FMO DATABASE

FMODB ID: X1NKZ

Calculation Name: 3KNB-B-Xray22

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KNB

Chain ID: B

ChEMBL ID:

UniProt ID: O75147

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	167
LigandCharge
Software	MIZUHO/ABINIT-MP 3.0

Total energy (hartree)

FMO2-HF: Electronic energy	-742096.412584
FMO2-HF: Nuclear repulsion	701833.288948
FMO2-HF: Total energy	-40263.123636
FMO2-MP2: Total energy	-40378.615455

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:9:ACE)

Summations of interaction energy for fragment #1(B:9: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.
14.125	2.527	8.233	5.687	-2.322	-0.011

Interaction energy analysis for fragmet #1(B:9:ACE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.071 / q_NPA : -0.010

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	11	GLY	0	0.069	0.081	3.337	1.741	2.335	-0.075	0.449	-0.968	-0.004
4	B	12	SER	0	0.010	-0.021	5.553	-0.106	-0.106	0.000	0.000	0.000	0.000
5	B	13	PRO	0	0.041	0.031	9.306	0.117	0.117	0.000	0.000	0.000	0.000
6	B	14	PRO	0	-0.016	0.005	11.988	-0.004	-0.004	0.000	0.000	0.000	0.000
7	B	15	CYS	0	-0.017	0.010	14.845	-0.016	-0.016	0.000	0.000	0.000	0.000
8	B	16	PHE	0	0.020	-0.006	17.658	0.018	0.018	0.000	0.000	0.000	0.000
9	B	17	LEU	0	0.017	0.027	19.893	-0.011	-0.011	0.000	0.000	0.000	0.000
10	B	18	ARG	1	0.898	0.953	21.503	0.008	0.008	0.000	0.000	0.000	0.000
11	B	19	PHE	0	-0.002	-0.001	24.497	0.005	0.005	0.000	0.000	0.000	0.000
12	B	20	PRO	0	0.061	0.051	25.628	0.002	0.002	0.000	0.000	0.000	0.000
13	B	21	ARG	1	0.889	0.946	28.642	0.027	0.027	0.000	0.000	0.000	0.000
14	B	22	PRO	0	0.027	0.022	32.137	0.003	0.003	0.000	0.000	0.000	0.000
15	B	23	VAL	0	0.018	0.025	34.618	-0.001	-0.001	0.000	0.000	0.000	0.000
16	B	24	ARG	1	0.875	0.909	37.220	0.005	0.005	0.000	0.000	0.000	0.000
17	B	25	VAL	0	0.015	0.021	40.439	0.000	0.000	0.000	0.000	0.000	0.000
18	B	26	VAL	0	0.009	0.016	42.488	0.000	0.000	0.000	0.000	0.000	0.000
19	B	27	SER	0	0.026	0.001	44.847	0.002	0.002	0.000	0.000	0.000	0.000
20	B	28	GLY	0	0.032	0.023	45.024	0.000	0.000	0.000	0.000	0.000	0.000
21	B	29	ALA	0	-0.003	0.002	43.013	0.001	0.001	0.000	0.000	0.000	0.000
22	B	30	GLU	-1	-0.814	-0.883	36.782	0.019	0.019	0.000	0.000	0.000	0.000
23	B	31	ALA	0	-0.058	-0.027	37.405	-0.003	-0.003	0.000	0.000	0.000	0.000
24	B	32	GLU	-1	-0.807	-0.898	30.315	0.025	0.025	0.000	0.000	0.000	0.000
25	B	33	LEU	0	-0.106	-0.026	30.263	-0.004	-0.004	0.000	0.000	0.000	0.000
26	B	34	LYS	1	0.940	0.978	25.495	-0.012	-0.012	0.000	0.000	0.000	0.000
27	B	35	CYS	0	-0.067	-0.042	23.945	-0.005	-0.005	0.000	0.000	0.000	0.000
28	B	36	VAL	0	0.015	0.000	20.394	0.006	0.006	0.000	0.000	0.000	0.000
29	B	37	VAL	0	0.004	0.006	16.826	-0.015	-0.015	0.000	0.000	0.000	0.000
30	B	38	LEU	0	0.002	0.009	14.939	0.018	0.018	0.000	0.000	0.000	0.000
31	B	39	GLY	0	0.053	0.015	11.947	-0.007	-0.007	0.000	0.000	0.000	0.000
32	B	40	GLU	-1	-0.902	-0.919	6.979	0.116	0.116	0.000	0.000	0.000	0.000
33	B	41	PRO	0	0.042	0.003	6.446	-0.093	-0.093	0.000	0.000	0.000	0.000
34	B	42	PRO	0	0.053	0.036	8.741	-0.082	-0.082	0.000	0.000	0.000	0.000
35	B	43	PRO	0	-0.051	-0.003	12.469	0.042	0.042	0.000	0.000	0.000	0.000
36	B	44	VAL	0	0.037	0.038	14.450	0.001	0.001	0.000	0.000	0.000	0.000
37	B	45	VAL	0	-0.033	-0.025	17.073	-0.021	-0.021	0.000	0.000	0.000	0.000
38	B	46	VAL	0	-0.025	-0.016	20.253	0.007	0.007	0.000	0.000	0.000	0.000
39	B	47	TRP	0	0.046	0.016	23.225	-0.012	-0.012	0.000	0.000	0.000	0.000
40	B	48	GLU	-1	-0.856	-0.916	26.633	0.022	0.022	0.000	0.000	0.000	0.000
41	B	49	LYS	1	0.893	0.942	29.021	-0.016	-0.016	0.000	0.000	0.000	0.000
42	B	50	GLY	0	-0.033	-0.010	32.595	0.002	0.002	0.000	0.000	0.000	0.000
43	B	51	GLY	0	-0.019	-0.007	30.689	0.000	0.000	0.000	0.000	0.000	0.000
44	B	52	GLN	0	0.008	0.020	30.630	0.006	0.006	0.000	0.000	0.000	0.000
45	B	53	GLN	0	-0.041	-0.012	26.790	0.003	0.003	0.000	0.000	0.000	0.000
46	B	54	LEU	0	-0.006	-0.010	28.998	-0.001	-0.001	0.000	0.000	0.000	0.000
47	B	55	ALA	0	0.014	0.012	29.258	0.005	0.005	0.000	0.000	0.000	0.000
48	B	56	ALA	0	0.016	0.024	29.992	-0.004	-0.004	0.000	0.000	0.000	0.000
49	B	57	SER	0	0.017	-0.002	31.825	0.001	0.001	0.000	0.000	0.000	0.000
50	B	58	GLU	-1	-0.844	-0.879	35.363	0.032	0.032	0.000	0.000	0.000	0.000
51	B	59	ARG	1	0.792	0.846	37.839	-0.021	-0.021	0.000	0.000	0.000	0.000
52	B	60	LEU	0	-0.030	0.001	32.634	-0.003	-0.003	0.000	0.000	0.000	0.000
53	B	61	SER	0	0.024	0.011	31.428	0.004	0.004	0.000	0.000	0.000	0.000
54	B	62	PHE	0	-0.017	-0.026	26.505	-0.004	-0.004	0.000	0.000	0.000	0.000
55	B	63	PRO	0	0.035	0.031	26.429	0.008	0.008	0.000	0.000	0.000	0.000
56	B	64	ALA	0	-0.059	-0.037	22.279	-0.004	-0.004	0.000	0.000	0.000	0.000
57	B	65	ASP	-1	-0.845	-0.887	22.953	0.064	0.064	0.000	0.000	0.000	0.000
58	B	66	GLY	0	0.059	0.037	18.617	-0.008	-0.008	0.000	0.000	0.000	0.000
59	B	67	ALA	0	0.025	0.012	17.714	0.001	0.001	0.000	0.000	0.000	0.000
60	B	68	GLU	-1	-1.007	-0.996	19.128	0.011	0.011	0.000	0.000	0.000	0.000
61	B	69	HIS	0	0.004	-0.020	18.843	0.019	0.019	0.000	0.000	0.000	0.000
62	B	70	GLY	0	0.032	0.024	24.099	-0.009	-0.009	0.000	0.000	0.000	0.000
63	B	71	LEU	0	-0.080	-0.017	27.700	0.005	0.005	0.000	0.000	0.000	0.000
64	B	72	LEU	0	0.003	0.000	30.051	-0.004	-0.004	0.000	0.000	0.000	0.000
65	B	73	LEU	0	-0.032	-0.025	33.140	0.002	0.002	0.000	0.000	0.000	0.000
66	B	74	THR	0	0.075	0.038	36.591	-0.001	-0.001	0.000	0.000	0.000	0.000
67	B	75	ALA	0	-0.008	-0.010	38.917	-0.002	-0.002	0.000	0.000	0.000	0.000
68	B	76	ALA	0	0.003	0.013	40.423	0.001	0.001	0.000	0.000	0.000	0.000
69	B	77	LEU	0	0.058	0.019	41.733	-0.001	-0.001	0.000	0.000	0.000	0.000
70	B	78	PRO	0	0.073	0.024	42.876	0.000	0.000	0.000	0.000	0.000	0.000
71	B	79	THR	0	-0.045	-0.022	42.026	-0.001	-0.001	0.000	0.000	0.000	0.000
72	B	80	ASP	-1	-0.762	-0.806	38.751	0.017	0.017	0.000	0.000	0.000	0.000
73	B	81	ALA	0	0.004	0.032	38.412	0.000	0.000	0.000	0.000	0.000	0.000
74	B	82	GLY	0	-0.014	-0.016	38.168	0.001	0.001	0.000	0.000	0.000	0.000
75	B	83	VAL	0	-0.025	-0.017	32.471	0.000	0.000	0.000	0.000	0.000	0.000
76	B	84	TYR	0	-0.008	-0.016	30.750	0.003	0.003	0.000	0.000	0.000	0.000
77	B	85	VAL	0	-0.009	-0.022	25.935	-0.005	-0.005	0.000	0.000	0.000	0.000
78	B	86	CYS	0	-0.016	0.013	23.586	0.006	0.006	0.000	0.000	0.000	0.000
79	B	87	ARG	1	0.929	0.968	19.987	-0.033	-0.033	0.000	0.000	0.000	0.000
80	B	88	ALA	0	0.010	0.020	17.478	0.015	0.015	0.000	0.000	0.000	0.000
81	B	89	ARG	1	0.925	0.945	15.223	-0.102	-0.102	0.000	0.000	0.000	0.000
82	B	90	ASN	0	0.014	-0.019	10.402	0.000	0.000	0.000	0.000	0.000	0.000
83	B	91	ALA	0	0.010	0.000	7.226	-0.027	-0.027	0.000	0.000	0.000	0.000
84	B	92	ALA	0	-0.006	0.025	8.169	-0.056	-0.056	0.000	0.000	0.000	0.000
85	B	93	GLY	0	0.033	0.018	9.663	-0.048	-0.048	0.000	0.000	0.000	0.000
86	B	94	GLU	-1	-0.847	-0.934	13.416	0.048	0.048	0.000	0.000	0.000	0.000
87	B	95	ALA	0	-0.034	0.000	16.605	-0.023	-0.023	0.000	0.000	0.000	0.000
88	B	96	TYR	0	-0.028	-0.025	19.205	0.018	0.018	0.000	0.000	0.000	0.000
89	B	97	ALA	0	-0.016	0.000	22.867	-0.009	-0.009	0.000	0.000	0.000	0.000
90	B	98	ALA	0	0.011	0.015	25.788	0.007	0.007	0.000	0.000	0.000	0.000
91	B	99	ALA	0	-0.026	-0.004	29.293	-0.004	-0.004	0.000	0.000	0.000	0.000
92	B	100	ALA	0	-0.023	-0.011	31.991	0.003	0.003	0.000	0.000	0.000	0.000
93	B	101	VAL	0	0.011	0.012	35.250	-0.001	-0.001	0.000	0.000	0.000	0.000
94	B	102	THR	0	-0.048	-0.038	37.687	0.000	0.000	0.000	0.000	0.000	0.000
95	B	103	VAL	0	0.003	0.006	41.379	0.000	0.000	0.000	0.000	0.000	0.000
96	B	104	LEU	0	-0.036	-0.004	43.753	-0.001	-0.001	0.000	0.000	0.000	0.000
97	B	105	GLU	-1	-0.863	-0.938	47.203	0.005	0.005	0.000	0.000	0.000	0.000
98	B	106	NME	0	-0.004	0.006	50.421	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	105	HOH	0	-0.038	-0.023	14.991	-0.005	-0.005	0.000	0.000	0.000	0.000
100	A	118	HOH	0	0.035	0.021	28.542	0.001	0.001	0.000	0.000	0.000	0.000
101	A	119	HOH	0	-0.039	-0.029	16.075	-0.012	-0.012	0.000	0.000	0.000	0.000
102	A	174	HOH	0	0.015	0.005	35.075	0.000	0.000	0.000	0.000	0.000	0.000
103	B	108	HOH	0	0.018	0.014	33.473	0.001	0.001	0.000	0.000	0.000	0.000
104	B	109	HOH	0	-0.038	-0.034	11.870	0.006	0.006	0.000	0.000	0.000	0.000
105	B	110	HOH	0	-0.043	-0.032	32.600	0.001	0.001	0.000	0.000	0.000	0.000
106	B	111	HOH	0	0.029	0.020	20.655	0.003	0.003	0.000	0.000	0.000	0.000
107	B	112	HOH	0	-0.027	-0.027	36.475	0.000	0.000	0.000	0.000	0.000	0.000
108	B	113	HOH	0	-0.045	-0.046	14.971	0.010	0.010	0.000	0.000	0.000	0.000
109	B	115	HOH	0	0.034	0.031	46.467	0.000	0.000	0.000	0.000	0.000	0.000
110	B	116	HOH	0	-0.008	0.001	43.489	0.000	0.000	0.000	0.000	0.000	0.000
111	B	118	HOH	0	-0.042	-0.037	19.835	0.005	0.005	0.000	0.000	0.000	0.000
112	B	120	HOH	0	-0.068	-0.051	33.871	-0.001	-0.001	0.000	0.000	0.000	0.000
113	B	121	HOH	0	-0.034	-0.032	35.433	0.000	0.000	0.000	0.000	0.000	0.000
114	B	122	HOH	0	-0.027	-0.022	42.590	0.000	0.000	0.000	0.000	0.000	0.000
115	B	123	HOH	0	-0.007	0.013	38.195	0.000	0.000	0.000	0.000	0.000	0.000
116	B	124	HOH	0	-0.045	-0.006	2.410	12.269	0.077	8.308	5.238	-1.354	-0.007
117	B	125	HOH	0	0.045	0.026	32.510	0.000	0.000	0.000	0.000	0.000	0.000
118	B	129	HOH	0	-0.025	-0.014	22.638	0.000	0.000	0.000	0.000	0.000	0.000
119	B	130	HOH	0	-0.045	-0.028	10.579	-0.047	-0.047	0.000	0.000	0.000	0.000
120	B	136	HOH	0	0.013	0.012	42.556	-0.001	-0.001	0.000	0.000	0.000	0.000
121	B	138	HOH	0	-0.029	-0.031	24.029	0.001	0.001	0.000	0.000	0.000	0.000
122	B	139	HOH	0	0.023	0.011	44.152	0.000	0.000	0.000	0.000	0.000	0.000
123	B	140	HOH	0	0.002	-0.020	31.187	0.000	0.000	0.000	0.000	0.000	0.000
124	B	142	HOH	0	0.029	0.018	25.823	0.003	0.003	0.000	0.000	0.000	0.000
125	B	143	HOH	0	-0.015	-0.032	40.834	0.000	0.000	0.000	0.000	0.000	0.000
126	B	145	HOH	0	0.021	0.013	38.968	0.000	0.000	0.000	0.000	0.000	0.000
127	B	148	HOH	0	0.043	0.029	19.960	0.005	0.005	0.000	0.000	0.000	0.000
128	B	149	HOH	0	-0.051	-0.043	36.705	0.001	0.001	0.000	0.000	0.000	0.000
129	B	153	HOH	0	-0.034	-0.031	23.213	-0.001	-0.001	0.000	0.000	0.000	0.000
130	B	154	HOH	0	-0.017	-0.022	31.665	-0.001	-0.001	0.000	0.000	0.000	0.000
131	B	156	HOH	0	0.027	0.007	31.609	0.000	0.000	0.000	0.000	0.000	0.000
132	B	157	HOH	0	0.053	0.047	37.644	0.001	0.001	0.000	0.000	0.000	0.000
133	B	158	HOH	0	-0.027	-0.043	6.754	0.066	0.066	0.000	0.000	0.000	0.000
134	B	159	HOH	0	-0.016	-0.010	11.979	0.003	0.003	0.000	0.000	0.000	0.000
135	B	160	HOH	0	-0.011	-0.013	23.989	0.001	0.001	0.000	0.000	0.000	0.000
136	B	161	HOH	0	0.031	0.041	9.122	-0.034	-0.034	0.000	0.000	0.000	0.000
137	B	162	HOH	0	0.004	-0.008	29.405	0.000	0.000	0.000	0.000	0.000	0.000
138	B	166	HOH	0	-0.029	-0.055	5.122	0.213	0.213	0.000	0.000	0.000	0.000
139	B	167	HOH	0	-0.061	-0.043	39.542	0.001	0.001	0.000	0.000	0.000	0.000
140	B	168	HOH	0	0.027	0.017	25.160	-0.003	-0.003	0.000	0.000	0.000	0.000
141	B	169	HOH	0	-0.053	-0.045	46.457	0.000	0.000	0.000	0.000	0.000	0.000
142	B	170	HOH	0	-0.001	-0.006	39.049	-0.001	-0.001	0.000	0.000	0.000	0.000
143	B	171	HOH	0	-0.036	-0.026	46.330	0.000	0.000	0.000	0.000	0.000	0.000
144	B	172	HOH	0	-0.007	-0.013	9.380	0.017	0.017	0.000	0.000	0.000	0.000
145	B	173	HOH	0	0.018	0.019	8.503	-0.145	-0.145	0.000	0.000	0.000	0.000
146	B	174	HOH	0	0.016	0.016	41.451	-0.001	-0.001	0.000	0.000	0.000	0.000
147	B	175	HOH	0	-0.029	-0.022	25.487	0.003	0.003	0.000	0.000	0.000	0.000
148	B	179	HOH	0	0.003	0.001	12.761	0.003	0.003	0.000	0.000	0.000	0.000
149	B	180	HOH	0	-0.034	-0.036	40.347	0.000	0.000	0.000	0.000	0.000	0.000
150	B	181	HOH	0	-0.045	-0.037	48.205	0.000	0.000	0.000	0.000	0.000	0.000
151	B	185	HOH	0	-0.004	-0.009	38.614	0.000	0.000	0.000	0.000	0.000	0.000
152	B	188	HOH	0	-0.023	-0.020	18.896	0.001	0.001	0.000	0.000	0.000	0.000
153	B	189	HOH	0	-0.032	-0.021	35.216	-0.001	-0.001	0.000	0.000	0.000	0.000
154	B	190	HOH	0	-0.035	-0.029	12.210	0.014	0.014	0.000	0.000	0.000	0.000
155	B	191	HOH	0	0.027	0.016	30.007	-0.001	-0.001	0.000	0.000	0.000	0.000
156	B	196	HOH	0	0.023	0.022	25.312	-0.001	-0.001	0.000	0.000	0.000	0.000
157	B	199	HOH	0	-0.028	-0.021	35.050	0.000	0.000	0.000	0.000	0.000	0.000
158	B	200	HOH	0	0.028	0.008	34.295	-0.002	-0.002	0.000	0.000	0.000	0.000
159	B	204	HOH	0	-0.004	0.000	42.465	0.000	0.000	0.000	0.000	0.000	0.000
160	B	205	HOH	0	-0.007	-0.002	33.977	0.001	0.001	0.000	0.000	0.000	0.000
161	B	215	HOH	0	-0.035	-0.032	8.421	0.053	0.053	0.000	0.000	0.000	0.000
162	B	217	HOH	0	-0.018	-0.033	38.085	0.001	0.001	0.000	0.000	0.000	0.000
163	B	221	HOH	0	0.030	0.021	47.751	0.000	0.000	0.000	0.000	0.000	0.000
164	B	227	HOH	0	-0.053	-0.032	34.512	0.000	0.000	0.000	0.000	0.000	0.000
165	B	229	HOH	0	0.006	0.006	35.305	0.000	0.000	0.000	0.000	0.000	0.000
166	B	249	HOH	0	-0.056	-0.056	22.612	0.005	0.005	0.000	0.000	0.000	0.000
167	B	259	HOH	0	0.005	-0.008	25.090	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:9:ACE)