FMO DATABASE

FMODB ID: MNL2Z

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	OptH
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	-1216296.681305
FMO2-HF: Nuclear repulsion	1164047.202791
FMO2-HF: Total energy	-52249.478514
FMO2-MP2: Total energy	-52405.506327

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.
-0.73600000000004	3.653	0.05	-2.106	-2.332	-0.001

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 : 0.996 / q_NPA : 0.985

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	0.018	3.825	3.663	6.728	-0.042	-1.713	-1.309	-0.002
4	A	190	GLU	-1	-0.927	-0.964	7.419	-34.606	-34.606	0.000	0.000	0.000	0.000
5	A	191	ILE	0	0.037	0.029	9.175	2.614	2.614	0.000	0.000	0.000	0.000
6	A	192	GLU	-1	-0.830	-0.920	12.805	-20.065	-20.065	0.000	0.000	0.000	0.000
7	A	193	ILE	0	-0.023	-0.006	15.558	0.969	0.969	0.000	0.000	0.000	0.000
8	A	194	ARG	1	0.792	0.861	19.110	13.176	13.176	0.000	0.000	0.000	0.000
9	A	195	THR	0	-0.018	-0.025	22.223	0.407	0.407	0.000	0.000	0.000	0.000
10	A	196	LYS	1	0.962	0.989	25.922	9.939	9.939	0.000	0.000	0.000	0.000
11	A	197	ILE	0	-0.029	-0.003	27.760	0.039	0.039	0.000	0.000	0.000	0.000
12	A	198	HIS	0	0.023	0.004	31.213	-0.013	-0.013	0.000	0.000	0.000	0.000
13	A	199	PRO	0	0.072	0.025	34.836	-0.016	-0.016	0.000	0.000	0.000	0.000
14	A	200	THR	0	-0.013	-0.004	37.662	0.063	0.063	0.000	0.000	0.000	0.000
15	A	201	GLU	-1	-0.876	-0.928	32.750	-9.895	-9.895	0.000	0.000	0.000	0.000
16	A	202	SER	0	-0.039	-0.016	33.584	-0.041	-0.041	0.000	0.000	0.000	0.000
17	A	203	GLU	-1	-0.824	-0.932	28.590	-11.126	-11.126	0.000	0.000	0.000	0.000
18	A	204	ASP	-1	-0.842	-0.930	28.840	-11.048	-11.048	0.000	0.000	0.000	0.000
19	A	205	LYS	1	0.928	0.950	28.645	8.868	8.868	0.000	0.000	0.000	0.000
20	A	206	VAL	0	0.050	0.035	26.659	-0.264	-0.264	0.000	0.000	0.000	0.000
21	A	207	LEU	0	0.049	0.021	24.073	-0.486	-0.486	0.000	0.000	0.000	0.000
22	A	208	LYS	1	0.866	0.942	23.798	10.155	10.155	0.000	0.000	0.000	0.000
23	A	209	ALA	0	0.005	0.008	24.791	-0.295	-0.295	0.000	0.000	0.000	0.000
24	A	210	ILE	0	-0.011	-0.003	20.327	-0.343	-0.343	0.000	0.000	0.000	0.000
25	A	211	ARG	1	0.884	0.928	19.506	14.807	14.807	0.000	0.000	0.000	0.000
26	A	212	ASN	0	-0.089	-0.030	20.944	-0.458	-0.458	0.000	0.000	0.000	0.000
27	A	213	ILE	0	-0.085	-0.043	19.670	0.103	0.103	0.000	0.000	0.000	0.000
28	A	214	PHE	0	-0.006	-0.027	15.481	-0.720	-0.720	0.000	0.000	0.000	0.000
29	A	215	PRO	0	0.013	-0.007	16.493	0.102	0.102	0.000	0.000	0.000	0.000
30	A	216	ASP	-1	-0.879	-0.935	12.024	-23.826	-23.826	0.000	0.000	0.000	0.000
31	A	217	ALA	0	-0.006	0.013	14.293	-1.103	-1.103	0.000	0.000	0.000	0.000
32	A	218	GLU	-1	-0.903	-0.944	14.161	-19.760	-19.760	0.000	0.000	0.000	0.000
33	A	219	ILE	0	-0.074	-0.062	16.730	-0.041	-0.041	0.000	0.000	0.000	0.000
34	A	220	GLU	-1	-0.914	-0.942	19.247	-15.651	-15.651	0.000	0.000	0.000	0.000
35	A	221	ILE	0	-0.049	-0.039	22.342	-0.039	-0.039	0.000	0.000	0.000	0.000
36	A	222	SER	0	-0.016	-0.007	25.947	0.141	0.141	0.000	0.000	0.000	0.000
37	A	223	GLU	-1	-0.913	-0.965	27.879	-9.355	-9.355	0.000	0.000	0.000	0.000
38	A	224	GLU	-1	-0.892	-0.939	30.509	-10.231	-10.231	0.000	0.000	0.000	0.000
39	A	225	GLY	0	-0.011	0.006	30.402	0.202	0.202	0.000	0.000	0.000	0.000
40	A	226	GLU	-1	-0.896	-0.924	26.460	-11.513	-11.513	0.000	0.000	0.000	0.000
41	A	227	VAL	0	-0.008	-0.008	22.793	-0.253	-0.253	0.000	0.000	0.000	0.000
42	A	228	TYR	0	0.007	-0.007	20.056	-0.256	-0.256	0.000	0.000	0.000	0.000
43	A	229	GLY	0	0.033	0.011	18.378	0.011	0.011	0.000	0.000	0.000	0.000
44	A	230	ARG	1	0.848	0.931	12.525	21.283	21.283	0.000	0.000	0.000	0.000
45	A	231	ALA	0	0.040	0.026	13.007	0.375	0.375	0.000	0.000	0.000	0.000
46	A	232	TYR	0	-0.019	-0.015	7.682	-3.009	-3.009	0.000	0.000	0.000	0.000
47	A	233	SER	0	-0.009	0.012	9.907	-0.257	-0.257	0.000	0.000	0.000	0.000
48	A	234	LEU	0	0.012	-0.012	10.241	1.801	1.801	0.000	0.000	0.000	0.000
49	A	235	ASP	-1	-0.908	-0.947	13.872	-20.744	-20.744	0.000	0.000	0.000	0.000
50	A	236	ARG	1	0.951	0.980	15.738	15.217	15.217	0.000	0.000	0.000	0.000
51	A	237	PHE	0	0.049	0.009	16.503	0.926	0.926	0.000	0.000	0.000	0.000
52	A	238	ARG	1	0.866	0.932	14.359	19.520	19.520	0.000	0.000	0.000	0.000
53	A	239	GLU	-1	-0.950	-0.971	18.694	-14.509	-14.509	0.000	0.000	0.000	0.000
54	A	240	LEU	0	-0.025	-0.008	21.412	0.859	0.859	0.000	0.000	0.000	0.000
55	A	241	LEU	0	0.005	0.014	19.428	0.677	0.677	0.000	0.000	0.000	0.000
56	A	242	ARG	0	-0.032	0.004	18.022	-0.168	-0.168	0.000	0.000	0.000	0.000
57	A	243	LYS	1	0.900	0.941	24.419	13.124	13.124	0.000	0.000	0.000	0.000
58	A	244	GLN	0	-0.005	0.016	26.695	0.554	0.554	0.000	0.000	0.000	0.000
59	A	245	ARG	1	0.896	0.945	27.643	10.509	10.509	0.000	0.000	0.000	0.000
60	A	246	ILE	0	0.015	0.022	25.762	0.329	0.329	0.000	0.000	0.000	0.000
61	A	247	LEU	0	0.028	-0.006	21.355	-0.464	-0.464	0.000	0.000	0.000	0.000
62	A	248	ASP	-1	-0.857	-0.922	23.547	-10.703	-10.703	0.000	0.000	0.000	0.000
63	A	249	THR	0	0.019	-0.003	25.725	-0.013	-0.013	0.000	0.000	0.000	0.000
64	A	250	ALA	0	0.001	0.020	21.245	-0.162	-0.162	0.000	0.000	0.000	0.000
65	A	251	ARG	1	0.906	0.937	19.364	12.464	12.464	0.000	0.000	0.000	0.000
66	A	252	SER	0	-0.052	-0.020	21.476	-0.092	-0.092	0.000	0.000	0.000	0.000
67	A	253	GLU	-1	-0.829	-0.926	22.930	-11.168	-11.168	0.000	0.000	0.000	0.000
68	A	254	ILE	0	-0.057	-0.026	16.661	-0.391	-0.391	0.000	0.000	0.000	0.000
69	A	255	LEU	0	-0.071	-0.045	19.189	-0.366	-0.366	0.000	0.000	0.000	0.000
70	A	256	LYS	1	0.874	0.942	20.828	10.765	10.765	0.000	0.000	0.000	0.000
71	A	257	GLY	0	0.060	0.046	21.292	0.271	0.271	0.000	0.000	0.000	0.000
72	A	258	ARG	1	0.903	0.964	15.777	13.990	13.990	0.000	0.000	0.000	0.000
73	A	259	ASN	0	0.044	0.020	17.697	1.067	1.067	0.000	0.000	0.000	0.000
74	A	260	GLY	0	0.005	0.008	16.551	0.259	0.259	0.000	0.000	0.000	0.000
75	A	261	LYS	1	0.866	0.934	9.306	21.223	21.223	0.000	0.000	0.000	0.000
76	A	262	GLU	-1	-0.920	-0.965	12.067	-18.876	-18.876	0.000	0.000	0.000	0.000
77	A	263	VAL	0	-0.031	-0.013	14.201	0.910	0.910	0.000	0.000	0.000	0.000
78	A	264	THR	0	0.001	0.000	16.349	-0.902	-0.902	0.000	0.000	0.000	0.000
79	A	265	ILE	0	-0.002	0.016	19.150	0.597	0.597	0.000	0.000	0.000	0.000
80	A	266	TYR	0	0.020	0.001	21.518	-0.469	-0.469	0.000	0.000	0.000	0.000
81	A	267	LEU	0	-0.006	0.005	21.732	0.343	0.343	0.000	0.000	0.000	0.000
82	A	268	ASN	0	0.049	0.017	25.392	0.131	0.131	0.000	0.000	0.000	0.000
83	A	269	LYS	1	0.908	0.972	27.751	10.414	10.414	0.000	0.000	0.000	0.000
84	A	270	GLN	0	0.039	0.023	28.769	0.045	0.045	0.000	0.000	0.000	0.000
85	A	271	THR	0	-0.024	-0.008	29.286	0.053	0.053	0.000	0.000	0.000	0.000
86	A	272	ALA	0	0.054	0.038	25.715	-0.028	-0.028	0.000	0.000	0.000	0.000
87	A	273	THR	0	-0.007	-0.026	27.192	-0.248	-0.248	0.000	0.000	0.000	0.000
88	A	274	VAL	0	-0.046	-0.017	29.599	0.072	0.072	0.000	0.000	0.000	0.000
89	A	275	SER	0	-0.089	-0.057	25.422	-0.072	-0.072	0.000	0.000	0.000	0.000
90	A	276	ARG	1	0.964	0.986	26.621	9.385	9.385	0.000	0.000	0.000	0.000
91	A	277	ILE	0	-0.008	0.012	23.187	-0.044	-0.044	0.000	0.000	0.000	0.000
92	A	278	ASN	0	-0.013	-0.012	26.461	0.258	0.258	0.000	0.000	0.000	0.000
93	A	279	PHE	0	0.020	0.009	21.556	-0.247	-0.247	0.000	0.000	0.000	0.000
94	A	280	CYS	0	-0.062	-0.026	26.824	0.377	0.377	0.000	0.000	0.000	0.000
95	A	281	ASP	-1	-0.864	-0.930	27.846	-9.891	-9.891	0.000	0.000	0.000	0.000
96	A	282	GLU	-1	-0.905	-0.980	27.228	-10.990	-10.990	0.000	0.000	0.000	0.000
97	A	283	ASN	0	-0.056	-0.026	29.396	0.042	0.042	0.000	0.000	0.000	0.000
98	A	284	ALA	0	-0.011	0.007	31.293	0.245	0.245	0.000	0.000	0.000	0.000
99	A	285	VAL	0	0.042	0.006	33.105	-0.129	-0.129	0.000	0.000	0.000	0.000
100	A	286	LEU	0	-0.053	-0.032	34.295	-0.122	-0.122	0.000	0.000	0.000	0.000
101	A	287	SER	0	0.015	0.000	29.658	-0.173	-0.173	0.000	0.000	0.000	0.000
102	A	288	PRO	0	0.013	0.024	27.342	-0.130	-0.130	0.000	0.000	0.000	0.000
103	A	289	ILE	0	0.004	0.018	22.157	-0.135	-0.135	0.000	0.000	0.000	0.000
104	A	290	LYS	1	0.923	0.955	19.149	14.930	14.930	0.000	0.000	0.000	0.000
105	A	291	VAL	0	-0.017	-0.015	17.107	-0.499	-0.499	0.000	0.000	0.000	0.000
106	A	292	THR	0	0.020	0.018	14.800	0.682	0.682	0.000	0.000	0.000	0.000
107	A	293	PHE	0	-0.003	0.001	12.129	-1.192	-1.192	0.000	0.000	0.000	0.000
108	A	294	ARG	1	0.920	0.942	9.113	24.989	24.989	0.000	0.000	0.000	0.000
109	A	295	LEU	0	-0.040	-0.006	7.846	-3.243	-3.243	0.000	0.000	0.000	0.000
110	A	296	ASN	0	-0.043	-0.023	4.251	5.915	6.150	0.000	-0.036	-0.199	0.000
111	A	297	ASN	0	-0.018	-0.015	3.255	0.976	1.688	0.089	-0.296	-0.505	0.001
112	A	298	ILE	0	-0.012	-0.003	3.926	-1.615	-1.238	0.003	-0.061	-0.319	0.000
113	A	299	PRO	0	0.019	0.017	6.122	0.949	0.949	0.000	0.000	0.000	0.000
114	A	300	PHE	0	0.107	0.031	9.873	-0.213	-0.213	0.000	0.000	0.000	0.000
115	A	301	SER	0	-0.043	-0.025	12.399	0.200	0.200	0.000	0.000	0.000	0.000
116	A	302	ARG	1	1.003	1.002	8.826	21.528	21.528	0.000	0.000	0.000	0.000
117	A	303	PHE	0	0.002	0.006	10.275	-0.322	-0.322	0.000	0.000	0.000	0.000
118	A	304	LEU	0	0.014	0.007	11.743	0.056	0.056	0.000	0.000	0.000	0.000
119	A	305	ASP	-1	-0.810	-0.909	15.467	-14.255	-14.255	0.000	0.000	0.000	0.000
120	A	306	TYR	0	-0.058	-0.023	11.703	-0.010	-0.010	0.000	0.000	0.000	0.000
121	A	307	ILE	0	-0.028	-0.016	13.388	-0.044	-0.044	0.000	0.000	0.000	0.000
122	A	308	ALA	0	-0.031	-0.017	16.117	0.645	0.645	0.000	0.000	0.000	0.000
123	A	309	PRO	0	0.007	0.015	18.204	0.360	0.360	0.000	0.000	0.000	0.000
124	A	310	GLU	-1	-0.924	-0.956	20.101	-11.156	-11.156	0.000	0.000	0.000	0.000
125	A	311	THR	0	0.031	-0.002	23.466	-0.076	-0.076	0.000	0.000	0.000	0.000
126	A	312	LYS	1	0.876	0.952	25.620	9.650	9.650	0.000	0.000	0.000	0.000
127	A	313	ASP	-1	-0.847	-0.918	23.318	-10.810	-10.810	0.000	0.000	0.000	0.000
128	A	314	GLY	0	-0.032	-0.019	21.112	-0.398	-0.398	0.000	0.000	0.000	0.000
129	A	315	ARG	1	0.944	0.961	18.252	15.273	15.273	0.000	0.000	0.000	0.000
130	A	316	PRO	0	-0.030	-0.004	13.730	-0.143	-0.143	0.000	0.000	0.000	0.000
131	A	317	VAL	0	0.014	-0.001	10.347	-0.351	-0.351	0.000	0.000	0.000	0.000

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