FMO DATABASE

FMODB ID: YY132

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

Total energy (hartree)

FMO2-HF: Electronic energy	-345271.81291
FMO2-HF: Nuclear repulsion	321767.703509
FMO2-HF: Total energy	-23504.1094
FMO2-MP2: Total energy	-23575.361559

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.
-18.351	-13.607	9.069	-4.851	-8.96	0.047

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 : 0.087 / q_NPA : 0.025

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	0.919	0.943	1.990	-2.132	0.174	4.542	-2.769	-4.078	0.022
4	B	55	VAL	0	0.067	0.052	2.375	-3.560	-2.131	4.503	-1.750	-4.182	0.023
5	B	56	VAL	0	0.120	0.056	3.796	-3.151	-2.657	0.019	-0.201	-0.312	0.001
6	B	57	ASP	-1	-1.006	-0.985	6.253	0.663	0.663	0.000	0.000	0.000	0.000
7	B	58	ALA	0	0.036	0.004	6.662	-0.568	-0.568	0.000	0.000	0.000	0.000
8	B	59	GLN	0	0.043	0.028	6.738	-0.678	-0.678	0.000	0.000	0.000	0.000
9	B	60	LYS	1	0.934	0.969	9.788	-0.888	-0.888	0.000	0.000	0.000	0.000
10	B	61	ALA	0	-0.089	-0.040	11.233	-0.209	-0.209	0.000	0.000	0.000	0.000
11	B	62	VAL	0	0.026	0.001	12.014	-0.180	-0.180	0.000	0.000	0.000	0.000
12	B	63	GLU	-1	-0.826	-0.892	13.787	0.422	0.422	0.000	0.000	0.000	0.000
13	B	64	LEU	0	-0.001	0.001	15.834	-0.089	-0.089	0.000	0.000	0.000	0.000
14	B	65	PHE	0	-0.011	0.009	16.965	-0.082	-0.082	0.000	0.000	0.000	0.000
15	B	66	LYS	1	0.957	0.989	17.296	-0.667	-0.667	0.000	0.000	0.000	0.000
16	B	67	ARG	1	0.856	0.914	17.607	-0.509	-0.509	0.000	0.000	0.000	0.000
17	B	68	THR	0	-0.063	-0.053	21.098	-0.046	-0.046	0.000	0.000	0.000	0.000
18	B	69	ARG	1	0.959	0.998	22.226	-0.355	-0.355	0.000	0.000	0.000	0.000
19	B	70	THR	0	0.064	0.046	22.723	-0.021	-0.021	0.000	0.000	0.000	0.000
20	B	71	VAL	0	0.092	0.034	22.507	0.044	0.044	0.000	0.000	0.000	0.000
21	B	72	ALA	0	-0.014	0.003	22.275	0.029	0.029	0.000	0.000	0.000	0.000
22	B	73	THR	0	0.006	-0.050	19.096	0.049	0.049	0.000	0.000	0.000	0.000
23	B	74	HIS	0	0.041	0.042	17.684	0.049	0.049	0.000	0.000	0.000	0.000
24	B	75	ARG	1	0.967	0.986	17.469	-0.300	-0.300	0.000	0.000	0.000	0.000
25	B	76	LYS	1	0.929	0.962	14.404	-0.509	-0.509	0.000	0.000	0.000	0.000
26	B	77	ALA	0	0.020	0.009	13.432	0.148	0.148	0.000	0.000	0.000	0.000
27	B	78	GLN	0	0.045	0.020	12.637	0.170	0.170	0.000	0.000	0.000	0.000
28	B	79	ARG	1	0.970	0.983	12.797	-0.330	-0.330	0.000	0.000	0.000	0.000
29	B	80	ALA	0	0.013	0.015	9.520	0.125	0.125	0.000	0.000	0.000	0.000
30	B	81	VAL	0	0.048	0.013	8.346	0.716	0.716	0.000	0.000	0.000	0.000
31	B	82	ASN	0	0.002	-0.004	8.768	0.494	0.494	0.000	0.000	0.000	0.000
32	B	83	LEU	0	-0.088	-0.031	7.765	-0.196	-0.196	0.000	0.000	0.000	0.000
33	B	84	ILE	0	-0.052	-0.011	3.722	-0.761	-0.246	0.005	-0.131	-0.388	0.001
34	B	85	HIS	0	0.041	-0.003	5.961	-0.776	-0.776	0.000	0.000	0.000	0.000
35	B	86	PHE	0	0.052	0.052	6.103	-0.396	-0.396	0.000	0.000	0.000	0.000
36	B	87	GLN	0	0.038	-0.012	7.672	0.875	0.875	0.000	0.000	0.000	0.000
37	B	88	HIS	0	0.058	0.028	10.552	0.195	0.195	0.000	0.000	0.000	0.000
38	B	89	SER	0	0.028	0.034	5.658	-0.842	-0.842	0.000	0.000	0.000	0.000
39	B	90	TYR	0	0.067	0.003	8.416	-0.080	-0.080	0.000	0.000	0.000	0.000
40	B	91	GLU	-1	-0.875	-0.950	6.647	1.389	1.389	0.000	0.000	0.000	0.000
41	B	92	LYS	1	0.844	0.946	7.352	-2.396	-2.396	0.000	0.000	0.000	0.000
42	B	93	LYS	1	0.938	0.972	8.822	-1.671	-1.671	0.000	0.000	0.000	0.000
43	B	94	LYS	1	0.947	0.987	11.810	-0.982	-0.982	0.000	0.000	0.000	0.000
44	B	95	LEU	0	-0.007	-0.021	7.957	-0.233	-0.233	0.000	0.000	0.000	0.000
45	B	96	GLN	0	-0.008	-0.005	11.922	0.027	0.027	0.000	0.000	0.000	0.000
46	B	97	ARG	1	0.991	1.000	13.778	-0.752	-0.752	0.000	0.000	0.000	0.000
47	B	98	GLN	0	0.013	-0.007	15.302	-0.167	-0.167	0.000	0.000	0.000	0.000
48	B	99	ILE	0	-0.055	-0.011	14.235	-0.094	-0.094	0.000	0.000	0.000	0.000
49	B	100	ASP	-1	-0.817	-0.923	17.296	0.683	0.683	0.000	0.000	0.000	0.000
50	B	101	LEU	0	-0.062	-0.035	19.796	-0.079	-0.079	0.000	0.000	0.000	0.000
51	B	102	VAL	0	-0.054	-0.010	19.567	-0.055	-0.055	0.000	0.000	0.000	0.000
52	B	103	LEU	0	-0.034	-0.037	20.152	-0.041	-0.041	0.000	0.000	0.000	0.000
53	B	104	LYS	1	0.912	0.977	23.605	-0.374	-0.374	0.000	0.000	0.000	0.000
54	B	105	TYR	0	0.032	0.017	25.833	-0.034	-0.034	0.000	0.000	0.000	0.000
55	B	106	ASN	0	-0.036	-0.016	25.435	0.008	0.008	0.000	0.000	0.000	0.000
56	B	107	THR	0	0.050	0.042	27.635	0.004	0.004	0.000	0.000	0.000	0.000
57	B	108	LEU	0	-0.073	-0.031	22.523	-0.005	-0.005	0.000	0.000	0.000	0.000
58	B	109	LYS	1	1.001	1.006	26.553	-0.233	-0.233	0.000	0.000	0.000	0.000

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