FMO DATABASE

FMODB ID: 9GYL2

Calculation Name: 4MQD-A-Xray322

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4MQD

Chain ID: A

ChEMBL ID:

UniProt ID: P12669

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:

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

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	134
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1223296.088549
FMO2-HF: Nuclear repulsion	1170035.394401
FMO2-HF: Total energy	-53260.694148
FMO2-MP2: Total energy	-53415.219532

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:ACE )

Summations of interaction energy for fragment #1(A:-1: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.
0.226	0.993	-0.005	-0.364	-0.397	0

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / q_NPA : -0.015

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	1	MET	0	-0.013	0.004	3.847	1.238	2.005	-0.005	-0.364	-0.397
4	A	2	ILE	0	0.052	0.040	6.269	0.118	0.118	0.000	0.000	0.000
5	A	3	LYS	1	0.878	0.952	9.028	0.387	0.387	0.000	0.000	0.000
6	A	4	SER	0	0.025	0.012	12.799	-0.019	-0.019	0.000	0.000	0.000
7	A	5	TRP	0	-0.021	-0.006	15.656	0.027	0.027	0.000	0.000	0.000
8	A	6	LYS	1	0.923	0.963	19.582	0.071	0.071	0.000	0.000	0.000
9	A	7	PRO	0	0.035	0.015	22.773	-0.006	-0.006	0.000	0.000	0.000
10	A	8	GLN	0	-0.034	-0.012	24.844	0.016	0.016	0.000	0.000	0.000
11	A	9	GLU	-1	-0.907	-0.944	27.402	-0.060	-0.060	0.000	0.000	0.000
12	A	10	LEU	0	-0.046	-0.034	29.685	0.000	0.000	0.000	0.000	0.000
13	A	11	SER	0	-0.059	-0.026	32.363	0.003	0.003	0.000	0.000	0.000
14	A	12	ILE	0	-0.021	0.003	31.628	-0.001	-0.001	0.000	0.000	0.000
15	A	13	SER	0	0.004	-0.008	35.602	0.006	0.006	0.000	0.000	0.000
16	A	14	TYR	0	-0.047	-0.039	37.426	-0.002	-0.002	0.000	0.000	0.000
17	A	15	HIS	0	0.037	0.011	36.586	-0.002	-0.002	0.000	0.000	0.000
18	A	16	GLN	0	0.059	0.046	33.370	-0.006	-0.006	0.000	0.000	0.000
19	A	17	PHE	0	-0.023	-0.003	26.328	0.004	0.004	0.000	0.000	0.000
20	A	18	THR	0	0.035	0.032	29.443	-0.005	-0.005	0.000	0.000	0.000
21	A	19	VAL	0	-0.003	0.007	22.981	0.001	0.001	0.000	0.000	0.000
22	A	20	PHE	0	-0.022	-0.012	26.425	0.001	0.001	0.000	0.000	0.000
23	A	21	GLN	0	0.053	0.010	23.870	-0.011	-0.011	0.000	0.000	0.000
24	A	22	LYS	1	0.885	0.955	24.108	0.133	0.133	0.000	0.000	0.000
25	A	23	ASP	-1	-0.903	-0.956	27.169	-0.086	-0.086	0.000	0.000	0.000
26	A	24	SER	0	-0.024	-0.016	29.785	0.002	0.002	0.000	0.000	0.000
27	A	25	THR	0	-0.018	-0.024	32.046	0.000	0.000	0.000	0.000	0.000
28	A	26	PRO	0	-0.019	0.015	31.656	0.003	0.003	0.000	0.000	0.000
29	A	27	PRO	0	0.010	0.002	33.914	0.004	0.004	0.000	0.000	0.000
30	A	28	VAL	0	-0.024	-0.018	35.409	-0.004	-0.004	0.000	0.000	0.000
31	A	29	MET	0	-0.036	-0.010	31.856	0.004	0.004	0.000	0.000	0.000
32	A	30	ASP	-1	-0.922	-0.968	36.640	-0.060	-0.060	0.000	0.000	0.000
33	A	31	TRP	0	-0.051	-0.013	31.868	-0.004	-0.004	0.000	0.000	0.000
34	A	32	THR	0	0.031	0.015	38.468	0.003	0.003	0.000	0.000	0.000
35	A	33	ASP	-1	-0.836	-0.933	38.800	-0.059	-0.059	0.000	0.000	0.000
36	A	34	GLU	-1	-0.991	-0.985	36.235	-0.076	-0.076	0.000	0.000	0.000
37	A	35	ALA	0	-0.018	-0.012	34.596	-0.005	-0.005	0.000	0.000	0.000
38	A	36	ILE	0	-0.017	-0.011	33.984	-0.006	-0.006	0.000	0.000	0.000
39	A	37	GLU	-1	-0.953	-0.967	34.641	-0.083	-0.083	0.000	0.000	0.000
40	A	38	LYS	1	0.927	0.970	31.066	0.089	0.089	0.000	0.000	0.000
41	A	39	GLY	0	0.017	0.017	30.086	-0.009	-0.009	0.000	0.000	0.000
42	A	40	TYR	0	-0.093	-0.066	28.266	-0.008	-0.008	0.000	0.000	0.000
43	A	41	ALA	0	0.045	0.027	30.324	0.006	0.006	0.000	0.000	0.000
44	A	42	ALA	0	-0.017	-0.004	28.422	-0.004	-0.004	0.000	0.000	0.000
45	A	43	ALA	0	0.007	-0.013	30.202	0.008	0.008	0.000	0.000	0.000
46	A	44	ASP	-1	-0.960	-0.968	30.651	-0.111	-0.111	0.000	0.000	0.000
47	A	45	GLY	0	0.061	0.044	27.015	-0.009	-0.009	0.000	0.000	0.000
48	A	46	ALA	0	-0.051	-0.030	26.898	-0.008	-0.008	0.000	0.000	0.000
49	A	47	ILE	0	0.010	0.005	23.785	0.003	0.003	0.000	0.000	0.000
50	A	48	SER	0	-0.015	-0.021	27.819	-0.002	-0.002	0.000	0.000	0.000
51	A	49	PHE	0	-0.004	-0.022	23.718	-0.003	-0.003	0.000	0.000	0.000
52	A	50	GLU	-1	-0.874	-0.940	29.488	-0.077	-0.077	0.000	0.000	0.000
53	A	51	ALA	0	-0.061	-0.033	31.136	-0.005	-0.005	0.000	0.000	0.000
54	A	52	GLN	0	0.007	-0.024	32.917	0.006	0.006	0.000	0.000	0.000
55	A	53	ARG	1	0.861	0.923	35.251	0.067	0.067	0.000	0.000	0.000
56	A	54	ASN	0	0.024	0.025	36.270	-0.006	-0.006	0.000	0.000	0.000
57	A	55	THR	0	0.004	-0.005	35.162	0.005	0.005	0.000	0.000	0.000
58	A	56	LYS	1	0.910	0.964	35.365	0.044	0.044	0.000	0.000	0.000
59	A	57	ALA	0	0.035	0.032	30.866	0.001	0.001	0.000	0.000	0.000
60	A	58	PHE	0	0.019	0.001	27.341	0.000	0.000	0.000	0.000	0.000
61	A	59	ILE	0	0.010	0.009	23.994	-0.006	-0.006	0.000	0.000	0.000
62	A	60	LEU	0	-0.012	-0.020	20.974	0.002	0.002	0.000	0.000	0.000
63	A	61	PHE	0	0.031	0.025	17.538	-0.014	-0.014	0.000	0.000	0.000
64	A	62	ARG	1	0.929	0.945	14.761	0.223	0.223	0.000	0.000	0.000
65	A	63	LEU	0	0.023	0.025	11.148	0.020	0.020	0.000	0.000	0.000
66	A	64	ASN	0	-0.014	-0.018	8.238	-0.040	-0.040	0.000	0.000	0.000
67	A	65	SER	0	-0.026	-0.002	9.193	-0.061	-0.061	0.000	0.000	0.000
68	A	66	SER	0	0.014	-0.002	9.297	-0.022	-0.022	0.000	0.000	0.000
69	A	67	GLU	-1	-0.991	-0.987	11.356	-0.079	-0.079	0.000	0.000	0.000
70	A	68	THR	0	-0.023	-0.017	14.655	-0.012	-0.012	0.000	0.000	0.000
71	A	69	VAL	0	0.011	0.008	17.342	0.013	0.013	0.000	0.000	0.000
72	A	70	ASN	0	-0.043	-0.034	20.586	0.006	0.006	0.000	0.000	0.000
73	A	71	SER	0	0.002	0.004	23.369	0.010	0.010	0.000	0.000	0.000
74	A	72	TYR	0	-0.030	-0.020	23.406	-0.011	-0.011	0.000	0.000	0.000
75	A	73	GLU	-1	-0.837	-0.913	27.203	-0.064	-0.064	0.000	0.000	0.000
76	A	74	LYS	1	0.872	0.932	28.130	0.100	0.100	0.000	0.000	0.000
77	A	75	LYS	1	0.934	0.979	19.305	0.196	0.196	0.000	0.000	0.000
78	A	76	VAL	0	-0.003	0.014	24.406	0.005	0.005	0.000	0.000	0.000
79	A	77	THR	0	-0.022	-0.019	19.380	-0.007	-0.007	0.000	0.000	0.000
80	A	78	VAL	0	-0.018	-0.009	21.636	0.014	0.014	0.000	0.000	0.000
81	A	79	PRO	0	-0.001	0.003	20.388	-0.023	-0.023	0.000	0.000	0.000
82	A	80	PHE	0	0.000	-0.007	20.030	0.024	0.024	0.000	0.000	0.000
83	A	81	HIS	0	-0.018	-0.020	19.548	-0.014	-0.014	0.000	0.000	0.000
84	A	82	VAL	0	-0.047	-0.004	18.808	0.022	0.022	0.000	0.000	0.000
85	A	83	THR	0	-0.021	-0.026	21.024	0.000	0.000	0.000	0.000	0.000
86	A	84	GLU	-1	-0.888	-0.966	23.048	-0.119	-0.119	0.000	0.000	0.000
87	A	85	ASN	0	-0.083	-0.045	18.259	-0.023	-0.023	0.000	0.000	0.000
88	A	86	GLY	0	-0.001	0.006	20.786	0.022	0.022	0.000	0.000	0.000
89	A	87	ILE	0	-0.016	0.004	20.867	0.002	0.002	0.000	0.000	0.000
90	A	88	HIS	0	-0.016	0.000	23.755	0.005	0.005	0.000	0.000	0.000
91	A	89	ILE	0	-0.002	-0.001	23.161	-0.008	-0.008	0.000	0.000	0.000
92	A	90	GLU	-1	-0.904	-0.949	27.465	-0.074	-0.074	0.000	0.000	0.000
93	A	91	SER	0	0.024	-0.002	31.182	-0.001	-0.001	0.000	0.000	0.000
94	A	92	ILE	0	0.012	0.005	34.030	0.002	0.002	0.000	0.000	0.000
95	A	93	MET	0	-0.025	-0.017	37.621	0.003	0.003	0.000	0.000	0.000
96	A	94	SER	0	0.002	0.024	33.762	0.001	0.001	0.000	0.000	0.000
97	A	95	LYS	1	0.937	0.957	32.935	0.067	0.067	0.000	0.000	0.000
98	A	96	ARG	1	0.963	0.994	30.266	0.083	0.083	0.000	0.000	0.000
99	A	97	LEU	0	-0.041	-0.014	26.685	0.002	0.002	0.000	0.000	0.000
100	A	98	SER	0	0.012	-0.015	25.612	0.001	0.001	0.000	0.000	0.000
101	A	99	PHE	0	-0.017	-0.017	20.260	0.003	0.003	0.000	0.000	0.000
102	A	100	ASP	-1	-0.939	-0.972	18.552	-0.183	-0.183	0.000	0.000	0.000
103	A	101	LEU	0	-0.005	0.006	15.411	-0.025	-0.025	0.000	0.000	0.000
104	A	102	PRO	0	0.037	0.007	13.400	0.035	0.035	0.000	0.000	0.000
105	A	103	LYS	1	0.941	0.988	16.619	0.164	0.164	0.000	0.000	0.000
106	A	104	GLY	0	0.010	0.011	16.252	-0.034	-0.034	0.000	0.000	0.000
107	A	105	ASP	-1	-0.842	-0.887	16.479	-0.234	-0.234	0.000	0.000	0.000
108	A	106	TYR	0	-0.022	-0.042	13.440	-0.103	-0.103	0.000	0.000	0.000
109	A	107	GLN	0	-0.010	-0.011	15.441	0.077	0.077	0.000	0.000	0.000
110	A	108	LEU	0	-0.017	-0.004	16.672	-0.031	-0.031	0.000	0.000	0.000
111	A	109	THR	0	-0.001	0.007	18.003	0.036	0.036	0.000	0.000	0.000
112	A	110	CYS	0	-0.045	-0.012	20.161	-0.002	-0.002	0.000	0.000	0.000
113	A	111	TRP	0	0.007	-0.010	17.095	0.009	0.009	0.000	0.000	0.000
114	A	112	THR	0	0.010	-0.005	24.038	0.004	0.004	0.000	0.000	0.000
115	A	113	VAL	0	0.008	-0.005	24.950	0.003	0.003	0.000	0.000	0.000
116	A	114	PRO	0	0.038	0.027	28.139	0.002	0.002	0.000	0.000	0.000
117	A	115	ALA	0	-0.002	-0.007	31.351	0.001	0.001	0.000	0.000	0.000
118	A	116	GLU	-1	-0.981	-0.980	32.943	-0.046	-0.046	0.000	0.000	0.000
119	A	117	MET	0	-0.054	-0.019	29.460	0.000	0.000	0.000	0.000	0.000
120	A	118	SER	0	-0.055	-0.037	28.124	-0.005	-0.005	0.000	0.000	0.000
121	A	119	ASP	-1	-0.910	-0.956	25.740	-0.066	-0.066	0.000	0.000	0.000
122	A	120	LEU	0	-0.051	-0.034	25.911	0.004	0.004	0.000	0.000	0.000
123	A	121	HIS	0	-0.065	-0.022	29.839	0.003	0.003	0.000	0.000	0.000
124	A	122	ALA	0	0.022	-0.004	31.733	0.003	0.003	0.000	0.000	0.000
125	A	123	ASP	-1	-0.806	-0.893	30.997	-0.072	-0.072	0.000	0.000	0.000
126	A	124	THR	0	-0.030	-0.009	25.348	-0.001	-0.001	0.000	0.000	0.000
127	A	125	TYR	0	0.045	0.027	25.987	-0.001	-0.001	0.000	0.000	0.000
128	A	126	ILE	0	-0.025	-0.002	19.579	-0.005	-0.005	0.000	0.000	0.000
129	A	127	ILE	0	0.009	-0.007	20.041	-0.002	-0.002	0.000	0.000	0.000
130	A	128	ASP	-1	-0.876	-0.942	14.102	-0.482	-0.482	0.000	0.000	0.000
131	A	129	ALA	0	0.000	0.004	15.453	0.013	0.013	0.000	0.000	0.000
132	A	130	VAL	0	0.012	0.003	10.897	-0.082	-0.082	0.000	0.000	0.000
133	A	131	SER	0	-0.013	-0.024	9.611	0.047	0.047	0.000	0.000	0.000
134	A	132	VAL	-1	-0.949	-0.962	11.249	-0.562	-0.562	0.000	0.000	0.000

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