FMO DATABASE

FMODB ID: XYVK2

Calculation Name: 1ZKK-D-Xray26

Preferred Name: Histone H4

Target Type: SINGLE PROTEIN

Ligand Name: s-adenosyl-l-homocysteine

ligand 3-letter code: SAH

PDB ID: 1ZKK

Chain ID: D

ChEMBL ID: CHEMBL5876

UniProt ID: P62805

Base Structure: X-ray

Registration Date: 2018-07-26

Reference:

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water	Apo structure with with a 3 angstrom solvent shell.
Procedure	Auto-FMO protocol ver. 1.20180227

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	168
LigandCharge
Software	MIZUHO/ABINIT-MP 3.0

Total energy (hartree)

FMO2-HF: Electronic energy	-1617398.958556
FMO2-HF: Nuclear repulsion	1550428.333679
FMO2-HF: Total energy	-66970.624877
FMO2-MP2: Total energy	-67163.787224

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(D:191:ACE)

Summations of interaction energy for fragment #1(D:191: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.
0.767	1.657	-0.011	-0.428	-0.451	0

Interaction energy analysis for fragmet #1(D:191:ACE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.032 / q_NPA : 0.006

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].
3	D	193	LYS	1	0.913	0.954	3.853	1.277	2.167	-0.011	-0.428	-0.451
4	D	194	SER	0	-0.027	-0.020	7.146	-0.067	-0.067	0.000	0.000	0.000
5	D	195	LYS	1	1.004	0.986	9.347	0.255	0.255	0.000	0.000	0.000
6	D	196	ALA	0	0.025	0.014	12.792	0.017	0.017	0.000	0.000	0.000
7	D	197	GLU	-1	-0.764	-0.870	8.386	-0.382	-0.382	0.000	0.000	0.000
8	D	198	LEU	0	-0.012	-0.016	10.765	0.015	0.015	0.000	0.000	0.000
9	D	199	GLN	0	-0.013	-0.009	13.383	0.042	0.042	0.000	0.000	0.000
10	D	200	SER	0	-0.036	-0.009	15.156	0.030	0.030	0.000	0.000	0.000
11	D	201	GLU	-1	-0.807	-0.899	11.635	-0.405	-0.405	0.000	0.000	0.000
12	D	202	GLU	-1	-0.911	-0.958	16.121	-0.209	-0.209	0.000	0.000	0.000
13	D	203	ARG	1	0.825	0.895	18.483	0.125	0.125	0.000	0.000	0.000
14	D	204	LYS	1	0.831	0.910	17.837	0.115	0.115	0.000	0.000	0.000
15	D	205	ARG	1	0.907	0.954	15.397	0.281	0.281	0.000	0.000	0.000
16	D	206	ILE	0	0.008	0.011	21.361	0.014	0.014	0.000	0.000	0.000
17	D	207	ASP	-1	-0.717	-0.857	24.099	-0.091	-0.091	0.000	0.000	0.000
18	D	208	GLU	-1	-0.800	-0.876	22.563	-0.085	-0.085	0.000	0.000	0.000
19	D	209	LEU	0	-0.052	-0.022	24.683	0.008	0.008	0.000	0.000	0.000
20	D	210	ILE	0	-0.067	-0.029	27.592	0.007	0.007	0.000	0.000	0.000
21	D	211	GLU	-1	-0.967	-0.984	29.054	-0.050	-0.050	0.000	0.000	0.000
22	D	212	SER	0	-0.100	-0.037	29.078	0.006	0.006	0.000	0.000	0.000
23	D	213	GLY	0	0.002	0.002	31.314	0.005	0.005	0.000	0.000	0.000
24	D	214	LYS	1	0.912	0.944	31.391	0.050	0.050	0.000	0.000	0.000
25	D	215	GLU	-1	-0.817	-0.903	32.226	-0.058	-0.058	0.000	0.000	0.000
26	D	216	GLU	-1	-0.910	-0.953	29.627	-0.066	-0.066	0.000	0.000	0.000
27	D	217	GLY	0	-0.041	-0.027	31.008	-0.006	-0.006	0.000	0.000	0.000
28	D	218	MET	0	-0.003	0.013	31.982	-0.002	-0.002	0.000	0.000	0.000
29	D	219	LYS	1	0.952	0.984	35.256	0.053	0.053	0.000	0.000	0.000
30	D	220	ILE	0	0.018	0.013	38.988	-0.002	-0.002	0.000	0.000	0.000
31	D	221	ASP	-1	-0.904	-0.946	42.239	-0.041	-0.041	0.000	0.000	0.000
32	D	222	LEU	0	-0.062	-0.039	44.608	0.000	0.000	0.000	0.000	0.000
33	D	223	ILE	0	-0.024	0.000	43.457	0.000	0.000	0.000	0.000	0.000
34	D	224	ASP	-1	-0.904	-0.963	47.370	-0.033	-0.033	0.000	0.000	0.000
35	D	225	GLY	0	-0.021	-0.011	49.942	-0.001	-0.001	0.000	0.000	0.000
36	D	226	LYS	1	0.808	0.891	43.730	0.050	0.050	0.000	0.000	0.000
37	D	227	GLY	0	0.013	0.032	48.621	0.000	0.000	0.000	0.000	0.000
38	D	228	ARG	1	0.814	0.878	45.449	0.037	0.037	0.000	0.000	0.000
39	D	229	GLY	0	0.080	0.054	43.006	-0.001	-0.001	0.000	0.000	0.000
40	D	230	VAL	0	-0.028	-0.008	37.073	0.001	0.001	0.000	0.000	0.000
41	D	231	ILE	0	-0.014	0.003	37.819	-0.002	-0.002	0.000	0.000	0.000
42	D	232	ALA	0	0.032	0.023	32.635	0.000	0.000	0.000	0.000	0.000
43	D	233	THR	0	-0.056	-0.049	33.898	0.001	0.001	0.000	0.000	0.000
44	D	234	LYS	1	0.933	0.973	26.252	0.108	0.108	0.000	0.000	0.000
45	D	235	GLN	0	-0.017	-0.010	26.873	-0.004	-0.004	0.000	0.000	0.000
46	D	236	PHE	0	-0.006	0.002	26.083	-0.001	-0.001	0.000	0.000	0.000
47	D	237	SER	0	0.016	0.012	22.103	0.001	0.001	0.000	0.000	0.000
48	D	238	ARG	1	0.917	0.955	23.110	0.161	0.161	0.000	0.000	0.000
49	D	239	GLY	0	-0.071	-0.038	22.222	-0.020	-0.020	0.000	0.000	0.000
50	D	240	ASP	-1	-0.826	-0.898	22.030	-0.183	-0.183	0.000	0.000	0.000
51	D	241	PHE	0	-0.009	-0.023	23.989	0.011	0.011	0.000	0.000	0.000
52	D	242	VAL	0	-0.038	-0.014	26.276	0.000	0.000	0.000	0.000	0.000
53	D	243	VAL	0	0.005	-0.011	29.515	0.005	0.005	0.000	0.000	0.000
54	D	244	GLU	-1	-0.795	-0.886	32.023	-0.067	-0.067	0.000	0.000	0.000
55	D	245	TYR	0	-0.038	-0.038	33.475	0.003	0.003	0.000	0.000	0.000
56	D	246	HIS	0	-0.051	-0.027	36.051	0.004	0.004	0.000	0.000	0.000
57	D	247	GLY	0	0.023	-0.011	38.243	0.002	0.002	0.000	0.000	0.000
58	D	248	ASP	-1	-0.908	-0.934	41.215	-0.035	-0.035	0.000	0.000	0.000
59	D	249	LEU	0	-0.025	-0.005	38.448	-0.001	-0.001	0.000	0.000	0.000
60	D	250	ILE	0	-0.011	0.009	42.149	0.002	0.002	0.000	0.000	0.000
61	D	251	GLU	-1	-0.778	-0.884	44.356	-0.032	-0.032	0.000	0.000	0.000
62	D	252	ILE	0	0.005	-0.011	46.227	0.001	0.001	0.000	0.000	0.000
63	D	253	THR	0	-0.103	-0.072	48.599	0.001	0.001	0.000	0.000	0.000
64	D	254	ASP	-1	-0.813	-0.926	49.484	-0.028	-0.028	0.000	0.000	0.000
65	D	255	ALA	0	0.016	0.013	47.882	0.000	0.000	0.000	0.000	0.000
66	D	256	LYS	1	0.964	0.979	49.946	0.029	0.029	0.000	0.000	0.000
67	D	257	LYS	1	0.893	0.950	53.123	0.024	0.024	0.000	0.000	0.000
68	D	258	ARG	1	0.846	0.913	48.061	0.032	0.032	0.000	0.000	0.000
69	D	259	GLU	-1	-0.838	-0.880	50.647	-0.034	-0.034	0.000	0.000	0.000
70	D	260	ALA	0	-0.049	-0.023	53.828	0.001	0.001	0.000	0.000	0.000
71	D	261	LEU	0	-0.046	-0.024	56.339	0.001	0.001	0.000	0.000	0.000
72	D	262	TYR	0	0.003	-0.044	50.089	0.001	0.001	0.000	0.000	0.000
73	D	263	ALA	0	-0.020	-0.004	55.955	0.000	0.000	0.000	0.000	0.000
74	D	264	GLN	0	-0.118	-0.056	57.932	0.001	0.001	0.000	0.000	0.000
75	D	265	ASP	-1	-0.849	-0.897	58.329	-0.024	-0.024	0.000	0.000	0.000
76	D	266	PRO	0	-0.015	0.001	57.628	-0.001	-0.001	0.000	0.000	0.000
77	D	267	SER	0	-0.107	-0.067	56.858	-0.001	-0.001	0.000	0.000	0.000
78	D	268	THR	0	-0.031	-0.014	52.546	-0.001	-0.001	0.000	0.000	0.000
79	D	269	GLY	0	0.019	0.004	51.508	-0.001	-0.001	0.000	0.000	0.000
80	D	270	CYS	0	-0.053	-0.042	49.055	0.001	0.001	0.000	0.000	0.000
81	D	271	TYR	0	0.062	0.049	45.112	-0.002	-0.002	0.000	0.000	0.000
82	D	272	MET	0	-0.043	0.006	44.688	-0.001	-0.001	0.000	0.000	0.000
83	D	273	TYR	0	0.013	0.005	37.511	-0.001	-0.001	0.000	0.000	0.000
84	D	274	TYR	0	-0.040	-0.068	41.931	0.000	0.000	0.000	0.000	0.000
85	D	275	PHE	0	-0.017	-0.012	37.396	-0.003	-0.003	0.000	0.000	0.000
86	D	276	GLN	0	0.033	0.044	39.270	0.005	0.005	0.000	0.000	0.000
87	D	277	TYR	0	-0.020	-0.049	33.583	-0.003	-0.003	0.000	0.000	0.000
88	D	278	LEU	0	0.015	0.004	34.839	0.003	0.003	0.000	0.000	0.000
89	D	279	SER	0	-0.026	-0.012	38.452	0.002	0.002	0.000	0.000	0.000
90	D	280	LYS	1	0.941	0.983	41.411	0.036	0.036	0.000	0.000	0.000
91	D	281	THR	0	-0.041	-0.050	41.969	-0.002	-0.002	0.000	0.000	0.000
92	D	282	TYR	0	-0.032	-0.016	40.573	0.003	0.003	0.000	0.000	0.000
93	D	283	CYS	0	-0.013	-0.005	42.860	-0.001	-0.001	0.000	0.000	0.000
94	D	284	VAL	0	-0.011	0.016	38.454	0.001	0.001	0.000	0.000	0.000
95	D	285	ASP	-1	-0.696	-0.814	41.924	-0.036	-0.036	0.000	0.000	0.000
96	D	286	ALA	0	-0.005	0.003	42.437	0.001	0.001	0.000	0.000	0.000
97	D	287	THR	0	0.015	-0.021	44.562	0.000	0.000	0.000	0.000	0.000
98	D	288	ARG	1	0.955	0.984	45.198	0.033	0.033	0.000	0.000	0.000
99	D	289	GLU	-1	-0.759	-0.858	46.694	-0.038	-0.038	0.000	0.000	0.000
100	D	290	THR	0	-0.054	-0.035	43.157	0.000	0.000	0.000	0.000	0.000
101	D	291	ASN	0	-0.022	-0.018	40.877	-0.001	-0.001	0.000	0.000	0.000
102	D	292	ARG	1	0.915	0.966	35.149	0.052	0.052	0.000	0.000	0.000
103	D	293	LEU	0	0.047	0.002	36.500	0.002	0.002	0.000	0.000	0.000
104	D	294	GLY	0	0.020	0.018	37.256	0.000	0.000	0.000	0.000	0.000
105	D	295	ARG	1	0.788	0.880	37.875	0.040	0.040	0.000	0.000	0.000
106	D	296	LEU	0	-0.047	-0.025	40.911	0.002	0.002	0.000	0.000	0.000
107	D	297	ILE	0	-0.046	0.003	36.004	0.000	0.000	0.000	0.000	0.000
108	D	298	ASN	0	-0.014	0.000	40.283	0.002	0.002	0.000	0.000	0.000
109	D	299	HIS	0	0.016	0.015	40.596	-0.004	-0.004	0.000	0.000	0.000
110	D	300	SER	0	-0.039	-0.035	39.617	0.002	0.002	0.000	0.000	0.000
111	D	301	LYS	1	0.840	0.925	39.584	0.047	0.047	0.000	0.000	0.000
112	D	302	CYS	0	-0.090	-0.033	37.536	-0.004	-0.004	0.000	0.000	0.000
113	D	303	GLY	0	0.023	0.018	36.747	0.000	0.000	0.000	0.000	0.000
114	D	304	ASN	0	-0.057	-0.041	32.248	-0.004	-0.004	0.000	0.000	0.000
115	D	305	CYS	0	0.003	0.020	31.290	-0.009	-0.009	0.000	0.000	0.000
116	D	306	GLN	0	-0.025	-0.016	30.508	0.004	0.004	0.000	0.000	0.000
117	D	307	THR	0	0.015	0.015	31.354	-0.004	-0.004	0.000	0.000	0.000
118	D	308	LYS	1	0.872	0.934	26.675	0.127	0.127	0.000	0.000	0.000
119	D	309	LEU	0	-0.002	0.013	31.451	0.003	0.003	0.000	0.000	0.000
120	D	310	HIS	0	-0.102	-0.077	24.860	-0.008	-0.008	0.000	0.000	0.000
121	D	311	ASP	-1	-0.829	-0.884	29.185	-0.059	-0.059	0.000	0.000	0.000
122	D	312	ILE	0	-0.003	-0.009	27.899	-0.008	-0.008	0.000	0.000	0.000
123	D	313	ASP	-1	-0.931	-0.963	29.093	-0.040	-0.040	0.000	0.000	0.000
124	D	314	GLY	0	0.020	0.018	30.842	0.005	0.005	0.000	0.000	0.000
125	D	315	VAL	0	-0.037	-0.012	33.072	0.003	0.003	0.000	0.000	0.000
126	D	316	PRO	0	-0.059	-0.016	33.033	-0.006	-0.006	0.000	0.000	0.000
127	D	317	HIS	1	0.884	0.915	31.758	0.067	0.067	0.000	0.000	0.000
128	D	318	LEU	0	0.017	0.022	32.928	-0.005	-0.005	0.000	0.000	0.000
129	D	319	ILE	0	-0.005	0.005	27.540	0.002	0.002	0.000	0.000	0.000
130	D	320	LEU	0	0.013	0.015	31.642	-0.002	-0.002	0.000	0.000	0.000
131	D	321	ILE	0	-0.020	-0.005	25.818	-0.004	-0.004	0.000	0.000	0.000
132	D	322	ALA	0	0.070	0.039	26.473	0.007	0.007	0.000	0.000	0.000
133	D	323	SER	0	-0.044	-0.033	26.845	-0.013	-0.013	0.000	0.000	0.000
134	D	324	ARG	1	0.738	0.820	27.013	0.089	0.089	0.000	0.000	0.000
135	D	325	ASP	-1	-0.824	-0.905	24.515	-0.168	-0.168	0.000	0.000	0.000
136	D	326	ILE	0	-0.066	-0.023	27.206	0.010	0.010	0.000	0.000	0.000
137	D	327	ALA	0	0.017	0.006	29.620	-0.004	-0.004	0.000	0.000	0.000
138	D	328	ALA	0	-0.003	-0.015	31.821	0.003	0.003	0.000	0.000	0.000
139	D	329	GLY	0	-0.026	-0.023	33.486	0.002	0.002	0.000	0.000	0.000
140	D	330	GLU	-1	-0.755	-0.846	33.353	-0.084	-0.084	0.000	0.000	0.000
141	D	331	GLU	-1	-0.730	-0.868	36.850	-0.053	-0.053	0.000	0.000	0.000
142	D	332	LEU	0	-0.048	-0.022	33.050	-0.004	-0.004	0.000	0.000	0.000
143	D	333	LEU	0	-0.023	-0.010	36.093	0.005	0.005	0.000	0.000	0.000
144	D	334	TYR	0	0.004	-0.002	35.769	-0.006	-0.006	0.000	0.000	0.000
145	D	335	ASP	-1	-0.794	-0.893	37.351	-0.057	-0.057	0.000	0.000	0.000
146	D	336	TYR	0	0.004	-0.044	39.239	0.000	0.000	0.000	0.000	0.000
147	D	337	GLY	0	-0.038	-0.009	41.620	0.001	0.001	0.000	0.000	0.000
148	D	338	ASP	-1	-0.817	-0.877	42.244	-0.039	-0.039	0.000	0.000	0.000
149	D	339	ARG	1	0.872	0.913	40.015	0.058	0.058	0.000	0.000	0.000
150	D	340	SER	0	-0.040	-0.013	47.518	0.002	0.002	0.000	0.000	0.000
151	D	341	LYS	1	0.933	0.957	50.812	0.030	0.030	0.000	0.000	0.000
152	D	342	ALA	0	0.004	-0.005	53.976	0.000	0.000	0.000	0.000	0.000
153	D	343	SER	0	0.020	-0.007	50.510	0.001	0.001	0.000	0.000	0.000
154	D	344	ILE	0	-0.020	-0.015	49.513	0.000	0.000	0.000	0.000	0.000
155	D	345	GLU	-1	-0.963	-0.995	52.126	-0.030	-0.030	0.000	0.000	0.000
156	D	346	ALA	0	-0.015	0.009	55.346	0.001	0.001	0.000	0.000	0.000
157	D	347	HIS	0	-0.008	0.005	51.183	0.000	0.000	0.000	0.000	0.000
158	D	348	PRO	0	0.009	0.004	51.158	-0.002	-0.002	0.000	0.000	0.000
159	D	349	TRP	0	0.043	0.011	46.057	-0.002	-0.002	0.000	0.000	0.000
160	D	350	LEU	0	0.040	0.029	45.983	-0.002	-0.002	0.000	0.000	0.000
161	D	351	LYS	1	0.841	0.914	46.406	0.035	0.035	0.000	0.000	0.000
162	D	352	HIS	-1	-0.796	-0.885	43.690	-0.055	-0.055	0.000	0.000	0.000
163	D	2803	SAH	0	0.026	0.043	78.884	0.001	0.001	0.000	0.000	0.000
164	D	2810	HOH	0	-0.014	-0.021	83.987	0.000	0.000	0.000	0.000	0.000
165	D	2826	HOH	0	-0.036	-0.035	84.865	0.000	0.000	0.000	0.000	0.000
166	D	2878	HOH	0	0.034	0.027	86.039	0.000	0.000	0.000	0.000	0.000
167	D	2889	HOH	0	-0.025	-0.028	82.165	0.000	0.000	0.000	0.000	0.000
168	D	2892	HOH	0	0.015	0.013	78.180	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:191:ACE)