FMO DATABASE

FMODB ID: 9GNJ2

Calculation Name: 3SSD-A-Xray320

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	157
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1623918.967033
FMO2-HF: Nuclear repulsion	1561872.223627
FMO2-HF: Total energy	-62046.743405
FMO2-MP2: Total energy	-62231.351695

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:1:ACE )

Summations of interaction energy for fragment #1(A:1:ACE )

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.
2.36	3.218	-0.005	-0.42	-0.432	-0.001

Interaction energy analysis for fragmet #1(A:1:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.001 / q_NPA : -0.012

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	3	SER	0	-0.036	-0.008	3.852	1.089	1.947	-0.005	-0.420	-0.432	-0.001
4	A	4	ILE	0	0.072	0.028	6.942	-0.019	-0.019	0.000	0.000	0.000	0.000
5	A	5	GLN	0	0.040	0.005	10.286	-0.017	-0.017	0.000	0.000	0.000	0.000
6	A	6	PRO	0	0.036	0.025	10.161	0.076	0.076	0.000	0.000	0.000	0.000
7	A	7	TRP	0	0.001	0.005	9.007	0.211	0.211	0.000	0.000	0.000	0.000
8	A	8	ILE	0	0.030	0.011	14.028	0.063	0.063	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.884	-0.945	16.038	-0.198	-0.198	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.863	0.947	16.470	0.364	0.364	0.000	0.000	0.000	0.000
11	A	11	PHE	0	-0.003	0.009	18.010	0.031	0.031	0.000	0.000	0.000	0.000
12	A	12	ILE	0	0.044	0.028	19.830	0.026	0.026	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.932	0.967	20.786	0.204	0.204	0.000	0.000	0.000	0.000
14	A	14	GLN	0	-0.076	-0.036	21.741	-0.005	-0.005	0.000	0.000	0.000	0.000
15	A	15	ALA	0	-0.021	-0.023	23.849	0.016	0.016	0.000	0.000	0.000	0.000
16	A	16	GLN	0	-0.058	-0.024	25.825	0.017	0.017	0.000	0.000	0.000	0.000
17	A	17	GLN	0	-0.023	-0.018	25.264	0.009	0.009	0.000	0.000	0.000	0.000
18	A	18	GLN	0	-0.021	0.017	28.380	0.007	0.007	0.000	0.000	0.000	0.000
19	A	19	ARG	1	0.991	0.993	28.868	0.115	0.115	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.017	-0.018	25.317	0.003	0.003	0.000	0.000	0.000	0.000
21	A	21	GLN	0	0.061	0.013	26.592	-0.006	-0.006	0.000	0.000	0.000	0.000
22	A	22	SER	0	-0.035	-0.007	23.091	-0.007	-0.007	0.000	0.000	0.000	0.000
23	A	23	THR	0	0.060	0.020	20.422	-0.007	-0.007	0.000	0.000	0.000	0.000
24	A	24	LYS	1	0.951	0.980	18.900	0.184	0.184	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.938	-0.951	17.165	-0.289	-0.289	0.000	0.000	0.000	0.000
26	A	26	TYR	0	-0.013	-0.047	14.538	-0.018	-0.018	0.000	0.000	0.000	0.000
27	A	27	PRO	0	0.043	0.041	10.123	0.060	0.060	0.000	0.000	0.000	0.000
28	A	28	THR	0	0.028	-0.004	12.172	0.049	0.049	0.000	0.000	0.000	0.000
29	A	29	SER	0	-0.081	-0.028	9.964	0.109	0.109	0.000	0.000	0.000	0.000
30	A	30	TYR	0	0.038	-0.009	7.248	-0.138	-0.138	0.000	0.000	0.000	0.000
31	A	31	ARG	1	0.935	0.975	7.787	0.238	0.238	0.000	0.000	0.000	0.000
32	A	32	ASN	0	-0.002	0.005	9.147	0.076	0.076	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.010	0.023	11.490	0.052	0.052	0.000	0.000	0.000	0.000
34	A	34	ARG	1	0.835	0.890	12.926	0.074	0.074	0.000	0.000	0.000	0.000
35	A	35	VAL	0	-0.010	0.002	12.443	0.027	0.027	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.864	0.940	15.331	0.185	0.185	0.000	0.000	0.000	0.000
37	A	37	LEU	0	0.009	0.022	17.467	0.009	0.009	0.000	0.000	0.000	0.000
38	A	38	SER	0	-0.007	0.007	20.842	0.011	0.011	0.000	0.000	0.000	0.000
39	A	39	PHE	0	0.044	0.020	21.383	0.006	0.006	0.000	0.000	0.000	0.000
40	A	40	GLY	0	-0.007	-0.009	26.706	0.011	0.011	0.000	0.000	0.000	0.000
41	A	41	TYR	0	-0.014	-0.011	28.697	-0.009	-0.009	0.000	0.000	0.000	0.000
42	A	42	GLY	0	0.020	0.026	31.047	0.007	0.007	0.000	0.000	0.000	0.000
43	A	43	ASN	0	0.006	0.013	34.111	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	44	PHE	0	-0.011	-0.015	29.197	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	45	THR	0	-0.027	-0.001	28.443	0.009	0.009	0.000	0.000	0.000	0.000
46	A	46	SER	0	0.013	-0.009	30.643	-0.006	-0.006	0.000	0.000	0.000	0.000
47	A	47	ILE	0	-0.030	-0.013	27.890	0.000	0.000	0.000	0.000	0.000	0.000
48	A	48	PRO	0	-0.039	-0.015	25.068	-0.004	-0.004	0.000	0.000	0.000	0.000
49	A	49	TRP	0	0.013	0.014	21.913	0.000	0.000	0.000	0.000	0.000	0.000
50	A	50	PHE	0	0.011	-0.012	14.396	-0.015	-0.015	0.000	0.000	0.000	0.000
51	A	51	ALA	0	-0.005	-0.008	19.285	0.009	0.009	0.000	0.000	0.000	0.000
52	A	52	PHE	0	0.018	0.000	12.704	-0.039	-0.039	0.000	0.000	0.000	0.000
53	A	53	LEU	0	-0.029	-0.010	16.775	0.029	0.029	0.000	0.000	0.000	0.000
54	A	54	GLY	0	0.093	0.040	17.445	-0.013	-0.013	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.921	-0.973	18.908	-0.055	-0.055	0.000	0.000	0.000	0.000
56	A	56	GLY	0	-0.038	-0.026	21.092	0.008	0.008	0.000	0.000	0.000	0.000
57	A	57	GLN	0	-0.040	0.006	22.006	0.005	0.005	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.806	-0.905	22.765	-0.144	-0.144	0.000	0.000	0.000	0.000
59	A	59	ALA	0	0.022	0.010	23.817	0.005	0.005	0.000	0.000	0.000	0.000
60	A	60	SER	0	-0.016	0.005	25.111	0.005	0.005	0.000	0.000	0.000	0.000
61	A	61	ASN	0	0.016	-0.019	27.571	0.009	0.009	0.000	0.000	0.000	0.000
62	A	62	GLY	0	0.084	0.048	25.807	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	63	ILE	0	0.022	0.029	24.676	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	64	TYR	0	-0.053	-0.064	20.372	-0.007	-0.007	0.000	0.000	0.000	0.000
65	A	65	PRO	0	0.014	0.035	17.443	0.003	0.003	0.000	0.000	0.000	0.000
66	A	66	VAL	0	-0.032	-0.012	19.669	-0.019	-0.019	0.000	0.000	0.000	0.000
67	A	67	ILE	0	0.008	0.011	16.933	0.010	0.010	0.000	0.000	0.000	0.000
68	A	68	LEU	0	-0.015	-0.021	21.163	-0.008	-0.008	0.000	0.000	0.000	0.000
69	A	69	TYR	0	0.011	-0.011	24.427	0.005	0.005	0.000	0.000	0.000	0.000
70	A	70	TYR	0	0.012	-0.032	26.130	0.002	0.002	0.000	0.000	0.000	0.000
71	A	71	LYS	1	0.898	0.952	28.818	0.112	0.112	0.000	0.000	0.000	0.000
72	A	72	ASP	-1	-0.925	-0.956	30.866	-0.068	-0.068	0.000	0.000	0.000	0.000
73	A	73	PHE	0	-0.064	-0.039	32.807	0.005	0.005	0.000	0.000	0.000	0.000
74	A	74	ASP	-1	-0.813	-0.888	30.426	-0.077	-0.077	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.832	-0.911	28.545	-0.067	-0.067	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.044	-0.019	20.920	-0.008	-0.008	0.000	0.000	0.000	0.000
77	A	77	VAL	0	0.026	-0.006	25.131	0.007	0.007	0.000	0.000	0.000	0.000
78	A	78	LEU	0	-0.049	-0.001	19.083	-0.015	-0.015	0.000	0.000	0.000	0.000
79	A	79	ALA	0	0.009	-0.005	22.557	0.014	0.014	0.000	0.000	0.000	0.000
80	A	80	TYR	0	0.037	0.004	22.611	-0.012	-0.012	0.000	0.000	0.000	0.000
81	A	81	GLY	0	-0.004	-0.019	23.584	0.006	0.006	0.000	0.000	0.000	0.000
82	A	82	ILE	0	0.009	0.007	25.333	0.003	0.003	0.000	0.000	0.000	0.000
83	A	83	SER	0	-0.032	0.001	28.142	-0.003	-0.003	0.000	0.000	0.000	0.000
84	A	84	ASP	-1	-0.820	-0.914	29.257	-0.061	-0.061	0.000	0.000	0.000	0.000
85	A	85	THR	0	-0.121	-0.061	31.931	0.002	0.002	0.000	0.000	0.000	0.000
86	A	86	ASN	0	-0.029	-0.018	32.141	0.008	0.008	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.900	-0.944	32.337	-0.040	-0.040	0.000	0.000	0.000	0.000
88	A	88	PRO	0	-0.053	-0.002	29.178	0.000	0.000	0.000	0.000	0.000	0.000
89	A	89	HIS	0	0.006	0.001	29.750	0.003	0.003	0.000	0.000	0.000	0.000
90	A	90	ALA	0	-0.028	-0.010	27.148	0.004	0.004	0.000	0.000	0.000	0.000
91	A	91	GLN	0	0.048	0.016	29.116	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	92	TRP	0	-0.060	-0.042	21.410	0.002	0.002	0.000	0.000	0.000	0.000
93	A	93	GLN	0	0.006	0.009	27.041	0.006	0.006	0.000	0.000	0.000	0.000
94	A	94	PHE	0	0.027	-0.006	26.384	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	95	SER	0	-0.005	-0.006	27.221	0.000	0.000	0.000	0.000	0.000	0.000
96	A	96	SER	0	-0.041	-0.005	29.660	0.003	0.003	0.000	0.000	0.000	0.000
97	A	97	ASP	-1	-0.920	-0.962	31.389	-0.009	-0.009	0.000	0.000	0.000	0.000
98	A	98	ILE	0	-0.031	-0.013	31.155	-0.002	-0.002	0.000	0.000	0.000	0.000
99	A	99	PRO	0	0.022	0.022	28.072	0.000	0.000	0.000	0.000	0.000	0.000
100	A	100	LYS	1	0.875	0.927	31.169	0.024	0.024	0.000	0.000	0.000	0.000
101	A	101	THR	0	0.054	0.031	31.433	-0.004	-0.004	0.000	0.000	0.000	0.000
102	A	102	ILE	0	0.012	-0.004	27.705	0.001	0.001	0.000	0.000	0.000	0.000
103	A	103	ALA	0	-0.030	-0.027	31.927	0.001	0.001	0.000	0.000	0.000	0.000
104	A	104	GLU	-1	-0.840	-0.909	35.598	-0.026	-0.026	0.000	0.000	0.000	0.000
105	A	105	TYR	0	-0.035	0.004	31.348	0.003	0.003	0.000	0.000	0.000	0.000
106	A	106	PHE	0	0.026	-0.008	30.866	0.000	0.000	0.000	0.000	0.000	0.000
107	A	107	GLN	0	0.012	0.011	35.740	0.000	0.000	0.000	0.000	0.000	0.000
108	A	108	ALA	0	-0.026	-0.024	37.879	0.002	0.002	0.000	0.000	0.000	0.000
109	A	109	THR	0	-0.061	-0.011	34.967	0.002	0.002	0.000	0.000	0.000	0.000
110	A	110	SER	0	-0.051	-0.043	37.202	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	111	GLY	0	-0.014	0.016	39.022	0.000	0.000	0.000	0.000	0.000	0.000
112	A	112	VAL	0	-0.045	-0.011	37.467	0.001	0.001	0.000	0.000	0.000	0.000
113	A	113	TYR	0	0.044	0.010	38.172	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	114	PRO	0	-0.025	0.010	33.670	-0.002	-0.002	0.000	0.000	0.000	0.000
115	A	115	LYS	1	0.944	0.956	35.378	0.061	0.061	0.000	0.000	0.000	0.000
116	A	116	LYS	1	0.950	0.980	31.884	0.078	0.078	0.000	0.000	0.000	0.000
117	A	117	TYR	0	0.042	0.025	28.857	-0.002	-0.002	0.000	0.000	0.000	0.000
118	A	118	GLY	0	0.026	0.017	30.846	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	119	GLN	0	0.032	0.000	31.979	0.006	0.006	0.000	0.000	0.000	0.000
120	A	120	SER	0	-0.004	0.020	27.694	0.000	0.000	0.000	0.000	0.000	0.000
121	A	121	TYR	0	0.020	0.013	27.794	0.003	0.003	0.000	0.000	0.000	0.000
122	A	122	TYR	0	-0.013	-0.035	27.014	-0.007	-0.007	0.000	0.000	0.000	0.000
123	A	123	ALA	0	-0.003	0.010	23.628	0.006	0.006	0.000	0.000	0.000	0.000
124	A	124	CYS	0	-0.070	-0.032	23.112	0.004	0.004	0.000	0.000	0.000	0.000
125	A	125	SER	0	-0.001	0.011	25.066	-0.008	-0.008	0.000	0.000	0.000	0.000
126	A	126	GLN	0	-0.014	0.004	21.393	0.008	0.008	0.000	0.000	0.000	0.000
127	A	127	LYS	1	1.038	1.028	26.525	0.046	0.046	0.000	0.000	0.000	0.000
128	A	128	VAL	0	-0.027	-0.008	24.948	-0.002	-0.002	0.000	0.000	0.000	0.000
129	A	129	SER	0	-0.075	-0.048	26.667	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	130	GLN	0	-0.048	-0.030	29.042	0.004	0.004	0.000	0.000	0.000	0.000
131	A	131	GLY	0	-0.014	0.007	25.289	0.004	0.004	0.000	0.000	0.000	0.000
132	A	132	ILE	0	-0.028	-0.014	19.824	0.003	0.003	0.000	0.000	0.000	0.000
133	A	133	ASP	-1	-0.866	-0.937	18.428	-0.091	-0.091	0.000	0.000	0.000	0.000
134	A	134	TYR	0	0.055	-0.005	15.559	-0.003	-0.003	0.000	0.000	0.000	0.000
135	A	135	THR	0	0.033	0.005	13.288	-0.043	-0.043	0.000	0.000	0.000	0.000
136	A	136	ARG	1	0.955	0.996	14.967	0.071	0.071	0.000	0.000	0.000	0.000
137	A	137	PHE	0	-0.006	-0.006	17.745	0.008	0.008	0.000	0.000	0.000	0.000
138	A	138	ALA	0	0.017	0.010	12.523	-0.004	-0.004	0.000	0.000	0.000	0.000
139	A	139	SER	0	-0.015	0.010	14.185	0.010	0.010	0.000	0.000	0.000	0.000
140	A	140	MET	0	0.010	-0.009	15.358	0.018	0.018	0.000	0.000	0.000	0.000
141	A	141	LEU	0	0.026	0.010	13.471	0.006	0.006	0.000	0.000	0.000	0.000
142	A	142	ASP	-1	-0.883	-0.930	11.268	-0.172	-0.172	0.000	0.000	0.000	0.000
143	A	143	ASN	0	-0.004	-0.007	14.069	0.037	0.037	0.000	0.000	0.000	0.000
144	A	144	ILE	0	0.044	0.042	17.404	0.007	0.007	0.000	0.000	0.000	0.000
145	A	145	ILE	0	-0.029	-0.018	12.793	0.002	0.002	0.000	0.000	0.000	0.000
146	A	146	ASN	0	-0.044	-0.037	14.521	0.008	0.008	0.000	0.000	0.000	0.000
147	A	147	ASP	-1	-0.849	-0.925	16.748	0.000	0.000	0.000	0.000	0.000	0.000
148	A	148	TYR	0	-0.072	-0.053	17.509	-0.004	-0.004	0.000	0.000	0.000	0.000
149	A	149	LYS	1	0.840	0.885	11.986	0.052	0.052	0.000	0.000	0.000	0.000
150	A	150	LEU	0	-0.026	-0.004	18.547	0.010	0.010	0.000	0.000	0.000	0.000
151	A	151	ILE	0	0.024	0.022	21.211	0.003	0.003	0.000	0.000	0.000	0.000
152	A	152	PHE	0	-0.101	-0.043	20.094	-0.002	-0.002	0.000	0.000	0.000	0.000
153	A	153	ASN	0	-0.043	-0.004	19.169	0.003	0.003	0.000	0.000	0.000	0.000
154	A	154	SER	0	-0.021	-0.029	23.398	0.008	0.008	0.000	0.000	0.000	0.000
155	A	155	GLY	0	0.003	0.023	27.251	-0.003	-0.003	0.000	0.000	0.000	0.000
156	A	156	LYS	1	0.917	0.956	26.099	0.035	0.035	0.000	0.000	0.000	0.000
157	A	157	NME	0	0.055	0.037	25.241	-0.003	-0.003	0.000	0.000	0.000	0.000

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