FMO DATABASE

FMODB ID: 9GR92

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	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	153
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1476988.611134
FMO2-HF: Nuclear repulsion	1417863.517452
FMO2-HF: Total energy	-59125.093682
FMO2-MP2: Total energy	-59300.638215

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.
-22.561	-11.343	12.149	-7.994	-15.375	-0.041

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 : -0.063 / 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	0.023	0.022	3.808	1.248	3.158	-0.026	-0.768	-1.116	0.001
4	X	365	GLY	0	-0.002	0.009	6.214	-0.352	-0.352	0.000	0.000	0.000	0.000
5	X	366	THR	0	0.032	0.000	8.341	0.653	0.653	0.000	0.000	0.000	0.000
6	X	367	VAL	0	0.013	0.020	6.764	0.328	0.328	0.000	0.000	0.000	0.000
7	X	368	PRO	0	-0.032	-0.029	9.232	-0.404	-0.404	0.000	0.000	0.000	0.000
8	X	369	GLY	0	0.022	0.014	12.142	0.194	0.194	0.000	0.000	0.000	0.000
9	X	370	VAL	0	-0.039	-0.005	11.024	0.003	0.003	0.000	0.000	0.000	0.000
10	X	371	GLU	-1	-0.897	-0.951	13.992	1.101	1.101	0.000	0.000	0.000	0.000
11	X	372	VAL	0	-0.081	-0.057	16.425	0.006	0.006	0.000	0.000	0.000	0.000
12	X	373	GLY	0	-0.011	-0.012	17.532	-0.056	-0.056	0.000	0.000	0.000	0.000
13	X	374	ASP	-1	-0.849	-0.888	16.369	1.013	1.013	0.000	0.000	0.000	0.000
14	X	375	GLU	-1	-0.973	-1.005	17.472	0.487	0.487	0.000	0.000	0.000	0.000
15	X	376	PHE	0	0.004	-0.007	14.355	0.068	0.068	0.000	0.000	0.000	0.000
16	X	377	GLN	0	-0.022	-0.008	17.982	-0.143	-0.143	0.000	0.000	0.000	0.000
17	X	378	TYR	0	0.012	-0.004	17.599	-0.114	-0.114	0.000	0.000	0.000	0.000
18	X	379	ARG	1	0.893	0.930	10.636	0.066	0.066	0.000	0.000	0.000	0.000
19	X	380	MET	0	-0.015	-0.020	11.961	0.113	0.113	0.000	0.000	0.000	0.000
20	X	381	GLU	-1	-0.819	-0.915	12.892	1.032	1.032	0.000	0.000	0.000	0.000
21	X	382	LEU	0	0.017	0.014	10.129	0.250	0.250	0.000	0.000	0.000	0.000
22	X	383	ASN	0	-0.108	-0.051	8.292	0.996	0.996	0.000	0.000	0.000	0.000
23	X	384	LEU	0	0.014	0.004	8.145	0.779	0.779	0.000	0.000	0.000	0.000
24	X	385	LEU	0	-0.010	-0.003	9.680	0.243	0.243	0.000	0.000	0.000	0.000
25	X	386	GLY	0	-0.010	0.003	5.410	0.497	0.497	0.000	0.000	0.000	0.000
26	X	387	ILE	0	-0.022	0.009	5.214	1.934	1.934	0.000	0.000	0.000	0.000
27	X	388	HIS	0	-0.007	0.007	5.884	0.129	0.129	0.000	0.000	0.000	0.000
28	X	389	ARG	1	0.875	0.938	2.454	0.701	1.938	5.358	-1.590	-5.006	0.001
29	X	390	PRO	0	-0.022	0.011	5.649	-0.086	-0.086	0.000	0.000	0.000	0.000
30	X	391	SER	0	0.051	0.023	8.879	0.254	0.254	0.000	0.000	0.000	0.000
31	X	392	GLN	0	-0.012	-0.017	12.491	0.033	0.033	0.000	0.000	0.000	0.000
32	X	393	SER	0	0.002	0.010	9.520	0.141	0.141	0.000	0.000	0.000	0.000
33	X	394	GLY	0	0.065	0.042	10.336	0.107	0.107	0.000	0.000	0.000	0.000
34	X	395	ILE	0	0.024	0.030	7.165	0.141	0.141	0.000	0.000	0.000	0.000
35	X	396	ASP	-1	-0.795	-0.892	3.297	-5.682	-4.362	0.293	-0.622	-0.991	-0.003
36	X	397	TYR	0	0.017	0.008	3.540	0.588	1.286	0.025	-0.182	-0.541	0.000
37	X	398	MET	0	-0.037	-0.009	2.257	-12.230	-9.121	4.226	-2.812	-4.523	-0.023
38	X	399	LYS	1	0.926	0.956	3.599	3.457	3.753	0.023	-0.101	-0.219	0.000
39	X	400	ASP	-1	-0.847	-0.926	6.334	-1.700	-1.700	0.000	0.000	0.000	0.000
40	X	401	ASP	-1	-0.916	-0.957	8.638	-0.817	-0.817	0.000	0.000	0.000	0.000
41	X	402	GLY	0	0.033	0.015	11.553	0.158	0.158	0.000	0.000	0.000	0.000
42	X	403	GLY	0	-0.088	-0.050	11.805	-0.177	-0.177	0.000	0.000	0.000	0.000
43	X	404	GLU	-1	-0.933	-0.958	11.899	-1.268	-1.268	0.000	0.000	0.000	0.000
44	X	405	LEU	0	-0.048	-0.022	7.338	-0.328	-0.328	0.000	0.000	0.000	0.000
45	X	406	VAL	0	0.078	0.033	6.509	0.570	0.570	0.000	0.000	0.000	0.000
46	X	407	ALA	0	0.001	-0.011	5.554	-1.609	-1.609	0.000	0.000	0.000	0.000
47	X	408	THR	0	0.021	-0.002	2.215	-8.877	-6.798	2.246	-1.741	-2.584	-0.018
48	X	409	SER	0	-0.021	-0.045	4.505	1.638	1.732	-0.001	-0.010	-0.083	0.000
49	X	410	ILE	0	-0.002	0.006	6.545	-0.909	-0.909	0.000	0.000	0.000	0.000
50	X	411	VAL	0	-0.023	-0.008	9.450	0.335	0.335	0.000	0.000	0.000	0.000
51	X	412	SER	0	-0.038	-0.011	12.256	-0.125	-0.125	0.000	0.000	0.000	0.000
52	X	413	SER	0	0.072	0.018	15.817	0.073	0.073	0.000	0.000	0.000	0.000
53	X	414	GLY	0	0.025	0.017	18.268	0.011	0.011	0.000	0.000	0.000	0.000
54	X	415	GLY	0	-0.073	-0.054	19.048	-0.016	-0.016	0.000	0.000	0.000	0.000
55	X	416	TYR	0	0.030	-0.003	17.285	-0.021	-0.021	0.000	0.000	0.000	0.000
56	X	417	ASN	0	-0.015	0.026	20.873	-0.004	-0.004	0.000	0.000	0.000	0.000
57	X	418	ASP	-1	-0.792	-0.874	17.799	-0.260	-0.260	0.000	0.000	0.000	0.000
58	X	419	VAL	0	-0.041	-0.027	20.655	0.029	0.029	0.000	0.000	0.000	0.000
59	X	420	LEU	0	0.005	-0.010	18.104	-0.002	-0.002	0.000	0.000	0.000	0.000
60	X	421	ASP	-1	-0.849	-0.889	22.330	0.030	0.030	0.000	0.000	0.000	0.000
61	X	422	ASN	0	-0.040	-0.038	23.822	0.019	0.019	0.000	0.000	0.000	0.000
62	X	423	SER	0	-0.034	-0.029	24.772	0.012	0.012	0.000	0.000	0.000	0.000
63	X	424	ASP	-1	-0.843	-0.915	21.894	0.086	0.086	0.000	0.000	0.000	0.000
64	X	425	VAL	0	-0.034	-0.020	20.610	-0.013	-0.013	0.000	0.000	0.000	0.000
65	X	426	LEU	0	0.024	0.032	15.967	0.003	0.003	0.000	0.000	0.000	0.000
66	X	427	ILE	0	-0.024	-0.016	18.914	-0.051	-0.051	0.000	0.000	0.000	0.000
67	X	428	TYR	0	-0.006	-0.021	12.524	-0.049	-0.049	0.000	0.000	0.000	0.000
68	X	429	THR	0	-0.016	-0.020	17.178	-0.046	-0.046	0.000	0.000	0.000	0.000
69	X	430	GLY	0	0.039	0.031	15.420	-0.066	-0.066	0.000	0.000	0.000	0.000
70	X	431	GLN	0	-0.038	-0.003	11.514	-0.091	-0.091	0.000	0.000	0.000	0.000
71	X	432	GLY	0	0.027	0.000	15.838	-0.035	-0.035	0.000	0.000	0.000	0.000
72	X	433	GLY	0	0.076	0.010	18.475	0.049	0.049	0.000	0.000	0.000	0.000
73	X	434	ASN	0	-0.119	-0.088	21.451	0.020	0.020	0.000	0.000	0.000	0.000
74	X	435	VAL	0	0.050	0.039	21.285	0.046	0.046	0.000	0.000	0.000	0.000
75	X	436	GLY	0	0.037	0.029	22.037	-0.009	-0.009	0.000	0.000	0.000	0.000
76	X	437	LYS	1	0.853	0.933	18.210	0.071	0.071	0.000	0.000	0.000	0.000
77	X	438	LYS	1	0.795	0.890	19.493	0.307	0.307	0.000	0.000	0.000	0.000
78	X	439	LYS	1	0.894	0.929	22.124	0.292	0.292	0.000	0.000	0.000	0.000
79	X	440	ASN	0	-0.016	-0.019	25.112	-0.014	-0.014	0.000	0.000	0.000	0.000
80	X	441	ASN	0	0.000	0.008	27.376	0.011	0.011	0.000	0.000	0.000	0.000
81	X	442	GLU	-1	-0.764	-0.840	24.545	-0.285	-0.285	0.000	0.000	0.000	0.000
82	X	443	PRO	0	0.030	0.015	28.181	0.006	0.006	0.000	0.000	0.000	0.000
83	X	444	PRO	0	0.027	0.025	26.800	-0.031	-0.031	0.000	0.000	0.000	0.000
84	X	445	LYS	1	0.884	0.950	22.135	0.500	0.500	0.000	0.000	0.000	0.000
85	X	446	ASP	-1	-0.777	-0.888	24.138	-0.387	-0.387	0.000	0.000	0.000	0.000
86	X	447	GLN	0	-0.113	-0.068	18.842	-0.054	-0.054	0.000	0.000	0.000	0.000
87	X	448	GLN	0	0.044	0.012	18.343	0.043	0.043	0.000	0.000	0.000	0.000
88	X	449	LEU	0	0.013	0.019	15.929	-0.097	-0.097	0.000	0.000	0.000	0.000
89	X	450	VAL	0	0.022	0.002	14.157	-0.019	-0.019	0.000	0.000	0.000	0.000
90	X	451	THR	0	-0.012	-0.011	9.354	0.010	0.010	0.000	0.000	0.000	0.000
91	X	452	GLY	0	0.083	0.036	8.757	-0.146	-0.146	0.000	0.000	0.000	0.000
92	X	453	ASN	0	0.024	0.016	9.740	0.053	0.053	0.000	0.000	0.000	0.000
93	X	454	LEU	0	-0.028	-0.006	12.445	0.115	0.115	0.000	0.000	0.000	0.000
94	X	455	ALA	0	-0.006	0.003	7.708	0.064	0.064	0.000	0.000	0.000	0.000
95	X	456	LEU	0	0.019	0.003	9.803	0.132	0.132	0.000	0.000	0.000	0.000
96	X	457	LYS	1	0.923	0.971	11.062	0.895	0.895	0.000	0.000	0.000	0.000
97	X	458	ASN	0	-0.009	-0.010	11.592	0.307	0.307	0.000	0.000	0.000	0.000
98	X	459	SER	0	-0.030	-0.032	9.526	-0.057	-0.057	0.000	0.000	0.000	0.000
99	X	460	ILE	0	-0.059	0.004	11.887	0.174	0.174	0.000	0.000	0.000	0.000
100	X	461	ASN	0	-0.042	-0.028	15.548	0.120	0.120	0.000	0.000	0.000	0.000
101	X	462	LYS	1	0.891	0.956	11.792	0.929	0.929	0.000	0.000	0.000	0.000
102	X	463	LYS	1	0.932	0.981	14.278	0.362	0.362	0.000	0.000	0.000	0.000
103	X	464	ASN	0	-0.006	0.015	8.054	-0.047	-0.047	0.000	0.000	0.000	0.000
104	X	465	PRO	0	0.026	-0.005	10.580	-0.052	-0.052	0.000	0.000	0.000	0.000
105	X	466	VAL	0	-0.035	0.001	7.974	-0.009	-0.009	0.000	0.000	0.000	0.000
106	X	467	ARG	1	0.779	0.864	3.452	-8.481	-8.006	0.005	-0.168	-0.312	0.001
107	X	468	VAL	0	0.039	0.026	9.442	-0.322	-0.322	0.000	0.000	0.000	0.000
108	X	469	ILE	0	-0.007	0.004	9.770	0.164	0.164	0.000	0.000	0.000	0.000
109	X	470	ARG	1	0.909	0.964	13.304	-0.476	-0.476	0.000	0.000	0.000	0.000
110	X	471	GLY	0	-0.062	-0.057	16.714	0.062	0.062	0.000	0.000	0.000	0.000
111	X	472	ILE	0	-0.054	-0.018	18.620	-0.048	-0.048	0.000	0.000	0.000	0.000
112	X	473	LYS	1	1.000	0.996	22.095	-0.076	-0.076	0.000	0.000	0.000	0.000
113	X	484	LYS	1	0.977	0.975	21.469	-0.368	-0.368	0.000	0.000	0.000	0.000
114	X	485	ASN	0	-0.048	-0.019	19.981	-0.076	-0.076	0.000	0.000	0.000	0.000
115	X	486	TYR	0	-0.079	-0.040	15.738	-0.110	-0.110	0.000	0.000	0.000	0.000
116	X	487	VAL	0	0.083	0.056	17.438	0.049	0.049	0.000	0.000	0.000	0.000
117	X	488	TYR	0	-0.014	-0.004	11.444	0.044	0.044	0.000	0.000	0.000	0.000
118	X	489	ASP	-1	-0.764	-0.884	14.652	0.316	0.316	0.000	0.000	0.000	0.000
119	X	490	GLY	0	0.041	0.039	14.362	-0.090	-0.090	0.000	0.000	0.000	0.000
120	X	491	LEU	0	-0.083	-0.051	10.714	0.022	0.022	0.000	0.000	0.000	0.000
121	X	492	TYR	0	-0.001	-0.024	12.671	-0.121	-0.121	0.000	0.000	0.000	0.000
122	X	493	LEU	0	0.005	0.010	12.811	0.000	0.000	0.000	0.000	0.000	0.000
123	X	494	VAL	0	0.002	-0.003	12.120	0.014	0.014	0.000	0.000	0.000	0.000
124	X	495	GLU	-1	-0.895	-0.962	15.025	-0.112	-0.112	0.000	0.000	0.000	0.000
125	X	496	GLU	-1	-0.901	-0.966	18.440	-0.261	-0.261	0.000	0.000	0.000	0.000
126	X	497	TYR	0	0.007	-0.011	17.564	-0.046	-0.046	0.000	0.000	0.000	0.000
127	X	498	TRP	0	-0.050	-0.030	19.563	0.017	0.017	0.000	0.000	0.000	0.000
128	X	499	GLU	-1	-0.897	-0.965	21.697	-0.481	-0.481	0.000	0.000	0.000	0.000
129	X	500	GLU	-1	-0.841	-0.912	23.958	-0.215	-0.215	0.000	0.000	0.000	0.000
130	X	501	THR	0	-0.020	-0.013	26.117	-0.022	-0.022	0.000	0.000	0.000	0.000
131	X	502	GLY	0	0.043	0.024	27.814	0.020	0.020	0.000	0.000	0.000	0.000
132	X	503	SER	0	0.016	0.001	28.857	-0.001	-0.001	0.000	0.000	0.000	0.000
133	X	504	HIS	0	-0.035	-0.014	26.696	0.015	0.015	0.000	0.000	0.000	0.000
134	X	505	GLY	0	-0.020	-0.011	31.590	-0.003	-0.003	0.000	0.000	0.000	0.000
135	X	506	LYS	1	0.878	0.949	26.669	0.279	0.279	0.000	0.000	0.000	0.000
136	X	507	LEU	0	0.018	0.019	23.033	0.013	0.013	0.000	0.000	0.000	0.000
137	X	508	VAL	0	-0.048	-0.030	21.478	-0.026	-0.026	0.000	0.000	0.000	0.000
138	X	509	PHE	0	0.014	0.007	17.980	-0.001	-0.001	0.000	0.000	0.000	0.000
139	X	510	LYS	1	0.853	0.941	19.288	0.291	0.291	0.000	0.000	0.000	0.000
140	X	511	PHE	0	0.005	-0.012	15.179	-0.047	-0.047	0.000	0.000	0.000	0.000
141	X	512	LYS	1	0.946	0.992	17.436	0.208	0.208	0.000	0.000	0.000	0.000
142	X	513	LEU	0	-0.028	-0.022	12.437	-0.043	-0.043	0.000	0.000	0.000	0.000
143	X	514	ARG	1	0.875	0.938	16.987	0.051	0.051	0.000	0.000	0.000	0.000
144	X	515	ARG	1	0.797	0.886	17.308	-0.407	-0.407	0.000	0.000	0.000	0.000
145	X	516	ILE	0	-0.035	-0.017	15.053	-0.036	-0.036	0.000	0.000	0.000	0.000
146	X	517	PRO	0	0.033	0.006	18.854	0.050	0.050	0.000	0.000	0.000	0.000
147	X	518	GLY	0	0.018	0.003	21.243	0.025	0.025	0.000	0.000	0.000	0.000
148	X	519	GLN	0	-0.059	-0.015	16.412	0.162	0.162	0.000	0.000	0.000	0.000
149	X	520	PRO	0	0.056	0.024	19.736	-0.053	-0.053	0.000	0.000	0.000	0.000
150	X	521	GLU	-1	-0.905	-0.940	21.658	0.274	0.274	0.000	0.000	0.000	0.000
151	X	522	LEU	0	-0.030	-0.017	19.302	0.030	0.030	0.000	0.000	0.000	0.000
152	X	523	PRO	0	0.016	0.014	23.736	-0.040	-0.040	0.000	0.000	0.000	0.000
153	X	524	TRP	0	-0.015	-0.005	23.111	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)