FMO DATABASE

FMODB ID: YNQQ2

Calculation Name: 1AWC-B-Xray372

Preferred Name:

Target Type:

Ligand Name: 5-bromo-2'-deoxyuridine-5'-monophosphate

ligand 3-letter code: BRU

PDB ID: 1AWC

Chain ID: B

ChEMBL ID:

UniProt ID: Q00420

Base Structure: X-ray

Registration Date: 2023-09-26

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1428965.982224
FMO2-HF: Nuclear repulsion	1369792.38967
FMO2-HF: Total energy	-59173.592554
FMO2-MP2: Total energy	-59346.260555

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(B:5:ASP)

Summations of interaction energy for fragment #1(B:5:ASP)

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.
-96.011	-95.62	22.007	-9.515	-12.883	0.14

Interaction energy analysis for fragmet #1(B:5:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.826 / q_NPA : -0.923

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	B	7	GLY	0	0.052	0.034	1.886	-20.477	-22.605	10.544	-4.258	-4.157	0.050
4	B	8	LYS	1	0.825	0.902	1.924	-103.829	-102.527	11.451	-4.705	-8.048	0.087
5	B	9	LYS	1	0.875	0.935	3.784	-43.266	-42.436	0.010	-0.435	-0.405	0.002
6	B	10	LEU	0	0.010	0.011	5.506	-6.838	-6.838	0.000	0.000	0.000	0.000
7	B	11	LEU	0	-0.029	-0.010	5.720	-5.033	-5.033	0.000	0.000	0.000	0.000
8	B	12	GLU	-1	-0.788	-0.866	6.794	27.775	27.775	0.000	0.000	0.000	0.000
9	B	13	ALA	0	-0.010	0.005	9.344	-3.207	-3.207	0.000	0.000	0.000	0.000
10	B	14	ALA	0	-0.034	-0.025	10.957	-2.549	-2.549	0.000	0.000	0.000	0.000
11	B	15	ARG	1	0.799	0.860	9.937	-28.705	-28.705	0.000	0.000	0.000	0.000
12	B	16	ALA	0	-0.028	-0.008	13.392	-1.668	-1.668	0.000	0.000	0.000	0.000
13	B	17	GLY	0	0.026	0.024	15.131	-1.062	-1.062	0.000	0.000	0.000	0.000
14	B	18	GLN	0	-0.030	-0.019	13.005	0.413	0.413	0.000	0.000	0.000	0.000
15	B	19	ASP	-1	-0.816	-0.908	14.915	17.140	17.140	0.000	0.000	0.000	0.000
16	B	20	ASP	-1	-0.764	-0.866	16.260	16.383	16.383	0.000	0.000	0.000	0.000
17	B	21	GLU	-1	-0.870	-0.916	10.490	27.200	27.200	0.000	0.000	0.000	0.000
18	B	22	VAL	0	0.009	-0.003	11.467	1.867	1.867	0.000	0.000	0.000	0.000
19	B	23	ARG	1	0.759	0.839	12.566	-15.276	-15.276	0.000	0.000	0.000	0.000
20	B	24	ILE	0	-0.003	0.002	12.059	0.220	0.220	0.000	0.000	0.000	0.000
21	B	25	LEU	0	-0.043	-0.021	7.179	1.220	1.220	0.000	0.000	0.000	0.000
22	B	26	MET	0	-0.043	-0.017	9.939	1.101	1.101	0.000	0.000	0.000	0.000
23	B	27	ALA	0	-0.016	0.005	11.687	-0.439	-0.439	0.000	0.000	0.000	0.000
24	B	28	ASN	0	-0.061	-0.034	9.979	-1.953	-1.953	0.000	0.000	0.000	0.000
25	B	29	GLY	0	0.003	0.016	10.177	0.758	0.758	0.000	0.000	0.000	0.000
26	B	30	ALA	0	-0.057	-0.027	6.076	2.982	2.982	0.000	0.000	0.000	0.000
27	B	31	PRO	0	0.004	0.007	3.901	-3.062	-2.773	0.003	-0.109	-0.183	0.001
28	B	32	PHE	0	0.045	0.013	5.713	6.134	6.134	0.000	0.000	0.000	0.000
29	B	33	THR	0	-0.069	-0.026	4.686	0.087	0.185	-0.001	-0.008	-0.090	0.000
30	B	34	THR	0	0.047	0.014	7.126	-2.528	-2.528	0.000	0.000	0.000	0.000
31	B	35	ASP	-1	-0.802	-0.882	7.488	31.565	31.565	0.000	0.000	0.000	0.000
32	B	36	TRP	0	0.019	-0.005	9.536	-1.050	-1.050	0.000	0.000	0.000	0.000
33	B	37	LEU	0	-0.006	0.001	11.541	-1.948	-1.948	0.000	0.000	0.000	0.000
34	B	38	GLY	0	0.009	0.009	12.663	-1.685	-1.685	0.000	0.000	0.000	0.000
35	B	39	THR	0	-0.031	-0.027	12.982	-1.379	-1.379	0.000	0.000	0.000	0.000
36	B	40	SER	0	0.016	-0.021	10.943	3.114	3.114	0.000	0.000	0.000	0.000
37	B	41	PRO	0	0.039	-0.002	8.857	-1.485	-1.485	0.000	0.000	0.000	0.000
38	B	42	LEU	0	0.041	0.027	11.596	-1.321	-1.321	0.000	0.000	0.000	0.000
39	B	43	HIS	0	-0.010	0.021	14.851	0.137	0.137	0.000	0.000	0.000	0.000
40	B	44	LEU	0	0.001	0.005	11.180	-0.970	-0.970	0.000	0.000	0.000	0.000
41	B	45	ALA	0	-0.007	-0.008	15.130	-1.053	-1.053	0.000	0.000	0.000	0.000
42	B	46	ALA	0	-0.002	-0.009	16.836	-1.014	-1.014	0.000	0.000	0.000	0.000
43	B	47	GLN	0	0.004	-0.005	18.189	0.026	0.026	0.000	0.000	0.000	0.000
44	B	48	TYR	0	-0.030	-0.028	16.131	-0.199	-0.199	0.000	0.000	0.000	0.000
45	B	49	GLY	0	0.063	0.055	20.580	-0.418	-0.418	0.000	0.000	0.000	0.000
46	B	50	HIS	0	-0.008	0.005	17.238	-1.057	-1.057	0.000	0.000	0.000	0.000
47	B	51	PHE	0	0.001	-0.003	19.861	0.676	0.676	0.000	0.000	0.000	0.000
48	B	52	SER	0	0.049	0.018	21.014	0.145	0.145	0.000	0.000	0.000	0.000
49	B	53	THR	0	0.040	0.011	14.988	0.063	0.063	0.000	0.000	0.000	0.000
50	B	54	THR	0	-0.001	-0.011	16.905	1.055	1.055	0.000	0.000	0.000	0.000
51	B	55	GLU	-1	-0.872	-0.918	18.735	13.214	13.214	0.000	0.000	0.000	0.000
52	B	56	VAL	0	-0.019	-0.009	15.663	-0.048	-0.048	0.000	0.000	0.000	0.000
53	B	57	LEU	0	0.000	-0.007	12.251	0.554	0.554	0.000	0.000	0.000	0.000
54	B	58	LEU	0	-0.020	0.001	15.978	0.175	0.175	0.000	0.000	0.000	0.000
55	B	59	ARG	1	0.859	0.908	19.221	-13.512	-13.512	0.000	0.000	0.000	0.000
56	B	60	ALA	0	-0.018	0.001	15.192	-0.344	-0.344	0.000	0.000	0.000	0.000
57	B	61	GLY	0	-0.022	-0.003	16.379	0.629	0.629	0.000	0.000	0.000	0.000
58	B	62	VAL	0	-0.043	-0.012	13.034	0.167	0.167	0.000	0.000	0.000	0.000
59	B	63	SER	0	-0.025	-0.019	15.766	-1.544	-1.544	0.000	0.000	0.000	0.000
60	B	64	ARG	1	0.860	0.914	17.526	-14.474	-14.474	0.000	0.000	0.000	0.000
61	B	65	ASP	-1	-0.820	-0.909	20.319	13.699	13.699	0.000	0.000	0.000	0.000
62	B	66	ALA	0	-0.016	-0.012	15.757	-0.074	-0.074	0.000	0.000	0.000	0.000
63	B	67	ARG	1	0.831	0.900	17.627	-14.199	-14.199	0.000	0.000	0.000	0.000
64	B	68	THR	0	0.020	0.023	16.536	0.779	0.779	0.000	0.000	0.000	0.000
65	B	69	LYS	1	0.867	0.908	13.922	-22.340	-22.340	0.000	0.000	0.000	0.000
66	B	70	VAL	0	-0.019	-0.020	18.851	-0.651	-0.651	0.000	0.000	0.000	0.000
67	B	71	ASP	-1	-0.868	-0.933	21.084	13.083	13.083	0.000	0.000	0.000	0.000
68	B	72	ARG	1	0.848	0.929	21.063	-13.841	-13.841	0.000	0.000	0.000	0.000
69	B	73	THR	0	0.040	0.006	20.086	0.997	0.997	0.000	0.000	0.000	0.000
70	B	74	PRO	0	-0.020	-0.030	17.565	-0.186	-0.186	0.000	0.000	0.000	0.000
71	B	75	LEU	0	0.057	0.039	20.125	-0.242	-0.242	0.000	0.000	0.000	0.000
72	B	76	HIS	0	-0.004	0.022	23.332	0.118	0.118	0.000	0.000	0.000	0.000
73	B	77	MET	0	-0.055	-0.011	18.279	-0.568	-0.568	0.000	0.000	0.000	0.000
74	B	78	ALA	0	-0.002	0.003	22.678	-0.365	-0.365	0.000	0.000	0.000	0.000
75	B	79	ALA	0	-0.003	-0.011	24.302	-0.373	-0.373	0.000	0.000	0.000	0.000
76	B	80	SER	0	-0.017	-0.011	25.582	-0.568	-0.568	0.000	0.000	0.000	0.000
77	B	81	GLU	-1	-0.845	-0.922	23.275	12.973	12.973	0.000	0.000	0.000	0.000
78	B	82	GLY	0	0.044	0.032	26.443	-0.150	-0.150	0.000	0.000	0.000	0.000
79	B	83	HIS	0	-0.025	-0.004	23.688	-0.641	-0.641	0.000	0.000	0.000	0.000
80	B	84	ALA	0	0.060	0.017	27.188	0.260	0.260	0.000	0.000	0.000	0.000
81	B	85	ASN	0	0.012	0.001	26.057	-0.065	-0.065	0.000	0.000	0.000	0.000
82	B	86	ILE	0	-0.035	-0.003	21.729	0.149	0.149	0.000	0.000	0.000	0.000
83	B	87	VAL	0	0.025	0.013	24.909	0.267	0.267	0.000	0.000	0.000	0.000
84	B	88	GLU	-1	-0.771	-0.859	26.991	9.888	9.888	0.000	0.000	0.000	0.000
85	B	89	VAL	0	-0.027	-0.007	23.518	-0.028	-0.028	0.000	0.000	0.000	0.000
86	B	90	LEU	0	0.019	0.005	20.596	0.315	0.315	0.000	0.000	0.000	0.000
87	B	91	LEU	0	0.008	0.015	24.397	0.030	0.030	0.000	0.000	0.000	0.000
88	B	92	LYS	1	0.798	0.892	27.870	-10.263	-10.263	0.000	0.000	0.000	0.000
89	B	93	HIS	0	-0.095	-0.053	23.443	0.132	0.132	0.000	0.000	0.000	0.000
90	B	94	GLY	0	-0.023	-0.013	24.741	0.441	0.441	0.000	0.000	0.000	0.000
91	B	95	ALA	0	-0.032	-0.005	23.905	-0.010	-0.010	0.000	0.000	0.000	0.000
92	B	96	ASP	-1	-0.860	-0.937	25.503	10.479	10.479	0.000	0.000	0.000	0.000
93	B	97	VAL	0	0.008	-0.008	27.921	0.267	0.267	0.000	0.000	0.000	0.000
94	B	98	ASN	0	-0.042	-0.005	30.366	-0.240	-0.240	0.000	0.000	0.000	0.000
95	B	99	ALA	0	0.008	0.013	25.820	-0.023	-0.023	0.000	0.000	0.000	0.000
96	B	100	LYS	1	0.857	0.933	27.970	-10.008	-10.008	0.000	0.000	0.000	0.000
97	B	101	ASP	-1	-0.710	-0.838	25.416	12.211	12.211	0.000	0.000	0.000	0.000
98	B	102	MET	0	-0.023	-0.007	23.639	-0.567	-0.567	0.000	0.000	0.000	0.000
99	B	103	LEU	0	-0.035	-0.025	27.140	-0.445	-0.445	0.000	0.000	0.000	0.000
100	B	104	LYS	1	0.795	0.890	29.946	-9.690	-9.690	0.000	0.000	0.000	0.000
101	B	105	MET	0	0.025	0.028	29.861	-0.331	-0.331	0.000	0.000	0.000	0.000
102	B	106	THR	0	0.055	0.004	29.233	0.480	0.480	0.000	0.000	0.000	0.000
103	B	107	ALA	0	0.015	-0.006	27.804	0.047	0.047	0.000	0.000	0.000	0.000
104	B	108	LEU	0	0.072	0.042	29.241	-0.019	-0.019	0.000	0.000	0.000	0.000
105	B	109	HIS	0	0.010	0.044	32.282	0.118	0.118	0.000	0.000	0.000	0.000
106	B	110	TRP	0	-0.020	-0.036	27.862	-0.020	-0.020	0.000	0.000	0.000	0.000
107	B	111	ALA	0	-0.002	0.007	30.940	-0.001	-0.001	0.000	0.000	0.000	0.000
108	B	112	THR	0	-0.008	-0.023	32.255	-0.234	-0.234	0.000	0.000	0.000	0.000
109	B	113	GLU	-1	-0.934	-0.960	32.629	9.147	9.147	0.000	0.000	0.000	0.000
110	B	114	HIS	0	-0.071	-0.028	28.605	-0.311	-0.311	0.000	0.000	0.000	0.000
111	B	115	ASN	0	-0.024	-0.012	33.291	-0.292	-0.292	0.000	0.000	0.000	0.000
112	B	116	HIS	0	0.018	0.025	29.927	-0.400	-0.400	0.000	0.000	0.000	0.000
113	B	117	GLN	0	0.040	0.010	34.652	0.136	0.136	0.000	0.000	0.000	0.000
114	B	118	GLU	-1	-0.898	-0.953	35.052	8.710	8.710	0.000	0.000	0.000	0.000
115	B	119	VAL	0	-0.073	-0.039	30.407	0.168	0.168	0.000	0.000	0.000	0.000
116	B	120	VAL	0	0.020	0.014	33.223	0.108	0.108	0.000	0.000	0.000	0.000
117	B	121	GLU	-1	-0.833	-0.918	35.778	7.922	7.922	0.000	0.000	0.000	0.000
118	B	122	LEU	0	-0.116	-0.054	30.833	-0.076	-0.076	0.000	0.000	0.000	0.000
119	B	123	LEU	0	0.001	-0.017	29.885	0.069	0.069	0.000	0.000	0.000	0.000
120	B	124	ILE	0	0.029	0.024	33.920	-0.017	-0.017	0.000	0.000	0.000	0.000
121	B	125	LYS	1	0.896	0.956	36.600	-8.832	-8.832	0.000	0.000	0.000	0.000
122	B	126	TYR	0	-0.122	-0.079	32.652	-0.019	-0.019	0.000	0.000	0.000	0.000
123	B	127	GLY	0	-0.002	0.005	34.558	0.172	0.172	0.000	0.000	0.000	0.000
124	B	128	ALA	0	-0.042	-0.023	33.899	0.049	0.049	0.000	0.000	0.000	0.000
125	B	129	ASP	-1	-0.898	-0.959	35.351	8.199	8.199	0.000	0.000	0.000	0.000
126	B	130	VAL	0	0.018	0.001	36.990	0.198	0.198	0.000	0.000	0.000	0.000
127	B	131	HIS	0	-0.036	-0.024	39.162	-0.005	-0.005	0.000	0.000	0.000	0.000
128	B	132	THR	0	-0.030	-0.015	34.818	0.048	0.048	0.000	0.000	0.000	0.000
129	B	133	GLN	0	-0.033	-0.010	37.581	0.020	0.020	0.000	0.000	0.000	0.000
130	B	134	SER	0	0.032	0.014	34.479	0.172	0.172	0.000	0.000	0.000	0.000
131	B	135	LYS	1	0.785	0.883	30.121	-10.868	-10.868	0.000	0.000	0.000	0.000
132	B	136	PHE	0	0.027	0.005	33.146	-0.113	-0.113	0.000	0.000	0.000	0.000
133	B	137	CYS	0	-0.053	-0.028	37.943	-0.249	-0.249	0.000	0.000	0.000	0.000
134	B	138	LYS	1	0.794	0.918	38.466	-7.971	-7.971	0.000	0.000	0.000	0.000
135	B	139	THR	0	-0.011	-0.031	38.019	0.293	0.293	0.000	0.000	0.000	0.000
136	B	140	ALA	0	0.035	0.010	36.906	0.100	0.100	0.000	0.000	0.000	0.000
137	B	141	PHE	0	0.059	0.030	38.282	-0.021	-0.021	0.000	0.000	0.000	0.000
138	B	142	ASP	-1	-0.811	-0.880	40.676	7.609	7.609	0.000	0.000	0.000	0.000
139	B	143	ILE	0	0.029	0.036	35.176	-0.066	-0.066	0.000	0.000	0.000	0.000
140	B	144	SER	0	0.012	0.003	39.350	0.031	0.031	0.000	0.000	0.000	0.000
141	B	145	ILE	0	-0.001	0.010	41.337	-0.119	-0.119	0.000	0.000	0.000	0.000
142	B	146	ASP	-1	-0.892	-0.943	40.679	7.788	7.788	0.000	0.000	0.000	0.000
143	B	147	ASN	0	-0.085	-0.055	37.531	0.038	0.038	0.000	0.000	0.000	0.000
144	B	148	GLY	0	-0.032	0.002	41.532	-0.041	-0.041	0.000	0.000	0.000	0.000
145	B	149	ASN	0	-0.047	-0.033	40.388	-0.217	-0.217	0.000	0.000	0.000	0.000
146	B	150	GLU	-1	-0.836	-0.956	43.798	6.970	6.970	0.000	0.000	0.000	0.000
147	B	151	ASP	-1	-0.948	-0.953	44.007	7.051	7.051	0.000	0.000	0.000	0.000
148	B	152	LEU	0	-0.018	-0.017	38.413	0.088	0.088	0.000	0.000	0.000	0.000
149	B	153	ALA	0	0.019	0.007	42.368	0.027	0.027	0.000	0.000	0.000	0.000
150	B	154	GLU	-1	-0.963	-0.989	44.709	6.457	6.457	0.000	0.000	0.000	0.000
151	B	155	ILE	0	-0.066	-0.021	40.509	-0.063	-0.063	0.000	0.000	0.000	0.000
152	B	156	LEU	0	-0.026	-0.011	38.785	0.176	0.176	0.000	0.000	0.000	0.000
153	B	157	GLN	0	-0.111	-0.039	42.873	-0.075	-0.075	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:5:ASP)