FMO DATABASE

FMODB ID: P89MY

Calculation Name: 3KGK-A-Xray22

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KGK

Chain ID: A

ChEMBL ID:

UniProt ID: P46003

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	163
LigandCharge
Software	MIZUHO/ABINIT-MP 3.0

Total energy (hartree)

FMO2-HF: Electronic energy	-791109.928262
FMO2-HF: Nuclear repulsion	749382.938764
FMO2-HF: Total energy	-41726.989498
FMO2-MP2: Total energy	-41846.208112

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:MET)

Summations of interaction energy for fragment #1(A:1: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.
-15.455	-6.648	12.517	-7.95	-13.37	-0.04

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.055 / q_NPA : -0.021

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	THR	0	-0.029	-0.001	2.614	-4.480	-1.754	0.749	-1.577	-1.898	-0.013
4	A	4	LEU	0	-0.024	-0.018	5.268	0.789	0.877	-0.001	-0.005	-0.081	0.000
5	A	5	MET	0	0.008	0.015	7.747	-0.156	-0.156	0.000	0.000	0.000	0.000
6	A	6	VAL	0	-0.034	-0.023	11.430	0.159	0.159	0.000	0.000	0.000	0.000
7	A	7	PHE	0	0.031	0.009	13.994	-0.061	-0.061	0.000	0.000	0.000	0.000
8	A	8	ASP	-1	-0.717	-0.838	17.655	-0.039	-0.039	0.000	0.000	0.000	0.000
9	A	9	PRO	0	0.027	0.010	19.776	-0.015	-0.015	0.000	0.000	0.000	0.000
10	A	10	ALA	0	0.009	-0.006	23.257	-0.018	-0.018	0.000	0.000	0.000	0.000
11	A	11	NME	0	0.040	0.058	25.748	0.014	0.014	0.000	0.000	0.000	0.000
12	A	23	ACE	0	0.044	-0.014	27.213	0.001	0.001	0.000	0.000	0.000	0.000
13	A	24	GLN	0	-0.038	-0.028	23.399	-0.018	-0.018	0.000	0.000	0.000	0.000
14	A	25	ALA	0	0.044	0.030	21.134	0.001	0.001	0.000	0.000	0.000	0.000
15	A	26	LEU	0	0.072	0.034	19.703	0.015	0.015	0.000	0.000	0.000	0.000
16	A	27	VAL	0	0.015	0.025	19.444	-0.018	-0.018	0.000	0.000	0.000	0.000
17	A	28	ASP	-1	-0.787	-0.890	18.756	0.087	0.087	0.000	0.000	0.000	0.000
18	A	29	PHE	0	0.017	0.004	12.430	0.010	0.010	0.000	0.000	0.000	0.000
19	A	30	SER	0	0.028	0.022	14.753	-0.027	-0.027	0.000	0.000	0.000	0.000
20	A	31	THR	0	0.027	0.015	15.144	-0.074	-0.074	0.000	0.000	0.000	0.000
21	A	32	ASP	-1	-0.795	-0.879	12.361	0.199	0.199	0.000	0.000	0.000	0.000
22	A	33	VAL	0	-0.010	0.001	10.650	0.012	0.012	0.000	0.000	0.000	0.000
23	A	34	GLN	0	-0.010	0.004	10.237	-0.156	-0.156	0.000	0.000	0.000	0.000
24	A	35	TRP	0	0.023	0.018	8.919	-0.047	-0.047	0.000	0.000	0.000	0.000
25	A	36	LEU	0	0.022	0.020	5.905	-0.166	-0.166	0.000	0.000	0.000	0.000
26	A	37	LYS	1	0.883	0.941	6.091	0.227	0.227	0.000	0.000	0.000	0.000
27	A	38	GLN	0	-0.029	-0.012	8.251	-0.279	-0.279	0.000	0.000	0.000	0.000
28	A	39	SER	0	-0.015	-0.005	4.779	0.060	0.124	-0.001	-0.002	-0.060	0.000
29	A	40	GLY	0	-0.045	0.002	4.375	-1.196	-1.047	-0.001	-0.030	-0.118	0.000
30	A	41	VAL	0	-0.012	0.004	2.327	-2.625	-1.464	1.832	-0.649	-2.344	0.000
31	A	42	GLN	0	0.033	0.021	3.524	1.187	1.367	0.007	0.081	-0.267	0.000
32	A	43	ILE	0	-0.023	-0.023	6.081	0.242	0.242	0.000	0.000	0.000	0.000
33	A	44	GLU	-1	-0.904	-0.934	8.577	-0.827	-0.827	0.000	0.000	0.000	0.000
34	A	45	ARG	1	0.764	0.846	11.983	0.243	0.243	0.000	0.000	0.000	0.000
35	A	46	PHE	0	0.017	0.017	13.992	-0.026	-0.026	0.000	0.000	0.000	0.000
36	A	47	ASN	0	0.036	-0.001	18.302	0.053	0.053	0.000	0.000	0.000	0.000
37	A	48	LEU	0	0.062	0.020	21.640	-0.016	-0.016	0.000	0.000	0.000	0.000
38	A	49	ALA	0	-0.031	0.010	25.078	0.003	0.003	0.000	0.000	0.000	0.000
39	A	50	GLN	0	0.008	0.019	23.163	-0.009	-0.009	0.000	0.000	0.000	0.000
40	A	51	GLN	0	0.035	0.027	20.162	0.007	0.007	0.000	0.000	0.000	0.000
41	A	52	PRO	0	0.057	0.030	22.617	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	53	MET	0	0.022	-0.005	24.994	0.015	0.015	0.000	0.000	0.000	0.000
43	A	54	SER	0	0.069	0.038	19.384	0.005	0.005	0.000	0.000	0.000	0.000
44	A	55	PHE	0	-0.061	-0.033	20.858	0.002	0.002	0.000	0.000	0.000	0.000
45	A	56	VAL	0	-0.024	-0.004	22.684	0.021	0.021	0.000	0.000	0.000	0.000
46	A	57	GLN	0	-0.005	0.000	22.138	-0.009	-0.009	0.000	0.000	0.000	0.000
47	A	58	ASN	0	0.028	0.034	16.286	0.038	0.038	0.000	0.000	0.000	0.000
48	A	59	GLU	-1	-0.780	-0.895	20.243	-0.033	-0.033	0.000	0.000	0.000	0.000
49	A	60	LYS	1	0.878	0.947	16.055	-0.112	-0.112	0.000	0.000	0.000	0.000
50	A	61	VAL	0	-0.003	0.006	18.355	0.028	0.028	0.000	0.000	0.000	0.000
51	A	62	LYS	1	0.899	0.974	20.856	0.046	0.046	0.000	0.000	0.000	0.000
52	A	63	ALA	0	0.043	0.027	23.750	0.010	0.010	0.000	0.000	0.000	0.000
53	A	64	PHE	0	-0.010	-0.008	21.807	0.014	0.014	0.000	0.000	0.000	0.000
54	A	65	ILE	0	-0.042	-0.019	23.757	0.006	0.006	0.000	0.000	0.000	0.000
55	A	66	GLU	-1	-0.920	-0.941	25.973	0.018	0.018	0.000	0.000	0.000	0.000
56	A	67	ALA	0	-0.011	0.003	26.783	0.004	0.004	0.000	0.000	0.000	0.000
57	A	68	SER	0	-0.044	-0.029	25.762	0.012	0.012	0.000	0.000	0.000	0.000
58	A	69	GLY	0	0.062	0.055	27.749	0.001	0.001	0.000	0.000	0.000	0.000
59	A	70	ALA	0	0.010	-0.024	26.040	0.007	0.007	0.000	0.000	0.000	0.000
60	A	71	GLU	-1	-0.866	-0.913	25.906	0.028	0.028	0.000	0.000	0.000	0.000
61	A	72	GLY	0	0.006	0.017	25.288	0.012	0.012	0.000	0.000	0.000	0.000
62	A	73	LEU	0	-0.035	0.002	20.747	0.022	0.022	0.000	0.000	0.000	0.000
63	A	74	PRO	0	0.010	0.001	17.614	0.002	0.002	0.000	0.000	0.000	0.000
64	A	75	LEU	0	-0.010	0.007	16.890	0.039	0.039	0.000	0.000	0.000	0.000
65	A	76	LEU	0	-0.040	-0.024	12.063	-0.042	-0.042	0.000	0.000	0.000	0.000
66	A	77	LEU	0	0.018	0.008	12.305	0.076	0.076	0.000	0.000	0.000	0.000
67	A	78	LEU	0	-0.001	-0.001	5.992	-0.108	-0.108	0.000	0.000	0.000	0.000
68	A	79	ASP	-1	-0.774	-0.877	6.612	-0.680	-0.680	0.000	0.000	0.000	0.000
69	A	80	GLY	0	0.004	0.003	9.120	0.115	0.115	0.000	0.000	0.000	0.000
70	A	81	GLU	-1	-0.935	-0.963	11.893	0.304	0.304	0.000	0.000	0.000	0.000
71	A	82	THR	0	-0.020	-0.032	12.893	0.033	0.033	0.000	0.000	0.000	0.000
72	A	83	VAL	0	-0.012	0.007	11.093	0.072	0.072	0.000	0.000	0.000	0.000
73	A	84	MET	0	-0.087	-0.035	14.296	0.046	0.046	0.000	0.000	0.000	0.000
74	A	85	ALA	0	0.005	-0.001	16.527	-0.045	-0.045	0.000	0.000	0.000	0.000
75	A	86	GLY	0	0.081	0.064	19.488	0.015	0.015	0.000	0.000	0.000	0.000
76	A	87	ARG	1	0.758	0.867	17.916	-0.406	-0.406	0.000	0.000	0.000	0.000
77	A	88	TYR	0	0.005	-0.030	15.881	0.020	0.020	0.000	0.000	0.000	0.000
78	A	89	PRO	0	-0.026	0.007	12.507	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	90	LYS	1	0.985	0.977	15.240	-0.345	-0.345	0.000	0.000	0.000	0.000
80	A	91	ARG	1	0.930	0.940	12.035	-0.042	-0.042	0.000	0.000	0.000	0.000
81	A	92	ALA	0	0.021	0.008	11.617	0.178	0.178	0.000	0.000	0.000	0.000
82	A	93	GLU	-1	-0.731	-0.828	12.335	0.705	0.705	0.000	0.000	0.000	0.000
83	A	94	LEU	0	0.044	0.020	8.862	0.228	0.228	0.000	0.000	0.000	0.000
84	A	95	ALA	0	0.017	0.009	7.580	0.745	0.745	0.000	0.000	0.000	0.000
85	A	96	ARG	1	0.859	0.917	7.826	-0.515	-0.515	0.000	0.000	0.000	0.000
86	A	97	TRP	0	-0.039	-0.031	7.795	0.264	0.264	0.000	0.000	0.000	0.000
87	A	98	PHE	0	0.003	-0.009	2.817	-2.056	-1.161	2.656	-0.926	-2.624	0.004
88	A	99	GLY	0	0.010	0.022	3.548	1.057	2.522	0.599	-0.715	-1.349	-0.011
89	A	100	ILE	0	-0.015	-0.003	4.290	-0.932	-0.734	-0.001	-0.022	-0.176	0.000
90	A	101	PRO	0	0.030	0.014	5.747	-0.032	-0.032	0.000	0.000	0.000	0.000
91	A	102	LEU	0	0.012	0.010	8.879	-0.132	-0.132	0.000	0.000	0.000	0.000
92	A	103	ASP	-1	-0.875	-0.936	11.971	0.126	0.126	0.000	0.000	0.000	0.000
93	A	104	LYS	1	0.889	0.938	12.929	-0.345	-0.345	0.000	0.000	0.000	0.000
94	A	105	VAL	0	0.013	0.016	16.902	-0.033	-0.033	0.000	0.000	0.000	0.000
95	A	0	NME	0	0.008	0.012	19.834	0.024	0.024	0.000	0.000	0.000	0.000
96	A	111	HOH	0	-0.015	-0.017	17.118	0.039	0.039	0.000	0.000	0.000	0.000
97	A	116	HOH	0	-0.022	-0.011	16.109	0.047	0.047	0.000	0.000	0.000	0.000
98	A	117	HOH	0	-0.007	-0.007	27.209	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	118	HOH	0	-0.033	-0.023	20.226	-0.006	-0.006	0.000	0.000	0.000	0.000
100	A	120	HOH	0	-0.032	-0.024	12.278	-0.028	-0.028	0.000	0.000	0.000	0.000
101	A	121	HOH	0	-0.032	-0.021	18.659	0.008	0.008	0.000	0.000	0.000	0.000
102	A	122	HOH	0	-0.027	-0.015	4.025	0.267	0.494	0.017	-0.085	-0.158	0.000
103	A	123	HOH	0	-0.016	-0.013	16.083	-0.030	-0.030	0.000	0.000	0.000	0.000
104	A	124	HOH	0	0.002	-0.004	16.567	0.001	0.001	0.000	0.000	0.000	0.000
105	A	127	HOH	0	-0.027	-0.030	28.674	0.005	0.005	0.000	0.000	0.000	0.000
106	A	128	HOH	0	-0.013	-0.020	21.794	0.009	0.009	0.000	0.000	0.000	0.000
107	A	129	HOH	0	-0.051	-0.029	24.232	0.006	0.006	0.000	0.000	0.000	0.000
108	A	131	HOH	0	0.017	0.012	9.522	0.068	0.068	0.000	0.000	0.000	0.000
109	A	135	HOH	0	-0.046	-0.032	27.667	0.005	0.005	0.000	0.000	0.000	0.000
110	A	136	HOH	0	0.043	0.024	21.098	0.002	0.002	0.000	0.000	0.000	0.000
111	A	137	HOH	0	0.017	0.008	17.794	0.007	0.007	0.000	0.000	0.000	0.000
112	A	139	HOH	0	-0.010	-0.015	14.810	0.006	0.006	0.000	0.000	0.000	0.000
113	A	140	HOH	0	0.005	0.010	19.965	0.010	0.010	0.000	0.000	0.000	0.000
114	A	143	HOH	0	0.032	0.017	2.568	-5.541	-5.419	4.388	-2.377	-2.133	-0.003
115	A	144	HOH	0	0.050	0.038	17.134	-0.021	-0.021	0.000	0.000	0.000	0.000
116	A	149	HOH	0	-0.056	-0.050	4.129	0.744	0.798	0.000	-0.015	-0.039	0.000
117	A	151	HOH	0	-0.006	0.000	14.056	0.016	0.016	0.000	0.000	0.000	0.000
118	A	152	HOH	0	-0.022	-0.018	10.003	0.138	0.138	0.000	0.000	0.000	0.000
119	A	153	HOH	0	0.033	0.020	14.758	-0.012	-0.012	0.000	0.000	0.000	0.000
120	A	154	HOH	0	0.021	0.009	2.490	-0.406	0.829	0.785	-0.924	-1.096	-0.007
121	A	155	HOH	0	-0.037	-0.020	31.286	0.000	0.000	0.000	0.000	0.000	0.000
122	A	156	HOH	0	-0.003	0.020	26.501	0.004	0.004	0.000	0.000	0.000	0.000
123	A	157	HOH	0	0.037	0.021	30.275	-0.002	-0.002	0.000	0.000	0.000	0.000
124	A	158	HOH	0	-0.017	-0.012	9.788	-0.011	-0.011	0.000	0.000	0.000	0.000
125	A	159	HOH	0	-0.012	-0.011	21.491	0.012	0.012	0.000	0.000	0.000	0.000
126	A	161	HOH	0	-0.002	-0.001	18.373	0.008	0.008	0.000	0.000	0.000	0.000
127	A	163	HOH	0	0.026	0.020	26.376	-0.006	-0.006	0.000	0.000	0.000	0.000
128	A	167	HOH	0	0.001	-0.019	26.163	-0.007	-0.007	0.000	0.000	0.000	0.000
129	A	169	HOH	0	-0.055	-0.039	18.623	-0.005	-0.005	0.000	0.000	0.000	0.000
130	A	170	HOH	0	0.019	0.004	18.513	-0.006	-0.006	0.000	0.000	0.000	0.000
131	A	171	HOH	0	0.005	-0.001	29.050	-0.003	-0.003	0.000	0.000	0.000	0.000
132	A	173	HOH	0	-0.062	-0.052	24.512	0.006	0.006	0.000	0.000	0.000	0.000
133	A	174	HOH	0	-0.027	-0.023	7.771	0.092	0.092	0.000	0.000	0.000	0.000
134	A	175	HOH	0	-0.046	-0.039	9.033	0.030	0.030	0.000	0.000	0.000	0.000
135	A	179	HOH	0	-0.028	-0.033	2.491	-2.522	-2.279	1.488	-0.704	-1.027	-0.010
136	A	180	HOH	0	0.025	0.022	14.183	0.018	0.018	0.000	0.000	0.000	0.000
137	A	183	HOH	0	-0.061	-0.038	9.144	-0.047	-0.047	0.000	0.000	0.000	0.000
138	A	185	HOH	0	-0.083	-0.051	19.938	0.010	0.010	0.000	0.000	0.000	0.000
139	A	186	HOH	0	-0.033	-0.021	6.680	0.102	0.102	0.000	0.000	0.000	0.000
140	A	190	HOH	0	-0.030	-0.020	17.003	0.006	0.006	0.000	0.000	0.000	0.000
141	A	194	HOH	0	-0.034	-0.019	24.058	-0.007	-0.007	0.000	0.000	0.000	0.000
142	A	195	HOH	0	0.008	-0.004	19.787	-0.014	-0.014	0.000	0.000	0.000	0.000
143	A	196	HOH	0	-0.039	-0.020	9.069	-0.059	-0.059	0.000	0.000	0.000	0.000
144	A	199	HOH	0	0.031	0.025	7.887	0.132	0.132	0.000	0.000	0.000	0.000
145	A	203	HOH	0	-0.053	-0.035	17.939	-0.010	-0.010	0.000	0.000	0.000	0.000
146	A	209	HOH	0	-0.032	-0.024	9.228	-0.053	-0.053	0.000	0.000	0.000	0.000
147	A	210	HOH	0	-0.039	-0.025	28.608	0.005	0.005	0.000	0.000	0.000	0.000
148	A	211	HOH	0	-0.038	-0.043	24.677	0.001	0.001	0.000	0.000	0.000	0.000
149	A	212	HOH	0	-0.040	-0.031	23.650	-0.002	-0.002	0.000	0.000	0.000	0.000
150	A	213	HOH	0	-0.035	-0.024	27.468	0.003	0.003	0.000	0.000	0.000	0.000
151	A	217	HOH	0	-0.005	-0.008	10.915	0.010	0.010	0.000	0.000	0.000	0.000
152	A	220	HOH	0	-0.008	-0.009	27.087	0.002	0.002	0.000	0.000	0.000	0.000
153	A	222	HOH	0	0.024	0.019	23.229	-0.002	-0.002	0.000	0.000	0.000	0.000
154	A	223	HOH	0	0.002	0.006	19.913	-0.011	-0.011	0.000	0.000	0.000	0.000
155	A	224	HOH	0	-0.052	-0.034	31.622	0.000	0.000	0.000	0.000	0.000	0.000
156	A	228	HOH	0	-0.004	-0.004	15.455	0.009	0.009	0.000	0.000	0.000	0.000
157	A	229	HOH	0	-0.042	-0.030	16.075	-0.015	-0.015	0.000	0.000	0.000	0.000
158	A	230	HOH	0	0.007	0.007	14.784	0.022	0.022	0.000	0.000	0.000	0.000
159	A	242	HOH	0	-0.029	-0.016	21.197	-0.010	-0.010	0.000	0.000	0.000	0.000
160	A	244	HOH	0	0.023	0.013	31.417	0.000	0.000	0.000	0.000	0.000	0.000
161	A	266	HOH	0	-0.055	-0.031	26.227	0.006	0.006	0.000	0.000	0.000	0.000
162	B	112	HOH	0	-0.029	-0.018	23.744	0.007	0.007	0.000	0.000	0.000	0.000
163	B	125	HOH	0	-0.030	-0.017	28.232	-0.002	-0.002	0.000	0.000	0.000	0.000

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