FMO DATABASE

FMODB ID: 14YRZ

Calculation Name: 2NOJ-B-Xray372

Preferred Name: Complement C3

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2NOJ

Chain ID: B

ChEMBL ID: CHEMBL4917

UniProt ID: P01024

Base Structure: X-ray

Registration Date: 2023-03-13

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	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	58
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-344635.585762
FMO2-HF: Nuclear repulsion	321130.661633
FMO2-HF: Total energy	-23504.924129
FMO2-MP2: Total energy	-23576.019422

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(B:52:ASN)

Summations of interaction energy for fragment #1(B:52:ASN)

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.
-26.193	-20.743	5.071	-3.79	-6.729	0.041

Interaction energy analysis for fragmet #1(B:52:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.069 / q_NPA : 0.018

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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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	B	54	LYS	1	0.913	0.952	2.185	-12.023	-10.197	3.699	-2.186	-3.339	0.025
4	B	55	VAL	0	0.011	0.014	2.492	-9.520	-6.562	1.364	-1.428	-2.892	0.016
5	B	56	VAL	0	0.093	0.051	3.281	-1.750	-1.229	0.009	-0.173	-0.357	0.000
6	B	57	ASP	-1	-0.875	-0.929	5.835	3.471	3.471	0.000	0.000	0.000	0.000
7	B	58	ALA	0	0.001	0.000	7.156	-0.833	-0.833	0.000	0.000	0.000	0.000
8	B	59	GLN	0	0.001	-0.010	6.511	-0.324	-0.324	0.000	0.000	0.000	0.000
9	B	60	LYS	1	0.885	0.944	9.086	-2.587	-2.587	0.000	0.000	0.000	0.000
10	B	61	ALA	0	-0.052	-0.018	11.712	-0.204	-0.204	0.000	0.000	0.000	0.000
11	B	62	VAL	0	0.042	0.008	12.626	-0.173	-0.173	0.000	0.000	0.000	0.000
12	B	63	GLU	-1	-0.797	-0.889	13.913	0.281	0.281	0.000	0.000	0.000	0.000
13	B	64	LEU	0	-0.024	-0.001	15.746	-0.064	-0.064	0.000	0.000	0.000	0.000
14	B	65	PHE	0	-0.016	-0.003	17.305	-0.071	-0.071	0.000	0.000	0.000	0.000
15	B	66	LYS	1	0.899	0.950	16.571	-0.389	-0.389	0.000	0.000	0.000	0.000
16	B	67	ARG	1	0.876	0.941	17.197	-0.524	-0.524	0.000	0.000	0.000	0.000
17	B	68	THR	0	-0.047	-0.040	21.347	-0.035	-0.035	0.000	0.000	0.000	0.000
18	B	69	ARG	1	0.913	0.976	22.677	-0.314	-0.314	0.000	0.000	0.000	0.000
19	B	70	THR	0	0.068	0.050	23.147	-0.011	-0.011	0.000	0.000	0.000	0.000
20	B	71	VAL	0	0.068	0.025	22.641	0.047	0.047	0.000	0.000	0.000	0.000
21	B	72	ALA	0	0.003	0.004	22.030	0.042	0.042	0.000	0.000	0.000	0.000
22	B	73	THR	0	0.004	-0.023	18.959	0.074	0.074	0.000	0.000	0.000	0.000
23	B	74	HIS	0	0.049	0.039	17.782	0.069	0.069	0.000	0.000	0.000	0.000
24	B	75	ARG	1	0.976	0.983	17.596	-0.490	-0.490	0.000	0.000	0.000	0.000
25	B	76	LYS	1	0.934	0.973	14.565	-1.033	-1.033	0.000	0.000	0.000	0.000
26	B	77	ALA	0	0.014	0.006	13.447	0.232	0.232	0.000	0.000	0.000	0.000
27	B	78	GLN	0	0.028	-0.003	12.814	0.130	0.130	0.000	0.000	0.000	0.000
28	B	79	ARG	1	0.968	0.984	13.199	-1.092	-1.092	0.000	0.000	0.000	0.000
29	B	80	ALA	0	-0.013	-0.007	9.324	0.177	0.177	0.000	0.000	0.000	0.000
30	B	81	VAL	0	0.048	0.017	8.550	0.668	0.668	0.000	0.000	0.000	0.000
31	B	82	ASN	0	0.020	0.009	9.715	0.010	0.010	0.000	0.000	0.000	0.000
32	B	83	LEU	0	-0.027	-0.011	8.217	-0.104	-0.104	0.000	0.000	0.000	0.000
33	B	84	ILE	0	-0.020	0.009	4.958	0.489	0.634	-0.001	-0.003	-0.141	0.000
34	B	85	HIS	0	0.047	0.007	6.394	-0.522	-0.522	0.000	0.000	0.000	0.000
35	B	86	PHE	0	0.047	0.033	5.697	-0.411	-0.411	0.000	0.000	0.000	0.000
36	B	87	GLN	0	0.076	0.025	7.553	0.169	0.169	0.000	0.000	0.000	0.000
37	B	88	HIS	0	0.093	0.044	10.960	0.098	0.098	0.000	0.000	0.000	0.000
38	B	89	SER	0	0.001	0.017	5.895	-0.082	-0.082	0.000	0.000	0.000	0.000
39	B	90	TYR	0	0.078	0.030	8.762	0.382	0.382	0.000	0.000	0.000	0.000
40	B	91	GLU	-1	-0.798	-0.906	6.550	-0.204	-0.204	0.000	0.000	0.000	0.000
41	B	92	LYS	1	0.804	0.917	8.137	-0.640	-0.640	0.000	0.000	0.000	0.000
42	B	93	LYS	1	0.887	0.929	9.348	0.494	0.494	0.000	0.000	0.000	0.000
43	B	94	LYS	1	0.894	0.966	11.544	0.383	0.383	0.000	0.000	0.000	0.000
44	B	95	LEU	0	-0.011	-0.020	8.091	0.069	0.069	0.000	0.000	0.000	0.000
45	B	96	GLN	0	-0.008	-0.005	12.366	0.143	0.143	0.000	0.000	0.000	0.000
46	B	97	ARG	1	1.019	1.015	14.822	-0.047	-0.047	0.000	0.000	0.000	0.000
47	B	98	GLN	0	-0.031	-0.018	14.761	-0.017	-0.017	0.000	0.000	0.000	0.000
48	B	99	ILE	0	-0.041	-0.012	15.113	0.020	0.020	0.000	0.000	0.000	0.000
49	B	100	ASP	-1	-0.804	-0.902	18.236	0.264	0.264	0.000	0.000	0.000	0.000
50	B	101	LEU	0	-0.051	-0.030	20.129	-0.032	-0.032	0.000	0.000	0.000	0.000
51	B	102	VAL	0	-0.011	0.005	20.806	-0.016	-0.016	0.000	0.000	0.000	0.000
52	B	103	LEU	0	-0.009	-0.026	21.380	-0.010	-0.010	0.000	0.000	0.000	0.000
53	B	104	LYS	1	0.890	0.964	24.443	-0.116	-0.116	0.000	0.000	0.000	0.000
54	B	105	TYR	0	0.033	0.019	26.051	-0.026	-0.026	0.000	0.000	0.000	0.000
55	B	106	ASN	0	-0.037	-0.024	25.972	0.014	0.014	0.000	0.000	0.000	0.000
56	B	107	THR	0	0.051	0.035	27.723	0.011	0.011	0.000	0.000	0.000	0.000
57	B	108	LEU	0	-0.035	-0.010	23.546	0.014	0.014	0.000	0.000	0.000	0.000
58	B	109	LYS	1	0.950	0.970	27.168	-0.280	-0.280	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:52:ASN)