FMO DATABASE

FMODB ID: 227KR

Calculation Name: 3KOP-A-Xray317

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3KOP

Chain ID: A

ChEMBL ID:

UniProt ID: A0JVT3

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 1.20200129
Remarks	Structural optimization was performed under the unconstrained condition of hydrogen and heavy atoms fixed using MOE with Auto-FMO protocol as OptH.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	162
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1553498.897009
FMO2-HF: Nuclear repulsion	1491932.73031
FMO2-HF: Total energy	-61566.166699
FMO2-MP2: Total energy	-61744.86204

3D Structure Molmil

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:0:ACE )

Summations of interaction energy for fragment #1(A:0: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.
0.63	1.416	-0.006	-0.332	-0.448	0

Interaction energy analysis for fragmet #1(A:0:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.001 / q_NPA : -0.012

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	A	2	ALA	0	0.022	0.028	3.819	1.036	1.822	-0.006	-0.332	-0.448
4	A	3	ARG	1	0.828	0.903	6.919	0.133	0.133	0.000	0.000	0.000
5	A	4	TYR	0	0.055	0.017	9.370	0.041	0.041	0.000	0.000	0.000
6	A	5	ILE	0	-0.008	-0.004	13.038	0.025	0.025	0.000	0.000	0.000
7	A	6	ASN	0	0.000	-0.001	16.262	-0.019	-0.019	0.000	0.000	0.000
8	A	7	ILE	0	-0.006	-0.007	19.648	0.017	0.017	0.000	0.000	0.000
9	A	8	THR	0	0.014	-0.021	22.552	-0.007	-0.007	0.000	0.000	0.000
10	A	9	LEU	0	-0.020	-0.002	25.995	0.008	0.008	0.000	0.000	0.000
11	A	10	GLU	-1	-0.787	-0.891	28.323	-0.067	-0.067	0.000	0.000	0.000
12	A	11	LYS	1	0.848	0.933	31.203	0.037	0.037	0.000	0.000	0.000
13	A	12	ARG	1	0.710	0.815	33.138	0.043	0.043	0.000	0.000	0.000
14	A	13	GLY	0	0.018	0.031	31.121	-0.002	-0.002	0.000	0.000	0.000
15	A	14	VAL	0	-0.030	-0.007	28.259	-0.005	-0.005	0.000	0.000	0.000
16	A	15	THR	0	-0.008	0.002	23.068	0.003	0.003	0.000	0.000	0.000
17	A	16	CYS	0	-0.067	0.001	22.762	-0.001	-0.001	0.000	0.000	0.000
18	A	17	LYS	1	0.981	0.995	15.999	0.287	0.287	0.000	0.000	0.000
19	A	18	ALA	0	0.016	0.004	16.801	0.003	0.003	0.000	0.000	0.000
20	A	19	LEU	0	-0.020	-0.002	9.559	-0.041	-0.041	0.000	0.000	0.000
21	A	20	LEU	0	-0.032	-0.018	10.502	0.067	0.067	0.000	0.000	0.000
22	A	21	LEU	0	-0.002	0.002	10.054	-0.068	-0.068	0.000	0.000	0.000
23	A	22	ASP	-1	-0.798	-0.905	6.991	0.016	0.016	0.000	0.000	0.000
24	A	23	ASP	-1	-0.912	-0.951	7.634	0.117	0.117	0.000	0.000	0.000
25	A	24	VAL	0	-0.024	-0.018	8.779	0.064	0.064	0.000	0.000	0.000
26	A	25	ALA	0	-0.024	-0.014	12.081	-0.001	-0.001	0.000	0.000	0.000
27	A	26	PRO	0	0.017	0.035	10.136	-0.013	-0.013	0.000	0.000	0.000
28	A	27	ARG	1	0.798	0.878	11.637	-0.161	-0.161	0.000	0.000	0.000
29	A	28	THR	0	-0.014	-0.038	14.858	-0.018	-0.018	0.000	0.000	0.000
30	A	29	SER	0	0.010	0.015	11.446	-0.041	-0.041	0.000	0.000	0.000
31	A	30	LYS	1	0.820	0.891	12.037	-0.258	-0.258	0.000	0.000	0.000
32	A	31	ALA	0	-0.011	0.003	13.303	-0.020	-0.020	0.000	0.000	0.000
33	A	32	VAL	0	0.033	0.012	16.364	-0.013	-0.013	0.000	0.000	0.000
34	A	33	TRP	0	0.002	-0.004	11.958	-0.021	-0.021	0.000	0.000	0.000
35	A	34	ASP	-1	-0.855	-0.931	13.760	0.118	0.118	0.000	0.000	0.000
36	A	35	ALA	0	-0.019	0.003	15.977	-0.005	-0.005	0.000	0.000	0.000
37	A	36	LEU	0	-0.109	-0.001	16.342	-0.010	-0.010	0.000	0.000	0.000
38	A	37	PRO	0	-0.016	-0.031	19.545	-0.001	-0.001	0.000	0.000	0.000
39	A	38	GLN	0	-0.034	-0.023	21.872	0.013	0.013	0.000	0.000	0.000
40	A	39	SER	0	-0.029	-0.043	24.010	-0.007	-0.007	0.000	0.000	0.000
41	A	40	SER	0	-0.011	-0.008	27.199	0.006	0.006	0.000	0.000	0.000
42	A	41	GLN	0	-0.065	-0.031	30.475	-0.004	-0.004	0.000	0.000	0.000
43	A	42	VAL	0	-0.024	0.006	30.467	0.001	0.001	0.000	0.000	0.000
44	A	43	PHE	0	0.000	-0.003	32.220	0.004	0.004	0.000	0.000	0.000
45	A	44	HIS	0	0.049	0.064	32.530	-0.006	-0.006	0.000	0.000	0.000
46	A	45	GLY	0	0.007	0.017	33.362	0.004	0.004	0.000	0.000	0.000
47	A	46	LYS	1	0.929	0.958	34.385	0.010	0.010	0.000	0.000	0.000
48	A	47	TYR	0	-0.004	-0.011	32.437	0.001	0.001	0.000	0.000	0.000
49	A	48	ALA	0	0.002	0.018	31.059	0.000	0.000	0.000	0.000	0.000
50	A	49	ARG	1	0.864	0.925	32.166	0.022	0.022	0.000	0.000	0.000
51	A	50	ASN	0	-0.057	-0.008	31.166	-0.001	-0.001	0.000	0.000	0.000
52	A	51	GLU	-1	-0.850	-0.937	28.601	-0.024	-0.024	0.000	0.000	0.000
53	A	52	ILE	0	-0.004	0.002	28.161	0.003	0.003	0.000	0.000	0.000
54	A	53	TYR	0	0.054	0.056	27.905	0.000	0.000	0.000	0.000	0.000
55	A	54	ASN	0	-0.018	-0.006	26.048	0.003	0.003	0.000	0.000	0.000
56	A	55	LEU	0	0.009	-0.004	28.558	0.004	0.004	0.000	0.000	0.000
57	A	56	VAL	0	-0.011	0.001	25.481	-0.002	-0.002	0.000	0.000	0.000
58	A	57	PRO	0	-0.007	-0.018	28.777	0.004	0.004	0.000	0.000	0.000
59	A	58	ALA	0	0.007	0.006	26.234	-0.001	-0.001	0.000	0.000	0.000
60	A	59	PHE	0	0.048	0.017	20.068	-0.001	-0.001	0.000	0.000	0.000
61	A	60	ALA	0	-0.013	0.012	20.467	0.006	0.006	0.000	0.000	0.000
62	A	61	PRO	0	-0.018	-0.016	20.040	-0.001	-0.001	0.000	0.000	0.000
63	A	62	LYS	1	0.923	0.951	21.324	-0.125	-0.125	0.000	0.000	0.000
64	A	63	GLU	-1	-0.776	-0.862	21.509	0.056	0.056	0.000	0.000	0.000
65	A	64	PRO	0	-0.001	0.027	18.586	0.014	0.014	0.000	0.000	0.000
66	A	65	GLY	0	0.020	0.012	20.305	0.013	0.013	0.000	0.000	0.000
67	A	66	ALA	0	0.012	0.016	21.485	-0.002	-0.002	0.000	0.000	0.000
68	A	67	GLU	-1	-0.826	-0.911	15.257	0.170	0.170	0.000	0.000	0.000
69	A	68	ASN	0	-0.005	-0.010	16.722	-0.006	-0.006	0.000	0.000	0.000
70	A	69	THR	0	-0.025	-0.010	18.853	-0.014	-0.014	0.000	0.000	0.000
71	A	70	THR	0	0.045	0.039	22.389	-0.001	-0.001	0.000	0.000	0.000
72	A	71	VAL	0	0.017	0.000	24.770	0.001	0.001	0.000	0.000	0.000
73	A	72	THR	0	-0.054	-0.038	26.830	0.000	0.000	0.000	0.000	0.000
74	A	73	PRO	0	0.014	0.032	25.081	-0.003	-0.003	0.000	0.000	0.000
75	A	74	ILE	0	-0.040	-0.024	22.010	0.001	0.001	0.000	0.000	0.000
76	A	75	PRO	0	-0.047	-0.036	24.684	-0.001	-0.001	0.000	0.000	0.000
77	A	76	GLY	0	0.040	0.019	22.154	-0.006	-0.006	0.000	0.000	0.000
78	A	77	ASP	-1	-0.814	-0.888	20.583	-0.062	-0.062	0.000	0.000	0.000
79	A	78	VAL	0	-0.025	-0.014	18.935	0.002	0.002	0.000	0.000	0.000
80	A	79	CYS	0	-0.064	-0.037	19.722	0.006	0.006	0.000	0.000	0.000
81	A	80	TYR	0	-0.010	-0.025	20.215	-0.001	-0.001	0.000	0.000	0.000
82	A	81	PHE	0	0.001	0.001	22.449	0.008	0.008	0.000	0.000	0.000
83	A	82	THR	0	-0.030	-0.022	25.112	0.000	0.000	0.000	0.000	0.000
84	A	83	PHE	0	0.002	0.002	27.019	0.001	0.001	0.000	0.000	0.000
85	A	84	THR	0	-0.017	-0.016	30.796	0.002	0.002	0.000	0.000	0.000
86	A	85	SER	0	-0.014	-0.042	33.690	-0.003	-0.003	0.000	0.000	0.000
87	A	86	ASN	0	-0.002	0.000	36.697	-0.004	-0.004	0.000	0.000	0.000
88	A	87	ASP	-1	-0.811	-0.877	33.536	0.018	0.018	0.000	0.000	0.000
89	A	88	LEU	0	-0.008	-0.006	32.192	-0.002	-0.002	0.000	0.000	0.000
90	A	89	LYS	1	0.896	0.947	36.820	-0.011	-0.011	0.000	0.000	0.000
91	A	90	THR	0	0.047	0.019	40.191	0.001	0.001	0.000	0.000	0.000
92	A	91	PRO	0	0.008	-0.023	42.431	-0.002	-0.002	0.000	0.000	0.000
93	A	92	SER	0	-0.062	-0.040	41.271	-0.001	-0.001	0.000	0.000	0.000
94	A	93	HIS	1	0.919	0.976	35.716	-0.002	-0.002	0.000	0.000	0.000
95	A	94	GLY	0	-0.057	-0.022	40.696	-0.002	-0.002	0.000	0.000	0.000
96	A	95	TYR	0	-0.024	-0.028	34.704	0.000	0.000	0.000	0.000	0.000
97	A	96	NME	0	-0.014	-0.005	40.860	-0.001	-0.001	0.000	0.000	0.000
98	A	103	ACE	0	0.004	-0.011	40.586	0.000	0.000	0.000	0.000	0.000
99	A	104	VAL	0	-0.037	-0.023	36.847	0.000	0.000	0.000	0.000	0.000
100	A	105	GLN	0	-0.026	0.001	33.724	0.001	0.001	0.000	0.000	0.000
101	A	106	THR	0	0.022	-0.003	28.134	-0.002	-0.002	0.000	0.000	0.000
102	A	107	ILE	0	-0.042	-0.012	29.833	-0.001	-0.001	0.000	0.000	0.000
103	A	108	VAL	0	0.020	0.018	23.495	0.003	0.003	0.000	0.000	0.000
104	A	109	ASP	-1	-0.885	-0.942	26.809	-0.016	-0.016	0.000	0.000	0.000
105	A	110	LEU	0	-0.024	-0.010	21.496	0.004	0.004	0.000	0.000	0.000
106	A	111	ALA	0	0.031	0.014	24.110	-0.005	-0.005	0.000	0.000	0.000
107	A	112	VAL	0	0.018	0.004	23.312	-0.006	-0.006	0.000	0.000	0.000
108	A	113	PHE	0	0.010	-0.004	24.651	0.007	0.007	0.000	0.000	0.000
109	A	114	TYR	0	0.018	-0.038	25.565	-0.010	-0.010	0.000	0.000	0.000
110	A	115	GLY	0	0.020	0.001	28.031	-0.002	-0.002	0.000	0.000	0.000
111	A	116	ARG	1	0.939	0.972	29.033	0.040	0.040	0.000	0.000	0.000
112	A	117	ASN	0	-0.041	-0.020	30.647	0.001	0.001	0.000	0.000	0.000
113	A	118	ASN	0	0.046	0.009	28.920	0.002	0.002	0.000	0.000	0.000
114	A	119	LEU	0	0.016	0.001	31.342	0.001	0.001	0.000	0.000	0.000
115	A	120	LEU	0	-0.007	0.021	27.070	-0.001	-0.001	0.000	0.000	0.000
116	A	121	LEU	0	-0.040	-0.015	31.451	0.004	0.004	0.000	0.000	0.000
117	A	122	ASN	0	0.020	0.004	34.851	-0.001	-0.001	0.000	0.000	0.000
118	A	123	GLY	0	0.009	-0.014	37.576	0.002	0.002	0.000	0.000	0.000
119	A	124	ASP	-1	-0.893	-0.903	38.322	0.004	0.004	0.000	0.000	0.000
120	A	125	THR	0	-0.042	-0.036	35.940	0.002	0.002	0.000	0.000	0.000
121	A	126	GLY	0	0.023	0.024	37.175	0.002	0.002	0.000	0.000	0.000
122	A	127	TRP	0	-0.013	-0.017	31.986	-0.002	-0.002	0.000	0.000	0.000
123	A	128	VAL	0	-0.014	-0.006	29.838	0.003	0.003	0.000	0.000	0.000
124	A	129	PRO	0	0.007	-0.016	26.575	-0.003	-0.003	0.000	0.000	0.000
125	A	130	GLY	0	0.034	0.034	24.691	0.002	0.002	0.000	0.000	0.000
126	A	131	ASN	0	-0.016	-0.036	19.361	-0.002	-0.002	0.000	0.000	0.000
127	A	132	VAL	0	0.036	0.017	17.876	-0.009	-0.009	0.000	0.000	0.000
128	A	133	PHE	0	-0.004	-0.004	15.458	0.011	0.011	0.000	0.000	0.000
129	A	134	ALA	0	0.007	0.008	14.474	-0.019	-0.019	0.000	0.000	0.000
130	A	135	THR	0	0.012	0.011	15.057	0.016	0.016	0.000	0.000	0.000
131	A	136	ILE	0	-0.012	-0.025	16.816	-0.034	-0.034	0.000	0.000	0.000
132	A	137	VAL	0	-0.060	-0.029	15.458	0.002	0.002	0.000	0.000	0.000
133	A	138	GLU	-1	-0.941	-0.972	18.336	-0.262	-0.262	0.000	0.000	0.000
134	A	139	GLY	0	0.065	0.028	21.272	0.005	0.005	0.000	0.000	0.000
135	A	140	LEU	0	-0.005	-0.006	23.636	0.010	0.010	0.000	0.000	0.000
136	A	141	ASP	-1	-0.901	-0.946	25.281	-0.081	-0.081	0.000	0.000	0.000
137	A	142	GLU	-1	-0.868	-0.950	27.824	-0.097	-0.097	0.000	0.000	0.000
138	A	143	MET	0	-0.001	-0.002	25.421	0.011	0.011	0.000	0.000	0.000
139	A	144	ALA	0	0.012	0.002	28.367	0.009	0.009	0.000	0.000	0.000
140	A	145	ALA	0	-0.038	-0.011	30.323	0.007	0.007	0.000	0.000	0.000
141	A	146	ALA	0	0.024	0.005	31.120	0.005	0.005	0.000	0.000	0.000
142	A	147	CYS	0	-0.031	-0.017	29.811	0.005	0.005	0.000	0.000	0.000
143	A	148	GLN	0	0.012	0.003	32.761	0.007	0.007	0.000	0.000	0.000
144	A	149	ASP	-1	-0.835	-0.904	35.802	-0.038	-0.038	0.000	0.000	0.000
145	A	150	ILE	0	-0.035	-0.004	32.425	0.003	0.003	0.000	0.000	0.000
146	A	151	TRP	0	-0.096	-0.043	36.638	0.004	0.004	0.000	0.000	0.000
147	A	152	MET	0	-0.047	-0.023	38.247	0.003	0.003	0.000	0.000	0.000
148	A	153	GLY	0	0.007	0.005	40.063	0.002	0.002	0.000	0.000	0.000
149	A	154	GLY	0	-0.055	-0.015	40.065	0.001	0.001	0.000	0.000	0.000
150	A	155	ALA	0	0.031	-0.001	36.215	-0.003	-0.003	0.000	0.000	0.000
151	A	156	ARG	1	0.914	0.960	37.414	0.019	0.019	0.000	0.000	0.000
152	A	157	ASP	-1	-0.907	-0.956	38.254	-0.028	-0.028	0.000	0.000	0.000
153	A	158	GLU	-1	-0.768	-0.863	33.060	-0.051	-0.051	0.000	0.000	0.000
154	A	159	THR	0	-0.025	-0.014	29.775	0.005	0.005	0.000	0.000	0.000
155	A	160	LEU	0	-0.014	0.006	25.975	-0.005	-0.005	0.000	0.000	0.000
156	A	161	THR	0	0.010	-0.014	24.132	0.010	0.010	0.000	0.000	0.000
157	A	162	PHE	0	0.007	0.019	20.349	-0.011	-0.011	0.000	0.000	0.000
158	A	163	SER	0	0.041	0.001	19.877	0.007	0.007	0.000	0.000	0.000
159	A	164	ARG	1	0.905	0.957	14.429	0.047	0.047	0.000	0.000	0.000
160	A	165	ALA	0	-0.033	-0.004	15.183	0.012	0.012	0.000	0.000	0.000
161	A	166	GLU	-1	-0.938	-0.976	14.293	-0.254	-0.254	0.000	0.000	0.000
162	A	167	NME	0	-0.043	-0.010	13.189	-0.027	-0.027	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:ACE )