FMO DATABASE

FMODB ID: 39Q8L

Calculation Name: 3K7U-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3K7U

Chain ID: C

ChEMBL ID:

UniProt ID: Q38B90

Base Structure: X-ray

Registration Date: 2023-06-21

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	OptHSide
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	103
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-745484.561626
FMO2-HF: Nuclear repulsion	705081.612047
FMO2-HF: Total energy	-40402.949579
FMO2-MP2: Total energy	-40521.167105

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(C:21:SER)

Summations of interaction energy for fragment #1(C:21:SER)

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.
-20.202	-12.555	4.174	-5.456	-6.365	0.026

Interaction energy analysis for fragmet #1(C:21:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.038 / q_NPA : 0.013

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

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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	C	23	ASN	0	-0.028	-0.017	2.233	-8.777	-4.490	2.365	-3.317	-3.336	0.031
4	C	24	SER	0	0.004	-0.001	2.373	-4.839	-2.504	1.793	-1.673	-2.455	-0.008
5	C	25	VAL	0	-0.017	0.003	3.594	0.718	0.881	0.009	-0.072	-0.100	0.000
6	C	26	THR	0	0.017	-0.012	7.207	-0.158	-0.158	0.000	0.000	0.000	0.000
7	C	27	LEU	0	-0.026	0.004	9.739	0.077	0.077	0.000	0.000	0.000	0.000
8	C	28	VAL	0	0.024	-0.002	13.224	0.021	0.021	0.000	0.000	0.000	0.000
9	C	29	GLY	0	0.033	0.013	16.449	0.006	0.006	0.000	0.000	0.000	0.000
10	C	30	VAL	0	-0.060	-0.023	19.429	0.010	0.010	0.000	0.000	0.000	0.000
11	C	31	VAL	0	-0.003	0.009	19.712	0.003	0.003	0.000	0.000	0.000	0.000
12	C	32	HIS	1	0.854	0.909	21.974	0.043	0.043	0.000	0.000	0.000	0.000
13	C	33	ASP	-1	-0.873	-0.936	23.161	0.011	0.011	0.000	0.000	0.000	0.000
14	C	34	ILE	0	-0.027	-0.004	22.344	0.012	0.012	0.000	0.000	0.000	0.000
15	C	35	GLN	0	-0.042	-0.020	23.181	0.000	0.000	0.000	0.000	0.000	0.000
16	C	36	SER	0	-0.002	-0.024	22.988	0.009	0.009	0.000	0.000	0.000	0.000
17	C	37	GLY	0	0.009	0.006	23.577	-0.013	-0.013	0.000	0.000	0.000	0.000
18	C	38	PHE	0	0.045	0.031	23.249	0.010	0.010	0.000	0.000	0.000	0.000
19	C	39	VAL	0	-0.053	-0.008	18.755	-0.013	-0.013	0.000	0.000	0.000	0.000
20	C	40	TYR	0	-0.047	-0.031	20.409	-0.009	-0.009	0.000	0.000	0.000	0.000
21	C	41	GLU	-1	-0.881	-0.940	22.861	0.200	0.200	0.000	0.000	0.000	0.000
22	C	42	ASP	-1	-0.960	-0.975	18.893	0.404	0.404	0.000	0.000	0.000	0.000
23	C	43	ALA	0	0.009	0.005	21.185	-0.021	-0.021	0.000	0.000	0.000	0.000
24	C	44	VAL	0	-0.038	-0.030	17.415	0.033	0.033	0.000	0.000	0.000	0.000
25	C	45	THR	0	-0.049	-0.032	18.979	-0.029	-0.029	0.000	0.000	0.000	0.000
26	C	46	GLN	0	0.010	0.009	18.302	0.033	0.033	0.000	0.000	0.000	0.000
27	C	47	PHE	0	-0.015	-0.015	16.228	-0.011	-0.011	0.000	0.000	0.000	0.000
28	C	48	THR	0	0.037	0.028	18.706	0.006	0.006	0.000	0.000	0.000	0.000
29	C	49	LEU	0	-0.049	-0.023	14.974	-0.004	-0.004	0.000	0.000	0.000	0.000
30	C	50	THR	0	-0.018	-0.020	18.576	-0.007	-0.007	0.000	0.000	0.000	0.000
31	C	51	THR	0	0.039	0.026	16.114	-0.010	-0.010	0.000	0.000	0.000	0.000
32	C	52	THR	0	-0.059	-0.051	19.559	0.029	0.029	0.000	0.000	0.000	0.000
33	C	53	SER	0	0.020	0.008	20.451	-0.020	-0.020	0.000	0.000	0.000	0.000
34	C	54	ILE	0	-0.023	-0.008	22.861	0.014	0.014	0.000	0.000	0.000	0.000
35	C	66	GLU	-1	-0.892	-0.918	20.745	-0.212	-0.212	0.000	0.000	0.000	0.000
36	C	67	LYS	1	0.839	0.903	22.929	0.103	0.103	0.000	0.000	0.000	0.000
37	C	68	ASP	-1	-0.857	-0.911	18.799	-0.134	-0.134	0.000	0.000	0.000	0.000
38	C	69	HIS	0	0.007	-0.011	20.012	-0.013	-0.013	0.000	0.000	0.000	0.000
39	C	70	HIS	0	0.029	0.024	15.194	0.038	0.038	0.000	0.000	0.000	0.000
40	C	71	THR	0	0.018	0.011	16.727	0.005	0.005	0.000	0.000	0.000	0.000
41	C	72	ILE	0	-0.012	-0.004	13.244	0.018	0.018	0.000	0.000	0.000	0.000
42	C	73	ARG	1	0.876	0.938	14.015	-0.202	-0.202	0.000	0.000	0.000	0.000
43	C	74	CYS	0	-0.024	0.005	13.599	0.039	0.039	0.000	0.000	0.000	0.000
44	C	75	PHE	0	0.045	0.003	13.493	-0.009	-0.009	0.000	0.000	0.000	0.000
45	C	76	GLY	0	0.050	0.022	15.876	0.027	0.027	0.000	0.000	0.000	0.000
46	C	77	GLU	-1	-0.907	-0.943	18.243	0.189	0.189	0.000	0.000	0.000	0.000
47	C	78	LEU	0	0.039	0.017	20.822	-0.023	-0.023	0.000	0.000	0.000	0.000
48	C	79	PHE	0	-0.005	0.010	13.917	-0.020	-0.020	0.000	0.000	0.000	0.000
49	C	80	SER	0	-0.018	-0.023	18.784	-0.043	-0.043	0.000	0.000	0.000	0.000
50	C	81	ALA	0	0.043	0.035	19.939	-0.031	-0.031	0.000	0.000	0.000	0.000
51	C	82	GLU	-1	-0.907	-0.970	19.695	0.171	0.171	0.000	0.000	0.000	0.000
52	C	83	VAL	0	-0.026	-0.027	17.295	-0.027	-0.027	0.000	0.000	0.000	0.000
53	C	84	LYS	1	0.891	0.942	20.704	-0.088	-0.088	0.000	0.000	0.000	0.000
54	C	85	GLN	0	-0.064	-0.032	23.770	-0.021	-0.021	0.000	0.000	0.000	0.000
55	C	86	LYS	1	0.894	0.942	23.646	-0.066	-0.066	0.000	0.000	0.000	0.000
56	C	87	VAL	0	0.011	0.031	19.698	-0.015	-0.015	0.000	0.000	0.000	0.000
57	C	88	LYS	1	0.915	0.947	23.154	0.007	0.007	0.000	0.000	0.000	0.000
58	C	89	GLU	-1	-0.760	-0.866	24.799	-0.019	-0.019	0.000	0.000	0.000	0.000
59	C	90	GLY	0	-0.010	-0.010	25.562	-0.001	-0.001	0.000	0.000	0.000	0.000
60	C	91	ASN	0	-0.055	-0.025	23.035	0.000	0.000	0.000	0.000	0.000	0.000
61	C	92	VAL	0	0.071	0.040	20.780	-0.003	-0.003	0.000	0.000	0.000	0.000
62	C	93	VAL	0	-0.010	-0.013	16.864	0.012	0.012	0.000	0.000	0.000	0.000
63	C	94	CYS	0	0.007	0.008	12.691	-0.044	-0.044	0.000	0.000	0.000	0.000
64	C	95	VAL	0	-0.034	-0.010	10.755	0.055	0.055	0.000	0.000	0.000	0.000
65	C	96	ASN	0	0.029	0.022	7.198	-0.312	-0.312	0.000	0.000	0.000	0.000
66	C	97	GLY	0	0.056	0.010	6.811	0.301	0.301	0.000	0.000	0.000	0.000
67	C	98	ARG	1	0.846	0.938	3.476	-7.562	-6.700	0.007	-0.394	-0.474	0.003
68	C	99	LEU	0	0.061	0.020	6.118	-0.029	-0.029	0.000	0.000	0.000	0.000
69	C	100	ARG	1	0.858	0.939	8.851	-0.575	-0.575	0.000	0.000	0.000	0.000
70	C	101	LEU	0	0.062	0.025	11.456	-0.111	-0.111	0.000	0.000	0.000	0.000
71	C	102	SER	0	-0.036	-0.016	14.832	0.044	0.044	0.000	0.000	0.000	0.000
72	C	103	PRO	0	0.029	-0.001	17.612	-0.029	-0.029	0.000	0.000	0.000	0.000
73	C	104	GLN	0	-0.011	-0.014	20.649	-0.031	-0.031	0.000	0.000	0.000	0.000
74	C	105	LEU	0	-0.021	-0.023	23.456	-0.004	-0.004	0.000	0.000	0.000	0.000
75	C	106	GLU	-1	-0.879	-0.916	26.307	0.094	0.094	0.000	0.000	0.000	0.000
76	C	107	PRO	0	-0.132	-0.032	26.612	-0.002	-0.002	0.000	0.000	0.000	0.000
77	C	108	SER	0	0.122	0.109	29.555	-0.011	-0.011	0.000	0.000	0.000	0.000
78	C	109	CYS	0	0.027	-0.045	31.652	-0.005	-0.005	0.000	0.000	0.000	0.000
79	C	110	ASN	0	-0.054	-0.041	31.631	0.002	0.002	0.000	0.000	0.000	0.000
80	C	111	LYS	1	0.948	0.977	30.075	-0.107	-0.107	0.000	0.000	0.000	0.000
81	C	112	HIS	0	-0.032	-0.018	25.220	0.017	0.017	0.000	0.000	0.000	0.000
82	C	113	PHE	0	0.048	0.020	22.508	-0.004	-0.004	0.000	0.000	0.000	0.000
83	C	114	TYR	0	-0.003	-0.004	19.054	0.002	0.002	0.000	0.000	0.000	0.000
84	C	115	PHE	0	0.018	0.009	18.111	0.021	0.021	0.000	0.000	0.000	0.000
85	C	116	PRO	0	-0.013	0.006	15.270	0.044	0.044	0.000	0.000	0.000	0.000
86	C	117	TYR	0	0.011	-0.007	13.266	0.008	0.008	0.000	0.000	0.000	0.000
87	C	118	ILE	0	0.009	0.003	9.034	0.068	0.068	0.000	0.000	0.000	0.000
88	C	119	GLN	0	0.002	0.022	9.260	0.068	0.068	0.000	0.000	0.000	0.000
89	C	120	VAL	0	0.003	-0.001	8.692	0.010	0.010	0.000	0.000	0.000	0.000
90	C	121	GLN	0	0.017	-0.011	9.795	0.082	0.082	0.000	0.000	0.000	0.000
91	C	122	PRO	0	0.026	0.067	10.112	0.142	0.142	0.000	0.000	0.000	0.000
92	C	123	PRO	0	0.011	-0.029	9.652	0.029	0.029	0.000	0.000	0.000	0.000
93	C	124	HIS	0	0.010	0.007	5.945	0.761	0.761	0.000	0.000	0.000	0.000
94	C	125	GLY	0	0.003	0.001	6.568	-0.501	-0.501	0.000	0.000	0.000	0.000
95	C	126	GLN	0	-0.032	-0.021	8.528	0.070	0.070	0.000	0.000	0.000	0.000
96	C	127	VAL	0	0.015	-0.002	11.727	-0.104	-0.104	0.000	0.000	0.000	0.000
97	C	128	ALA	0	0.018	0.022	14.603	0.040	0.040	0.000	0.000	0.000	0.000
98	C	129	VAL	0	0.018	0.002	16.762	-0.026	-0.026	0.000	0.000	0.000	0.000
99	C	130	ILE	0	-0.011	0.004	18.329	0.000	0.000	0.000	0.000	0.000	0.000
100	C	131	HIS	0	-0.018	-0.022	22.035	0.013	0.013	0.000	0.000	0.000	0.000
101	C	132	GLY	0	0.047	0.025	25.737	-0.006	-0.006	0.000	0.000	0.000	0.000
102	C	133	ASP	-1	-0.877	-0.923	28.715	-0.066	-0.066	0.000	0.000	0.000	0.000
103	C	134	ARG	1	0.817	0.906	30.600	0.046	0.046	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:21:SER)