FMO DATABASE

FMODB ID: J3N19

Calculation Name: 3KOP-A-Xray372

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: 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:

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. 2.20220422
Remarks

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	-1539792.156312
FMO2-HF: Nuclear repulsion	1478567.893295
FMO2-HF: Total energy	-61224.263016
FMO2-MP2: Total energy	-61401.882613

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: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.
-7.569	-3.84	1.522	-2.216	-3.034	-0.022

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 : -0.039 / q_NPA : -0.035

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	0.829	0.903	2.555	-3.613	-0.088	1.523	-2.200	-2.847	-0.022
4	A	4	TYR	0	0.051	0.015	4.463	0.939	1.143	-0.001	-0.016	-0.187	0.000
5	A	5	ILE	0	-0.007	-0.003	7.158	-0.036	-0.036	0.000	0.000	0.000	0.000
6	A	6	ASN	0	0.002	-0.001	10.332	0.072	0.072	0.000	0.000	0.000	0.000
7	A	7	ILE	0	-0.009	-0.008	13.209	0.002	0.002	0.000	0.000	0.000	0.000
8	A	8	THR	0	0.012	-0.022	16.661	0.012	0.012	0.000	0.000	0.000	0.000
9	A	9	LEU	0	-0.019	-0.001	19.536	0.008	0.008	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.786	-0.891	21.794	-0.375	-0.375	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.847	0.933	24.451	0.202	0.202	0.000	0.000	0.000	0.000
12	A	12	ARG	1	0.710	0.815	26.661	0.222	0.222	0.000	0.000	0.000	0.000
13	A	13	GLY	0	0.017	0.030	23.903	0.011	0.011	0.000	0.000	0.000	0.000
14	A	14	VAL	0	-0.030	-0.007	21.997	0.004	0.004	0.000	0.000	0.000	0.000
15	A	15	THR	0	-0.008	0.002	16.046	-0.029	-0.029	0.000	0.000	0.000	0.000
16	A	16	CYS	0	-0.068	0.001	16.841	0.021	0.021	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.980	0.994	9.179	0.916	0.916	0.000	0.000	0.000	0.000
18	A	18	ALA	0	0.021	0.007	11.877	0.097	0.097	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.025	-0.004	7.310	-0.336	-0.336	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.032	-0.018	8.397	0.397	0.397	0.000	0.000	0.000	0.000
21	A	21	LEU	0	-0.006	0.001	8.704	-0.296	-0.296	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.795	-0.905	6.223	-3.097	-3.097	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.907	-0.949	8.137	-0.149	-0.149	0.000	0.000	0.000	0.000
24	A	24	VAL	0	-0.025	-0.019	9.223	0.108	0.108	0.000	0.000	0.000	0.000
25	A	25	ALA	0	-0.026	-0.014	11.974	0.069	0.069	0.000	0.000	0.000	0.000
26	A	26	PRO	0	0.017	0.034	10.481	-0.144	-0.144	0.000	0.000	0.000	0.000
27	A	27	ARG	1	0.799	0.878	11.567	0.225	0.225	0.000	0.000	0.000	0.000
28	A	28	THR	0	-0.015	-0.038	14.635	0.002	0.002	0.000	0.000	0.000	0.000
29	A	29	SER	0	0.010	0.016	10.253	-0.054	-0.054	0.000	0.000	0.000	0.000
30	A	30	LYS	1	0.818	0.890	11.385	0.725	0.725	0.000	0.000	0.000	0.000
31	A	31	ALA	0	-0.009	0.004	12.321	0.012	0.012	0.000	0.000	0.000	0.000
32	A	32	VAL	0	0.035	0.013	14.018	0.040	0.040	0.000	0.000	0.000	0.000
33	A	33	TRP	0	-0.001	-0.005	6.349	-0.150	-0.150	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.855	-0.932	11.650	-0.981	-0.981	0.000	0.000	0.000	0.000
35	A	35	ALA	0	-0.017	0.003	13.325	0.080	0.080	0.000	0.000	0.000	0.000
36	A	36	LEU	0	-0.114	-0.002	11.679	0.063	0.063	0.000	0.000	0.000	0.000
37	A	37	PRO	0	-0.013	-0.029	15.006	-0.011	-0.011	0.000	0.000	0.000	0.000
38	A	38	GLN	0	-0.030	-0.022	16.793	0.088	0.088	0.000	0.000	0.000	0.000
39	A	39	SER	0	-0.028	-0.044	19.505	-0.007	-0.007	0.000	0.000	0.000	0.000
40	A	40	SER	0	-0.017	-0.008	22.109	0.031	0.031	0.000	0.000	0.000	0.000
41	A	41	GLN	0	-0.062	-0.031	25.593	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	42	VAL	0	-0.019	0.008	25.799	-0.009	-0.009	0.000	0.000	0.000	0.000
43	A	43	PHE	0	-0.005	-0.004	27.702	0.033	0.033	0.000	0.000	0.000	0.000
44	A	44	HIS	0	0.052	0.065	28.591	-0.021	-0.021	0.000	0.000	0.000	0.000
45	A	45	GLY	0	0.007	0.018	30.074	0.009	0.009	0.000	0.000	0.000	0.000
46	A	46	LYS	1	0.924	0.955	31.490	0.160	0.160	0.000	0.000	0.000	0.000
47	A	47	TYR	0	0.003	-0.009	31.407	0.012	0.012	0.000	0.000	0.000	0.000
48	A	48	ALA	0	0.001	0.019	29.612	0.008	0.008	0.000	0.000	0.000	0.000
49	A	49	ARG	1	0.861	0.924	30.404	0.139	0.139	0.000	0.000	0.000	0.000
50	A	50	ASN	0	-0.052	-0.007	28.508	0.004	0.004	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.854	-0.939	26.164	-0.286	-0.286	0.000	0.000	0.000	0.000
52	A	52	ILE	0	-0.001	0.003	23.367	0.023	0.023	0.000	0.000	0.000	0.000
53	A	53	TYR	0	0.056	0.058	24.297	-0.016	-0.016	0.000	0.000	0.000	0.000
54	A	54	ASN	0	-0.023	-0.007	21.610	0.017	0.017	0.000	0.000	0.000	0.000
55	A	55	LEU	0	0.009	-0.004	25.390	-0.004	-0.004	0.000	0.000	0.000	0.000
56	A	56	VAL	0	-0.015	0.001	22.233	0.013	0.013	0.000	0.000	0.000	0.000
57	A	57	PRO	0	0.000	-0.015	25.691	0.009	0.009	0.000	0.000	0.000	0.000
58	A	58	ALA	0	0.008	0.006	24.247	-0.026	-0.026	0.000	0.000	0.000	0.000
59	A	59	PHE	0	0.048	0.017	18.046	0.005	0.005	0.000	0.000	0.000	0.000
60	A	60	ALA	0	-0.012	0.013	19.572	-0.016	-0.016	0.000	0.000	0.000	0.000
61	A	61	PRO	0	-0.021	-0.017	19.578	0.039	0.039	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.922	0.950	21.148	0.288	0.288	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.777	-0.861	20.975	-0.406	-0.406	0.000	0.000	0.000	0.000
64	A	64	PRO	0	0.002	0.028	18.118	0.027	0.027	0.000	0.000	0.000	0.000
65	A	65	GLY	0	0.016	0.010	19.989	0.028	0.028	0.000	0.000	0.000	0.000
66	A	66	ALA	0	0.014	0.016	21.277	-0.029	-0.029	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.825	-0.910	15.401	-0.492	-0.492	0.000	0.000	0.000	0.000
68	A	68	ASN	0	-0.007	-0.010	16.567	0.031	0.031	0.000	0.000	0.000	0.000
69	A	69	THR	0	-0.025	-0.010	18.870	-0.015	-0.015	0.000	0.000	0.000	0.000
70	A	70	THR	0	0.043	0.038	22.209	0.033	0.033	0.000	0.000	0.000	0.000
71	A	71	VAL	0	0.019	0.000	24.440	-0.008	-0.008	0.000	0.000	0.000	0.000
72	A	72	THR	0	-0.055	-0.039	26.481	0.017	0.017	0.000	0.000	0.000	0.000
73	A	73	PRO	0	0.013	0.032	24.349	0.002	0.002	0.000	0.000	0.000	0.000
74	A	74	ILE	0	-0.041	-0.024	20.958	0.037	0.037	0.000	0.000	0.000	0.000
75	A	75	PRO	0	-0.045	-0.037	22.925	-0.022	-0.022	0.000	0.000	0.000	0.000
76	A	76	GLY	0	0.040	0.019	19.490	0.002	0.002	0.000	0.000	0.000	0.000
77	A	77	ASP	-1	-0.813	-0.888	18.179	-0.438	-0.438	0.000	0.000	0.000	0.000
78	A	78	VAL	0	-0.029	-0.015	16.110	0.016	0.016	0.000	0.000	0.000	0.000
79	A	79	CYS	0	-0.062	-0.037	18.371	-0.022	-0.022	0.000	0.000	0.000	0.000
80	A	80	TYR	0	-0.011	-0.025	18.779	-0.026	-0.026	0.000	0.000	0.000	0.000
81	A	81	PHE	0	0.001	0.001	21.344	0.027	0.027	0.000	0.000	0.000	0.000
82	A	82	THR	0	-0.026	-0.021	24.329	-0.014	-0.014	0.000	0.000	0.000	0.000
83	A	83	PHE	0	-0.005	-0.001	26.169	0.020	0.020	0.000	0.000	0.000	0.000
84	A	84	THR	0	-0.025	-0.020	29.886	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	85	SER	0	0.013	-0.029	32.718	-0.002	-0.002	0.000	0.000	0.000	0.000
86	A	86	ASN	0	-0.023	-0.012	35.154	0.008	0.008	0.000	0.000	0.000	0.000
87	A	87	ASP	-1	-0.813	-0.879	32.743	-0.180	-0.180	0.000	0.000	0.000	0.000
88	A	88	LEU	0	-0.008	-0.005	30.450	0.006	0.006	0.000	0.000	0.000	0.000
89	A	89	LYS	1	0.917	0.958	35.107	0.173	0.173	0.000	0.000	0.000	0.000
90	A	90	THR	0	0.048	0.018	38.218	0.006	0.006	0.000	0.000	0.000	0.000
91	A	91	PRO	0	0.004	-0.024	40.714	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	92	SER	0	-0.062	-0.041	40.041	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	93	HIS	1	0.922	0.979	33.965	0.172	0.172	0.000	0.000	0.000	0.000
94	A	94	GLY	0	-0.055	-0.017	37.966	-0.005	-0.005	0.000	0.000	0.000	0.000
95	A	95	TYR	0	-0.042	-0.039	31.891	0.006	0.006	0.000	0.000	0.000	0.000
96	A	104	VAL	0	-0.040	-0.031	36.093	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	105	GLN	0	-0.026	-0.009	31.740	-0.006	-0.006	0.000	0.000	0.000	0.000
98	A	106	THR	0	0.020	-0.001	27.187	0.012	0.012	0.000	0.000	0.000	0.000
99	A	107	ILE	0	-0.035	-0.009	27.763	-0.006	-0.006	0.000	0.000	0.000	0.000
100	A	108	VAL	0	0.019	0.016	21.550	0.008	0.008	0.000	0.000	0.000	0.000
101	A	109	ASP	-1	-0.887	-0.943	25.027	-0.313	-0.313	0.000	0.000	0.000	0.000
102	A	110	LEU	0	-0.027	-0.011	18.855	-0.030	-0.030	0.000	0.000	0.000	0.000
103	A	111	ALA	0	0.034	0.015	21.679	0.015	0.015	0.000	0.000	0.000	0.000
104	A	112	VAL	0	0.013	0.002	19.444	-0.047	-0.047	0.000	0.000	0.000	0.000
105	A	113	PHE	0	0.013	-0.003	21.847	0.050	0.050	0.000	0.000	0.000	0.000
106	A	114	TYR	0	0.017	-0.039	22.651	-0.016	-0.016	0.000	0.000	0.000	0.000
107	A	115	GLY	0	0.019	0.002	24.628	0.017	0.017	0.000	0.000	0.000	0.000
108	A	116	ARG	1	0.938	0.972	26.888	0.128	0.128	0.000	0.000	0.000	0.000
109	A	117	ASN	0	-0.039	-0.020	28.766	0.004	0.004	0.000	0.000	0.000	0.000
110	A	118	ASN	0	0.046	0.008	27.486	0.018	0.018	0.000	0.000	0.000	0.000
111	A	119	LEU	0	0.017	0.002	30.624	0.003	0.003	0.000	0.000	0.000	0.000
112	A	120	LEU	0	-0.004	0.022	26.204	0.002	0.002	0.000	0.000	0.000	0.000
113	A	121	LEU	0	-0.043	-0.016	30.714	0.005	0.005	0.000	0.000	0.000	0.000
114	A	122	ASN	0	0.022	0.005	34.197	0.009	0.009	0.000	0.000	0.000	0.000
115	A	123	GLY	0	0.009	-0.014	36.798	0.005	0.005	0.000	0.000	0.000	0.000
116	A	124	ASP	-1	-0.893	-0.903	37.531	-0.138	-0.138	0.000	0.000	0.000	0.000
117	A	125	THR	0	-0.041	-0.036	35.367	0.004	0.004	0.000	0.000	0.000	0.000
118	A	126	GLY	0	0.020	0.024	36.722	0.005	0.005	0.000	0.000	0.000	0.000
119	A	127	TRP	0	-0.013	-0.018	31.694	-0.008	-0.008	0.000	0.000	0.000	0.000
120	A	128	VAL	0	-0.012	-0.005	29.093	0.001	0.001	0.000	0.000	0.000	0.000
121	A	129	PRO	0	0.006	-0.015	26.279	-0.011	-0.011	0.000	0.000	0.000	0.000
122	A	130	GLY	0	0.035	0.035	24.006	-0.004	-0.004	0.000	0.000	0.000	0.000
123	A	131	ASN	0	-0.015	-0.036	18.778	0.056	0.056	0.000	0.000	0.000	0.000
124	A	132	VAL	0	0.030	0.014	17.102	-0.046	-0.046	0.000	0.000	0.000	0.000
125	A	133	PHE	0	0.002	-0.002	13.950	0.001	0.001	0.000	0.000	0.000	0.000
126	A	134	ALA	0	0.007	0.008	12.831	-0.209	-0.209	0.000	0.000	0.000	0.000
127	A	135	THR	0	0.017	0.013	13.032	0.163	0.163	0.000	0.000	0.000	0.000
128	A	136	ILE	0	-0.016	-0.027	13.666	-0.128	-0.128	0.000	0.000	0.000	0.000
129	A	137	VAL	0	-0.058	-0.029	11.184	0.056	0.056	0.000	0.000	0.000	0.000
130	A	138	GLU	-1	-0.943	-0.973	12.154	-0.557	-0.557	0.000	0.000	0.000	0.000
131	A	139	GLY	0	0.065	0.029	15.901	-0.046	-0.046	0.000	0.000	0.000	0.000
132	A	140	LEU	0	-0.005	-0.006	19.032	0.002	0.002	0.000	0.000	0.000	0.000
133	A	141	ASP	-1	-0.900	-0.946	20.611	-0.204	-0.204	0.000	0.000	0.000	0.000
134	A	142	GLU	-1	-0.870	-0.950	22.135	-0.250	-0.250	0.000	0.000	0.000	0.000
135	A	143	MET	0	-0.002	-0.002	19.782	0.022	0.022	0.000	0.000	0.000	0.000
136	A	144	ALA	0	0.013	0.003	22.970	0.012	0.012	0.000	0.000	0.000	0.000
137	A	145	ALA	0	-0.041	-0.012	25.697	0.016	0.016	0.000	0.000	0.000	0.000
138	A	146	ALA	0	0.025	0.005	25.435	0.014	0.014	0.000	0.000	0.000	0.000
139	A	147	CYS	0	-0.032	-0.016	24.933	0.001	0.001	0.000	0.000	0.000	0.000
140	A	148	GLN	0	0.014	0.003	27.904	0.017	0.017	0.000	0.000	0.000	0.000
141	A	149	ASP	-1	-0.833	-0.903	30.579	-0.162	-0.162	0.000	0.000	0.000	0.000
142	A	150	ILE	0	-0.035	-0.004	27.183	0.007	0.007	0.000	0.000	0.000	0.000
143	A	151	TRP	0	-0.096	-0.043	31.499	0.012	0.012	0.000	0.000	0.000	0.000
144	A	152	MET	0	-0.047	-0.024	33.744	0.010	0.010	0.000	0.000	0.000	0.000
145	A	153	GLY	0	0.008	0.006	34.829	0.009	0.009	0.000	0.000	0.000	0.000
146	A	154	GLY	0	-0.057	-0.016	34.908	0.003	0.003	0.000	0.000	0.000	0.000
147	A	155	ALA	0	0.035	0.001	31.170	-0.008	-0.008	0.000	0.000	0.000	0.000
148	A	156	ARG	1	0.911	0.958	31.936	0.144	0.144	0.000	0.000	0.000	0.000
149	A	157	ASP	-1	-0.907	-0.956	32.274	-0.169	-0.169	0.000	0.000	0.000	0.000
150	A	158	GLU	-1	-0.767	-0.864	26.773	-0.268	-0.268	0.000	0.000	0.000	0.000
151	A	159	THR	0	-0.027	-0.013	24.035	0.006	0.006	0.000	0.000	0.000	0.000
152	A	160	LEU	0	-0.010	0.007	20.966	-0.004	-0.004	0.000	0.000	0.000	0.000
153	A	161	THR	0	0.010	-0.014	17.992	0.003	0.003	0.000	0.000	0.000	0.000
154	A	162	PHE	0	0.002	0.017	15.512	-0.034	-0.034	0.000	0.000	0.000	0.000
155	A	163	SER	0	0.044	0.003	13.868	0.017	0.017	0.000	0.000	0.000	0.000
156	A	164	ARG	1	0.902	0.956	8.639	1.075	1.075	0.000	0.000	0.000	0.000
157	A	165	ALA	0	-0.030	0.001	7.891	0.232	0.232	0.000	0.000	0.000	0.000
158	A	166	GLU	-1	-0.976	-0.986	6.091	-1.460	-1.460	0.000	0.000	0.000	0.000

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