FMO DATABASE

FMODB ID: 141YZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1617816.042479
FMO2-HF: Nuclear repulsion	1555939.352661
FMO2-HF: Total energy	-61876.689819
FMO2-MP2: Total energy	-62060.798141

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.
-102.645	-91.429	3.927	-6.1	-9.045	0.067

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 : -0.913 / q_NPA : -0.975

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	0.049	0.015	3.625	1.237	3.268	0.013	-0.773	-1.271	0.002
4	A	5	GLN	0	0.042	0.001	4.705	0.045	0.121	-0.001	-0.007	-0.069	0.000
5	A	6	PRO	0	0.028	0.021	5.975	-2.368	-2.368	0.000	0.000	0.000	0.000
6	A	7	TRP	0	-0.008	-0.002	3.240	-5.999	-5.404	0.009	-0.092	-0.512	0.001
7	A	8	ILE	0	0.034	0.017	8.235	-2.404	-2.404	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.836	-0.906	10.510	18.177	18.177	0.000	0.000	0.000	0.000
9	A	10	LYS	1	0.833	0.916	10.537	-27.202	-27.202	0.000	0.000	0.000	0.000
10	A	11	PHE	0	-0.004	0.010	12.118	-1.448	-1.448	0.000	0.000	0.000	0.000
11	A	12	ILE	0	0.062	0.031	13.753	-1.479	-1.479	0.000	0.000	0.000	0.000
12	A	13	LYS	1	0.851	0.916	15.860	-19.010	-19.010	0.000	0.000	0.000	0.000
13	A	14	GLN	0	-0.062	-0.027	15.531	0.145	0.145	0.000	0.000	0.000	0.000
14	A	15	ALA	0	-0.016	-0.018	17.838	-0.943	-0.943	0.000	0.000	0.000	0.000
15	A	16	GLN	0	-0.062	-0.031	19.712	-1.061	-1.061	0.000	0.000	0.000	0.000
16	A	17	GLN	0	-0.044	-0.027	20.252	-0.389	-0.389	0.000	0.000	0.000	0.000
17	A	18	GLN	0	0.011	0.035	22.423	-0.321	-0.321	0.000	0.000	0.000	0.000
18	A	19	ARG	1	0.989	0.990	22.753	-12.932	-12.932	0.000	0.000	0.000	0.000
19	A	20	SER	0	-0.009	-0.013	19.358	-0.153	-0.153	0.000	0.000	0.000	0.000
20	A	21	GLN	0	0.056	0.009	19.681	0.482	0.482	0.000	0.000	0.000	0.000
21	A	22	SER	0	-0.035	0.004	15.978	0.535	0.535	0.000	0.000	0.000	0.000
22	A	23	THR	0	0.055	0.009	13.205	0.221	0.221	0.000	0.000	0.000	0.000
23	A	24	LYS	1	0.889	0.939	11.685	-17.893	-17.893	0.000	0.000	0.000	0.000
24	A	25	ASP	-1	-0.871	-0.915	10.776	22.852	22.852	0.000	0.000	0.000	0.000
25	A	26	TYR	0	-0.011	-0.029	7.879	-0.599	-0.599	0.000	0.000	0.000	0.000
26	A	27	PRO	0	0.045	0.045	3.067	-7.377	-5.424	0.363	-1.043	-1.274	0.009
27	A	28	THR	0	0.045	0.003	4.904	-2.132	-2.163	-0.001	-0.005	0.037	0.000
28	A	29	SER	0	-0.049	-0.014	4.125	-12.004	-11.911	-0.001	-0.090	-0.002	0.000
29	A	30	TYR	0	0.005	-0.023	2.478	9.316	15.513	3.512	-4.261	-5.448	0.051
30	A	31	ARG	1	0.840	0.927	3.495	-47.356	-47.054	0.033	0.171	-0.506	0.004
31	A	32	ASN	0	-0.026	-0.011	5.813	-6.440	-6.440	0.000	0.000	0.000	0.000
32	A	33	LEU	0	-0.015	0.020	6.853	-5.381	-5.381	0.000	0.000	0.000	0.000
33	A	34	ARG	1	0.829	0.898	6.981	-16.524	-16.524	0.000	0.000	0.000	0.000
34	A	35	VAL	0	-0.002	0.003	5.702	-2.294	-2.294	0.000	0.000	0.000	0.000
35	A	36	LYS	1	0.807	0.886	8.592	-22.711	-22.711	0.000	0.000	0.000	0.000
36	A	37	LEU	0	0.002	0.018	10.328	-0.482	-0.482	0.000	0.000	0.000	0.000
37	A	38	SER	0	-0.008	0.002	13.914	-0.976	-0.976	0.000	0.000	0.000	0.000
38	A	39	PHE	0	0.049	0.021	14.877	-0.305	-0.305	0.000	0.000	0.000	0.000
39	A	40	GLY	0	0.004	0.000	19.851	-0.913	-0.913	0.000	0.000	0.000	0.000
40	A	41	TYR	0	-0.019	-0.011	21.478	0.669	0.669	0.000	0.000	0.000	0.000
41	A	42	GLY	0	0.023	0.026	23.748	-0.509	-0.509	0.000	0.000	0.000	0.000
42	A	43	ASN	0	-0.004	0.008	27.003	-0.047	-0.047	0.000	0.000	0.000	0.000
43	A	44	PHE	0	-0.007	-0.010	22.454	0.395	0.395	0.000	0.000	0.000	0.000
44	A	45	THR	0	-0.006	0.009	21.792	-0.649	-0.649	0.000	0.000	0.000	0.000
45	A	46	SER	0	-0.002	-0.017	24.178	0.311	0.311	0.000	0.000	0.000	0.000
46	A	47	ILE	0	-0.044	-0.020	21.793	-0.015	-0.015	0.000	0.000	0.000	0.000
47	A	48	PRO	0	-0.024	-0.005	18.771	0.414	0.414	0.000	0.000	0.000	0.000
48	A	49	TRP	0	0.008	0.012	15.264	0.142	0.142	0.000	0.000	0.000	0.000
49	A	50	PHE	0	0.013	-0.009	7.835	0.625	0.625	0.000	0.000	0.000	0.000
50	A	51	ALA	0	-0.001	-0.003	12.882	-0.431	-0.431	0.000	0.000	0.000	0.000
51	A	52	PHE	0	0.017	-0.005	6.762	2.967	2.967	0.000	0.000	0.000	0.000
52	A	53	LEU	0	-0.008	0.002	10.704	-1.735	-1.735	0.000	0.000	0.000	0.000
53	A	54	GLY	0	0.090	0.038	11.846	1.908	1.908	0.000	0.000	0.000	0.000
54	A	55	GLU	-1	-0.852	-0.930	13.880	15.476	15.476	0.000	0.000	0.000	0.000
55	A	56	GLY	0	0.039	0.014	16.301	-0.678	-0.678	0.000	0.000	0.000	0.000
56	A	57	GLN	0	-0.041	0.002	16.321	-1.246	-1.246	0.000	0.000	0.000	0.000
57	A	58	GLU	-1	-0.767	-0.877	16.777	20.700	20.700	0.000	0.000	0.000	0.000
58	A	59	ALA	0	0.023	0.016	17.090	-0.432	-0.432	0.000	0.000	0.000	0.000
59	A	60	SER	0	-0.009	0.008	18.587	-0.374	-0.374	0.000	0.000	0.000	0.000
60	A	61	ASN	0	0.014	-0.013	21.224	-0.707	-0.707	0.000	0.000	0.000	0.000
61	A	62	GLY	0	0.114	0.060	19.927	0.502	0.502	0.000	0.000	0.000	0.000
62	A	63	ILE	0	0.008	0.030	19.429	-0.227	-0.227	0.000	0.000	0.000	0.000
63	A	64	TYR	0	-0.043	-0.050	14.612	1.014	1.014	0.000	0.000	0.000	0.000
64	A	65	PRO	0	0.017	0.032	12.598	-0.795	-0.795	0.000	0.000	0.000	0.000
65	A	66	VAL	0	-0.028	-0.013	13.912	1.184	1.184	0.000	0.000	0.000	0.000
66	A	67	ILE	0	-0.005	0.008	11.300	-0.689	-0.689	0.000	0.000	0.000	0.000
67	A	68	LEU	0	-0.017	-0.017	15.318	0.262	0.262	0.000	0.000	0.000	0.000
68	A	69	TYR	0	0.023	-0.004	18.212	-0.229	-0.229	0.000	0.000	0.000	0.000
69	A	70	TYR	0	0.008	-0.024	19.921	-0.211	-0.211	0.000	0.000	0.000	0.000
70	A	71	LYS	1	0.885	0.937	22.250	-13.686	-13.686	0.000	0.000	0.000	0.000
71	A	72	ASP	-1	-0.840	-0.906	24.692	10.842	10.842	0.000	0.000	0.000	0.000
72	A	73	PHE	0	-0.052	-0.030	26.797	-0.389	-0.389	0.000	0.000	0.000	0.000
73	A	74	ASP	-1	-0.809	-0.867	24.845	12.261	12.261	0.000	0.000	0.000	0.000
74	A	75	GLU	-1	-0.771	-0.831	22.998	12.270	12.270	0.000	0.000	0.000	0.000
75	A	76	LEU	0	-0.025	-0.008	15.309	0.383	0.383	0.000	0.000	0.000	0.000
76	A	77	VAL	0	0.014	-0.012	19.350	-0.217	-0.217	0.000	0.000	0.000	0.000
77	A	78	LEU	0	-0.051	0.000	14.151	0.937	0.937	0.000	0.000	0.000	0.000
78	A	79	ALA	0	0.016	-0.004	17.415	-0.974	-0.974	0.000	0.000	0.000	0.000
79	A	80	TYR	0	0.009	-0.004	17.626	1.102	1.102	0.000	0.000	0.000	0.000
80	A	81	GLY	0	0.006	-0.016	18.256	-0.867	-0.867	0.000	0.000	0.000	0.000
81	A	82	ILE	0	0.014	0.009	19.746	0.243	0.243	0.000	0.000	0.000	0.000
82	A	83	SER	0	-0.024	0.000	21.930	0.066	0.066	0.000	0.000	0.000	0.000
83	A	84	ASP	-1	-0.805	-0.913	23.060	11.830	11.830	0.000	0.000	0.000	0.000
84	A	85	THR	0	-0.110	-0.052	25.481	-0.150	-0.150	0.000	0.000	0.000	0.000
85	A	86	ASN	0	-0.032	-0.025	25.658	-0.773	-0.773	0.000	0.000	0.000	0.000
86	A	87	GLU	-1	-0.894	-0.934	26.194	10.652	10.652	0.000	0.000	0.000	0.000
87	A	88	PRO	0	-0.066	-0.008	23.423	0.005	0.005	0.000	0.000	0.000	0.000
88	A	89	HIS	0	0.018	0.011	24.825	-0.468	-0.468	0.000	0.000	0.000	0.000
89	A	90	ALA	0	-0.028	-0.015	22.159	-0.268	-0.268	0.000	0.000	0.000	0.000
90	A	91	GLN	0	0.034	0.011	24.253	-0.029	-0.029	0.000	0.000	0.000	0.000
91	A	92	TRP	0	-0.057	-0.041	16.834	0.571	0.571	0.000	0.000	0.000	0.000
92	A	93	GLN	0	0.004	0.007	23.215	-0.864	-0.864	0.000	0.000	0.000	0.000
93	A	94	PHE	0	0.023	-0.005	22.482	0.579	0.579	0.000	0.000	0.000	0.000
94	A	95	SER	0	-0.009	-0.008	25.457	-0.381	-0.381	0.000	0.000	0.000	0.000
95	A	96	SER	0	-0.065	-0.041	27.356	-0.465	-0.465	0.000	0.000	0.000	0.000
96	A	97	ASP	-1	-0.882	-0.920	28.802	10.396	10.396	0.000	0.000	0.000	0.000
97	A	98	ILE	0	-0.034	-0.016	27.872	0.427	0.427	0.000	0.000	0.000	0.000
98	A	99	PRO	0	0.011	0.019	24.305	-0.316	-0.316	0.000	0.000	0.000	0.000
99	A	100	LYS	1	0.858	0.908	27.399	-9.801	-9.801	0.000	0.000	0.000	0.000
100	A	101	THR	0	0.054	0.026	26.959	0.447	0.447	0.000	0.000	0.000	0.000
101	A	102	ILE	0	-0.001	-0.005	22.400	-0.130	-0.130	0.000	0.000	0.000	0.000
102	A	103	ALA	0	-0.022	-0.023	26.712	-0.210	-0.210	0.000	0.000	0.000	0.000
103	A	104	GLU	-1	-0.826	-0.893	30.239	9.371	9.371	0.000	0.000	0.000	0.000
104	A	105	TYR	0	-0.017	-0.014	26.242	-0.283	-0.283	0.000	0.000	0.000	0.000
105	A	106	PHE	0	0.013	-0.003	24.977	-0.096	-0.096	0.000	0.000	0.000	0.000
106	A	107	GLN	0	-0.004	0.002	30.341	-0.191	-0.191	0.000	0.000	0.000	0.000
107	A	108	ALA	0	-0.024	-0.023	33.031	-0.284	-0.284	0.000	0.000	0.000	0.000
108	A	109	THR	0	-0.065	-0.023	29.891	-0.199	-0.199	0.000	0.000	0.000	0.000
109	A	110	SER	0	-0.032	-0.032	31.457	0.003	0.003	0.000	0.000	0.000	0.000
110	A	111	GLY	0	-0.025	0.011	33.640	-0.134	-0.134	0.000	0.000	0.000	0.000
111	A	112	VAL	0	-0.043	-0.013	31.635	-0.206	-0.206	0.000	0.000	0.000	0.000
112	A	113	TYR	0	0.048	0.011	32.442	0.201	0.201	0.000	0.000	0.000	0.000
113	A	114	PRO	0	-0.032	0.006	27.758	0.048	0.048	0.000	0.000	0.000	0.000
114	A	115	LYS	1	0.862	0.908	29.003	-10.451	-10.451	0.000	0.000	0.000	0.000
115	A	116	LYS	1	0.889	0.940	24.997	-12.437	-12.437	0.000	0.000	0.000	0.000
116	A	117	TYR	0	0.024	0.016	21.688	0.074	0.074	0.000	0.000	0.000	0.000
117	A	118	GLY	0	0.023	0.013	25.130	0.259	0.259	0.000	0.000	0.000	0.000
118	A	119	GLN	0	0.019	0.004	26.262	-0.386	-0.386	0.000	0.000	0.000	0.000
119	A	120	SER	0	0.005	0.018	22.236	0.298	0.298	0.000	0.000	0.000	0.000
120	A	121	TYR	0	0.027	0.013	23.268	-0.314	-0.314	0.000	0.000	0.000	0.000
121	A	122	TYR	0	-0.020	-0.021	22.285	0.837	0.837	0.000	0.000	0.000	0.000
122	A	123	ALA	0	-0.002	0.009	19.306	-0.267	-0.267	0.000	0.000	0.000	0.000
123	A	124	CYS	0	-0.060	-0.031	18.908	-0.189	-0.189	0.000	0.000	0.000	0.000
124	A	125	SER	0	-0.001	-0.011	20.222	0.497	0.497	0.000	0.000	0.000	0.000
125	A	126	GLN	0	-0.022	0.004	17.274	-0.648	-0.648	0.000	0.000	0.000	0.000
126	A	127	LYS	1	0.953	0.965	21.765	-11.168	-11.168	0.000	0.000	0.000	0.000
127	A	128	VAL	0	-0.023	-0.010	19.685	0.260	0.260	0.000	0.000	0.000	0.000
128	A	129	SER	0	-0.077	-0.061	21.842	0.127	0.127	0.000	0.000	0.000	0.000
129	A	130	GLN	0	-0.032	-0.023	24.476	-0.182	-0.182	0.000	0.000	0.000	0.000
130	A	131	GLY	0	-0.008	0.011	21.277	-0.119	-0.119	0.000	0.000	0.000	0.000
131	A	132	ILE	0	-0.052	-0.018	15.474	0.056	0.056	0.000	0.000	0.000	0.000
132	A	133	ASP	-1	-0.811	-0.894	16.110	17.258	17.258	0.000	0.000	0.000	0.000
133	A	134	TYR	0	0.081	0.009	11.583	0.609	0.609	0.000	0.000	0.000	0.000
134	A	135	THR	0	0.036	0.006	11.441	2.259	2.259	0.000	0.000	0.000	0.000
135	A	136	ARG	1	0.891	0.956	12.511	-14.541	-14.541	0.000	0.000	0.000	0.000
136	A	137	PHE	0	0.023	-0.005	13.019	0.083	0.083	0.000	0.000	0.000	0.000
137	A	138	ALA	0	0.009	0.008	8.776	0.434	0.434	0.000	0.000	0.000	0.000
138	A	139	SER	0	-0.027	0.005	10.684	0.404	0.404	0.000	0.000	0.000	0.000
139	A	140	MET	0	0.024	-0.008	12.799	-0.186	-0.186	0.000	0.000	0.000	0.000
140	A	141	LEU	0	0.025	0.014	8.879	-0.299	-0.299	0.000	0.000	0.000	0.000
141	A	142	ASP	-1	-0.816	-0.896	8.625	32.589	32.589	0.000	0.000	0.000	0.000
142	A	143	ASN	0	-0.018	-0.012	11.416	-0.159	-0.159	0.000	0.000	0.000	0.000
143	A	144	ILE	0	0.053	0.052	14.757	-0.433	-0.433	0.000	0.000	0.000	0.000
144	A	145	ILE	0	-0.034	-0.022	8.475	-0.004	-0.004	0.000	0.000	0.000	0.000
145	A	146	ASN	0	-0.039	-0.033	12.673	1.174	1.174	0.000	0.000	0.000	0.000
146	A	147	ASP	-1	-0.796	-0.897	14.698	15.316	15.316	0.000	0.000	0.000	0.000
147	A	148	TYR	0	-0.088	-0.070	13.107	-0.114	-0.114	0.000	0.000	0.000	0.000
148	A	149	LYS	1	0.869	0.908	9.376	-29.127	-29.127	0.000	0.000	0.000	0.000
149	A	150	LEU	0	-0.008	0.016	15.738	-0.642	-0.642	0.000	0.000	0.000	0.000
150	A	151	ILE	0	0.020	0.019	19.100	-0.643	-0.643	0.000	0.000	0.000	0.000
151	A	152	PHE	0	-0.099	-0.045	16.801	-0.307	-0.307	0.000	0.000	0.000	0.000
152	A	153	ASN	0	-0.098	-0.052	17.476	-0.118	-0.118	0.000	0.000	0.000	0.000
153	A	154	SER	0	-0.001	-0.013	21.247	-0.820	-0.820	0.000	0.000	0.000	0.000
154	A	155	GLY	0	-0.006	0.023	24.843	-0.122	-0.122	0.000	0.000	0.000	0.000
155	A	156	LYS	1	0.877	0.934	20.968	-14.265	-14.265	0.000	0.000	0.000	0.000

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