FMO DATABASE

FMODB ID: 7GK7K

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1477235.4454
FMO2-HF: Nuclear repulsion	1418109.315576
FMO2-HF: Total energy	-59126.129824
FMO2-MP2: Total energy	-59301.595775

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.
-30.977	-25.86	26.64	-11.857	-19.899	-0.055

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 : -0.025 / q_NPA : -0.041

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	0.014	0.018	3.694	2.285	4.703	0.010	-1.102	-1.327	0.004
4	X	365	GLY	0	0.018	0.014	6.189	-0.389	-0.389	0.000	0.000	0.000	0.000
5	X	366	THR	0	0.013	-0.007	7.877	0.680	0.680	0.000	0.000	0.000	0.000
6	X	367	VAL	0	0.001	0.016	6.774	0.129	0.129	0.000	0.000	0.000	0.000
7	X	368	PRO	0	-0.018	-0.027	9.453	-0.238	-0.238	0.000	0.000	0.000	0.000
8	X	369	GLY	0	0.014	0.021	12.311	0.084	0.084	0.000	0.000	0.000	0.000
9	X	370	VAL	0	-0.036	-0.010	10.970	0.064	0.064	0.000	0.000	0.000	0.000
10	X	371	GLU	-1	-0.905	-0.958	13.591	0.718	0.718	0.000	0.000	0.000	0.000
11	X	372	VAL	0	-0.078	-0.053	15.870	0.013	0.013	0.000	0.000	0.000	0.000
12	X	373	GLY	0	0.027	0.006	17.253	-0.066	-0.066	0.000	0.000	0.000	0.000
13	X	374	ASP	-1	-0.871	-0.910	15.930	0.658	0.658	0.000	0.000	0.000	0.000
14	X	375	GLU	-1	-0.916	-0.968	16.980	0.319	0.319	0.000	0.000	0.000	0.000
15	X	376	PHE	0	0.002	-0.013	14.321	0.082	0.082	0.000	0.000	0.000	0.000
16	X	377	GLN	0	-0.024	-0.021	17.573	-0.113	-0.113	0.000	0.000	0.000	0.000
17	X	378	TYR	0	-0.002	-0.015	17.284	-0.090	-0.090	0.000	0.000	0.000	0.000
18	X	379	ARG	1	0.852	0.903	10.212	0.126	0.126	0.000	0.000	0.000	0.000
19	X	380	MET	0	-0.001	-0.007	12.154	0.103	0.103	0.000	0.000	0.000	0.000
20	X	381	GLU	-1	-0.748	-0.862	13.054	0.756	0.756	0.000	0.000	0.000	0.000
21	X	382	LEU	0	0.019	0.008	9.782	0.170	0.170	0.000	0.000	0.000	0.000
22	X	383	ASN	0	-0.101	-0.053	8.407	0.684	0.684	0.000	0.000	0.000	0.000
23	X	384	LEU	0	0.003	0.006	8.268	0.629	0.629	0.000	0.000	0.000	0.000
24	X	385	LEU	0	0.008	0.007	9.844	0.016	0.016	0.000	0.000	0.000	0.000
25	X	386	GLY	0	-0.009	-0.004	5.628	0.067	0.067	0.000	0.000	0.000	0.000
26	X	387	ILE	0	-0.001	0.023	5.009	2.305	2.380	-0.001	0.000	-0.074	0.000
27	X	388	HIS	0	-0.010	-0.007	5.262	0.007	0.007	0.000	0.000	0.000	0.000
28	X	389	ARG	1	0.877	0.928	2.317	-1.937	0.343	4.348	-1.577	-5.051	0.002
29	X	390	PRO	0	-0.034	-0.004	5.563	-0.042	-0.042	0.000	0.000	0.000	0.000
30	X	391	SER	0	0.056	0.031	8.754	0.094	0.094	0.000	0.000	0.000	0.000
31	X	392	GLN	0	0.001	-0.006	12.080	-0.029	-0.029	0.000	0.000	0.000	0.000
32	X	393	SER	0	-0.024	-0.019	8.947	0.127	0.127	0.000	0.000	0.000	0.000
33	X	394	GLY	0	0.068	0.044	9.931	0.027	0.027	0.000	0.000	0.000	0.000
34	X	395	ILE	0	0.019	0.031	7.214	0.058	0.058	0.000	0.000	0.000	0.000
35	X	396	ASP	-1	-0.781	-0.859	3.068	-6.939	-5.425	0.558	-0.781	-1.290	-0.005
36	X	397	TYR	0	0.014	0.004	2.974	0.090	1.201	0.107	-0.355	-0.863	-0.001
37	X	398	MET	0	-0.017	0.014	1.965	-13.020	-13.592	11.034	-4.354	-6.108	-0.041
38	X	399	LYS	1	0.863	0.934	3.904	2.278	2.569	0.009	-0.100	-0.199	0.000
39	X	400	ASP	-1	-0.797	-0.894	6.130	-1.157	-1.157	0.000	0.000	0.000	0.000
40	X	401	ASP	-1	-0.854	-0.900	8.595	-0.649	-0.649	0.000	0.000	0.000	0.000
41	X	402	GLY	0	0.035	0.008	11.358	0.140	0.140	0.000	0.000	0.000	0.000
42	X	403	GLY	0	-0.035	-0.030	12.342	-0.077	-0.077	0.000	0.000	0.000	0.000
43	X	404	GLU	-1	-0.913	-0.934	12.267	-0.968	-0.968	0.000	0.000	0.000	0.000
44	X	405	LEU	0	-0.056	-0.033	7.625	-0.257	-0.257	0.000	0.000	0.000	0.000
45	X	406	VAL	0	0.070	0.027	6.581	0.399	0.399	0.000	0.000	0.000	0.000
46	X	407	ALA	0	0.025	0.008	5.568	-1.478	-1.478	0.000	0.000	0.000	0.000
47	X	408	THR	0	0.011	0.012	1.882	-10.186	-13.142	10.562	-3.199	-4.408	-0.017
48	X	409	SER	0	-0.017	-0.021	4.101	1.660	1.823	-0.001	-0.036	-0.125	0.000
49	X	410	ILE	0	-0.017	-0.011	5.940	-0.959	-0.959	0.000	0.000	0.000	0.000
50	X	411	VAL	0	0.016	0.009	8.954	0.331	0.331	0.000	0.000	0.000	0.000
51	X	412	SER	0	-0.042	-0.016	11.758	-0.077	-0.077	0.000	0.000	0.000	0.000
52	X	413	SER	0	0.055	0.004	15.278	0.080	0.080	0.000	0.000	0.000	0.000
53	X	414	GLY	0	0.041	0.029	17.685	0.017	0.017	0.000	0.000	0.000	0.000
54	X	415	GLY	0	-0.030	-0.037	19.060	0.006	0.006	0.000	0.000	0.000	0.000
55	X	416	TYR	0	-0.028	-0.028	16.939	-0.028	-0.028	0.000	0.000	0.000	0.000
56	X	417	ASN	0	0.006	0.018	20.466	-0.005	-0.005	0.000	0.000	0.000	0.000
57	X	418	ASP	-1	-0.753	-0.823	17.105	-0.321	-0.321	0.000	0.000	0.000	0.000
58	X	419	VAL	0	-0.043	-0.020	20.266	0.031	0.031	0.000	0.000	0.000	0.000
59	X	420	LEU	0	0.004	-0.001	17.381	-0.013	-0.013	0.000	0.000	0.000	0.000
60	X	421	ASP	-1	-0.842	-0.896	21.674	-0.027	-0.027	0.000	0.000	0.000	0.000
61	X	422	ASN	0	-0.041	-0.034	23.288	0.011	0.011	0.000	0.000	0.000	0.000
62	X	423	SER	0	-0.043	-0.027	24.217	0.009	0.009	0.000	0.000	0.000	0.000
63	X	424	ASP	-1	-0.823	-0.905	21.607	-0.011	-0.011	0.000	0.000	0.000	0.000
64	X	425	VAL	0	-0.040	-0.020	20.323	-0.015	-0.015	0.000	0.000	0.000	0.000
65	X	426	LEU	0	-0.002	0.012	15.215	0.006	0.006	0.000	0.000	0.000	0.000
66	X	427	ILE	0	-0.014	-0.009	18.488	-0.044	-0.044	0.000	0.000	0.000	0.000
67	X	428	TYR	0	0.019	0.005	12.577	-0.041	-0.041	0.000	0.000	0.000	0.000
68	X	429	THR	0	-0.027	-0.027	16.507	-0.002	-0.002	0.000	0.000	0.000	0.000
69	X	430	GLY	0	0.010	0.014	15.347	-0.082	-0.082	0.000	0.000	0.000	0.000
70	X	431	GLN	0	-0.007	0.007	10.872	-0.072	-0.072	0.000	0.000	0.000	0.000
71	X	432	GLY	0	0.030	0.010	15.564	-0.016	-0.016	0.000	0.000	0.000	0.000
72	X	433	GLY	0	0.051	0.006	18.254	0.037	0.037	0.000	0.000	0.000	0.000
73	X	434	ASN	0	-0.088	-0.055	21.437	0.014	0.014	0.000	0.000	0.000	0.000
74	X	435	VAL	0	0.037	0.032	21.164	0.037	0.037	0.000	0.000	0.000	0.000
75	X	436	GLY	0	0.025	0.006	21.329	-0.017	-0.017	0.000	0.000	0.000	0.000
76	X	437	LYS	1	0.849	0.938	17.679	0.106	0.106	0.000	0.000	0.000	0.000
77	X	438	LYS	1	0.807	0.884	19.292	0.223	0.223	0.000	0.000	0.000	0.000
78	X	439	LYS	1	0.886	0.922	21.894	0.184	0.184	0.000	0.000	0.000	0.000
79	X	440	ASN	0	-0.011	-0.011	24.791	-0.010	-0.010	0.000	0.000	0.000	0.000
80	X	441	ASN	0	-0.004	0.004	27.188	0.012	0.012	0.000	0.000	0.000	0.000
81	X	442	GLU	-1	-0.749	-0.835	24.117	-0.187	-0.187	0.000	0.000	0.000	0.000
82	X	443	PRO	0	0.034	0.014	27.708	-0.005	-0.005	0.000	0.000	0.000	0.000
83	X	444	PRO	0	0.011	0.015	26.496	-0.021	-0.021	0.000	0.000	0.000	0.000
84	X	445	LYS	1	0.849	0.919	22.306	0.374	0.374	0.000	0.000	0.000	0.000
85	X	446	ASP	-1	-0.746	-0.842	24.502	-0.290	-0.290	0.000	0.000	0.000	0.000
86	X	447	GLN	0	-0.046	-0.037	18.879	-0.033	-0.033	0.000	0.000	0.000	0.000
87	X	448	GLN	0	0.042	0.006	18.422	0.004	0.004	0.000	0.000	0.000	0.000
88	X	449	LEU	0	0.020	0.032	16.033	-0.083	-0.083	0.000	0.000	0.000	0.000
89	X	450	VAL	0	0.014	-0.001	14.335	-0.012	-0.012	0.000	0.000	0.000	0.000
90	X	451	THR	0	-0.004	-0.016	9.367	-0.001	-0.001	0.000	0.000	0.000	0.000
91	X	452	GLY	0	0.076	0.038	8.675	-0.236	-0.236	0.000	0.000	0.000	0.000
92	X	453	ASN	0	-0.007	-0.005	9.630	0.029	0.029	0.000	0.000	0.000	0.000
93	X	454	LEU	0	-0.031	-0.007	12.132	0.087	0.087	0.000	0.000	0.000	0.000
94	X	455	ALA	0	0.006	0.010	7.526	0.067	0.067	0.000	0.000	0.000	0.000
95	X	456	LEU	0	0.020	0.003	9.648	0.095	0.095	0.000	0.000	0.000	0.000
96	X	457	LYS	1	0.920	0.970	11.234	0.752	0.752	0.000	0.000	0.000	0.000
97	X	458	ASN	0	-0.025	-0.018	11.494	0.259	0.259	0.000	0.000	0.000	0.000
98	X	459	SER	0	-0.010	-0.031	9.506	-0.035	-0.035	0.000	0.000	0.000	0.000
99	X	460	ILE	0	-0.042	0.018	11.931	0.145	0.145	0.000	0.000	0.000	0.000
100	X	461	ASN	0	-0.039	-0.016	15.531	0.131	0.131	0.000	0.000	0.000	0.000
101	X	462	LYS	1	0.816	0.867	11.463	0.819	0.819	0.000	0.000	0.000	0.000
102	X	463	LYS	1	0.856	0.934	14.045	0.395	0.395	0.000	0.000	0.000	0.000
103	X	464	ASN	0	0.011	0.032	7.870	-0.070	-0.070	0.000	0.000	0.000	0.000
104	X	465	PRO	0	0.016	-0.005	10.544	-0.061	-0.061	0.000	0.000	0.000	0.000
105	X	466	VAL	0	-0.027	-0.002	7.295	0.086	0.086	0.000	0.000	0.000	0.000
106	X	467	ARG	1	0.785	0.873	3.256	-8.646	-7.853	0.014	-0.353	-0.454	0.003
107	X	468	VAL	0	0.018	0.012	8.839	-0.282	-0.282	0.000	0.000	0.000	0.000
108	X	469	ILE	0	-0.031	-0.014	8.753	0.166	0.166	0.000	0.000	0.000	0.000
109	X	470	ARG	1	0.861	0.926	12.686	-0.298	-0.298	0.000	0.000	0.000	0.000
110	X	471	GLY	0	-0.029	-0.029	16.285	0.053	0.053	0.000	0.000	0.000	0.000
111	X	472	ILE	0	-0.046	-0.012	18.089	-0.033	-0.033	0.000	0.000	0.000	0.000
112	X	473	LYS	1	0.990	0.997	21.731	-0.031	-0.031	0.000	0.000	0.000	0.000
113	X	484	LYS	1	0.943	0.963	21.005	-0.268	-0.268	0.000	0.000	0.000	0.000
114	X	485	ASN	0	-0.101	-0.050	19.652	-0.053	-0.053	0.000	0.000	0.000	0.000
115	X	486	TYR	0	-0.069	-0.046	15.137	-0.079	-0.079	0.000	0.000	0.000	0.000
116	X	487	VAL	0	0.069	0.052	16.687	0.032	0.032	0.000	0.000	0.000	0.000
117	X	488	TYR	0	-0.037	-0.011	11.333	0.042	0.042	0.000	0.000	0.000	0.000
118	X	489	ASP	-1	-0.758	-0.862	14.208	0.145	0.145	0.000	0.000	0.000	0.000
119	X	490	GLY	0	0.097	0.049	13.822	-0.052	-0.052	0.000	0.000	0.000	0.000
120	X	491	LEU	0	-0.059	-0.031	10.314	0.002	0.002	0.000	0.000	0.000	0.000
121	X	492	TYR	0	-0.005	-0.028	12.233	-0.101	-0.101	0.000	0.000	0.000	0.000
122	X	493	LEU	0	-0.002	0.007	12.545	-0.001	-0.001	0.000	0.000	0.000	0.000
123	X	494	VAL	0	0.007	-0.005	12.176	0.004	0.004	0.000	0.000	0.000	0.000
124	X	495	GLU	-1	-0.842	-0.891	14.989	-0.152	-0.152	0.000	0.000	0.000	0.000
125	X	496	GLU	-1	-0.857	-0.924	18.529	-0.241	-0.241	0.000	0.000	0.000	0.000
126	X	497	TYR	0	-0.068	-0.074	17.570	-0.056	-0.056	0.000	0.000	0.000	0.000
127	X	498	TRP	0	-0.024	-0.014	19.490	0.023	0.023	0.000	0.000	0.000	0.000
128	X	499	GLU	-1	-0.854	-0.921	21.337	-0.454	-0.454	0.000	0.000	0.000	0.000
129	X	500	GLU	-1	-0.842	-0.920	23.754	-0.225	-0.225	0.000	0.000	0.000	0.000
130	X	501	THR	0	-0.017	-0.008	26.006	-0.015	-0.015	0.000	0.000	0.000	0.000
131	X	502	GLY	0	0.020	0.011	27.826	0.014	0.014	0.000	0.000	0.000	0.000
132	X	503	SER	0	0.006	-0.010	28.784	0.002	0.002	0.000	0.000	0.000	0.000
133	X	504	HIS	0	-0.021	-0.001	25.945	0.021	0.021	0.000	0.000	0.000	0.000
134	X	505	GLY	0	0.015	0.009	31.554	0.000	0.000	0.000	0.000	0.000	0.000
135	X	506	LYS	1	0.789	0.881	26.842	0.226	0.226	0.000	0.000	0.000	0.000
136	X	507	LEU	0	0.033	0.015	22.922	0.007	0.007	0.000	0.000	0.000	0.000
137	X	508	VAL	0	-0.023	-0.018	21.409	-0.019	-0.019	0.000	0.000	0.000	0.000
138	X	509	PHE	0	0.000	0.006	17.919	-0.002	-0.002	0.000	0.000	0.000	0.000
139	X	510	LYS	1	0.881	0.947	18.872	0.282	0.282	0.000	0.000	0.000	0.000
140	X	511	PHE	0	-0.003	-0.019	15.131	-0.046	-0.046	0.000	0.000	0.000	0.000
141	X	512	LYS	1	0.815	0.908	17.124	0.230	0.230	0.000	0.000	0.000	0.000
142	X	513	LEU	0	-0.009	-0.023	12.188	-0.037	-0.037	0.000	0.000	0.000	0.000
143	X	514	ARG	1	0.799	0.865	16.763	0.119	0.119	0.000	0.000	0.000	0.000
144	X	515	ARG	1	0.803	0.896	16.775	-0.213	-0.213	0.000	0.000	0.000	0.000
145	X	516	ILE	0	-0.024	-0.018	14.362	-0.020	-0.020	0.000	0.000	0.000	0.000
146	X	517	PRO	0	0.035	0.006	18.222	0.038	0.038	0.000	0.000	0.000	0.000
147	X	518	GLY	0	-0.003	0.001	20.891	0.016	0.016	0.000	0.000	0.000	0.000
148	X	519	GLN	0	-0.035	-0.012	15.746	0.114	0.114	0.000	0.000	0.000	0.000
149	X	520	PRO	0	0.041	0.019	19.662	-0.034	-0.034	0.000	0.000	0.000	0.000
150	X	521	GLU	-1	-0.918	-0.939	21.417	0.138	0.138	0.000	0.000	0.000	0.000
151	X	522	LEU	0	-0.019	-0.012	18.753	0.025	0.025	0.000	0.000	0.000	0.000
152	X	523	PRO	0	0.006	0.009	23.353	-0.025	-0.025	0.000	0.000	0.000	0.000
153	X	524	TRP	0	-0.006	0.013	21.982	0.001	0.001	0.000	0.000	0.000	0.000

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