FMO DATABASE

FMODB ID: 3QL6L

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	OptHSide
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	-1539656.147933
FMO2-HF: Nuclear repulsion	1478431.443525
FMO2-HF: Total energy	-61224.704408
FMO2-MP2: Total energy	-61402.303898

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.
-7.41	-3.443	1.521	-2.261	-3.228	-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 : -0.045 / 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	0.818	0.887	2.614	-4.080	-0.328	1.522	-2.241	-3.033	-0.021
4	A	4	TYR	0	0.050	0.012	4.328	0.925	1.140	-0.001	-0.020	-0.195	0.000
5	A	5	ILE	0	-0.006	-0.002	7.121	-0.034	-0.034	0.000	0.000	0.000	0.000
6	A	6	ASN	0	0.003	0.005	10.265	0.075	0.075	0.000	0.000	0.000	0.000
7	A	7	ILE	0	-0.007	-0.012	13.195	0.007	0.007	0.000	0.000	0.000	0.000
8	A	8	THR	0	0.031	0.018	16.625	0.020	0.020	0.000	0.000	0.000	0.000
9	A	9	LEU	0	0.000	0.018	19.521	0.006	0.006	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.808	-0.884	21.628	-0.337	-0.337	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.753	0.870	24.437	0.174	0.174	0.000	0.000	0.000	0.000
12	A	12	ARG	1	0.725	0.824	26.722	0.195	0.195	0.000	0.000	0.000	0.000
13	A	13	GLY	0	0.005	0.025	23.940	0.009	0.009	0.000	0.000	0.000	0.000
14	A	14	VAL	0	-0.035	-0.010	22.113	0.003	0.003	0.000	0.000	0.000	0.000
15	A	15	THR	0	-0.009	-0.029	16.085	-0.005	-0.005	0.000	0.000	0.000	0.000
16	A	16	CYS	0	-0.094	-0.018	16.892	0.020	0.020	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.888	0.913	9.235	0.714	0.714	0.000	0.000	0.000	0.000
18	A	18	ALA	0	0.023	0.009	11.861	0.092	0.092	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.020	0.002	7.488	-0.320	-0.320	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.032	-0.018	8.056	0.373	0.373	0.000	0.000	0.000	0.000
21	A	21	LEU	0	0.004	0.005	8.766	-0.230	-0.230	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.797	-0.896	6.303	-2.685	-2.685	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.901	-0.945	8.150	-0.013	-0.013	0.000	0.000	0.000	0.000
24	A	24	VAL	0	-0.035	-0.023	9.244	0.064	0.064	0.000	0.000	0.000	0.000
25	A	25	ALA	0	-0.019	-0.010	12.022	0.047	0.047	0.000	0.000	0.000	0.000
26	A	26	PRO	0	0.027	0.038	10.460	-0.134	-0.134	0.000	0.000	0.000	0.000
27	A	27	ARG	1	0.758	0.857	11.621	0.175	0.175	0.000	0.000	0.000	0.000
28	A	28	THR	0	-0.026	-0.049	14.698	-0.005	-0.005	0.000	0.000	0.000	0.000
29	A	29	SER	0	0.016	0.019	10.344	-0.051	-0.051	0.000	0.000	0.000	0.000
30	A	30	LYS	1	0.813	0.881	11.351	0.677	0.677	0.000	0.000	0.000	0.000
31	A	31	ALA	0	-0.006	0.004	12.327	0.008	0.008	0.000	0.000	0.000	0.000
32	A	32	VAL	0	0.032	0.012	13.878	0.035	0.035	0.000	0.000	0.000	0.000
33	A	33	TRP	0	0.013	0.007	5.715	-0.158	-0.158	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.848	-0.914	11.396	-0.873	-0.873	0.000	0.000	0.000	0.000
35	A	35	ALA	0	-0.013	-0.002	13.068	0.074	0.074	0.000	0.000	0.000	0.000
36	A	36	LEU	0	-0.105	0.010	11.592	0.062	0.062	0.000	0.000	0.000	0.000
37	A	37	PRO	0	-0.011	-0.029	14.667	-0.009	-0.009	0.000	0.000	0.000	0.000
38	A	38	GLN	0	-0.032	-0.023	16.509	0.079	0.079	0.000	0.000	0.000	0.000
39	A	39	SER	0	-0.021	-0.026	19.342	-0.007	-0.007	0.000	0.000	0.000	0.000
40	A	40	SER	0	-0.034	-0.017	21.980	0.029	0.029	0.000	0.000	0.000	0.000
41	A	41	GLN	0	-0.063	-0.037	25.469	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	42	VAL	0	-0.010	0.014	25.692	-0.008	-0.008	0.000	0.000	0.000	0.000
43	A	43	PHE	0	-0.016	-0.007	27.610	0.030	0.030	0.000	0.000	0.000	0.000
44	A	44	HIS	0	0.059	0.042	28.500	-0.019	-0.019	0.000	0.000	0.000	0.000
45	A	45	GLY	0	0.019	0.023	29.988	0.008	0.008	0.000	0.000	0.000	0.000
46	A	46	LYS	1	0.862	0.919	31.393	0.145	0.145	0.000	0.000	0.000	0.000
47	A	47	TYR	0	0.013	-0.009	31.226	0.012	0.012	0.000	0.000	0.000	0.000
48	A	48	ALA	0	0.001	0.023	29.491	0.007	0.007	0.000	0.000	0.000	0.000
49	A	49	ARG	1	0.842	0.915	30.319	0.119	0.119	0.000	0.000	0.000	0.000
50	A	50	ASN	0	-0.065	-0.012	28.510	0.004	0.004	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.842	-0.934	26.178	-0.239	-0.239	0.000	0.000	0.000	0.000
52	A	52	ILE	0	-0.002	0.001	23.361	0.020	0.020	0.000	0.000	0.000	0.000
53	A	53	TYR	0	0.044	0.030	24.185	-0.015	-0.015	0.000	0.000	0.000	0.000
54	A	54	ASN	0	-0.031	-0.017	21.596	0.014	0.014	0.000	0.000	0.000	0.000
55	A	55	LEU	0	0.011	0.006	25.232	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	56	VAL	0	0.000	0.004	21.984	0.012	0.012	0.000	0.000	0.000	0.000
57	A	57	PRO	0	-0.005	-0.014	25.487	0.009	0.009	0.000	0.000	0.000	0.000
58	A	58	ALA	0	0.008	0.005	23.965	-0.023	-0.023	0.000	0.000	0.000	0.000
59	A	59	PHE	0	0.051	0.015	17.806	0.003	0.003	0.000	0.000	0.000	0.000
60	A	60	ALA	0	-0.013	0.013	19.272	-0.014	-0.014	0.000	0.000	0.000	0.000
61	A	61	PRO	0	-0.011	-0.013	19.281	0.035	0.035	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.923	0.954	21.226	0.255	0.255	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.771	-0.854	21.048	-0.351	-0.351	0.000	0.000	0.000	0.000
64	A	64	PRO	0	-0.003	0.023	18.156	0.025	0.025	0.000	0.000	0.000	0.000
65	A	65	GLY	0	0.019	0.017	20.055	0.027	0.027	0.000	0.000	0.000	0.000
66	A	66	ALA	0	0.028	0.021	21.338	-0.026	-0.026	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.802	-0.892	15.676	-0.407	-0.407	0.000	0.000	0.000	0.000
68	A	68	ASN	0	-0.008	-0.003	16.424	0.027	0.027	0.000	0.000	0.000	0.000
69	A	69	THR	0	-0.001	0.005	18.912	-0.015	-0.015	0.000	0.000	0.000	0.000
70	A	70	THR	0	0.009	0.013	22.258	0.030	0.030	0.000	0.000	0.000	0.000
71	A	71	VAL	0	0.028	0.006	24.488	-0.008	-0.008	0.000	0.000	0.000	0.000
72	A	72	THR	0	-0.053	-0.033	26.598	0.014	0.014	0.000	0.000	0.000	0.000
73	A	73	PRO	0	0.016	0.033	24.408	0.003	0.003	0.000	0.000	0.000	0.000
74	A	74	ILE	0	-0.046	-0.025	20.965	0.031	0.031	0.000	0.000	0.000	0.000
75	A	75	PRO	0	-0.038	-0.034	23.025	-0.020	-0.020	0.000	0.000	0.000	0.000
76	A	76	GLY	0	0.036	0.017	19.603	0.003	0.003	0.000	0.000	0.000	0.000
77	A	77	ASP	-1	-0.809	-0.887	18.140	-0.375	-0.375	0.000	0.000	0.000	0.000
78	A	78	VAL	0	-0.030	-0.019	15.881	0.013	0.013	0.000	0.000	0.000	0.000
79	A	79	CYS	0	-0.062	-0.026	18.235	-0.008	-0.008	0.000	0.000	0.000	0.000
80	A	80	TYR	0	-0.015	-0.030	18.671	-0.025	-0.025	0.000	0.000	0.000	0.000
81	A	81	PHE	0	-0.007	0.000	21.214	0.024	0.024	0.000	0.000	0.000	0.000
82	A	82	THR	0	-0.031	-0.026	24.308	-0.011	-0.011	0.000	0.000	0.000	0.000
83	A	83	PHE	0	-0.008	-0.005	26.192	0.019	0.019	0.000	0.000	0.000	0.000
84	A	84	THR	0	-0.027	-0.041	29.674	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	85	SER	0	0.030	-0.014	32.423	-0.002	-0.002	0.000	0.000	0.000	0.000
86	A	86	ASN	0	-0.020	-0.007	34.880	0.005	0.005	0.000	0.000	0.000	0.000
87	A	87	ASP	-1	-0.809	-0.864	33.152	-0.154	-0.154	0.000	0.000	0.000	0.000
88	A	88	LEU	0	0.003	0.007	30.257	0.005	0.005	0.000	0.000	0.000	0.000
89	A	89	LYS	1	0.854	0.920	34.915	0.159	0.159	0.000	0.000	0.000	0.000
90	A	90	THR	0	0.032	0.012	38.019	0.005	0.005	0.000	0.000	0.000	0.000
91	A	91	PRO	0	0.019	-0.014	40.531	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	92	SER	0	-0.057	-0.056	40.279	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	93	HIS	1	0.904	0.971	33.899	0.147	0.147	0.000	0.000	0.000	0.000
94	A	94	GLY	0	-0.025	0.002	37.826	-0.005	-0.005	0.000	0.000	0.000	0.000
95	A	95	TYR	0	-0.036	-0.018	31.895	0.005	0.005	0.000	0.000	0.000	0.000
96	A	104	VAL	0	-0.034	-0.027	35.815	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	105	GLN	0	0.001	0.004	31.399	0.004	0.004	0.000	0.000	0.000	0.000
98	A	106	THR	0	0.033	0.003	26.979	0.010	0.010	0.000	0.000	0.000	0.000
99	A	107	ILE	0	-0.053	-0.023	27.521	-0.005	-0.005	0.000	0.000	0.000	0.000
100	A	108	VAL	0	0.028	0.020	21.303	0.007	0.007	0.000	0.000	0.000	0.000
101	A	109	ASP	-1	-0.886	-0.941	24.761	-0.272	-0.272	0.000	0.000	0.000	0.000
102	A	110	LEU	0	-0.022	-0.006	18.535	-0.025	-0.025	0.000	0.000	0.000	0.000
103	A	111	ALA	0	0.031	0.005	21.492	0.015	0.015	0.000	0.000	0.000	0.000
104	A	112	VAL	0	0.014	0.009	19.242	-0.041	-0.041	0.000	0.000	0.000	0.000
105	A	113	PHE	0	0.020	-0.002	21.769	0.043	0.043	0.000	0.000	0.000	0.000
106	A	114	TYR	0	0.022	-0.016	22.619	-0.014	-0.014	0.000	0.000	0.000	0.000
107	A	115	GLY	0	0.021	0.006	24.615	0.015	0.015	0.000	0.000	0.000	0.000
108	A	116	ARG	1	0.932	0.965	26.901	0.107	0.107	0.000	0.000	0.000	0.000
109	A	117	ASN	0	-0.030	-0.017	28.877	0.003	0.003	0.000	0.000	0.000	0.000
110	A	118	ASN	0	0.058	0.021	27.380	0.016	0.016	0.000	0.000	0.000	0.000
111	A	119	LEU	0	0.015	0.002	30.664	0.004	0.004	0.000	0.000	0.000	0.000
112	A	120	LEU	0	-0.007	0.022	26.253	0.001	0.001	0.000	0.000	0.000	0.000
113	A	121	LEU	0	-0.043	-0.017	30.774	0.005	0.005	0.000	0.000	0.000	0.000
114	A	122	ASN	0	0.027	0.006	34.220	0.008	0.008	0.000	0.000	0.000	0.000
115	A	123	GLY	0	0.020	-0.007	36.862	0.004	0.004	0.000	0.000	0.000	0.000
116	A	124	ASP	-1	-0.886	-0.883	37.588	-0.120	-0.120	0.000	0.000	0.000	0.000
117	A	125	THR	0	-0.035	-0.037	35.571	0.002	0.002	0.000	0.000	0.000	0.000
118	A	126	GLY	0	0.016	0.028	36.781	0.004	0.004	0.000	0.000	0.000	0.000
119	A	127	TRP	0	-0.017	-0.018	31.760	-0.007	-0.007	0.000	0.000	0.000	0.000
120	A	128	VAL	0	-0.007	-0.005	29.104	0.001	0.001	0.000	0.000	0.000	0.000
121	A	129	PRO	0	0.011	-0.012	26.297	-0.010	-0.010	0.000	0.000	0.000	0.000
122	A	130	GLY	0	0.037	0.031	24.070	-0.005	-0.005	0.000	0.000	0.000	0.000
123	A	131	ASN	0	-0.026	-0.041	18.852	0.052	0.052	0.000	0.000	0.000	0.000
124	A	132	VAL	0	0.028	0.013	17.321	-0.043	-0.043	0.000	0.000	0.000	0.000
125	A	133	PHE	0	-0.001	-0.011	13.784	0.004	0.004	0.000	0.000	0.000	0.000
126	A	134	ALA	0	0.002	0.005	12.829	-0.183	-0.183	0.000	0.000	0.000	0.000
127	A	135	THR	0	0.017	0.016	13.210	0.141	0.141	0.000	0.000	0.000	0.000
128	A	136	ILE	0	-0.020	-0.025	13.707	-0.117	-0.117	0.000	0.000	0.000	0.000
129	A	137	VAL	0	-0.047	-0.025	11.247	0.055	0.055	0.000	0.000	0.000	0.000
130	A	138	GLU	-1	-0.861	-0.908	11.965	-0.590	-0.590	0.000	0.000	0.000	0.000
131	A	139	GLY	0	0.074	0.035	16.016	-0.041	-0.041	0.000	0.000	0.000	0.000
132	A	140	LEU	0	-0.004	-0.004	19.133	0.003	0.003	0.000	0.000	0.000	0.000
133	A	141	ASP	-1	-0.909	-0.952	20.674	-0.183	-0.183	0.000	0.000	0.000	0.000
134	A	142	GLU	-1	-0.864	-0.944	22.180	-0.228	-0.228	0.000	0.000	0.000	0.000
135	A	143	MET	0	0.004	0.001	19.917	0.019	0.019	0.000	0.000	0.000	0.000
136	A	144	ALA	0	0.011	0.002	23.013	0.012	0.012	0.000	0.000	0.000	0.000
137	A	145	ALA	0	-0.039	-0.013	25.727	0.015	0.015	0.000	0.000	0.000	0.000
138	A	146	ALA	0	0.029	0.011	25.439	0.013	0.013	0.000	0.000	0.000	0.000
139	A	147	CYS	0	-0.041	-0.021	25.005	0.000	0.000	0.000	0.000	0.000	0.000
140	A	148	GLN	0	0.004	-0.004	27.898	0.017	0.017	0.000	0.000	0.000	0.000
141	A	149	ASP	-1	-0.825	-0.896	30.592	-0.143	-0.143	0.000	0.000	0.000	0.000
142	A	150	ILE	0	-0.023	-0.001	27.238	0.006	0.006	0.000	0.000	0.000	0.000
143	A	151	TRP	0	-0.108	-0.049	31.479	0.012	0.012	0.000	0.000	0.000	0.000
144	A	152	MET	0	-0.043	-0.021	33.717	0.009	0.009	0.000	0.000	0.000	0.000
145	A	153	GLY	0	0.005	0.007	34.808	0.008	0.008	0.000	0.000	0.000	0.000
146	A	154	GLY	0	-0.056	-0.013	34.873	0.002	0.002	0.000	0.000	0.000	0.000
147	A	155	ALA	0	0.046	0.004	31.121	-0.007	-0.007	0.000	0.000	0.000	0.000
148	A	156	ARG	1	0.931	0.974	31.873	0.125	0.125	0.000	0.000	0.000	0.000
149	A	157	ASP	-1	-0.834	-0.915	32.144	-0.146	-0.146	0.000	0.000	0.000	0.000
150	A	158	GLU	-1	-0.761	-0.860	26.818	-0.236	-0.236	0.000	0.000	0.000	0.000
151	A	159	THR	0	-0.040	-0.018	23.895	0.004	0.004	0.000	0.000	0.000	0.000
152	A	160	LEU	0	-0.005	0.011	20.936	-0.003	-0.003	0.000	0.000	0.000	0.000
153	A	161	THR	0	0.003	-0.047	17.949	0.001	0.001	0.000	0.000	0.000	0.000
154	A	162	PHE	0	-0.005	0.011	15.427	-0.031	-0.031	0.000	0.000	0.000	0.000
155	A	163	SER	0	0.040	-0.004	13.770	0.028	0.028	0.000	0.000	0.000	0.000
156	A	164	ARG	1	0.875	0.935	8.419	0.949	0.949	0.000	0.000	0.000	0.000
157	A	165	ALA	0	-0.019	0.003	7.917	0.219	0.219	0.000	0.000	0.000	0.000
158	A	166	GLU	-1	-0.981	-0.986	6.299	-1.304	-1.304	0.000	0.000	0.000	0.000

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