FMO DATABASE

FMODB ID: VRNM1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-344844.692277
FMO2-HF: Nuclear repulsion	321340.062948
FMO2-HF: Total energy	-23504.629329
FMO2-MP2: Total energy	-23575.790616

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.
-24.414	-19.231	5.239	-3.106	-7.316	0.046

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 : 0.068 / q_NPA : 0.017

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	0.873	0.927	2.459	-7.145	-4.635	3.441	-2.174	-3.778	0.026
4	B	55	VAL	0	0.031	0.031	2.512	-8.192	-6.062	1.797	-0.810	-3.117	0.020
5	B	56	VAL	0	0.095	0.055	3.831	-2.510	-2.179	0.002	-0.110	-0.223	0.000
6	B	57	ASP	-1	-0.832	-0.913	6.042	1.962	1.962	0.000	0.000	0.000	0.000
7	B	58	ALA	0	-0.010	-0.009	6.706	-0.950	-0.950	0.000	0.000	0.000	0.000
8	B	59	GLN	0	0.013	0.004	7.217	-0.583	-0.583	0.000	0.000	0.000	0.000
9	B	60	LYS	1	0.875	0.940	9.534	-2.326	-2.326	0.000	0.000	0.000	0.000
10	B	61	ALA	0	-0.100	-0.046	11.301	-0.253	-0.253	0.000	0.000	0.000	0.000
11	B	62	VAL	0	0.033	0.002	12.424	-0.211	-0.211	0.000	0.000	0.000	0.000
12	B	63	GLU	-1	-0.813	-0.898	14.076	0.418	0.418	0.000	0.000	0.000	0.000
13	B	64	LEU	0	-0.006	0.005	16.043	-0.094	-0.094	0.000	0.000	0.000	0.000
14	B	65	PHE	0	-0.018	0.001	17.194	-0.083	-0.083	0.000	0.000	0.000	0.000
15	B	66	LYS	1	0.930	0.975	17.346	-0.568	-0.568	0.000	0.000	0.000	0.000
16	B	67	ARG	1	0.856	0.917	17.653	-0.629	-0.629	0.000	0.000	0.000	0.000
17	B	68	THR	0	-0.065	-0.055	21.271	-0.045	-0.045	0.000	0.000	0.000	0.000
18	B	69	ARG	1	0.943	1.001	22.485	-0.378	-0.378	0.000	0.000	0.000	0.000
19	B	70	THR	0	0.054	0.026	22.943	-0.017	-0.017	0.000	0.000	0.000	0.000
20	B	71	VAL	0	0.084	0.032	22.705	0.048	0.048	0.000	0.000	0.000	0.000
21	B	72	ALA	0	-0.017	0.000	22.362	0.039	0.039	0.000	0.000	0.000	0.000
22	B	73	THR	0	0.014	-0.028	19.139	0.068	0.068	0.000	0.000	0.000	0.000
23	B	74	HIS	0	0.051	0.048	17.831	0.071	0.071	0.000	0.000	0.000	0.000
24	B	75	ARG	1	0.970	0.983	17.700	-0.478	-0.478	0.000	0.000	0.000	0.000
25	B	76	LYS	1	0.928	0.963	14.381	-1.004	-1.004	0.000	0.000	0.000	0.000
26	B	77	ALA	0	0.014	0.006	13.622	0.228	0.228	0.000	0.000	0.000	0.000
27	B	78	GLN	0	0.033	0.004	12.938	0.135	0.135	0.000	0.000	0.000	0.000
28	B	79	ARG	1	0.972	0.987	13.135	-0.911	-0.911	0.000	0.000	0.000	0.000
29	B	80	ALA	0	-0.003	0.005	9.555	0.212	0.212	0.000	0.000	0.000	0.000
30	B	81	VAL	0	0.062	0.017	8.518	0.747	0.747	0.000	0.000	0.000	0.000
31	B	82	ASN	0	-0.001	-0.001	9.242	0.185	0.185	0.000	0.000	0.000	0.000
32	B	83	LEU	0	-0.050	-0.019	8.234	-0.144	-0.144	0.000	0.000	0.000	0.000
33	B	84	ILE	0	-0.024	0.009	4.513	0.077	0.289	-0.001	-0.012	-0.198	0.000
34	B	85	HIS	0	0.047	0.008	6.097	-0.749	-0.749	0.000	0.000	0.000	0.000
35	B	86	PHE	0	0.039	0.032	5.900	-0.398	-0.398	0.000	0.000	0.000	0.000
36	B	87	GLN	0	0.065	0.016	7.763	0.560	0.560	0.000	0.000	0.000	0.000
37	B	88	HIS	0	0.061	0.025	11.269	0.167	0.167	0.000	0.000	0.000	0.000
38	B	89	SER	0	0.022	0.028	5.991	-0.388	-0.388	0.000	0.000	0.000	0.000
39	B	90	TYR	0	0.063	0.011	8.798	0.272	0.272	0.000	0.000	0.000	0.000
40	B	91	GLU	-1	-0.828	-0.930	6.641	0.459	0.459	0.000	0.000	0.000	0.000
41	B	92	LYS	1	0.831	0.928	8.210	-1.138	-1.138	0.000	0.000	0.000	0.000
42	B	93	LYS	1	0.934	0.965	9.728	-0.212	-0.212	0.000	0.000	0.000	0.000
43	B	94	LYS	1	0.933	0.988	11.890	-0.149	-0.149	0.000	0.000	0.000	0.000
44	B	95	LEU	0	-0.002	-0.017	8.533	-0.038	-0.038	0.000	0.000	0.000	0.000
45	B	96	GLN	0	-0.025	-0.015	12.601	0.148	0.148	0.000	0.000	0.000	0.000
46	B	97	ARG	1	1.003	1.007	14.527	-0.328	-0.328	0.000	0.000	0.000	0.000
47	B	98	GLN	0	-0.001	-0.003	15.493	-0.064	-0.064	0.000	0.000	0.000	0.000
48	B	99	ILE	0	-0.035	-0.005	14.571	-0.030	-0.030	0.000	0.000	0.000	0.000
49	B	100	ASP	-1	-0.804	-0.906	17.891	0.463	0.463	0.000	0.000	0.000	0.000
50	B	101	LEU	0	-0.071	-0.038	20.299	-0.055	-0.055	0.000	0.000	0.000	0.000
51	B	102	VAL	0	-0.027	-0.004	20.764	-0.035	-0.035	0.000	0.000	0.000	0.000
52	B	103	LEU	0	-0.033	-0.035	20.723	-0.023	-0.023	0.000	0.000	0.000	0.000
53	B	104	LYS	1	0.909	0.973	24.152	-0.237	-0.237	0.000	0.000	0.000	0.000
54	B	105	TYR	0	0.033	0.020	26.376	-0.030	-0.030	0.000	0.000	0.000	0.000
55	B	106	ASN	0	-0.041	-0.024	25.827	0.015	0.015	0.000	0.000	0.000	0.000
56	B	107	THR	0	0.048	0.040	28.122	0.000	0.000	0.000	0.000	0.000	0.000
57	B	108	LEU	0	-0.056	-0.025	23.090	0.005	0.005	0.000	0.000	0.000	0.000
58	B	109	LYS	1	1.007	1.009	26.753	-0.298	-0.298	0.000	0.000	0.000	0.000

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