FMO DATABASE

FMODB ID: MM7GZ

Calculation Name: 2NOJ-B-Xray311

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	59
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-348104.167398
FMO2-HF: Nuclear repulsion	324448.478004
FMO2-HF: Total energy	-23655.689394
FMO2-MP2: Total energy	-23727.3785

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:51:ACE )

Summations of interaction energy for fragment #1(B:51:ACE )

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.
3.415	4.146	-0.005	-0.338	-0.387	0

Interaction energy analysis for fragmet #1(B:51:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.078 / q_NPA : 0.033

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].
3	B	53	LYS	1	0.940	0.964	3.840	1.490	2.221	-0.005	-0.338	-0.387
4	B	54	LYS	1	0.920	0.943	6.754	0.776	0.776	0.000	0.000	0.000
5	B	55	VAL	0	0.069	0.053	5.841	0.217	0.217	0.000	0.000	0.000
6	B	56	VAL	0	0.115	0.052	5.750	0.197	0.197	0.000	0.000	0.000
7	B	57	ASP	-1	-1.006	-0.985	8.374	-0.178	-0.178	0.000	0.000	0.000
8	B	58	ALA	0	0.038	0.006	11.077	0.069	0.069	0.000	0.000	0.000
9	B	59	GLN	0	0.044	0.028	7.524	0.019	0.019	0.000	0.000	0.000
10	B	60	LYS	1	0.927	0.967	11.460	0.131	0.131	0.000	0.000	0.000
11	B	61	ALA	0	-0.083	-0.038	14.207	0.013	0.013	0.000	0.000	0.000
12	B	62	VAL	0	0.026	0.001	15.423	0.013	0.013	0.000	0.000	0.000
13	B	63	GLU	-1	-0.832	-0.895	15.827	0.063	0.063	0.000	0.000	0.000
14	B	64	LEU	0	-0.005	-0.001	17.687	0.002	0.002	0.000	0.000	0.000
15	B	65	PHE	0	-0.004	0.013	19.931	0.001	0.001	0.000	0.000	0.000
16	B	66	LYS	1	0.952	0.987	19.132	-0.033	-0.033	0.000	0.000	0.000
17	B	67	ARG	1	0.848	0.910	18.936	-0.033	-0.033	0.000	0.000	0.000
18	B	68	THR	0	-0.063	-0.054	23.720	0.000	0.000	0.000	0.000	0.000
19	B	69	ARG	1	0.946	0.990	25.227	-0.002	-0.002	0.000	0.000	0.000
20	B	70	THR	0	0.097	0.067	26.427	-0.003	-0.003	0.000	0.000	0.000
21	B	71	VAL	0	0.096	0.040	26.778	-0.005	-0.005	0.000	0.000	0.000
22	B	72	ALA	0	-0.019	-0.001	26.923	-0.007	-0.007	0.000	0.000	0.000
23	B	73	THR	0	-0.001	-0.054	22.972	-0.009	-0.009	0.000	0.000	0.000
24	B	74	HIS	0	0.039	0.041	22.065	-0.008	-0.008	0.000	0.000	0.000
25	B	75	ARG	1	0.965	0.985	22.517	0.064	0.064	0.000	0.000	0.000
26	B	76	LYS	1	0.925	0.961	18.274	0.069	0.069	0.000	0.000	0.000
27	B	77	ALA	0	0.020	0.008	18.035	-0.021	-0.021	0.000	0.000	0.000
28	B	78	GLN	0	0.043	0.019	17.733	-0.006	-0.006	0.000	0.000	0.000
29	B	79	ARG	1	0.970	0.983	18.855	0.136	0.136	0.000	0.000	0.000
30	B	80	ALA	0	0.015	0.015	14.634	-0.031	-0.031	0.000	0.000	0.000
31	B	81	VAL	0	0.043	0.012	14.052	-0.057	-0.057	0.000	0.000	0.000
32	B	82	ASN	0	0.004	-0.003	14.820	-0.033	-0.033	0.000	0.000	0.000
33	B	83	LEU	0	-0.091	-0.033	14.594	-0.021	-0.021	0.000	0.000	0.000
34	B	84	ILE	0	-0.055	-0.012	9.726	-0.071	-0.071	0.000	0.000	0.000
35	B	85	HIS	0	0.043	-0.003	12.496	0.038	0.038	0.000	0.000	0.000
36	B	86	PHE	0	0.052	0.052	10.504	0.053	0.053	0.000	0.000	0.000
37	B	87	GLN	0	0.036	-0.012	12.680	0.033	0.033	0.000	0.000	0.000
38	B	88	HIS	0	0.057	0.027	14.330	0.025	0.025	0.000	0.000	0.000
39	B	89	SER	0	0.028	0.034	9.029	0.073	0.073	0.000	0.000	0.000
40	B	90	TYR	0	0.066	0.002	10.647	0.028	0.028	0.000	0.000	0.000
41	B	91	GLU	-1	-0.878	-0.950	7.596	0.149	0.149	0.000	0.000	0.000
42	B	92	LYS	1	0.847	0.948	10.503	0.245	0.245	0.000	0.000	0.000
43	B	93	LYS	1	0.937	0.971	12.704	0.130	0.130	0.000	0.000	0.000
44	B	94	LYS	1	0.946	0.987	13.209	-0.065	-0.065	0.000	0.000	0.000
45	B	95	LEU	0	-0.006	-0.021	10.582	0.012	0.012	0.000	0.000	0.000
46	B	96	GLN	0	-0.009	-0.005	14.918	-0.017	-0.017	0.000	0.000	0.000
47	B	97	ARG	1	0.987	0.998	17.814	-0.009	-0.009	0.000	0.000	0.000
48	B	98	GLN	0	0.012	-0.008	17.329	0.002	0.002	0.000	0.000	0.000
49	B	99	ILE	0	-0.047	-0.007	18.600	0.003	0.003	0.000	0.000	0.000
50	B	100	ASP	-1	-0.819	-0.923	21.131	-0.046	-0.046	0.000	0.000	0.000
51	B	101	LEU	0	-0.071	-0.039	22.332	0.005	0.005	0.000	0.000	0.000
52	B	102	VAL	0	-0.049	-0.007	22.694	0.004	0.004	0.000	0.000	0.000
53	B	103	LEU	0	-0.026	-0.032	24.478	0.000	0.000	0.000	0.000	0.000
54	B	104	LYS	1	0.906	0.974	27.602	0.006	0.006	0.000	0.000	0.000
55	B	105	TYR	0	0.026	0.013	28.554	0.001	0.001	0.000	0.000	0.000
56	B	106	ASN	0	-0.035	-0.016	28.352	0.003	0.003	0.000	0.000	0.000
57	B	107	THR	0	0.021	0.024	31.053	-0.003	-0.003	0.000	0.000	0.000
58	B	108	LEU	0	-0.101	-0.044	26.931	0.001	0.001	0.000	0.000	0.000
59	B	109	LYS	0	0.093	0.047	30.407	0.002	0.002	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(B:51:ACE )