FMO DATABASE

FMODB ID: VR3N1

Calculation Name: 3SSD-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name: 5-methyl-2'-deoxy-cytidine-5'-monophosphate

ligand 3-letter code: 5CM

PDB ID: 3SSD

Chain ID: A

ChEMBL ID:
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UniProt ID: P15005

Base Structure: X-ray

Registration Date: 2023-06-20

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	155
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1616206.015326
FMO2-HF: Nuclear repulsion	1554330.171139
FMO2-HF: Total energy	-61875.844187
FMO2-MP2: Total energy	-62059.923985

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:2:GLU)

Summations of interaction energy for fragment #1(A:2: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.
-91.289	-81.663	6.054	-6.044	-9.637	0.061

Interaction energy analysis for fragmet #1(A:2:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.910 / q_NPA : -0.972

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	4	ILE	0	0.068	0.026	3.512	1.685	4.188	0.063	-0.980	-1.587	0.002
4	A	5	GLN	0	0.044	0.006	4.562	-0.048	0.032	-0.001	-0.009	-0.071	0.000
5	A	6	PRO	0	0.034	0.025	5.708	-2.474	-2.474	0.000	0.000	0.000	0.000
6	A	7	TRP	0	-0.002	0.004	3.047	-6.874	-6.156	0.019	-0.104	-0.633	0.001
7	A	8	ILE	0	0.030	0.011	8.008	-2.693	-2.693	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.883	-0.945	10.457	18.796	18.796	0.000	0.000	0.000	0.000
9	A	10	LYS	1	0.863	0.947	10.644	-27.854	-27.854	0.000	0.000	0.000	0.000
10	A	11	PHE	0	-0.005	0.008	11.786	-1.661	-1.661	0.000	0.000	0.000	0.000
11	A	12	ILE	0	0.050	0.030	13.461	-1.582	-1.582	0.000	0.000	0.000	0.000
12	A	13	LYS	1	0.926	0.965	15.695	-19.284	-19.284	0.000	0.000	0.000	0.000
13	A	14	GLN	0	-0.075	-0.036	15.360	0.190	0.190	0.000	0.000	0.000	0.000
14	A	15	ALA	0	-0.012	-0.019	17.505	-1.008	-1.008	0.000	0.000	0.000	0.000
15	A	16	GLN	0	-0.065	-0.027	19.274	-1.043	-1.043	0.000	0.000	0.000	0.000
16	A	17	GLN	0	-0.023	-0.018	19.540	-0.588	-0.588	0.000	0.000	0.000	0.000
17	A	18	GLN	0	-0.020	0.017	22.093	-0.449	-0.449	0.000	0.000	0.000	0.000
18	A	19	ARG	1	0.990	0.993	22.591	-13.303	-13.303	0.000	0.000	0.000	0.000
19	A	20	SER	0	-0.018	-0.018	19.063	-0.205	-0.205	0.000	0.000	0.000	0.000
20	A	21	GLN	0	0.063	0.013	19.500	0.515	0.515	0.000	0.000	0.000	0.000
21	A	22	SER	0	-0.036	-0.007	16.642	0.720	0.720	0.000	0.000	0.000	0.000
22	A	23	THR	0	0.060	0.020	13.006	0.180	0.180	0.000	0.000	0.000	0.000
23	A	24	LYS	1	0.951	0.980	11.892	-17.814	-17.814	0.000	0.000	0.000	0.000
24	A	25	ASP	-1	-0.939	-0.952	10.945	24.047	24.047	0.000	0.000	0.000	0.000
25	A	26	TYR	0	-0.013	-0.047	8.069	-0.459	-0.459	0.000	0.000	0.000	0.000
26	A	27	PRO	0	0.042	0.040	3.239	-8.292	-6.184	0.208	-1.050	-1.267	0.008
27	A	28	THR	0	0.028	-0.005	5.105	-2.089	-2.113	-0.001	-0.003	0.028	0.000
28	A	29	SER	0	-0.081	-0.029	4.762	-9.992	-10.026	-0.001	-0.036	0.072	0.000
29	A	30	TYR	0	0.037	-0.007	2.464	15.824	19.706	5.716	-3.837	-5.761	0.046
30	A	31	ARG	1	0.937	0.976	3.559	-45.974	-45.653	0.052	-0.022	-0.351	0.004
31	A	32	ASN	0	-0.003	0.004	6.547	-4.389	-4.389	0.000	0.000	0.000	0.000
32	A	33	LEU	0	-0.009	0.023	7.206	-4.642	-4.642	0.000	0.000	0.000	0.000
33	A	34	ARG	1	0.832	0.889	6.959	-16.380	-16.380	0.000	0.000	0.000	0.000
34	A	35	VAL	0	-0.010	0.002	4.712	-2.450	-2.378	-0.001	-0.003	-0.067	0.000
35	A	36	LYS	1	0.866	0.940	7.842	-24.081	-24.081	0.000	0.000	0.000	0.000
36	A	37	LEU	0	0.009	0.022	9.774	-0.498	-0.498	0.000	0.000	0.000	0.000
37	A	38	SER	0	-0.010	0.005	13.062	-1.063	-1.063	0.000	0.000	0.000	0.000
38	A	39	PHE	0	0.049	0.022	14.464	-0.365	-0.365	0.000	0.000	0.000	0.000
39	A	40	GLY	0	-0.006	-0.010	19.216	-0.963	-0.963	0.000	0.000	0.000	0.000
40	A	41	TYR	0	-0.020	-0.013	21.101	0.670	0.670	0.000	0.000	0.000	0.000
41	A	42	GLY	0	0.021	0.027	23.414	-0.528	-0.528	0.000	0.000	0.000	0.000
42	A	43	ASN	0	0.006	0.013	26.746	-0.035	-0.035	0.000	0.000	0.000	0.000
43	A	44	PHE	0	-0.011	-0.015	22.296	0.416	0.416	0.000	0.000	0.000	0.000
44	A	45	THR	0	-0.026	0.000	20.795	-0.722	-0.722	0.000	0.000	0.000	0.000
45	A	46	SER	0	0.014	-0.009	23.284	0.395	0.395	0.000	0.000	0.000	0.000
46	A	47	ILE	0	-0.033	-0.014	20.714	-0.006	-0.006	0.000	0.000	0.000	0.000
47	A	48	PRO	0	-0.035	-0.013	17.900	0.364	0.364	0.000	0.000	0.000	0.000
48	A	49	TRP	0	0.010	0.012	14.307	0.178	0.178	0.000	0.000	0.000	0.000
49	A	50	PHE	0	0.009	-0.012	7.053	0.644	0.644	0.000	0.000	0.000	0.000
50	A	51	ALA	0	-0.004	-0.006	11.938	-0.433	-0.433	0.000	0.000	0.000	0.000
51	A	52	PHE	0	0.012	-0.003	5.895	3.183	3.183	0.000	0.000	0.000	0.000
52	A	53	LEU	0	-0.023	-0.008	10.191	-1.976	-1.976	0.000	0.000	0.000	0.000
53	A	54	GLY	0	0.090	0.041	11.798	1.765	1.765	0.000	0.000	0.000	0.000
54	A	55	GLU	-1	-0.918	-0.974	13.969	16.669	16.669	0.000	0.000	0.000	0.000
55	A	56	GLY	0	-0.039	-0.026	16.504	-0.801	-0.801	0.000	0.000	0.000	0.000
56	A	57	GLN	0	-0.041	0.005	16.098	-1.197	-1.197	0.000	0.000	0.000	0.000
57	A	58	GLU	-1	-0.805	-0.903	16.512	20.518	20.518	0.000	0.000	0.000	0.000
58	A	59	ALA	0	0.022	0.009	16.413	-0.412	-0.412	0.000	0.000	0.000	0.000
59	A	60	SER	0	-0.015	0.005	17.915	-0.374	-0.374	0.000	0.000	0.000	0.000
60	A	61	ASN	0	0.016	-0.020	20.685	-0.794	-0.794	0.000	0.000	0.000	0.000
61	A	62	GLY	0	0.084	0.048	19.583	0.482	0.482	0.000	0.000	0.000	0.000
62	A	63	ILE	0	0.020	0.029	19.357	-0.244	-0.244	0.000	0.000	0.000	0.000
63	A	64	TYR	0	-0.054	-0.063	14.100	0.958	0.958	0.000	0.000	0.000	0.000
64	A	65	PRO	0	0.017	0.036	12.074	-0.789	-0.789	0.000	0.000	0.000	0.000
65	A	66	VAL	0	-0.034	-0.013	13.281	1.279	1.279	0.000	0.000	0.000	0.000
66	A	67	ILE	0	0.008	0.012	10.902	-0.783	-0.783	0.000	0.000	0.000	0.000
67	A	68	LEU	0	-0.018	-0.022	14.676	0.288	0.288	0.000	0.000	0.000	0.000
68	A	69	TYR	0	0.015	-0.009	17.811	-0.411	-0.411	0.000	0.000	0.000	0.000
69	A	70	TYR	0	0.011	-0.032	19.464	-0.214	-0.214	0.000	0.000	0.000	0.000
70	A	71	LYS	1	0.900	0.952	22.230	-14.260	-14.260	0.000	0.000	0.000	0.000
71	A	72	ASP	-1	-0.923	-0.956	24.334	10.953	10.953	0.000	0.000	0.000	0.000
72	A	73	PHE	0	-0.066	-0.040	26.550	-0.405	-0.405	0.000	0.000	0.000	0.000
73	A	74	ASP	-1	-0.812	-0.888	24.962	12.370	12.370	0.000	0.000	0.000	0.000
74	A	75	GLU	-1	-0.835	-0.912	22.906	12.712	12.712	0.000	0.000	0.000	0.000
75	A	76	LEU	0	-0.037	-0.016	15.167	0.473	0.473	0.000	0.000	0.000	0.000
76	A	77	VAL	0	0.022	-0.007	19.100	-0.229	-0.229	0.000	0.000	0.000	0.000
77	A	78	LEU	0	-0.053	-0.003	13.942	1.016	1.016	0.000	0.000	0.000	0.000
78	A	79	ALA	0	0.007	-0.005	16.824	-1.033	-1.033	0.000	0.000	0.000	0.000
79	A	80	TYR	0	0.037	0.005	17.020	1.174	1.174	0.000	0.000	0.000	0.000
80	A	81	GLY	0	-0.002	-0.018	17.702	-0.868	-0.868	0.000	0.000	0.000	0.000
81	A	82	ILE	0	0.007	0.005	19.126	0.203	0.203	0.000	0.000	0.000	0.000
82	A	83	SER	0	-0.032	0.001	21.293	0.105	0.105	0.000	0.000	0.000	0.000
83	A	84	ASP	-1	-0.816	-0.913	22.420	11.866	11.866	0.000	0.000	0.000	0.000
84	A	85	THR	0	-0.122	-0.061	24.672	-0.225	-0.225	0.000	0.000	0.000	0.000
85	A	86	ASN	0	-0.030	-0.018	25.162	-0.899	-0.899	0.000	0.000	0.000	0.000
86	A	87	GLU	-1	-0.899	-0.943	25.659	10.749	10.749	0.000	0.000	0.000	0.000
87	A	88	PRO	0	-0.058	-0.002	23.096	0.015	0.015	0.000	0.000	0.000	0.000
88	A	89	HIS	0	0.019	0.006	24.799	-0.427	-0.427	0.000	0.000	0.000	0.000
89	A	90	ALA	0	-0.035	-0.015	22.081	-0.259	-0.259	0.000	0.000	0.000	0.000
90	A	91	GLN	0	0.049	0.018	24.142	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	92	TRP	0	-0.056	-0.040	16.587	0.539	0.539	0.000	0.000	0.000	0.000
92	A	93	GLN	0	0.004	0.008	23.171	-0.894	-0.894	0.000	0.000	0.000	0.000
93	A	94	PHE	0	0.028	-0.005	22.304	0.580	0.580	0.000	0.000	0.000	0.000
94	A	95	SER	0	-0.005	-0.006	25.583	-0.368	-0.368	0.000	0.000	0.000	0.000
95	A	96	SER	0	-0.039	-0.006	27.458	-0.455	-0.455	0.000	0.000	0.000	0.000
96	A	97	ASP	-1	-0.921	-0.961	28.671	10.456	10.456	0.000	0.000	0.000	0.000
97	A	98	ILE	0	-0.031	-0.013	27.439	0.420	0.420	0.000	0.000	0.000	0.000
98	A	99	PRO	0	0.025	0.023	24.044	-0.312	-0.312	0.000	0.000	0.000	0.000
99	A	100	LYS	1	0.871	0.927	26.981	-9.915	-9.915	0.000	0.000	0.000	0.000
100	A	101	THR	0	0.052	0.030	26.421	0.469	0.469	0.000	0.000	0.000	0.000
101	A	102	ILE	0	0.010	-0.006	21.629	-0.131	-0.131	0.000	0.000	0.000	0.000
102	A	103	ALA	0	-0.026	-0.026	26.071	-0.212	-0.212	0.000	0.000	0.000	0.000
103	A	104	GLU	-1	-0.841	-0.910	29.519	9.376	9.376	0.000	0.000	0.000	0.000
104	A	105	TYR	0	-0.033	0.005	26.035	-0.327	-0.327	0.000	0.000	0.000	0.000
105	A	106	PHE	0	0.025	-0.008	24.814	-0.096	-0.096	0.000	0.000	0.000	0.000
106	A	107	GLN	0	0.012	0.010	29.984	-0.155	-0.155	0.000	0.000	0.000	0.000
107	A	108	ALA	0	-0.028	-0.025	32.899	-0.283	-0.283	0.000	0.000	0.000	0.000
108	A	109	THR	0	-0.057	-0.010	29.851	-0.210	-0.210	0.000	0.000	0.000	0.000
109	A	110	SER	0	-0.049	-0.042	31.494	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	111	GLY	0	-0.015	0.016	33.491	-0.127	-0.127	0.000	0.000	0.000	0.000
111	A	112	VAL	0	-0.049	-0.012	31.210	-0.212	-0.212	0.000	0.000	0.000	0.000
112	A	113	TYR	0	0.048	0.012	31.392	0.273	0.273	0.000	0.000	0.000	0.000
113	A	114	PRO	0	-0.029	0.009	26.933	0.055	0.055	0.000	0.000	0.000	0.000
114	A	115	LYS	1	0.947	0.957	28.181	-10.397	-10.397	0.000	0.000	0.000	0.000
115	A	116	LYS	1	0.949	0.979	24.279	-12.551	-12.551	0.000	0.000	0.000	0.000
116	A	117	TYR	0	0.043	0.026	21.471	0.170	0.170	0.000	0.000	0.000	0.000
117	A	118	GLY	0	0.025	0.016	24.294	0.270	0.270	0.000	0.000	0.000	0.000
118	A	119	GLN	0	0.028	-0.001	25.646	-0.376	-0.376	0.000	0.000	0.000	0.000
119	A	120	SER	0	0.000	0.020	21.571	0.336	0.336	0.000	0.000	0.000	0.000
120	A	121	TYR	0	0.017	0.013	22.684	-0.345	-0.345	0.000	0.000	0.000	0.000
121	A	122	TYR	0	-0.012	-0.035	21.669	0.827	0.827	0.000	0.000	0.000	0.000
122	A	123	ALA	0	0.000	0.010	19.098	-0.272	-0.272	0.000	0.000	0.000	0.000
123	A	124	CYS	0	-0.072	-0.033	18.681	-0.202	-0.202	0.000	0.000	0.000	0.000
124	A	125	SER	0	0.004	0.012	20.033	0.541	0.541	0.000	0.000	0.000	0.000
125	A	126	GLN	0	-0.021	0.003	17.216	-0.518	-0.518	0.000	0.000	0.000	0.000
126	A	127	LYS	1	1.040	1.029	21.622	-10.922	-10.922	0.000	0.000	0.000	0.000
127	A	128	VAL	0	-0.020	-0.006	19.456	0.273	0.273	0.000	0.000	0.000	0.000
128	A	129	SER	0	-0.080	-0.050	21.735	0.107	0.107	0.000	0.000	0.000	0.000
129	A	130	GLN	0	-0.048	-0.031	24.353	-0.217	-0.217	0.000	0.000	0.000	0.000
130	A	131	GLY	0	-0.016	0.007	21.164	-0.150	-0.150	0.000	0.000	0.000	0.000
131	A	132	ILE	0	-0.028	-0.013	15.353	0.080	0.080	0.000	0.000	0.000	0.000
132	A	133	ASP	-1	-0.866	-0.937	15.821	17.689	17.689	0.000	0.000	0.000	0.000
133	A	134	TYR	0	0.057	-0.005	11.460	0.350	0.350	0.000	0.000	0.000	0.000
134	A	135	THR	0	0.035	0.005	11.232	2.390	2.390	0.000	0.000	0.000	0.000
135	A	136	ARG	1	0.950	0.995	12.307	-14.891	-14.891	0.000	0.000	0.000	0.000
136	A	137	PHE	0	-0.007	-0.007	12.539	-0.075	-0.075	0.000	0.000	0.000	0.000
137	A	138	ALA	0	0.011	0.008	8.604	0.442	0.442	0.000	0.000	0.000	0.000
138	A	139	SER	0	-0.009	0.012	10.455	0.622	0.622	0.000	0.000	0.000	0.000
139	A	140	MET	0	0.008	-0.010	12.541	-0.342	-0.342	0.000	0.000	0.000	0.000
140	A	141	LEU	0	0.031	0.013	8.381	-0.347	-0.347	0.000	0.000	0.000	0.000
141	A	142	ASP	-1	-0.886	-0.931	8.408	31.884	31.884	0.000	0.000	0.000	0.000
142	A	143	ASN	0	-0.005	-0.008	11.162	-0.218	-0.218	0.000	0.000	0.000	0.000
143	A	144	ILE	0	0.046	0.043	14.511	-0.538	-0.538	0.000	0.000	0.000	0.000
144	A	145	ILE	0	-0.032	-0.019	8.412	-0.065	-0.065	0.000	0.000	0.000	0.000
145	A	146	ASN	0	-0.044	-0.037	12.689	1.010	1.010	0.000	0.000	0.000	0.000
146	A	147	ASP	-1	-0.849	-0.925	14.995	15.153	15.153	0.000	0.000	0.000	0.000
147	A	148	TYR	0	-0.070	-0.052	13.247	-0.096	-0.096	0.000	0.000	0.000	0.000
148	A	149	LYS	1	0.839	0.885	10.018	-28.042	-28.042	0.000	0.000	0.000	0.000
149	A	150	LEU	0	-0.024	-0.003	16.141	-0.623	-0.623	0.000	0.000	0.000	0.000
150	A	151	ILE	0	0.023	0.021	19.533	-0.663	-0.663	0.000	0.000	0.000	0.000
151	A	152	PHE	0	-0.094	-0.040	16.016	-0.358	-0.358	0.000	0.000	0.000	0.000
152	A	153	ASN	0	-0.046	-0.006	18.139	0.190	0.190	0.000	0.000	0.000	0.000
153	A	154	SER	0	-0.021	-0.028	21.825	-0.840	-0.840	0.000	0.000	0.000	0.000
154	A	155	GLY	0	0.003	0.027	25.336	-0.114	-0.114	0.000	0.000	0.000	0.000
155	A	156	LYS	1	0.969	0.989	21.953	-13.490	-13.490	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:GLU)