FMO DATABASE

FMODB ID: LJY19

Calculation Name: 3KOP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KOP

Chain ID: A

ChEMBL ID:

UniProt ID: A0JVT3

Base Structure: X-ray

Registration Date: 2023-06-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	158
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1540038.269569
FMO2-HF: Nuclear repulsion	1478813.441078
FMO2-HF: Total energy	-61224.82849
FMO2-MP2: Total energy	-61402.433068

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.
-7.469	-3.495	1.689	-2.28	-3.381	-0.021

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 : -0.042 / q_NPA : -0.032

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	ARG	1	0.813	0.880	2.593	-4.267	-0.510	1.690	-2.261	-3.185	-0.021
4	A	4	TYR	0	0.059	0.021	4.372	0.921	1.138	-0.001	-0.019	-0.196	0.000
5	A	5	ILE	0	-0.003	-0.002	7.160	0.000	0.000	0.000	0.000	0.000	0.000
6	A	6	ASN	0	0.033	0.021	10.413	0.052	0.052	0.000	0.000	0.000	0.000
7	A	7	ILE	0	-0.018	-0.018	13.247	0.009	0.009	0.000	0.000	0.000	0.000
8	A	8	THR	0	0.030	0.023	16.655	0.016	0.016	0.000	0.000	0.000	0.000
9	A	9	LEU	0	0.005	0.012	19.813	0.006	0.006	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.805	-0.886	21.575	-0.350	-0.350	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.748	0.863	24.609	0.178	0.178	0.000	0.000	0.000	0.000
12	A	12	ARG	1	0.730	0.821	26.924	0.205	0.205	0.000	0.000	0.000	0.000
13	A	13	GLY	0	0.000	0.022	24.422	0.009	0.009	0.000	0.000	0.000	0.000
14	A	14	VAL	0	-0.039	-0.010	22.490	-0.003	-0.003	0.000	0.000	0.000	0.000
15	A	15	THR	0	-0.013	-0.028	16.450	-0.005	-0.005	0.000	0.000	0.000	0.000
16	A	16	CYS	0	-0.080	-0.016	17.167	0.019	0.019	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.865	0.904	9.364	0.809	0.809	0.000	0.000	0.000	0.000
18	A	18	ALA	0	0.023	0.012	12.074	0.100	0.100	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.019	0.000	7.653	-0.298	-0.298	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.032	-0.022	7.640	0.341	0.341	0.000	0.000	0.000	0.000
21	A	21	LEU	0	0.015	0.012	8.783	-0.213	-0.213	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.824	-0.896	6.226	-2.515	-2.515	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.887	-0.939	7.969	-0.076	-0.076	0.000	0.000	0.000	0.000
24	A	24	VAL	0	-0.032	-0.023	9.130	0.099	0.099	0.000	0.000	0.000	0.000
25	A	25	ALA	0	-0.021	-0.010	11.987	0.050	0.050	0.000	0.000	0.000	0.000
26	A	26	PRO	0	0.025	0.030	10.233	-0.115	-0.115	0.000	0.000	0.000	0.000
27	A	27	ARG	1	0.734	0.836	11.455	0.163	0.163	0.000	0.000	0.000	0.000
28	A	28	THR	0	-0.016	-0.038	14.621	-0.011	-0.011	0.000	0.000	0.000	0.000
29	A	29	SER	0	0.011	0.002	10.485	-0.011	-0.011	0.000	0.000	0.000	0.000
30	A	30	LYS	1	0.840	0.898	10.932	0.643	0.643	0.000	0.000	0.000	0.000
31	A	31	ALA	0	-0.011	-0.004	12.076	0.008	0.008	0.000	0.000	0.000	0.000
32	A	32	VAL	0	0.028	0.015	13.936	0.038	0.038	0.000	0.000	0.000	0.000
33	A	33	TRP	0	0.012	0.012	5.810	-0.147	-0.147	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.839	-0.909	11.411	-0.834	-0.834	0.000	0.000	0.000	0.000
35	A	35	ALA	0	-0.008	-0.002	13.056	0.067	0.067	0.000	0.000	0.000	0.000
36	A	36	LEU	0	-0.088	0.010	11.528	0.052	0.052	0.000	0.000	0.000	0.000
37	A	37	PRO	0	-0.036	-0.033	14.365	-0.015	-0.015	0.000	0.000	0.000	0.000
38	A	38	GLN	0	-0.030	-0.028	16.292	0.081	0.081	0.000	0.000	0.000	0.000
39	A	39	SER	0	-0.029	-0.029	19.208	-0.007	-0.007	0.000	0.000	0.000	0.000
40	A	40	SER	0	-0.031	-0.024	22.089	0.028	0.028	0.000	0.000	0.000	0.000
41	A	41	GLN	0	-0.063	-0.039	25.652	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	42	VAL	0	-0.018	0.005	25.909	-0.006	-0.006	0.000	0.000	0.000	0.000
43	A	43	PHE	0	-0.028	-0.013	27.753	0.028	0.028	0.000	0.000	0.000	0.000
44	A	44	HIS	0	0.075	0.050	28.489	-0.019	-0.019	0.000	0.000	0.000	0.000
45	A	45	GLY	0	0.027	0.020	30.178	0.007	0.007	0.000	0.000	0.000	0.000
46	A	46	LYS	1	0.823	0.892	31.442	0.149	0.149	0.000	0.000	0.000	0.000
47	A	47	TYR	0	0.022	0.003	31.282	0.012	0.012	0.000	0.000	0.000	0.000
48	A	48	ALA	0	-0.006	0.017	29.732	0.007	0.007	0.000	0.000	0.000	0.000
49	A	49	ARG	1	0.847	0.910	30.290	0.119	0.119	0.000	0.000	0.000	0.000
50	A	50	ASN	0	-0.061	-0.005	28.635	0.004	0.004	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.854	-0.935	26.630	-0.235	-0.235	0.000	0.000	0.000	0.000
52	A	52	ILE	0	0.012	0.002	23.538	0.020	0.020	0.000	0.000	0.000	0.000
53	A	53	TYR	0	0.037	0.027	24.191	-0.017	-0.017	0.000	0.000	0.000	0.000
54	A	54	ASN	0	-0.023	-0.007	22.085	0.009	0.009	0.000	0.000	0.000	0.000
55	A	55	LEU	0	0.014	0.012	25.426	-0.004	-0.004	0.000	0.000	0.000	0.000
56	A	56	VAL	0	0.025	0.027	22.276	0.010	0.010	0.000	0.000	0.000	0.000
57	A	57	PRO	0	-0.001	-0.017	25.782	0.010	0.010	0.000	0.000	0.000	0.000
58	A	58	ALA	0	0.002	0.007	23.992	-0.023	-0.023	0.000	0.000	0.000	0.000
59	A	59	PHE	0	0.032	0.011	17.824	0.010	0.010	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.021	0.023	19.341	-0.025	-0.025	0.000	0.000	0.000	0.000
61	A	61	PRO	0	-0.033	-0.030	18.986	0.036	0.036	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.920	0.959	21.119	0.241	0.241	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.755	-0.838	20.993	-0.339	-0.339	0.000	0.000	0.000	0.000
64	A	64	PRO	0	-0.001	0.022	18.007	0.028	0.028	0.000	0.000	0.000	0.000
65	A	65	GLY	0	0.029	0.016	19.947	0.032	0.032	0.000	0.000	0.000	0.000
66	A	66	ALA	0	0.025	0.016	20.996	-0.026	-0.026	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.790	-0.868	15.420	-0.380	-0.380	0.000	0.000	0.000	0.000
68	A	68	ASN	0	-0.004	-0.002	16.142	0.031	0.031	0.000	0.000	0.000	0.000
69	A	69	THR	0	-0.021	0.008	18.539	-0.016	-0.016	0.000	0.000	0.000	0.000
70	A	70	THR	0	0.028	0.015	22.081	0.034	0.034	0.000	0.000	0.000	0.000
71	A	71	VAL	0	0.038	0.005	24.172	-0.006	-0.006	0.000	0.000	0.000	0.000
72	A	72	THR	0	-0.052	-0.025	26.758	0.013	0.013	0.000	0.000	0.000	0.000
73	A	73	PRO	0	0.015	0.032	24.528	0.005	0.005	0.000	0.000	0.000	0.000
74	A	74	ILE	0	-0.044	-0.024	21.198	0.030	0.030	0.000	0.000	0.000	0.000
75	A	75	PRO	0	-0.047	-0.037	23.037	-0.021	-0.021	0.000	0.000	0.000	0.000
76	A	76	GLY	0	0.061	0.039	19.484	0.002	0.002	0.000	0.000	0.000	0.000
77	A	77	ASP	-1	-0.827	-0.904	18.210	-0.383	-0.383	0.000	0.000	0.000	0.000
78	A	78	VAL	0	-0.018	-0.008	15.960	0.021	0.021	0.000	0.000	0.000	0.000
79	A	79	CYS	0	-0.057	-0.019	17.984	-0.013	-0.013	0.000	0.000	0.000	0.000
80	A	80	TYR	0	-0.003	-0.031	18.660	-0.024	-0.024	0.000	0.000	0.000	0.000
81	A	81	PHE	0	-0.016	-0.004	21.141	0.025	0.025	0.000	0.000	0.000	0.000
82	A	82	THR	0	-0.026	-0.028	24.149	-0.007	-0.007	0.000	0.000	0.000	0.000
83	A	83	PHE	0	-0.006	-0.001	25.987	0.018	0.018	0.000	0.000	0.000	0.000
84	A	84	THR	0	-0.031	-0.042	29.526	0.000	0.000	0.000	0.000	0.000	0.000
85	A	85	SER	0	-0.019	-0.055	32.323	-0.004	-0.004	0.000	0.000	0.000	0.000
86	A	86	ASN	0	-0.011	-0.006	35.121	0.003	0.003	0.000	0.000	0.000	0.000
87	A	87	ASP	-1	-0.820	-0.877	32.956	-0.149	-0.149	0.000	0.000	0.000	0.000
88	A	88	LEU	0	0.017	0.013	30.191	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	89	LYS	1	0.834	0.911	34.841	0.153	0.153	0.000	0.000	0.000	0.000
90	A	90	THR	0	0.019	0.008	37.905	0.006	0.006	0.000	0.000	0.000	0.000
91	A	91	PRO	0	0.004	-0.023	40.333	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	92	SER	0	-0.045	-0.051	40.632	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	93	HIS	1	0.890	0.970	33.630	0.147	0.147	0.000	0.000	0.000	0.000
94	A	94	GLY	0	-0.001	0.021	37.740	-0.004	-0.004	0.000	0.000	0.000	0.000
95	A	95	TYR	0	-0.038	-0.029	31.925	0.003	0.003	0.000	0.000	0.000	0.000
96	A	104	VAL	0	-0.003	0.011	36.157	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	105	GLN	0	0.039	0.029	31.583	0.007	0.007	0.000	0.000	0.000	0.000
98	A	106	THR	0	0.025	0.000	27.047	0.009	0.009	0.000	0.000	0.000	0.000
99	A	107	ILE	0	-0.066	-0.025	27.680	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	108	VAL	0	0.014	0.012	21.301	0.005	0.005	0.000	0.000	0.000	0.000
101	A	109	ASP	-1	-0.879	-0.945	24.745	-0.274	-0.274	0.000	0.000	0.000	0.000
102	A	110	LEU	0	-0.017	-0.003	18.816	-0.029	-0.029	0.000	0.000	0.000	0.000
103	A	111	ALA	0	0.046	0.010	21.670	0.015	0.015	0.000	0.000	0.000	0.000
104	A	112	VAL	0	0.003	-0.002	19.264	-0.050	-0.050	0.000	0.000	0.000	0.000
105	A	113	PHE	0	-0.002	-0.007	21.786	0.041	0.041	0.000	0.000	0.000	0.000
106	A	114	TYR	0	0.022	-0.009	22.847	-0.012	-0.012	0.000	0.000	0.000	0.000
107	A	115	GLY	0	0.038	0.010	24.920	0.015	0.015	0.000	0.000	0.000	0.000
108	A	116	ARG	1	0.925	0.961	27.075	0.113	0.113	0.000	0.000	0.000	0.000
109	A	117	ASN	0	-0.018	-0.012	29.281	0.004	0.004	0.000	0.000	0.000	0.000
110	A	118	ASN	0	0.043	0.018	27.488	0.017	0.017	0.000	0.000	0.000	0.000
111	A	119	LEU	0	0.019	-0.002	30.942	0.005	0.005	0.000	0.000	0.000	0.000
112	A	120	LEU	0	0.005	0.024	26.250	0.002	0.002	0.000	0.000	0.000	0.000
113	A	121	LEU	0	-0.047	-0.016	30.807	0.005	0.005	0.000	0.000	0.000	0.000
114	A	122	ASN	0	0.026	0.011	34.033	0.009	0.009	0.000	0.000	0.000	0.000
115	A	123	GLY	0	0.026	-0.003	36.900	0.005	0.005	0.000	0.000	0.000	0.000
116	A	124	ASP	-1	-0.847	-0.874	37.608	-0.116	-0.116	0.000	0.000	0.000	0.000
117	A	125	THR	0	-0.059	-0.045	35.398	0.001	0.001	0.000	0.000	0.000	0.000
118	A	126	GLY	0	0.025	0.033	36.824	0.004	0.004	0.000	0.000	0.000	0.000
119	A	127	TRP	0	-0.019	-0.025	31.735	-0.007	-0.007	0.000	0.000	0.000	0.000
120	A	128	VAL	0	-0.001	0.002	28.946	0.002	0.002	0.000	0.000	0.000	0.000
121	A	129	PRO	0	0.000	-0.020	26.240	-0.011	-0.011	0.000	0.000	0.000	0.000
122	A	130	GLY	0	0.036	0.027	23.962	-0.002	-0.002	0.000	0.000	0.000	0.000
123	A	131	ASN	0	-0.040	-0.045	18.634	0.046	0.046	0.000	0.000	0.000	0.000
124	A	132	VAL	0	0.019	0.005	17.109	-0.042	-0.042	0.000	0.000	0.000	0.000
125	A	133	PHE	0	0.002	-0.008	13.687	0.004	0.004	0.000	0.000	0.000	0.000
126	A	134	ALA	0	0.015	0.010	12.689	-0.189	-0.189	0.000	0.000	0.000	0.000
127	A	135	THR	0	0.008	0.007	13.343	0.147	0.147	0.000	0.000	0.000	0.000
128	A	136	ILE	0	-0.028	-0.025	13.799	-0.115	-0.115	0.000	0.000	0.000	0.000
129	A	137	VAL	0	-0.051	-0.028	11.470	0.050	0.050	0.000	0.000	0.000	0.000
130	A	138	GLU	-1	-0.850	-0.901	11.957	-0.689	-0.689	0.000	0.000	0.000	0.000
131	A	139	GLY	0	0.074	0.035	16.050	-0.036	-0.036	0.000	0.000	0.000	0.000
132	A	140	LEU	0	-0.003	-0.002	19.237	0.004	0.004	0.000	0.000	0.000	0.000
133	A	141	ASP	-1	-0.901	-0.947	20.732	-0.208	-0.208	0.000	0.000	0.000	0.000
134	A	142	GLU	-1	-0.875	-0.952	22.022	-0.264	-0.264	0.000	0.000	0.000	0.000
135	A	143	MET	0	0.009	0.009	20.118	0.022	0.022	0.000	0.000	0.000	0.000
136	A	144	ALA	0	0.020	0.008	23.254	0.014	0.014	0.000	0.000	0.000	0.000
137	A	145	ALA	0	-0.033	-0.010	25.855	0.017	0.017	0.000	0.000	0.000	0.000
138	A	146	ALA	0	0.027	0.013	25.546	0.013	0.013	0.000	0.000	0.000	0.000
139	A	147	CYS	0	-0.061	-0.031	25.095	-0.001	-0.001	0.000	0.000	0.000	0.000
140	A	148	GLN	0	-0.021	-0.024	27.925	0.022	0.022	0.000	0.000	0.000	0.000
141	A	149	ASP	-1	-0.817	-0.887	30.706	-0.150	-0.150	0.000	0.000	0.000	0.000
142	A	150	ILE	0	-0.020	-0.015	27.349	0.008	0.008	0.000	0.000	0.000	0.000
143	A	151	TRP	0	-0.096	-0.047	31.503	0.011	0.011	0.000	0.000	0.000	0.000
144	A	152	MET	0	-0.052	-0.024	33.840	0.010	0.010	0.000	0.000	0.000	0.000
145	A	153	GLY	0	-0.004	0.008	35.080	0.009	0.009	0.000	0.000	0.000	0.000
146	A	154	GLY	0	-0.036	-0.006	34.559	0.004	0.004	0.000	0.000	0.000	0.000
147	A	155	ALA	0	0.045	0.006	31.539	-0.007	-0.007	0.000	0.000	0.000	0.000
148	A	156	ARG	1	0.914	0.968	32.202	0.127	0.127	0.000	0.000	0.000	0.000
149	A	157	ASP	-1	-0.811	-0.901	32.435	-0.150	-0.150	0.000	0.000	0.000	0.000
150	A	158	GLU	-1	-0.772	-0.863	27.089	-0.244	-0.244	0.000	0.000	0.000	0.000
151	A	159	THR	0	-0.040	-0.020	24.141	0.005	0.005	0.000	0.000	0.000	0.000
152	A	160	LEU	0	-0.010	0.019	20.979	-0.005	-0.005	0.000	0.000	0.000	0.000
153	A	161	THR	0	-0.011	-0.046	18.027	0.011	0.011	0.000	0.000	0.000	0.000
154	A	162	PHE	0	0.013	0.018	15.684	-0.035	-0.035	0.000	0.000	0.000	0.000
155	A	163	SER	0	0.009	-0.017	13.954	0.036	0.036	0.000	0.000	0.000	0.000
156	A	164	ARG	1	0.874	0.930	8.518	0.889	0.889	0.000	0.000	0.000	0.000
157	A	165	ALA	0	-0.046	-0.016	7.937	0.201	0.201	0.000	0.000	0.000	0.000
158	A	166	GLU	-1	-0.976	-0.977	7.034	-1.269	-1.269	0.000	0.000	0.000	0.000

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