	0.000	0.000	0.000	0.000
47	X	408	THR	0	0.028	0.012	1.933	-10.376	-11.678	8.231	-2.897	-4.032	-0.016
48	X	409	SER	0	-0.016	-0.026	4.122	1.690	1.839	-0.001	-0.035	-0.113	0.000
49	X	410	ILE	0	-0.011	0.002	6.224	-0.834	-0.834	0.000	0.000	0.000	0.000
50	X	411	VAL	0	-0.017	-0.010	9.221	0.303	0.303	0.000	0.000	0.000	0.000
51	X	412	SER	0	-0.042	-0.028	12.077	-0.084	-0.084	0.000	0.000	0.000	0.000
52	X	413	SER	0	0.066	0.020	15.623	0.065	0.065	0.000	0.000	0.000	0.000
53	X	414	GLY	0	0.026	0.017	18.117	0.017	0.017	0.000	0.000	0.000	0.000
54	X	415	GLY	0	-0.077	-0.055	18.973	-0.006	-0.006	0.000	0.000	0.000	0.000
55	X	416	TYR	0	0.016	-0.017	17.024	-0.023	-0.023	0.000	0.000	0.000	0.000
56	X	417	ASN	0	0.004	0.024	20.780	-0.009	-0.009	0.000	0.000	0.000	0.000
57	X	418	ASP	-1	-0.768	-0.841	17.387	-0.275	-0.275	0.000	0.000	0.000	0.000
58	X	419	VAL	0	-0.053	-0.032	20.458	0.028	0.028	0.000	0.000	0.000	0.000
59	X	420	LEU	0	0.012	-0.005	17.846	-0.007	-0.007	0.000	0.000	0.000	0.000
60	X	421	ASP	-1	-0.836	-0.873	22.046	-0.018	-0.018	0.000	0.000	0.000	0.000
61	X	422	ASN	0	-0.043	-0.037	23.499	0.009	0.009	0.000	0.000	0.000	0.000
62	X	423	SER	0	-0.034	-0.040	24.496	0.009	0.009	0.000	0.000	0.000	0.000
63	X	424	ASP	-1	-0.836	-0.913	21.522	-0.006	-0.006	0.000	0.000	0.000	0.000
64	X	425	VAL	0	-0.030	-0.017	20.237	-0.015	-0.015	0.000	0.000	0.000	0.000
65	X	426	LEU	0	0.004	0.021	15.679	0.004	0.004	0.000	0.000	0.000	0.000
66	X	427	ILE	0	-0.014	-0.012	18.613	-0.042	-0.042	0.000	0.000	0.000	0.000
67	X	428	TYR	0	-0.005	-0.021	12.410	-0.044	-0.044	0.000	0.000	0.000	0.000
68	X	429	THR	0	-0.016	-0.013	16.960	-0.035	-0.035	0.000	0.000	0.000	0.000
69	X	430	GLY	0	0.034	0.027	15.337	-0.063	-0.063	0.000	0.000	0.000	0.000
70	X	431	GLN	0	-0.030	-0.004	11.252	-0.071	-0.071	0.000	0.000	0.000	0.000
71	X	432	GLY	0	0.034	0.004	15.842	-0.020	-0.020	0.000	0.000	0.000	0.000
72	X	433	GLY	0	0.058	0.008	18.384	0.034	0.034	0.000	0.000	0.000	0.000
73	X	434	ASN	0	-0.110	-0.070	21.345	0.014	0.014	0.000	0.000	0.000	0.000
74	X	435	VAL	0	0.055	0.042	21.350	0.035	0.035	0.000	0.000	0.000	0.000
75	X	436	GLY	0	0.043	0.030	22.058	-0.006	-0.006	0.000	0.000	0.000	0.000
76	X	437	LYS	1	0.860	0.944	18.101	0.085	0.085	0.000	0.000	0.000	0.000
77	X	438	LYS	1	0.799	0.885	19.458	0.221	0.221	0.000	0.000	0.000	0.000
78	X	439	LYS	1	0.891	0.925	22.066	0.181	0.181	0.000	0.000	0.000	0.000
79	X	440	ASN	0	-0.011	-0.014	25.001	-0.011	-0.011	0.000	0.000	0.000	0.000
80	X	441	ASN	0	-0.003	0.006	27.208	0.012	0.012	0.000	0.000	0.000	0.000
81	X	442	GLU	-1	-0.757	-0.842	24.283	-0.185	-0.185	0.000	0.000	0.000	0.000
82	X	443	PRO	0	0.026	0.017	28.102	0.001	0.001	0.000	0.000	0.000	0.000
83	X	444	PRO	0	0.023	0.015	26.712	-0.021	-0.021	0.000	0.000	0.000	0.000
84	X	445	LYS	1	0.870	0.936	21.939	0.375	0.375	0.000	0.000	0.000	0.000
85	X	446	ASP	-1	-0.751	-0.855	24.397	-0.288	-0.288	0.000	0.000	0.000	0.000
86	X	447	GLN	0	-0.059	-0.033	19.023	-0.034	-0.034	0.000	0.000	0.000	0.000
87	X	448	GLN	0	0.035	0.005	18.374	0.018	0.018	0.000	0.000	0.000	0.000
88	X	449	LEU	0	0.019	0.025	15.974	-0.083	-0.083	0.000	0.000	0.000	0.000
89	X	450	VAL	0	0.017	0.000	14.393	-0.007	-0.007	0.000	0.000	0.000	0.000
90	X	451	THR	0	-0.002	-0.014	9.585	-0.011	-0.011	0.000	0.000	0.000	0.000
91	X	452	GLY	0	0.088	0.043	8.633	-0.144	-0.144	0.000	0.000	0.000	0.000
92	X	453	ASN	0	0.008	0.006	9.616	0.020	0.020	0.000	0.000	0.000	0.000
93	X	454	LEU	0	-0.026	-0.005	12.341	0.088	0.088	0.000	0.000	0.000	0.000
94	X	455	ALA	0	-0.006	0.005	7.630	0.049	0.049	0.000	0.000	0.000	0.000
95	X	456	LEU	0	0.019	0.004	9.761	0.096	0.096	0.000	0.000	0.000	0.000
96	X	457	LYS	1	0.923	0.973	10.898	0.747	0.747	0.000	0.000	0.000	0.000
97	X	458	ASN	0	-0.006	-0.009	11.514	0.242	0.242	0.000	0.000	0.000	0.000
98	X	459	SER	0	-0.024	-0.036	9.300	-0.057	-0.057	0.000	0.000	0.000	0.000
99	X	460	ILE	0	-0.053	0.008	11.659	0.146	0.146	0.000	0.000	0.000	0.000
100	X	461	ASN	0	-0.031	-0.023	15.301	0.121	0.121	0.000	0.000	0.000	0.000
101	X	462	LYS	1	0.819	0.892	11.757	0.797	0.797	0.000	0.000	0.000	0.000
102	X	463	LYS	1	0.881	0.957	14.047	0.377	0.377	0.000	0.000	0.000	0.000
103	X	464	ASN	0	-0.011	0.025	7.764	-0.060	-0.060	0.000	0.000	0.000	0.000
104	X	465	PRO	0	0.026	-0.004	10.285	-0.056	-0.056	0.000	0.000	0.000	0.000
105	X	466	VAL	0	-0.041	-0.003	7.449	0.022	0.022	0.000	0.000	0.000	0.000
106	X	467	ARG	1	0.800	0.885	3.399	-7.607	-7.045	0.006	-0.225	-0.343	0.002
107	X	468	VAL	0	0.030	0.022	9.095	-0.302	-0.302	0.000	0.000	0.000	0.000
108	X	469	ILE	0	-0.015	-0.003	9.065	0.131	0.131	0.000	0.000	0.000	0.000
109	X	470	ARG	1	0.873	0.940	13.034	-0.296	-0.296	0.000	0.000	0.000	0.000
110	X	471	GLY	0	-0.053	-0.051	16.467	0.050	0.050	0.000	0.000	0.000	0.000
111	X	472	ILE	0	-0.049	-0.017	18.438	-0.037	-0.037	0.000	0.000	0.000	0.000
112	X	473	LYS	1	0.994	0.994	21.900	-0.026	-0.026	0.000	0.000	0.000	0.000
113	X	484	LYS	1	0.957	0.968	21.522	-0.250	-0.250	0.000	0.000	0.000	0.000
114	X	485	ASN	0	-0.071	-0.034	19.905	-0.051	-0.051	0.000	0.000	0.000	0.000
115	X	486	TYR	0	-0.070	-0.032	15.544	-0.076	-0.076	0.000	0.000	0.000	0.000
116	X	487	VAL	0	0.074	0.053	17.211	0.037	0.037	0.000	0.000	0.000	0.000
117	X	488	TYR	0	-0.025	-0.006	11.473	0.040	0.040	0.000	0.000	0.000	0.000
118	X	489	ASP	-1	-0.755	-0.872	14.310	0.144	0.144	0.000	0.000	0.000	0.000
119	X	490	GLY	0	0.063	0.042	14.141	-0.063	-0.063	0.000	0.000	0.000	0.000
120	X	491	LEU	0	-0.080	-0.054	10.350	0.024	0.024	0.000	0.000	0.000	0.000
121	X	492	TYR	0	0.003	-0.030	12.268	-0.091	-0.091	0.000	0.000	0.000	0.000
122	X	493	LEU	0	0.012	0.015	12.418	-0.003	-0.003	0.000	0.000	0.000	0.000
123	X	494	VAL	0	0.006	-0.006	11.873	0.009	0.009	0.000	0.000	0.000	0.000
124	X	495	GLU	-1	-0.834	-0.902	14.711	-0.141	-0.141	0.000	0.000	0.000	0.000
125	X	496	GLU	-1	-0.859	-0.928	18.167	-0.225	-0.225	0.000	0.000	0.000	0.000
126	X	497	TYR	0	-0.043	-0.037	17.384	-0.049	-0.049	0.000	0.000	0.000	0.000
127	X	498	TRP	0	-0.034	-0.014	19.366	0.018	0.018	0.000	0.000	0.000	0.000
128	X	499	GLU	-1	-0.861	-0.954	21.561	-0.418	-0.418	0.000	0.000	0.000	0.000
129	X	500	GLU	-1	-0.833	-0.913	23.849	-0.203	-0.203	0.000	0.000	0.000	0.000
130	X	501	THR	0	-0.017	-0.013	26.042	-0.016	-0.016	0.000	0.000	0.000	0.000
131	X	502	GLY	0	0.038	0.021	27.741	0.015	0.015	0.000	0.000	0.000	0.000
132	X	503	SER	0	0.006	0.000	28.791	0.001	0.001	0.000	0.000	0.000	0.000
133	X	504	HIS	0	-0.015	-0.017	26.386	0.017	0.017	0.000	0.000	0.000	0.000
134	X	505	GLY	0	-0.007	0.002	31.554	0.000	0.000	0.000	0.000	0.000	0.000
135	X	506	LYS	1	0.792	0.897	26.611	0.224	0.224	0.000	0.000	0.000	0.000
136	X	507	LEU	0	0.018	0.005	23.034	0.008	0.008	0.000	0.000	0.000	0.000
137	X	508	VAL	0	-0.034	-0.024	21.452	-0.019	-0.019	0.000	0.000	0.000	0.000
138	X	509	PHE	0	0.004	0.005	17.905	-0.002	-0.002	0.000	0.000	0.000	0.000
139	X	510	LYS	1	0.860	0.947	19.135	0.254	0.254	0.000	0.000	0.000	0.000
140	X	511	PHE	0	-0.001	-0.014	15.054	-0.039	-0.039	0.000	0.000	0.000	0.000
141	X	512	LYS	1	0.848	0.933	17.215	0.219	0.219	0.000	0.000	0.000	0.000
142	X	513	LEU	0	-0.014	-0.017	12.143	-0.040	-0.040	0.000	0.000	0.000	0.000
143	X	514	ARG	1	0.806	0.874	16.654	0.110	0.110	0.000	0.000	0.000	0.000
144	X	515	ARG	1	0.781	0.889	16.914	-0.209	-0.209	0.000	0.000	0.000	0.000
145	X	516	ILE	0	-0.027	-0.017	14.442	-0.021	-0.021	0.000	0.000	0.000	0.000
146	X	517	PRO	0	0.033	0.010	18.444	0.035	0.035	0.000	0.000	0.000	0.000
147	X	518	GLY	0	0.012	0.003	20.914	0.015	0.015	0.000	0.000	0.000	0.000
148	X	519	GLN	0	-0.048	-0.006	16.040	0.107	0.107	0.000	0.000	0.000	0.000
149	X	520	PRO	0	0.059	0.024	19.558	-0.032	-0.032	0.000	0.000	0.000	0.000
150	X	521	GLU	-1	-0.918	-0.944	21.419	0.140	0.140	0.000	0.000	0.000	0.000
151	X	522	LEU	0	-0.028	-0.008	18.975	0.021	0.021	0.000	0.000	0.000	0.000
152	X	523	PRO	0	0.022	0.015	23.467	-0.025	-0.025	0.000	0.000	0.000	0.000
153	X	524	TRP	0	-0.009	-0.003	22.648	0.002	0.002	0.000	0.000	0.000	0.000

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