FMO DATABASE

FMODB ID: GN3R1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1618553.499502
FMO2-HF: Nuclear repulsion	1556676.48056
FMO2-HF: Total energy	-61877.018942
FMO2-MP2: Total energy	-62061.121336

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.
-141.644	-143.368	26.605	-11.538	-13.341	0.152

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 : -0.838 / q_NPA : -0.921

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	0.044	0.019	3.880	-0.701	0.988	-0.017	-0.787	-0.886	0.002
4	A	5	GLN	0	0.043	0.008	5.491	0.118	0.118	0.000	0.000	0.000	0.000
5	A	6	PRO	0	0.031	0.017	6.794	-2.073	-2.073	0.000	0.000	0.000	0.000
6	A	7	TRP	0	-0.001	0.005	4.526	-3.990	-3.756	-0.001	-0.008	-0.224	0.000
7	A	8	ILE	0	0.039	0.020	8.958	-2.003	-2.003	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.842	-0.908	11.191	16.896	16.896	0.000	0.000	0.000	0.000
9	A	10	LYS	1	0.843	0.926	11.531	-23.792	-23.792	0.000	0.000	0.000	0.000
10	A	11	PHE	0	-0.012	0.004	12.804	-1.217	-1.217	0.000	0.000	0.000	0.000
11	A	12	ILE	0	0.069	0.026	14.415	-1.290	-1.290	0.000	0.000	0.000	0.000
12	A	13	LYS	1	0.819	0.909	16.321	-17.881	-17.881	0.000	0.000	0.000	0.000
13	A	14	GLN	0	-0.023	-0.012	16.229	0.004	0.004	0.000	0.000	0.000	0.000
14	A	15	ALA	0	-0.016	-0.013	18.448	-0.815	-0.815	0.000	0.000	0.000	0.000
15	A	16	GLN	0	-0.043	-0.027	20.175	-1.111	-1.111	0.000	0.000	0.000	0.000
16	A	17	GLN	0	-0.032	-0.025	20.972	-0.160	-0.160	0.000	0.000	0.000	0.000
17	A	18	GLN	0	-0.009	0.022	22.881	-0.227	-0.227	0.000	0.000	0.000	0.000
18	A	19	ARG	1	1.004	1.001	23.514	-12.222	-12.222	0.000	0.000	0.000	0.000
19	A	20	SER	0	-0.014	-0.017	20.505	-0.074	-0.074	0.000	0.000	0.000	0.000
20	A	21	GLN	0	0.035	0.012	20.444	0.538	0.538	0.000	0.000	0.000	0.000
21	A	22	SER	0	-0.052	-0.033	16.887	0.404	0.404	0.000	0.000	0.000	0.000
22	A	23	THR	0	0.052	0.012	14.051	0.274	0.274	0.000	0.000	0.000	0.000
23	A	24	LYS	1	0.889	0.935	12.635	-16.386	-16.386	0.000	0.000	0.000	0.000
24	A	25	ASP	-1	-0.843	-0.875	12.079	20.381	20.381	0.000	0.000	0.000	0.000
25	A	26	TYR	0	-0.018	-0.043	8.780	-0.989	-0.989	0.000	0.000	0.000	0.000
26	A	27	PRO	0	0.024	0.035	3.897	-3.282	-2.947	0.003	-0.098	-0.240	0.000
27	A	28	THR	0	0.040	0.003	6.041	0.011	0.011	0.000	0.000	0.000	0.000
28	A	29	SER	0	-0.077	-0.040	1.681	-25.850	-31.477	13.872	-5.473	-2.772	0.057
29	A	30	TYR	0	-0.021	-0.057	2.271	-0.845	2.637	7.344	-5.099	-5.727	0.050
30	A	31	ARG	1	0.826	0.922	1.975	-60.657	-62.960	5.400	0.154	-3.250	0.042
31	A	32	ASN	0	-0.036	-0.027	4.031	-15.333	-14.867	0.004	-0.227	-0.242	0.001
32	A	33	LEU	0	0.005	0.021	5.832	-9.285	-9.285	0.000	0.000	0.000	0.000
33	A	34	ARG	1	0.831	0.895	6.433	-16.530	-16.530	0.000	0.000	0.000	0.000
34	A	35	VAL	0	-0.015	0.008	5.861	-3.054	-3.054	0.000	0.000	0.000	0.000
35	A	36	LYS	1	0.792	0.877	8.238	-23.203	-23.203	0.000	0.000	0.000	0.000
36	A	37	LEU	0	0.002	0.015	10.978	-0.417	-0.417	0.000	0.000	0.000	0.000
37	A	38	SER	0	-0.013	-0.006	14.078	-1.013	-1.013	0.000	0.000	0.000	0.000
38	A	39	PHE	0	0.038	0.013	15.377	-0.264	-0.264	0.000	0.000	0.000	0.000
39	A	40	GLY	0	0.002	-0.003	20.410	-0.878	-0.878	0.000	0.000	0.000	0.000
40	A	41	TYR	0	-0.022	-0.008	21.837	0.782	0.782	0.000	0.000	0.000	0.000
41	A	42	GLY	0	0.025	0.033	24.301	-0.500	-0.500	0.000	0.000	0.000	0.000
42	A	43	ASN	0	-0.007	0.007	27.579	-0.125	-0.125	0.000	0.000	0.000	0.000
43	A	44	PHE	0	0.000	-0.013	22.970	0.480	0.480	0.000	0.000	0.000	0.000
44	A	45	THR	0	-0.009	0.005	22.275	-0.653	-0.653	0.000	0.000	0.000	0.000
45	A	46	SER	0	-0.033	-0.049	24.438	0.302	0.302	0.000	0.000	0.000	0.000
46	A	47	ILE	0	0.003	0.002	21.906	-0.005	-0.005	0.000	0.000	0.000	0.000
47	A	48	PRO	0	-0.048	-0.023	19.093	0.346	0.346	0.000	0.000	0.000	0.000
48	A	49	TRP	0	0.009	0.010	15.191	0.156	0.156	0.000	0.000	0.000	0.000
49	A	50	PHE	0	0.006	-0.011	8.227	0.474	0.474	0.000	0.000	0.000	0.000
50	A	51	ALA	0	0.008	0.013	12.598	-0.563	-0.563	0.000	0.000	0.000	0.000
51	A	52	PHE	0	0.017	-0.005	6.875	2.813	2.813	0.000	0.000	0.000	0.000
52	A	53	LEU	0	0.014	0.013	10.360	-1.313	-1.313	0.000	0.000	0.000	0.000
53	A	54	GLY	0	0.083	0.038	11.420	2.418	2.418	0.000	0.000	0.000	0.000
54	A	55	GLU	-1	-0.831	-0.893	13.278	16.644	16.644	0.000	0.000	0.000	0.000
55	A	56	GLY	0	0.053	0.016	15.794	-0.874	-0.874	0.000	0.000	0.000	0.000
56	A	57	GLN	0	-0.028	0.010	16.028	-1.365	-1.365	0.000	0.000	0.000	0.000
57	A	58	GLU	-1	-0.762	-0.887	16.025	21.629	21.629	0.000	0.000	0.000	0.000
58	A	59	ALA	0	0.014	0.017	16.962	-0.587	-0.587	0.000	0.000	0.000	0.000
59	A	60	SER	0	-0.003	0.001	18.512	-0.457	-0.457	0.000	0.000	0.000	0.000
60	A	61	ASN	0	0.021	-0.007	20.980	-0.616	-0.616	0.000	0.000	0.000	0.000
61	A	62	GLY	0	0.099	0.043	19.761	0.614	0.614	0.000	0.000	0.000	0.000
62	A	63	ILE	0	0.007	0.031	18.862	-0.298	-0.298	0.000	0.000	0.000	0.000
63	A	64	TYR	0	-0.042	-0.028	14.312	1.259	1.259	0.000	0.000	0.000	0.000
64	A	65	PRO	0	0.030	0.031	11.716	-1.035	-1.035	0.000	0.000	0.000	0.000
65	A	66	VAL	0	-0.045	-0.019	13.506	1.365	1.365	0.000	0.000	0.000	0.000
66	A	67	ILE	0	0.007	0.013	11.569	-0.692	-0.692	0.000	0.000	0.000	0.000
67	A	68	LEU	0	-0.017	-0.016	15.479	0.163	0.163	0.000	0.000	0.000	0.000
68	A	69	TYR	0	-0.001	-0.001	18.602	-0.325	-0.325	0.000	0.000	0.000	0.000
69	A	70	TYR	0	0.029	-0.014	20.216	-0.219	-0.219	0.000	0.000	0.000	0.000
70	A	71	LYS	1	0.844	0.923	22.522	-13.508	-13.508	0.000	0.000	0.000	0.000
71	A	72	ASP	-1	-0.815	-0.879	25.199	10.692	10.692	0.000	0.000	0.000	0.000
72	A	73	PHE	0	-0.022	-0.015	27.166	-0.379	-0.379	0.000	0.000	0.000	0.000
73	A	74	ASP	-1	-0.787	-0.863	25.150	12.190	12.190	0.000	0.000	0.000	0.000
74	A	75	GLU	-1	-0.741	-0.795	23.283	12.550	12.550	0.000	0.000	0.000	0.000
75	A	76	LEU	0	-0.011	-0.008	15.749	0.401	0.401	0.000	0.000	0.000	0.000
76	A	77	VAL	0	0.004	-0.008	19.905	-0.048	-0.048	0.000	0.000	0.000	0.000
77	A	78	LEU	0	-0.040	-0.014	14.163	1.005	1.005	0.000	0.000	0.000	0.000
78	A	79	ALA	0	-0.006	-0.014	17.402	-1.024	-1.024	0.000	0.000	0.000	0.000
79	A	80	TYR	0	0.010	-0.021	17.263	1.217	1.217	0.000	0.000	0.000	0.000
80	A	81	GLY	0	0.015	-0.005	17.859	-0.947	-0.947	0.000	0.000	0.000	0.000
81	A	82	ILE	0	0.011	0.009	19.351	0.301	0.301	0.000	0.000	0.000	0.000
82	A	83	SER	0	-0.007	0.011	21.830	0.081	0.081	0.000	0.000	0.000	0.000
83	A	84	ASP	-1	-0.773	-0.875	22.923	12.132	12.132	0.000	0.000	0.000	0.000
84	A	85	THR	0	-0.115	-0.050	24.982	-0.185	-0.185	0.000	0.000	0.000	0.000
85	A	86	ASN	0	-0.030	-0.031	25.437	-0.739	-0.739	0.000	0.000	0.000	0.000
86	A	87	GLU	-1	-0.896	-0.926	26.188	10.986	10.986	0.000	0.000	0.000	0.000
87	A	88	PRO	0	-0.069	-0.007	23.229	0.053	0.053	0.000	0.000	0.000	0.000
88	A	89	HIS	0	0.003	-0.005	23.948	-0.476	-0.476	0.000	0.000	0.000	0.000
89	A	90	ALA	0	-0.034	-0.012	21.362	-0.209	-0.209	0.000	0.000	0.000	0.000
90	A	91	GLN	0	0.025	0.002	23.379	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	92	TRP	0	-0.043	-0.036	16.071	0.638	0.638	0.000	0.000	0.000	0.000
92	A	93	GLN	0	-0.001	0.006	22.297	-0.895	-0.895	0.000	0.000	0.000	0.000
93	A	94	PHE	0	0.024	-0.006	21.641	0.617	0.617	0.000	0.000	0.000	0.000
94	A	95	SER	0	-0.010	-0.006	23.920	-0.424	-0.424	0.000	0.000	0.000	0.000
95	A	96	SER	0	-0.065	-0.038	26.273	-0.407	-0.407	0.000	0.000	0.000	0.000
96	A	97	ASP	-1	-0.891	-0.922	27.877	10.818	10.818	0.000	0.000	0.000	0.000
97	A	98	ILE	0	-0.013	-0.007	27.140	0.471	0.471	0.000	0.000	0.000	0.000
98	A	99	PRO	0	0.007	0.020	23.346	-0.356	-0.356	0.000	0.000	0.000	0.000
99	A	100	LYS	1	0.853	0.900	26.406	-10.004	-10.004	0.000	0.000	0.000	0.000
100	A	101	THR	0	0.066	0.030	26.378	0.440	0.440	0.000	0.000	0.000	0.000
101	A	102	ILE	0	-0.020	-0.014	22.158	-0.201	-0.201	0.000	0.000	0.000	0.000
102	A	103	ALA	0	-0.020	-0.019	26.543	-0.246	-0.246	0.000	0.000	0.000	0.000
103	A	104	GLU	-1	-0.818	-0.885	30.108	9.612	9.612	0.000	0.000	0.000	0.000
104	A	105	TYR	0	-0.032	-0.031	26.530	-0.273	-0.273	0.000	0.000	0.000	0.000
105	A	106	PHE	0	0.032	0.011	25.108	-0.094	-0.094	0.000	0.000	0.000	0.000
106	A	107	GLN	0	-0.006	0.017	30.442	-0.255	-0.255	0.000	0.000	0.000	0.000
107	A	108	ALA	0	-0.017	-0.016	33.267	-0.343	-0.343	0.000	0.000	0.000	0.000
108	A	109	THR	0	-0.062	-0.036	29.975	-0.233	-0.233	0.000	0.000	0.000	0.000
109	A	110	SER	0	-0.074	-0.058	31.551	0.070	0.070	0.000	0.000	0.000	0.000
110	A	111	GLY	0	-0.002	0.018	33.755	-0.118	-0.118	0.000	0.000	0.000	0.000
111	A	112	VAL	0	-0.040	-0.016	31.997	-0.215	-0.215	0.000	0.000	0.000	0.000
112	A	113	TYR	0	0.068	0.024	32.153	0.244	0.244	0.000	0.000	0.000	0.000
113	A	114	PRO	0	-0.051	-0.004	27.591	0.027	0.027	0.000	0.000	0.000	0.000
114	A	115	LYS	1	0.843	0.901	28.840	-10.526	-10.526	0.000	0.000	0.000	0.000
115	A	116	LYS	1	0.879	0.932	24.653	-12.724	-12.724	0.000	0.000	0.000	0.000
116	A	117	TYR	0	0.021	-0.004	21.158	-0.065	-0.065	0.000	0.000	0.000	0.000
117	A	118	GLY	0	0.026	0.017	24.844	0.249	0.249	0.000	0.000	0.000	0.000
118	A	119	GLN	0	0.011	-0.008	25.611	-0.358	-0.358	0.000	0.000	0.000	0.000
119	A	120	SER	0	-0.020	-0.001	21.803	0.221	0.221	0.000	0.000	0.000	0.000
120	A	121	TYR	0	0.024	0.012	22.927	-0.278	-0.278	0.000	0.000	0.000	0.000
121	A	122	TYR	0	-0.013	-0.024	21.864	0.920	0.920	0.000	0.000	0.000	0.000
122	A	123	ALA	0	-0.012	0.003	19.210	-0.220	-0.220	0.000	0.000	0.000	0.000
123	A	124	CYS	0	-0.053	-0.023	18.642	-0.105	-0.105	0.000	0.000	0.000	0.000
124	A	125	SER	0	-0.003	-0.016	20.412	0.420	0.420	0.000	0.000	0.000	0.000
125	A	126	GLN	0	-0.011	0.001	17.785	-0.691	-0.691	0.000	0.000	0.000	0.000
126	A	127	LYS	1	0.921	0.955	21.842	-11.295	-11.295	0.000	0.000	0.000	0.000
127	A	128	VAL	0	-0.015	-0.020	19.962	0.235	0.235	0.000	0.000	0.000	0.000
128	A	129	SER	0	-0.094	-0.077	22.290	-0.004	-0.004	0.000	0.000	0.000	0.000
129	A	130	GLN	0	-0.031	-0.022	24.906	-0.162	-0.162	0.000	0.000	0.000	0.000
130	A	131	GLY	0	0.021	0.019	22.196	-0.186	-0.186	0.000	0.000	0.000	0.000
131	A	132	ILE	0	-0.061	-0.019	16.026	0.225	0.225	0.000	0.000	0.000	0.000
132	A	133	ASP	-1	-0.795	-0.884	16.774	17.102	17.102	0.000	0.000	0.000	0.000
133	A	134	TYR	0	0.062	0.006	12.137	0.731	0.731	0.000	0.000	0.000	0.000
134	A	135	THR	0	0.016	0.010	12.028	2.155	2.155	0.000	0.000	0.000	0.000
135	A	136	ARG	1	0.889	0.946	13.013	-14.217	-14.217	0.000	0.000	0.000	0.000
136	A	137	PHE	0	0.013	-0.001	13.518	0.303	0.303	0.000	0.000	0.000	0.000
137	A	138	ALA	0	0.013	0.004	9.083	0.623	0.623	0.000	0.000	0.000	0.000
138	A	139	SER	0	-0.013	0.003	10.885	0.800	0.800	0.000	0.000	0.000	0.000
139	A	140	MET	0	0.024	0.005	12.933	-0.168	-0.168	0.000	0.000	0.000	0.000
140	A	141	LEU	0	0.004	0.001	8.663	-0.183	-0.183	0.000	0.000	0.000	0.000
141	A	142	ASP	-1	-0.796	-0.880	8.471	35.650	35.650	0.000	0.000	0.000	0.000
142	A	143	ASN	0	-0.028	-0.015	10.738	-0.118	-0.118	0.000	0.000	0.000	0.000
143	A	144	ILE	0	0.049	0.041	14.099	-0.370	-0.370	0.000	0.000	0.000	0.000
144	A	145	ILE	0	-0.050	-0.033	7.484	0.377	0.377	0.000	0.000	0.000	0.000
145	A	146	ASN	0	-0.019	-0.008	11.527	1.758	1.758	0.000	0.000	0.000	0.000
146	A	147	ASP	-1	-0.799	-0.883	13.495	16.441	16.441	0.000	0.000	0.000	0.000
147	A	148	TYR	0	-0.059	-0.060	12.246	0.000	0.000	0.000	0.000	0.000	0.000
148	A	149	LYS	1	0.836	0.907	8.091	-35.000	-35.000	0.000	0.000	0.000	0.000
149	A	150	LEU	0	0.006	0.021	14.453	-0.651	-0.651	0.000	0.000	0.000	0.000
150	A	151	ILE	0	0.012	0.013	17.909	-0.703	-0.703	0.000	0.000	0.000	0.000
151	A	152	PHE	0	-0.066	-0.040	15.847	-0.384	-0.384	0.000	0.000	0.000	0.000
152	A	153	ASN	0	-0.088	-0.039	16.285	-0.380	-0.380	0.000	0.000	0.000	0.000
153	A	154	SER	0	-0.054	-0.032	19.907	-0.969	-0.969	0.000	0.000	0.000	0.000
154	A	155	GLY	0	0.038	0.035	23.367	-0.345	-0.345	0.000	0.000	0.000	0.000
155	A	156	LYS	1	0.823	0.895	19.985	-15.618	-15.618	0.000	0.000	0.000	0.000

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