FMO DATABASE

FMODB ID: 2NM5R

Calculation Name: 3C9G-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3C9G

Chain ID: A

ChEMBL ID:

UniProt ID: O28876

Base Structure: X-ray

Registration Date: 2023-09-23

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	OptAll
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	131
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1221613.999128
FMO2-HF: Nuclear repulsion	1169363.259398
FMO2-HF: Total energy	-52250.73973
FMO2-MP2: Total energy	-52406.722418

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:187:LYS)

Summations of interaction energy for fragment #1(A:187:LYS)

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.
12.349	15.974	0.91	-1.931	-2.604	0.003

Interaction energy analysis for fragmet #1(A:187:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.982 / q_NPA : 0.971

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	189	VAL	0	0.030	0.027	3.872	6.171	8.458	-0.023	-1.229	-1.036	-0.001
4	A	190	GLU	-1	-0.776	-0.857	7.425	-31.354	-31.354	0.000	0.000	0.000	0.000
5	A	191	ILE	0	-0.028	0.006	9.692	2.068	2.068	0.000	0.000	0.000	0.000
6	A	192	GLU	-1	-0.786	-0.880	13.282	-19.223	-19.223	0.000	0.000	0.000	0.000
7	A	193	ILE	0	-0.020	-0.010	15.807	1.061	1.061	0.000	0.000	0.000	0.000
8	A	194	ARG	1	0.793	0.873	19.114	12.641	12.641	0.000	0.000	0.000	0.000
9	A	195	THR	0	-0.033	-0.030	22.375	0.286	0.286	0.000	0.000	0.000	0.000
10	A	196	LYS	1	0.869	0.927	26.093	10.191	10.191	0.000	0.000	0.000	0.000
11	A	197	ILE	0	-0.022	0.005	28.301	-0.014	-0.014	0.000	0.000	0.000	0.000
12	A	198	HIS	0	0.036	0.029	31.468	-0.003	-0.003	0.000	0.000	0.000	0.000
13	A	199	PRO	0	0.042	0.003	35.017	-0.020	-0.020	0.000	0.000	0.000	0.000
14	A	200	THR	0	0.001	0.012	37.819	0.134	0.134	0.000	0.000	0.000	0.000
15	A	201	GLU	-1	-0.813	-0.890	32.884	-9.813	-9.813	0.000	0.000	0.000	0.000
16	A	202	SER	0	0.005	-0.003	33.767	0.033	0.033	0.000	0.000	0.000	0.000
17	A	203	GLU	-1	-0.818	-0.921	28.626	-10.987	-10.987	0.000	0.000	0.000	0.000
18	A	204	ASP	-1	-0.775	-0.866	28.702	-10.547	-10.547	0.000	0.000	0.000	0.000
19	A	205	LYS	1	0.825	0.894	28.546	9.091	9.091	0.000	0.000	0.000	0.000
20	A	206	VAL	0	0.047	0.036	26.541	-0.221	-0.221	0.000	0.000	0.000	0.000
21	A	207	LEU	0	0.038	0.009	23.927	-0.511	-0.511	0.000	0.000	0.000	0.000
22	A	208	LYS	1	0.840	0.905	23.660	9.994	9.994	0.000	0.000	0.000	0.000
23	A	209	ALA	0	-0.016	-0.005	24.749	-0.332	-0.332	0.000	0.000	0.000	0.000
24	A	210	ILE	0	0.002	0.007	19.996	-0.346	-0.346	0.000	0.000	0.000	0.000
25	A	211	ARG	1	0.873	0.924	19.095	14.781	14.781	0.000	0.000	0.000	0.000
26	A	212	ASN	0	-0.067	-0.036	20.800	-0.418	-0.418	0.000	0.000	0.000	0.000
27	A	213	ILE	0	-0.084	-0.041	19.272	0.045	0.045	0.000	0.000	0.000	0.000
28	A	214	PHE	0	0.014	-0.013	15.054	-0.802	-0.802	0.000	0.000	0.000	0.000
29	A	215	PRO	0	0.025	0.012	16.444	0.133	0.133	0.000	0.000	0.000	0.000
30	A	216	ASP	-1	-0.793	-0.902	11.948	-23.631	-23.631	0.000	0.000	0.000	0.000
31	A	217	ALA	0	-0.033	-0.008	14.438	-0.763	-0.763	0.000	0.000	0.000	0.000
32	A	218	GLU	-1	-0.850	-0.916	15.261	-16.188	-16.188	0.000	0.000	0.000	0.000
33	A	219	ILE	0	-0.113	-0.070	16.933	-0.057	-0.057	0.000	0.000	0.000	0.000
34	A	220	GLU	-1	-0.914	-0.941	20.312	-14.737	-14.737	0.000	0.000	0.000	0.000
35	A	221	ILE	0	-0.040	-0.050	22.826	-0.023	-0.023	0.000	0.000	0.000	0.000
36	A	222	SER	0	-0.036	-0.027	26.401	-0.015	-0.015	0.000	0.000	0.000	0.000
37	A	223	GLU	-1	-0.919	-0.963	28.926	-9.102	-9.102	0.000	0.000	0.000	0.000
38	A	224	GLU	-1	-0.861	-0.913	30.341	-10.139	-10.139	0.000	0.000	0.000	0.000
39	A	225	GLY	0	0.006	0.014	31.174	0.182	0.182	0.000	0.000	0.000	0.000
40	A	226	GLU	-1	-0.818	-0.877	27.327	-11.093	-11.093	0.000	0.000	0.000	0.000
41	A	227	VAL	0	-0.004	-0.001	23.311	-0.214	-0.214	0.000	0.000	0.000	0.000
42	A	228	TYR	0	0.019	0.000	20.970	-0.234	-0.234	0.000	0.000	0.000	0.000
43	A	229	GLY	0	0.060	0.026	18.426	0.214	0.214	0.000	0.000	0.000	0.000
44	A	230	ARG	1	0.765	0.870	12.527	20.613	20.613	0.000	0.000	0.000	0.000
45	A	231	ALA	0	0.017	0.021	12.671	0.402	0.402	0.000	0.000	0.000	0.000
46	A	232	TYR	0	-0.065	-0.067	7.442	-2.031	-2.031	0.000	0.000	0.000	0.000
47	A	233	SER	0	-0.074	-0.036	9.157	-1.329	-1.329	0.000	0.000	0.000	0.000
48	A	234	LEU	0	0.028	-0.007	10.275	1.734	1.734	0.000	0.000	0.000	0.000
49	A	235	ASP	-1	-0.897	-0.930	12.244	-23.327	-23.327	0.000	0.000	0.000	0.000
50	A	236	ARG	1	0.888	0.948	15.036	15.527	15.527	0.000	0.000	0.000	0.000
51	A	237	PHE	0	0.078	0.027	16.644	1.002	1.002	0.000	0.000	0.000	0.000
52	A	238	ARG	1	0.818	0.898	14.191	21.447	21.447	0.000	0.000	0.000	0.000
53	A	239	GLU	-1	-0.832	-0.897	18.590	-13.785	-13.785	0.000	0.000	0.000	0.000
54	A	240	LEU	0	-0.034	-0.003	20.991	0.803	0.803	0.000	0.000	0.000	0.000
55	A	241	LEU	0	0.021	0.014	19.571	0.679	0.679	0.000	0.000	0.000	0.000
56	A	242	ARG	0	-0.016	0.016	17.708	-0.140	-0.140	0.000	0.000	0.000	0.000
57	A	243	LYS	1	0.821	0.884	23.607	13.713	13.713	0.000	0.000	0.000	0.000
58	A	244	GLN	0	-0.006	0.000	26.485	0.551	0.551	0.000	0.000	0.000	0.000
59	A	245	ARG	1	0.933	0.960	27.562	11.216	11.216	0.000	0.000	0.000	0.000
60	A	246	ILE	0	0.008	0.029	26.033	0.154	0.154	0.000	0.000	0.000	0.000
61	A	247	LEU	0	0.021	0.004	21.673	-0.516	-0.516	0.000	0.000	0.000	0.000
62	A	248	ASP	-1	-0.817	-0.908	23.559	-11.313	-11.313	0.000	0.000	0.000	0.000
63	A	249	THR	0	0.014	0.010	25.564	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	250	ALA	0	0.014	0.022	21.166	-0.142	-0.142	0.000	0.000	0.000	0.000
65	A	251	ARG	1	0.730	0.828	18.632	13.289	13.289	0.000	0.000	0.000	0.000
66	A	252	SER	0	-0.013	-0.027	21.502	-0.099	-0.099	0.000	0.000	0.000	0.000
67	A	253	GLU	-1	-0.822	-0.885	22.907	-11.475	-11.475	0.000	0.000	0.000	0.000
68	A	254	ILE	0	-0.029	-0.026	16.526	-0.344	-0.344	0.000	0.000	0.000	0.000
69	A	255	LEU	0	-0.055	-0.031	18.708	-0.432	-0.432	0.000	0.000	0.000	0.000
70	A	256	LYS	1	0.821	0.890	20.823	11.022	11.022	0.000	0.000	0.000	0.000
71	A	257	GLY	0	0.081	0.051	20.987	0.299	0.299	0.000	0.000	0.000	0.000
72	A	258	ARG	1	0.841	0.929	16.105	14.434	14.434	0.000	0.000	0.000	0.000
73	A	259	ASN	0	0.015	0.017	17.395	1.055	1.055	0.000	0.000	0.000	0.000
74	A	260	GLY	0	0.031	0.003	16.180	0.355	0.355	0.000	0.000	0.000	0.000
75	A	261	LYS	1	0.778	0.909	8.251	21.906	21.906	0.000	0.000	0.000	0.000
76	A	262	GLU	-1	-0.851	-0.939	11.363	-18.486	-18.486	0.000	0.000	0.000	0.000
77	A	263	VAL	0	-0.030	-0.009	13.993	0.791	0.791	0.000	0.000	0.000	0.000
78	A	264	THR	0	-0.027	-0.012	16.392	-0.834	-0.834	0.000	0.000	0.000	0.000
79	A	265	ILE	0	0.011	0.006	19.231	0.523	0.523	0.000	0.000	0.000	0.000
80	A	266	TYR	0	-0.020	-0.044	21.602	-0.540	-0.540	0.000	0.000	0.000	0.000
81	A	267	LEU	0	-0.009	-0.002	21.594	0.207	0.207	0.000	0.000	0.000	0.000
82	A	268	ASN	0	0.052	0.009	25.732	0.054	0.054	0.000	0.000	0.000	0.000
83	A	269	LYS	1	0.838	0.917	27.486	10.316	10.316	0.000	0.000	0.000	0.000
84	A	270	GLN	0	0.023	0.014	28.513	-0.027	-0.027	0.000	0.000	0.000	0.000
85	A	271	THR	0	-0.037	-0.014	29.205	0.169	0.169	0.000	0.000	0.000	0.000
86	A	272	ALA	0	0.029	0.025	25.366	-0.060	-0.060	0.000	0.000	0.000	0.000
87	A	273	THR	0	-0.009	-0.011	26.869	-0.242	-0.242	0.000	0.000	0.000	0.000
88	A	274	VAL	0	-0.040	-0.017	29.310	0.058	0.058	0.000	0.000	0.000	0.000
89	A	275	SER	0	-0.063	-0.034	25.056	-0.029	-0.029	0.000	0.000	0.000	0.000
90	A	276	ARG	1	0.971	0.996	26.057	9.495	9.495	0.000	0.000	0.000	0.000
91	A	277	ILE	0	0.010	0.013	23.148	-0.020	-0.020	0.000	0.000	0.000	0.000
92	A	278	ASN	0	-0.023	-0.019	26.418	0.273	0.273	0.000	0.000	0.000	0.000
93	A	279	PHE	0	0.035	0.008	21.813	-0.128	-0.128	0.000	0.000	0.000	0.000
94	A	280	CYS	0	-0.083	-0.036	26.965	0.359	0.359	0.000	0.000	0.000	0.000
95	A	281	ASP	-1	-0.850	-0.917	27.891	-9.922	-9.922	0.000	0.000	0.000	0.000
96	A	282	GLU	-1	-0.872	-0.921	26.924	-10.938	-10.938	0.000	0.000	0.000	0.000
97	A	283	ASN	0	-0.038	-0.020	29.224	0.067	0.067	0.000	0.000	0.000	0.000
98	A	284	ALA	0	-0.005	0.008	31.527	0.270	0.270	0.000	0.000	0.000	0.000
99	A	285	VAL	0	0.027	-0.005	33.359	-0.113	-0.113	0.000	0.000	0.000	0.000
100	A	286	LEU	0	-0.051	-0.019	34.469	-0.110	-0.110	0.000	0.000	0.000	0.000
101	A	287	SER	0	0.049	0.000	29.903	-0.271	-0.271	0.000	0.000	0.000	0.000
102	A	288	PRO	0	0.016	0.027	27.446	-0.183	-0.183	0.000	0.000	0.000	0.000
103	A	289	ILE	0	-0.009	0.002	22.055	-0.134	-0.134	0.000	0.000	0.000	0.000
104	A	290	LYS	1	0.912	0.958	18.967	15.097	15.097	0.000	0.000	0.000	0.000
105	A	291	VAL	0	-0.024	-0.006	16.997	-0.558	-0.558	0.000	0.000	0.000	0.000
106	A	292	THR	0	0.036	0.024	14.887	0.816	0.816	0.000	0.000	0.000	0.000
107	A	293	PHE	0	0.008	0.015	12.305	-1.244	-1.244	0.000	0.000	0.000	0.000
108	A	294	ARG	1	0.859	0.905	8.720	24.433	24.433	0.000	0.000	0.000	0.000
109	A	295	LEU	0	-0.015	-0.006	8.073	-3.060	-3.060	0.000	0.000	0.000	0.000
110	A	296	ASN	0	-0.038	-0.024	4.540	4.677	4.845	0.000	-0.024	-0.143	0.000
111	A	297	ASN	0	-0.005	-0.019	2.533	1.093	1.868	0.932	-0.610	-1.097	0.004
112	A	298	ILE	0	0.002	0.005	3.923	-2.979	-2.584	0.001	-0.068	-0.328	0.000
113	A	299	PRO	0	0.020	0.019	6.225	1.330	1.330	0.000	0.000	0.000	0.000
114	A	300	PHE	0	0.078	0.010	9.975	-0.354	-0.354	0.000	0.000	0.000	0.000
115	A	301	SER	0	-0.021	0.007	12.521	0.642	0.642	0.000	0.000	0.000	0.000
116	A	302	ARG	1	0.996	0.997	9.298	22.883	22.883	0.000	0.000	0.000	0.000
117	A	303	PHE	0	0.021	0.007	10.145	-0.663	-0.663	0.000	0.000	0.000	0.000
118	A	304	LEU	0	0.002	0.007	11.666	0.097	0.097	0.000	0.000	0.000	0.000
119	A	305	ASP	-1	-0.785	-0.893	15.018	-15.254	-15.254	0.000	0.000	0.000	0.000
120	A	306	TYR	0	-0.039	-0.011	11.180	0.289	0.289	0.000	0.000	0.000	0.000
121	A	307	ILE	0	-0.009	-0.008	13.413	0.131	0.131	0.000	0.000	0.000	0.000
122	A	308	ALA	0	0.004	0.006	16.080	0.628	0.628	0.000	0.000	0.000	0.000
123	A	309	PRO	0	0.029	0.030	18.285	0.259	0.259	0.000	0.000	0.000	0.000
124	A	310	GLU	-1	-0.812	-0.896	20.084	-11.711	-11.711	0.000	0.000	0.000	0.000
125	A	311	THR	0	-0.004	-0.016	23.553	-0.113	-0.113	0.000	0.000	0.000	0.000
126	A	312	LYS	1	0.855	0.925	25.725	10.006	10.006	0.000	0.000	0.000	0.000
127	A	313	ASP	-1	-0.836	-0.894	23.096	-11.805	-11.805	0.000	0.000	0.000	0.000
128	A	314	GLY	0	-0.039	-0.025	21.401	-0.396	-0.396	0.000	0.000	0.000	0.000
129	A	315	ARG	1	0.855	0.907	17.721	16.585	16.585	0.000	0.000	0.000	0.000
130	A	316	PRO	0	-0.023	0.001	13.639	-0.250	-0.250	0.000	0.000	0.000	0.000
131	A	317	VAL	0	0.007	0.006	10.820	-0.278	-0.278	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:187:LYS)