FMO DATABASE

FMODB ID: XVQM1

Calculation Name: 4YZU-B-Xray23

Preferred Name: Coagulation factor IX

Target Type: SINGLE PROTEIN

Ligand Name: n-[2-(5,6-dimethyl-1h-benzimidazol-2-yl)ethyl]-4-(4h-1,2,4-triazol-4-yl)benzamide

ligand 3-letter code: 4K6

PDB ID: 4YZU

Chain ID: B

ChEMBL ID: CHEMBL2016

UniProt ID: P00740

Base Structure: X-ray

Registration Date: 2018-06-07

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	145
LigandCharge	CL-=-1
Software	MIZUHO/ABINIT-MP 3.0

Total energy (hartree)

FMO2-HF: Electronic energy	-401073.588582
FMO2-HF: Nuclear repulsion	369916.055022
FMO2-HF: Total energy	-31157.53356
FMO2-MP2: Total energy	-31237.563967

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:84:MET)

Summations of interaction energy for fragment #1(B:84:MET)

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.
-1.147	3.045	2.368	-2.285	-4.274	-0.004

Interaction energy analysis for fragmet #1(B:84:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / q_NPA : 0.007

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	86	VAL	0	-0.041	-0.008	3.089	-1.065	1.499	0.999	-1.318	-2.245	0.001
4	B	87	THR	0	0.011	0.025	5.516	0.053	0.053	0.000	0.000	0.000	0.000
5	B	99	CYS	0	0.044	0.017	8.267	-0.023	-0.023	0.000	0.000	0.000	0.000
6	B	89	ASN	0	0.018	0.025	10.815	0.049	0.049	0.000	0.000	0.000	0.000
7	B	90	ILE	0	-0.026	0.013	5.272	0.045	0.045	0.000	0.000	0.000	0.000
8	B	91	LYS	1	0.868	0.902	5.535	0.606	0.606	0.000	0.000	0.000	0.000
9	B	92	ASN	0	0.013	0.008	8.807	0.014	0.014	0.000	0.000	0.000	0.000
10	B	93	GLY	0	0.038	0.019	6.953	0.063	0.063	0.000	0.000	0.000	0.000
11	B	94	ARG	1	0.853	0.917	2.662	1.011	1.578	0.952	-0.349	-1.170	0.000
12	B	109	CYS	0	-0.094	0.004	7.671	0.058	0.058	0.000	0.000	0.000	0.000
13	B	96	GLU	-1	-0.680	-0.788	11.127	-0.131	-0.131	0.000	0.000	0.000	0.000
14	B	97	GLN	0	0.011	0.011	13.953	0.002	0.002	0.000	0.000	0.000	0.000
15	B	98	PHE	0	0.014	0.013	15.772	-0.026	-0.026	0.000	0.000	0.000	0.000
16	B	100	LYS	1	0.899	0.959	13.728	0.208	0.208	0.000	0.000	0.000	0.000
17	B	101	ASN	0	0.032	-0.007	11.951	-0.061	-0.061	0.000	0.000	0.000	0.000
18	B	102	SER	0	-0.054	-0.036	12.747	0.075	0.075	0.000	0.000	0.000	0.000
19	B	103	ALA	0	0.029	0.011	13.682	-0.047	-0.047	0.000	0.000	0.000	0.000
20	B	104	ASP	-1	-0.868	-0.934	10.616	-0.286	-0.286	0.000	0.000	0.000	0.000
21	B	105	ASN	0	-0.012	-0.005	4.158	0.238	0.385	-0.001	-0.052	-0.094	0.000
22	B	106	LYS	1	0.897	0.952	7.425	0.049	0.049	0.000	0.000	0.000	0.000
23	B	107	VAL	0	-0.012	-0.014	8.267	-0.052	-0.052	0.000	0.000	0.000	0.000
24	B	108	VAL	0	0.014	0.014	10.734	0.066	0.066	0.000	0.000	0.000	0.000
25	B	110	SER	0	0.002	-0.007	13.782	0.026	0.026	0.000	0.000	0.000	0.000
26	B	124	CYS	0	-0.082	-0.019	14.975	-0.010	-0.010	0.000	0.000	0.000	0.000
27	B	112	THR	0	0.040	0.034	19.682	0.002	0.002	0.000	0.000	0.000	0.000
28	B	113	GLU	-1	-0.870	-0.930	23.080	-0.059	-0.059	0.000	0.000	0.000	0.000
29	B	114	GLY	0	0.058	0.037	26.390	0.000	0.000	0.000	0.000	0.000	0.000
30	B	115	TYR	0	-0.052	-0.038	21.695	0.005	0.005	0.000	0.000	0.000	0.000
31	B	116	ARG	1	0.891	0.948	21.330	0.020	0.020	0.000	0.000	0.000	0.000
32	B	117	LEU	0	-0.033	-0.019	14.488	-0.003	-0.003	0.000	0.000	0.000	0.000
33	B	118	ALA	0	-0.012	-0.015	16.373	0.014	0.014	0.000	0.000	0.000	0.000
34	B	119	GLU	-1	-0.912	-0.956	16.374	0.054	0.054	0.000	0.000	0.000	0.000
35	B	120	ASN	0	-0.014	-0.003	12.432	0.004	0.004	0.000	0.000	0.000	0.000
36	B	121	GLN	0	0.002	0.002	11.528	0.018	0.018	0.000	0.000	0.000	0.000
37	B	122	LYS	1	0.817	0.894	6.908	0.162	0.162	0.000	0.000	0.000	0.000
38	B	123	SER	0	0.009	-0.009	11.968	-0.024	-0.024	0.000	0.000	0.000	0.000
39	B	125	GLU	-1	-0.879	-0.939	18.441	-0.038	-0.038	0.000	0.000	0.000	0.000
40	B	126	PRO	0	-0.031	-0.004	21.549	-0.002	-0.002	0.000	0.000	0.000	0.000
41	B	127	ALA	0	-0.004	-0.004	25.162	0.007	0.007	0.000	0.000	0.000	0.000
42	B	128	VAL	0	-0.033	0.003	27.043	0.003	0.003	0.000	0.000	0.000	0.000
43	B	129	PRO	0	0.029	0.019	29.952	-0.001	-0.001	0.000	0.000	0.000	0.000
44	B	130	PHE	0	-0.001	0.006	31.753	0.001	0.001	0.000	0.000	0.000	0.000
45	B	131	PRO	0	-0.030	0.013	26.728	-0.002	-0.002	0.000	0.000	0.000	0.000
46	B	132	CYS	0	0.019	0.004	26.962	-0.002	-0.002	0.000	0.000	0.000	0.000
47	B	133	GLY	0	0.017	0.010	26.743	-0.003	-0.003	0.000	0.000	0.000	0.000
48	B	134	ARG	1	0.920	0.984	23.162	0.050	0.050	0.000	0.000	0.000	0.000
49	B	135	VAL	0	-0.018	-0.001	27.657	0.004	0.004	0.000	0.000	0.000	0.000
50	B	136	SER	0	0.009	0.011	29.115	0.000	0.000	0.000	0.000	0.000	0.000
51	B	137	VAL	0	0.016	0.013	31.436	0.004	0.004	0.000	0.000	0.000	0.000
52	B	138	SER	0	0.042	0.030	33.440	-0.003	-0.003	0.000	0.000	0.000	0.000
53	B	139	GLN	0	-0.016	-0.015	31.528	-0.001	-0.001	0.000	0.000	0.000	0.000
54	B	140	THR	0	-0.022	-0.001	34.225	0.000	0.000	0.000	0.000	0.000	0.000
55	B	0	NME	0	0.010	0.012	34.432	-0.001	-0.001	0.000	0.000	0.000	0.000
56	B	201	CL-	-1	-0.863	-0.917	21.290	-0.064	-0.064	0.000	0.000	0.000	0.000
57	A	427	HOH	0	0.055	0.034	33.402	0.000	0.000	0.000	0.000	0.000	0.000
58	A	433	HOH	0	0.033	0.022	25.867	0.001	0.001	0.000	0.000	0.000	0.000
59	A	464	HOH	0	0.004	0.001	29.156	0.000	0.000	0.000	0.000	0.000	0.000
60	A	471	HOH	0	-0.020	-0.013	26.153	0.001	0.001	0.000	0.000	0.000	0.000
61	A	505	HOH	0	-0.030	-0.019	36.972	0.000	0.000	0.000	0.000	0.000	0.000
62	A	506	HOH	0	0.008	0.002	35.943	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	642	HOH	0	0.009	0.002	38.194	-0.001	-0.001	0.000	0.000	0.000	0.000
64	B	301	HOH	0	-0.074	-0.057	19.308	0.003	0.003	0.000	0.000	0.000	0.000
65	B	302	HOH	0	-0.028	-0.029	24.519	-0.003	-0.003	0.000	0.000	0.000	0.000
66	B	303	HOH	0	-0.014	-0.022	2.817	-1.286	-0.545	0.417	-0.490	-0.668	-0.005
67	B	304	HOH	0	-0.026	-0.019	14.769	-0.008	-0.008	0.000	0.000	0.000	0.000
68	B	305	HOH	0	-0.012	-0.014	18.960	0.002	0.002	0.000	0.000	0.000	0.000
69	B	306	HOH	0	-0.003	-0.013	9.483	-0.033	-0.033	0.000	0.000	0.000	0.000
70	B	307	HOH	0	-0.007	-0.014	27.913	0.002	0.002	0.000	0.000	0.000	0.000
71	B	308	HOH	0	-0.018	-0.017	16.149	-0.003	-0.003	0.000	0.000	0.000	0.000
72	B	309	HOH	0	-0.041	-0.031	9.852	0.001	0.001	0.000	0.000	0.000	0.000
73	B	310	HOH	0	0.020	0.019	25.976	0.001	0.001	0.000	0.000	0.000	0.000
74	B	311	HOH	0	0.000	0.002	31.501	-0.001	-0.001	0.000	0.000	0.000	0.000
75	B	312	HOH	0	-0.031	-0.031	9.545	-0.016	-0.016	0.000	0.000	0.000	0.000
76	B	313	HOH	0	-0.025	-0.025	32.340	-0.001	-0.001	0.000	0.000	0.000	0.000
77	B	314	HOH	0	0.000	-0.004	13.194	0.011	0.011	0.000	0.000	0.000	0.000
78	B	315	HOH	0	-0.012	-0.016	24.644	0.002	0.002	0.000	0.000	0.000	0.000
79	B	316	HOH	0	-0.030	-0.025	31.382	0.000	0.000	0.000	0.000	0.000	0.000
80	B	317	HOH	0	-0.062	-0.045	17.486	0.002	0.002	0.000	0.000	0.000	0.000
81	B	318	HOH	0	-0.026	-0.024	11.581	-0.005	-0.005	0.000	0.000	0.000	0.000
82	B	319	HOH	0	-0.004	0.000	15.595	0.001	0.001	0.000	0.000	0.000	0.000
83	B	320	HOH	0	-0.078	-0.056	11.988	-0.017	-0.017	0.000	0.000	0.000	0.000
84	B	321	HOH	0	-0.017	-0.007	13.949	0.019	0.019	0.000	0.000	0.000	0.000
85	B	322	HOH	0	-0.024	-0.023	24.606	0.002	0.002	0.000	0.000	0.000	0.000
86	B	323	HOH	0	0.021	0.000	12.728	-0.005	-0.005	0.000	0.000	0.000	0.000
87	B	324	HOH	0	-0.040	-0.028	17.722	0.001	0.001	0.000	0.000	0.000	0.000
88	B	325	HOH	0	0.004	0.008	10.981	0.002	0.002	0.000	0.000	0.000	0.000
89	B	326	HOH	0	0.043	0.033	9.614	-0.034	-0.034	0.000	0.000	0.000	0.000
90	B	327	HOH	0	-0.004	-0.007	12.228	0.019	0.019	0.000	0.000	0.000	0.000
91	B	328	HOH	0	-0.024	-0.024	30.320	0.001	0.001	0.000	0.000	0.000	0.000
92	B	329	HOH	0	0.027	0.016	5.294	-0.172	-0.172	0.000	0.000	0.000	0.000
93	B	330	HOH	0	0.004	0.001	14.518	-0.002	-0.002	0.000	0.000	0.000	0.000
94	B	331	HOH	0	-0.016	-0.005	15.628	0.001	0.001	0.000	0.000	0.000	0.000
95	B	332	HOH	0	-0.022	-0.014	23.058	-0.001	-0.001	0.000	0.000	0.000	0.000
96	B	333	HOH	0	-0.009	0.000	17.202	0.015	0.015	0.000	0.000	0.000	0.000
97	B	334	HOH	0	-0.031	-0.021	17.144	0.005	0.005	0.000	0.000	0.000	0.000
98	B	335	HOH	0	0.019	0.008	27.112	0.000	0.000	0.000	0.000	0.000	0.000
99	B	336	HOH	0	-0.012	-0.008	12.104	0.000	0.000	0.000	0.000	0.000	0.000
100	B	337	HOH	0	-0.036	-0.035	9.774	0.038	0.038	0.000	0.000	0.000	0.000
101	B	338	HOH	0	-0.045	-0.026	31.241	-0.001	-0.001	0.000	0.000	0.000	0.000
102	B	339	HOH	0	-0.040	-0.024	29.556	0.001	0.001	0.000	0.000	0.000	0.000
103	B	340	HOH	0	0.020	0.009	23.399	0.003	0.003	0.000	0.000	0.000	0.000
104	B	341	HOH	0	-0.022	-0.011	20.044	0.002	0.002	0.000	0.000	0.000	0.000
105	B	342	HOH	0	0.031	0.016	20.644	-0.006	-0.006	0.000	0.000	0.000	0.000
106	B	343	HOH	0	0.037	0.022	10.464	-0.031	-0.031	0.000	0.000	0.000	0.000
107	B	344	HOH	0	-0.061	-0.033	30.844	-0.001	-0.001	0.000	0.000	0.000	0.000
108	B	345	HOH	0	0.000	-0.015	30.130	0.001	0.001	0.000	0.000	0.000	0.000
109	B	346	HOH	0	0.003	0.001	31.986	0.000	0.000	0.000	0.000	0.000	0.000
110	B	347	HOH	0	0.024	0.022	5.113	-0.129	-0.108	-0.001	0.000	-0.020	0.000
111	B	348	HOH	0	0.019	0.004	14.789	-0.012	-0.012	0.000	0.000	0.000	0.000
112	B	349	HOH	0	0.022	0.018	15.637	0.011	0.011	0.000	0.000	0.000	0.000
113	B	350	HOH	0	0.010	0.010	9.911	-0.016	-0.016	0.000	0.000	0.000	0.000
114	B	351	HOH	0	-0.021	-0.013	32.264	0.001	0.001	0.000	0.000	0.000	0.000
115	B	352	HOH	0	-0.039	-0.028	9.688	0.017	0.017	0.000	0.000	0.000	0.000
116	B	353	HOH	0	0.060	0.034	19.960	-0.004	-0.004	0.000	0.000	0.000	0.000
117	B	354	HOH	0	0.046	0.026	10.505	-0.031	-0.031	0.000	0.000	0.000	0.000
118	B	355	HOH	0	0.015	0.013	30.969	0.001	0.001	0.000	0.000	0.000	0.000
119	B	356	HOH	0	0.000	0.007	11.821	-0.007	-0.007	0.000	0.000	0.000	0.000
120	B	357	HOH	0	-0.012	-0.001	8.865	0.081	0.081	0.000	0.000	0.000	0.000
121	B	358	HOH	0	-0.016	-0.009	7.716	-0.069	-0.069	0.000	0.000	0.000	0.000
122	B	359	HOH	0	0.028	0.017	16.527	0.000	0.000	0.000	0.000	0.000	0.000
123	B	360	HOH	0	0.029	0.017	37.101	-0.001	-0.001	0.000	0.000	0.000	0.000
124	B	361	HOH	0	0.007	0.003	26.544	-0.001	-0.001	0.000	0.000	0.000	0.000
125	B	362	HOH	0	-0.015	-0.028	29.298	0.000	0.000	0.000	0.000	0.000	0.000
126	B	363	HOH	0	0.024	0.010	22.058	-0.006	-0.006	0.000	0.000	0.000	0.000
127	B	364	HOH	0	0.023	0.014	13.707	-0.007	-0.007	0.000	0.000	0.000	0.000
128	B	365	HOH	0	0.027	0.013	21.680	-0.004	-0.004	0.000	0.000	0.000	0.000
129	B	366	HOH	0	-0.002	-0.010	3.997	-0.403	-0.251	0.002	-0.076	-0.077	0.000
130	B	367	HOH	0	0.018	0.010	33.226	0.001	0.001	0.000	0.000	0.000	0.000
131	B	368	HOH	0	0.025	0.011	16.704	0.002	0.002	0.000	0.000	0.000	0.000
132	B	369	HOH	0	0.040	0.020	16.935	-0.007	-0.007	0.000	0.000	0.000	0.000
133	B	370	HOH	0	0.030	0.010	25.597	-0.002	-0.002	0.000	0.000	0.000	0.000
134	B	371	HOH	0	-0.020	-0.007	7.927	0.060	0.060	0.000	0.000	0.000	0.000
135	B	372	HOH	0	0.015	0.005	31.064	-0.001	-0.001	0.000	0.000	0.000	0.000
136	B	373	HOH	0	-0.014	-0.005	38.049	0.001	0.001	0.000	0.000	0.000	0.000
137	B	377	HOH	0	0.037	0.018	26.720	0.001	0.001	0.000	0.000	0.000	0.000
138	B	379	HOH	0	0.042	0.030	30.686	-0.001	-0.001	0.000	0.000	0.000	0.000
139	B	381	HOH	0	0.022	0.017	10.525	0.010	0.010	0.000	0.000	0.000	0.000
140	B	382	HOH	0	-0.042	-0.040	29.755	0.000	0.000	0.000	0.000	0.000	0.000
141	B	384	HOH	0	0.015	0.011	20.496	-0.005	-0.005	0.000	0.000	0.000	0.000
142	B	385	HOH	0	0.058	0.040	7.941	-0.046	-0.046	0.000	0.000	0.000	0.000
143	B	387	HOH	0	-0.018	-0.014	5.605	-0.084	-0.084	0.000	0.000	0.000	0.000
144	B	389	HOH	0	0.014	0.011	7.708	-0.012	-0.012	0.000	0.000	0.000	0.000
145	B	390	HOH	0	0.012	0.003	28.624	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:84:MET)