FMO DATABASE

FMODB ID: N29JQ

Calculation Name: 5GKM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5GKM

Chain ID: A

ChEMBL ID:

UniProt ID: Q94C10

Base Structure: X-ray

Registration Date: 2023-09-26

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	158
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1539445.574634
FMO2-HF: Nuclear repulsion	1477920.838562
FMO2-HF: Total energy	-61524.736072
FMO2-MP2: Total energy	-61702.307269

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:75:LEU)

Summations of interaction energy for fragment #1(A:75:LEU)

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.
-6.624	-3.847	13.334	-4.96	-11.149	-0.025

Interaction energy analysis for fragmet #1(A:75:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / 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	77	SER	0	-0.019	-0.026	3.852	-1.359	0.003	-0.018	-0.551	-0.793	0.001
4	A	78	MET	0	-0.037	0.011	2.216	0.268	-2.339	9.599	-1.901	-5.091	-0.005
5	A	79	VAL	0	0.025	0.002	4.271	-0.163	0.016	0.000	-0.052	-0.127	0.000
6	A	80	PHE	0	-0.019	-0.022	3.340	-0.241	0.335	0.018	-0.096	-0.498	0.000
7	A	81	GLU	-1	-0.883	-0.905	2.025	-2.990	-1.536	2.376	-1.613	-2.217	0.001
8	A	82	ARG	1	0.908	0.924	2.406	-1.946	-0.893	1.331	-0.641	-1.743	-0.022
9	A	83	PHE	0	0.001	0.011	4.617	0.621	0.742	-0.001	-0.009	-0.111	0.000
10	A	84	THR	0	0.002	-0.003	4.945	-0.611	-0.477	-0.001	-0.003	-0.129	0.000
11	A	85	GLU	-1	-0.813	-0.914	6.462	-0.324	-0.324	0.000	0.000	0.000	0.000
12	A	86	ARG	1	0.865	0.917	7.468	0.244	0.244	0.000	0.000	0.000	0.000
13	A	87	ALA	0	-0.020	-0.009	8.408	0.052	0.052	0.000	0.000	0.000	0.000
14	A	88	ILE	0	0.015	0.010	3.371	-0.401	0.104	0.030	-0.094	-0.440	0.000
15	A	89	ARG	1	0.762	0.865	6.637	0.328	0.328	0.000	0.000	0.000	0.000
16	A	90	ALA	0	0.026	0.011	9.195	0.054	0.054	0.000	0.000	0.000	0.000
17	A	91	ILE	0	-0.015	0.008	8.199	0.053	0.053	0.000	0.000	0.000	0.000
18	A	92	ILE	0	0.032	0.038	6.117	0.063	0.063	0.000	0.000	0.000	0.000
19	A	93	PHE	0	-0.055	-0.045	10.220	0.047	0.047	0.000	0.000	0.000	0.000
20	A	94	SER	0	-0.023	-0.042	12.820	0.022	0.022	0.000	0.000	0.000	0.000
21	A	95	GLN	0	0.002	0.014	10.441	0.021	0.021	0.000	0.000	0.000	0.000
22	A	96	LYS	1	0.903	0.951	14.030	0.142	0.142	0.000	0.000	0.000	0.000
23	A	97	GLU	-1	-0.766	-0.860	16.440	-0.112	-0.112	0.000	0.000	0.000	0.000
24	A	98	ALA	0	0.029	0.030	17.906	0.013	0.013	0.000	0.000	0.000	0.000
25	A	99	LYS	1	0.813	0.896	18.252	0.131	0.131	0.000	0.000	0.000	0.000
26	A	100	SER	0	-0.098	-0.077	20.175	0.013	0.013	0.000	0.000	0.000	0.000
27	A	101	LEU	0	0.039	0.039	22.566	0.007	0.007	0.000	0.000	0.000	0.000
28	A	102	GLY	0	-0.010	0.001	23.882	0.004	0.004	0.000	0.000	0.000	0.000
29	A	103	LYS	1	0.785	0.880	21.370	0.107	0.107	0.000	0.000	0.000	0.000
30	A	104	ASP	-1	-0.822	-0.928	20.176	-0.123	-0.123	0.000	0.000	0.000	0.000
31	A	105	MET	0	-0.004	0.018	17.941	-0.009	-0.009	0.000	0.000	0.000	0.000
32	A	106	VAL	0	0.007	0.018	14.417	0.011	0.011	0.000	0.000	0.000	0.000
33	A	107	TYR	0	0.002	-0.012	17.452	-0.017	-0.017	0.000	0.000	0.000	0.000
34	A	108	THR	0	0.006	-0.026	18.968	-0.009	-0.009	0.000	0.000	0.000	0.000
35	A	109	GLN	0	0.019	-0.006	20.147	-0.016	-0.016	0.000	0.000	0.000	0.000
36	A	110	HIS	0	0.045	0.024	18.501	-0.006	-0.006	0.000	0.000	0.000	0.000
37	A	111	LEU	0	0.000	-0.002	14.016	-0.008	-0.008	0.000	0.000	0.000	0.000
38	A	112	LEU	0	-0.023	-0.005	17.046	-0.007	-0.007	0.000	0.000	0.000	0.000
39	A	113	LEU	0	-0.008	-0.001	19.521	0.004	0.004	0.000	0.000	0.000	0.000
40	A	114	GLY	0	0.017	0.010	15.282	0.009	0.009	0.000	0.000	0.000	0.000
41	A	115	LEU	0	-0.029	-0.023	14.588	-0.005	-0.005	0.000	0.000	0.000	0.000
42	A	116	ILE	0	-0.043	-0.018	16.585	0.013	0.013	0.000	0.000	0.000	0.000
43	A	117	ALA	0	-0.014	-0.005	16.969	0.012	0.012	0.000	0.000	0.000	0.000
44	A	118	GLU	-1	-0.804	-0.900	12.498	-0.215	-0.215	0.000	0.000	0.000	0.000
45	A	119	ASP	-1	-0.820	-0.878	15.750	-0.123	-0.123	0.000	0.000	0.000	0.000
46	A	120	ARG	1	0.944	0.973	13.721	0.097	0.097	0.000	0.000	0.000	0.000
47	A	121	ASP	-1	-0.822	-0.880	20.021	-0.060	-0.060	0.000	0.000	0.000	0.000
48	A	122	PRO	0	-0.020	-0.010	22.813	0.000	0.000	0.000	0.000	0.000	0.000
49	A	123	GLN	0	-0.028	-0.019	26.065	0.002	0.002	0.000	0.000	0.000	0.000
50	A	124	GLY	0	0.029	0.026	25.027	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	125	PHE	0	0.000	-0.004	19.008	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	126	LEU	0	-0.024	0.000	20.331	0.003	0.003	0.000	0.000	0.000	0.000
53	A	127	GLY	0	0.019	0.016	23.572	0.006	0.006	0.000	0.000	0.000	0.000
54	A	128	SER	0	-0.092	-0.079	25.964	0.008	0.008	0.000	0.000	0.000	0.000
55	A	129	GLY	0	0.016	0.012	27.993	0.003	0.003	0.000	0.000	0.000	0.000
56	A	130	ILE	0	-0.063	-0.021	25.076	0.002	0.002	0.000	0.000	0.000	0.000
57	A	131	THR	0	0.026	0.000	25.100	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	132	ILE	0	0.038	0.000	20.740	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	133	ASP	-1	-0.855	-0.916	23.892	-0.076	-0.076	0.000	0.000	0.000	0.000
60	A	134	LYS	1	0.845	0.905	26.931	0.061	0.061	0.000	0.000	0.000	0.000
61	A	135	ALA	0	0.010	0.007	24.328	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	136	ARG	1	0.799	0.847	20.676	0.098	0.098	0.000	0.000	0.000	0.000
63	A	137	GLU	-1	-0.825	-0.885	25.919	-0.063	-0.063	0.000	0.000	0.000	0.000
64	A	138	ALA	0	-0.020	-0.007	28.455	0.002	0.002	0.000	0.000	0.000	0.000
65	A	139	VAL	0	-0.023	-0.022	24.175	0.000	0.000	0.000	0.000	0.000	0.000
66	A	140	TRP	0	0.018	0.006	27.435	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	141	SER	0	0.014	0.018	29.146	0.003	0.003	0.000	0.000	0.000	0.000
68	A	142	ILE	0	-0.139	-0.082	29.493	0.003	0.003	0.000	0.000	0.000	0.000
69	A	143	TRP	0	-0.040	-0.047	27.085	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	144	ASP	-1	-0.838	-0.898	28.392	-0.099	-0.099	0.000	0.000	0.000	0.000
71	A	145	GLU	-1	-0.892	-0.911	31.633	-0.058	-0.058	0.000	0.000	0.000	0.000
72	A	146	ALA	0	-0.042	-0.022	34.928	0.004	0.004	0.000	0.000	0.000	0.000
73	A	147	ASN	0	-0.064	-0.016	35.684	0.001	0.001	0.000	0.000	0.000	0.000
74	A	148	SER	0	0.077	0.045	31.194	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	149	ASP	-1	-0.813	-0.905	28.685	-0.115	-0.115	0.000	0.000	0.000	0.000
76	A	150	SER	0	0.028	0.003	29.859	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	151	LYS	1	0.780	0.894	27.649	0.126	0.126	0.000	0.000	0.000	0.000
78	A	152	GLN	0	-0.092	-0.029	24.563	-0.007	-0.007	0.000	0.000	0.000	0.000
79	A	153	GLU	-1	-0.892	-0.942	26.355	-0.094	-0.094	0.000	0.000	0.000	0.000
80	A	154	GLU	-1	-0.806	-0.870	21.338	-0.198	-0.198	0.000	0.000	0.000	0.000
81	A	155	ALA	0	0.030	0.024	24.244	0.003	0.003	0.000	0.000	0.000	0.000
82	A	156	SER	0	-0.032	-0.019	19.978	-0.011	-0.011	0.000	0.000	0.000	0.000
83	A	157	SER	0	0.012	-0.009	19.934	0.013	0.013	0.000	0.000	0.000	0.000
84	A	158	THR	0	-0.069	-0.034	17.989	-0.015	-0.015	0.000	0.000	0.000	0.000
85	A	159	SER	0	0.029	0.004	19.357	0.006	0.006	0.000	0.000	0.000	0.000
86	A	160	TYR	0	-0.001	-0.015	15.880	0.000	0.000	0.000	0.000	0.000	0.000
87	A	161	SER	0	0.032	0.019	16.256	0.008	0.008	0.000	0.000	0.000	0.000
88	A	162	LYS	1	0.815	0.880	10.540	0.149	0.149	0.000	0.000	0.000	0.000
89	A	163	SER	0	0.032	0.006	14.475	-0.010	-0.010	0.000	0.000	0.000	0.000
90	A	164	THR	0	0.001	-0.010	9.017	0.001	0.001	0.000	0.000	0.000	0.000
91	A	165	ASP	-1	-0.862	-0.886	10.190	-0.209	-0.209	0.000	0.000	0.000	0.000
92	A	166	MET	0	-0.070	-0.028	12.475	-0.004	-0.004	0.000	0.000	0.000	0.000
93	A	167	PRO	0	0.031	0.064	13.027	-0.038	-0.038	0.000	0.000	0.000	0.000
94	A	168	PHE	0	0.000	-0.017	9.860	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	169	SER	0	0.053	0.024	15.116	-0.009	-0.009	0.000	0.000	0.000	0.000
96	A	170	ILE	0	-0.011	-0.020	17.529	-0.030	-0.030	0.000	0.000	0.000	0.000
97	A	171	SER	0	0.006	-0.020	19.146	-0.018	-0.018	0.000	0.000	0.000	0.000
98	A	172	THR	0	0.027	0.012	14.420	-0.007	-0.007	0.000	0.000	0.000	0.000
99	A	173	LYS	1	0.910	0.956	13.827	0.339	0.339	0.000	0.000	0.000	0.000
100	A	174	ARG	1	0.934	0.978	15.557	0.171	0.171	0.000	0.000	0.000	0.000
101	A	175	VAL	0	-0.002	0.004	16.107	-0.006	-0.006	0.000	0.000	0.000	0.000
102	A	176	PHE	0	-0.032	-0.022	11.231	-0.025	-0.025	0.000	0.000	0.000	0.000
103	A	177	GLU	-1	-0.781	-0.875	13.555	-0.533	-0.533	0.000	0.000	0.000	0.000
104	A	178	ALA	0	0.032	0.014	15.189	0.008	0.008	0.000	0.000	0.000	0.000
105	A	179	ALA	0	-0.041	-0.009	13.632	0.017	0.017	0.000	0.000	0.000	0.000
106	A	180	VAL	0	-0.021	-0.025	10.661	-0.003	-0.003	0.000	0.000	0.000	0.000
107	A	181	GLU	-1	-0.922	-0.961	13.238	-0.229	-0.229	0.000	0.000	0.000	0.000
108	A	182	TYR	0	-0.013	-0.016	16.649	0.042	0.042	0.000	0.000	0.000	0.000
109	A	183	SER	0	-0.044	-0.041	12.105	0.050	0.050	0.000	0.000	0.000	0.000
110	A	184	ARG	1	0.860	0.918	12.937	0.446	0.446	0.000	0.000	0.000	0.000
111	A	185	THR	0	-0.049	-0.021	15.709	0.040	0.040	0.000	0.000	0.000	0.000
112	A	186	MET	0	-0.122	-0.064	17.445	0.017	0.017	0.000	0.000	0.000	0.000
113	A	187	ASP	-1	-0.937	-0.946	16.889	-0.039	-0.039	0.000	0.000	0.000	0.000
114	A	188	CYS	0	-0.051	-0.022	12.525	0.042	0.042	0.000	0.000	0.000	0.000
115	A	189	GLN	0	0.030	0.024	10.519	0.009	0.009	0.000	0.000	0.000	0.000
116	A	190	TYR	0	-0.012	-0.011	8.341	-0.016	-0.016	0.000	0.000	0.000	0.000
117	A	191	ILE	0	0.052	0.051	8.105	0.085	0.085	0.000	0.000	0.000	0.000
118	A	192	ALA	0	-0.027	-0.019	9.380	-0.141	-0.141	0.000	0.000	0.000	0.000
119	A	193	PRO	0	0.044	0.005	11.792	-0.011	-0.011	0.000	0.000	0.000	0.000
120	A	194	GLU	-1	-0.776	-0.869	13.904	-0.209	-0.209	0.000	0.000	0.000	0.000
121	A	195	HIS	0	0.071	0.041	13.719	-0.030	-0.030	0.000	0.000	0.000	0.000
122	A	196	ILE	0	-0.010	-0.014	10.964	0.005	0.005	0.000	0.000	0.000	0.000
123	A	197	ALA	0	-0.017	-0.001	15.514	0.024	0.024	0.000	0.000	0.000	0.000
124	A	198	VAL	0	0.003	0.004	18.835	0.019	0.019	0.000	0.000	0.000	0.000
125	A	199	GLY	0	0.047	0.040	18.591	0.016	0.016	0.000	0.000	0.000	0.000
126	A	200	LEU	0	-0.028	-0.011	18.779	0.016	0.016	0.000	0.000	0.000	0.000
127	A	201	PHE	0	-0.017	-0.039	20.414	0.015	0.015	0.000	0.000	0.000	0.000
128	A	202	THR	0	-0.034	-0.028	22.596	0.012	0.012	0.000	0.000	0.000	0.000
129	A	203	VAL	0	-0.031	-0.004	20.521	0.010	0.010	0.000	0.000	0.000	0.000
130	A	204	ASP	-1	-0.781	-0.883	21.995	-0.180	-0.180	0.000	0.000	0.000	0.000
131	A	205	ASP	-1	-0.813	-0.883	23.305	-0.150	-0.150	0.000	0.000	0.000	0.000
132	A	206	GLY	0	-0.007	-0.002	25.922	0.013	0.013	0.000	0.000	0.000	0.000
133	A	207	SER	0	-0.092	-0.077	24.180	0.013	0.013	0.000	0.000	0.000	0.000
134	A	208	ALA	0	0.026	0.002	23.023	0.008	0.008	0.000	0.000	0.000	0.000
135	A	209	GLY	0	0.065	0.022	24.987	0.008	0.008	0.000	0.000	0.000	0.000
136	A	210	ARG	1	0.847	0.929	28.428	0.114	0.114	0.000	0.000	0.000	0.000
137	A	211	VAL	0	0.032	0.016	25.386	0.007	0.007	0.000	0.000	0.000	0.000
138	A	212	LEU	0	0.008	0.003	25.476	0.007	0.007	0.000	0.000	0.000	0.000
139	A	213	LYS	1	0.948	0.977	28.964	0.081	0.081	0.000	0.000	0.000	0.000
140	A	214	ARG	1	0.869	0.935	31.261	0.080	0.080	0.000	0.000	0.000	0.000
141	A	215	LEU	0	-0.026	-0.024	27.215	0.004	0.004	0.000	0.000	0.000	0.000
142	A	216	GLY	0	-0.007	0.022	31.687	0.003	0.003	0.000	0.000	0.000	0.000
143	A	217	ALA	0	-0.012	0.007	29.423	0.002	0.002	0.000	0.000	0.000	0.000
144	A	218	ASN	0	-0.009	-0.024	31.216	-0.006	-0.006	0.000	0.000	0.000	0.000
145	A	219	MET	0	0.068	0.041	26.409	-0.003	-0.003	0.000	0.000	0.000	0.000
146	A	220	ASN	0	0.025	0.008	27.454	-0.012	-0.012	0.000	0.000	0.000	0.000
147	A	221	LEU	0	0.003	-0.001	28.624	-0.001	-0.001	0.000	0.000	0.000	0.000
148	A	222	LEU	0	0.024	0.023	24.868	0.001	0.001	0.000	0.000	0.000	0.000
149	A	223	THR	0	0.004	-0.005	23.547	-0.012	-0.012	0.000	0.000	0.000	0.000
150	A	224	ALA	0	-0.007	0.002	24.051	-0.004	-0.004	0.000	0.000	0.000	0.000
151	A	225	ALA	0	0.035	0.024	25.355	0.003	0.003	0.000	0.000	0.000	0.000
152	A	226	ALA	0	-0.003	0.002	20.165	0.001	0.001	0.000	0.000	0.000	0.000
153	A	227	LEU	0	0.015	-0.002	20.744	-0.003	-0.003	0.000	0.000	0.000	0.000
154	A	228	THR	0	-0.060	-0.043	22.339	0.011	0.011	0.000	0.000	0.000	0.000
155	A	229	ARG	1	0.735	0.820	19.089	0.137	0.137	0.000	0.000	0.000	0.000
156	A	230	LEU	0	-0.058	-0.025	15.727	0.007	0.007	0.000	0.000	0.000	0.000
157	A	231	LYS	1	0.912	0.976	19.176	0.081	0.081	0.000	0.000	0.000	0.000
158	A	232	GLY	0	-0.003	0.019	21.076	0.015	0.015	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:75:LEU)