Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 497NN

Calculation Name: 1FDP-A-Xray372

Preferred Name: Complement factor D

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1FDP

Chain ID: A

ChEMBL ID: CHEMBL2176771

UniProt ID: P00746

Base Structure: X-ray

Registration Date: 2023-09-20

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 215
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2453870.334477
FMO2-HF: Nuclear repulsion 2370626.595084
FMO2-HF: Total energy -83243.739393
FMO2-MP2: Total energy -83483.181074


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
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/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:17:LEU)


Summations of interaction energy for fragment #1(A:17:LEU)
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.
-0.2311.539-0.021-0.844-0.9050
Interaction energy analysis for fragmet #1(A:17:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.026 / q_NPA : -0.026
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   
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].
3A19GLY00.0120.0123.8570.3962.092-0.020-0.839-0.8370.000
4A20ARG10.9090.9346.588-0.118-0.1180.0000.0000.0000.000
5A21GLU-1-0.961-0.9629.2370.0540.0540.0000.0000.0000.000
6A22ALA00.0560.0308.333-0.069-0.0690.0000.0000.0000.000
7A23GLU-1-0.918-0.9517.380-0.444-0.4440.0000.0000.0000.000
8A24ALA0-0.082-0.0404.5530.0300.104-0.001-0.005-0.0680.000
9A25HIS00.0530.0336.642-0.046-0.0460.0000.0000.0000.000
10A26ALA0-0.017-0.0278.8030.0250.0250.0000.0000.0000.000
11A27ARG10.8180.89410.1530.2150.2150.0000.0000.0000.000
12A28PRO00.0200.0098.8460.0220.0220.0000.0000.0000.000
13A29TYR00.0470.04011.5670.0290.0290.0000.0000.0000.000
14A30MET0-0.033-0.00314.7130.0120.0120.0000.0000.0000.000
15A31ALA0-0.0030.00216.9340.0070.0070.0000.0000.0000.000
16A32SER0-0.038-0.05619.679-0.007-0.0070.0000.0000.0000.000
17A33VAL00.0160.00622.5920.0110.0110.0000.0000.0000.000
18A34GLN0-0.019-0.03424.585-0.003-0.0030.0000.0000.0000.000
19A35LEU00.0640.03228.0320.0060.0060.0000.0000.0000.000
20A36ASN0-0.035-0.03431.7320.0000.0000.0000.0000.0000.000
21A38GLY00.0040.00829.131-0.002-0.0020.0000.0000.0000.000
22A39ALA0-0.0070.01428.737-0.004-0.0040.0000.0000.0000.000
23A40HIS0-0.0160.01623.9170.0070.0070.0000.0000.0000.000
24A41LEU0-0.0140.01027.608-0.002-0.0020.0000.0000.0000.000
25A42CYS0-0.148-0.08127.417-0.007-0.0070.0000.0000.0000.000
26A43GLY00.0220.02623.3560.0030.0030.0000.0000.0000.000
27A44GLY00.0340.01421.9350.0050.0050.0000.0000.0000.000
28A45VAL0-0.019-0.01118.110-0.008-0.0080.0000.0000.0000.000
29A46LEU0-0.0030.01915.2630.0080.0080.0000.0000.0000.000
30A47VAL0-0.002-0.00617.728-0.002-0.0020.0000.0000.0000.000
31A48ALA0-0.008-0.00718.9700.0060.0060.0000.0000.0000.000
32A49GLU-1-0.919-0.96716.6370.2490.2490.0000.0000.0000.000
33A50GLN0-0.068-0.03718.7130.0050.0050.0000.0000.0000.000
34A51TRP00.0400.03221.492-0.011-0.0110.0000.0000.0000.000
35A52VAL00.0170.01020.7180.0020.0020.0000.0000.0000.000
36A53LEU0-0.040-0.01122.778-0.001-0.0010.0000.0000.0000.000
37A54SER00.012-0.01324.097-0.007-0.0070.0000.0000.0000.000
38A55ALA00.0280.01026.6960.0010.0010.0000.0000.0000.000
39A56ALA0-0.028-0.01630.2060.0020.0020.0000.0000.0000.000
40A57HIS10.7900.86831.9330.0120.0120.0000.0000.0000.000
41A59LEU0-0.076-0.03831.5700.0010.0010.0000.0000.0000.000
42A60GLU-1-0.835-0.91734.4060.0020.0020.0000.0000.0000.000
43A61ASP-1-0.967-0.98337.5760.0020.0020.0000.0000.0000.000
44A61ALA00.0130.02336.6020.0000.0000.0000.0000.0000.000
45A61ALA0-0.023-0.01337.5530.0010.0010.0000.0000.0000.000
46A61ASP-1-0.978-1.00938.8230.0190.0190.0000.0000.0000.000
47A62GLY0-0.052-0.02136.5660.0020.0020.0000.0000.0000.000
48A63LYS10.8480.93330.717-0.043-0.0430.0000.0000.0000.000
49A64VAL00.0450.02129.732-0.004-0.0040.0000.0000.0000.000
50A65GLN0-0.113-0.06326.6160.0010.0010.0000.0000.0000.000
51A66VAL00.0160.01721.604-0.008-0.0080.0000.0000.0000.000
52A67LEU0-0.013-0.00119.9540.0100.0100.0000.0000.0000.000
53A68LEU0-0.019-0.02116.578-0.010-0.0100.0000.0000.0000.000
54A69GLY00.0720.02113.6520.0060.0060.0000.0000.0000.000
55A70ALA0-0.036-0.01114.515-0.019-0.0190.0000.0000.0000.000
56A71HIS0-0.0090.01013.880-0.008-0.0080.0000.0000.0000.000
57A72SER0-0.009-0.02415.8290.0130.0130.0000.0000.0000.000
58A73LEU0-0.037-0.01919.1380.0120.0120.0000.0000.0000.000
59A74SER0-0.052-0.02722.0790.0070.0070.0000.0000.0000.000
60A75GLN0-0.0060.00218.489-0.012-0.0120.0000.0000.0000.000
61A76PRO0-0.0040.01219.8400.0090.0090.0000.0000.0000.000
62A77GLU-1-0.681-0.84614.925-0.138-0.1380.0000.0000.0000.000
63A78PRO00.0260.02012.3150.0250.0250.0000.0000.0000.000
64A79SER0-0.034-0.02611.6780.0310.0310.0000.0000.0000.000
65A80LYS10.7670.88813.7650.0680.0680.0000.0000.0000.000
66A81ARG10.9250.95417.298-0.173-0.1730.0000.0000.0000.000
67A82LEU0-0.0040.00119.404-0.008-0.0080.0000.0000.0000.000
68A83TYR00.0130.01417.9030.0240.0240.0000.0000.0000.000
69A84ASP-1-0.774-0.88924.2310.0490.0490.0000.0000.0000.000
70A85VAL0-0.004-0.01327.0160.0070.0070.0000.0000.0000.000
71A86LEU0-0.050-0.00728.693-0.002-0.0020.0000.0000.0000.000
72A87ARG10.8890.91930.357-0.064-0.0640.0000.0000.0000.000
73A88ALA00.0310.02030.4070.0020.0020.0000.0000.0000.000
74A89VAL0-0.038-0.02731.308-0.001-0.0010.0000.0000.0000.000
75A90PRO00.0620.03532.2240.0000.0000.0000.0000.0000.000
76A91HIS00.0030.01534.1440.0020.0020.0000.0000.0000.000
77A92PRO0-0.022-0.00735.408-0.001-0.0010.0000.0000.0000.000
78A93ASP-1-0.910-0.97238.6760.0120.0120.0000.0000.0000.000
79A94SER0-0.091-0.03636.780-0.002-0.0020.0000.0000.0000.000
80A95GLN0-0.006-0.02138.8290.0000.0000.0000.0000.0000.000
81A96PRO00.0520.01940.242-0.002-0.0020.0000.0000.0000.000
82A97ASP-1-1.013-1.00141.301-0.007-0.0070.0000.0000.0000.000
83A98THR0-0.0270.01240.171-0.001-0.0010.0000.0000.0000.000
84A99ILE0-0.017-0.00636.4610.0000.0000.0000.0000.0000.000
85A100ASP-1-0.946-0.97936.740-0.007-0.0070.0000.0000.0000.000
86A101HIS00.0440.03335.3170.0020.0020.0000.0000.0000.000
87A102ASP-1-0.702-0.80933.598-0.002-0.0020.0000.0000.0000.000
88A103LEU0-0.068-0.03328.680-0.002-0.0020.0000.0000.0000.000
89A104LEU00.0210.01329.5530.0030.0030.0000.0000.0000.000
90A105LEU0-0.025-0.00225.9940.0000.0000.0000.0000.0000.000
91A106LEU00.0020.00226.1670.0020.0020.0000.0000.0000.000
92A107GLN00.0460.04625.656-0.001-0.0010.0000.0000.0000.000
93A108LEU00.015-0.00821.073-0.004-0.0040.0000.0000.0000.000
94A109SER00.011-0.01025.2940.0030.0030.0000.0000.0000.000
95A110GLU-1-0.941-0.97422.1350.1610.1610.0000.0000.0000.000
96A111LYS10.9310.96519.663-0.190-0.1900.0000.0000.0000.000
97A112ALA00.0460.02417.2490.0090.0090.0000.0000.0000.000
98A113THR0-0.025-0.00813.6130.0160.0160.0000.0000.0000.000
99A114LEU0-0.014-0.00311.533-0.024-0.0240.0000.0000.0000.000
100A115GLY0-0.007-0.0148.6660.1180.1180.0000.0000.0000.000
101A118PRO0-0.048-0.0304.984-0.041-0.0410.0000.0000.0000.000
102A119ALA00.0600.0336.587-0.128-0.1280.0000.0000.0000.000
103A120VAL0-0.0060.0139.801-0.018-0.0180.0000.0000.0000.000
104A121ARG10.9470.9626.219-0.271-0.2710.0000.0000.0000.000
105A122PRO00.0120.00412.023-0.036-0.0360.0000.0000.0000.000
106A123LEU0-0.0130.00213.9150.0000.0000.0000.0000.0000.000
107A124PRO0-0.030-0.02214.7790.0050.0050.0000.0000.0000.000
108A124TRP00.0370.02218.040-0.019-0.0190.0000.0000.0000.000
109A125GLN0-0.002-0.00521.6350.0130.0130.0000.0000.0000.000
110A126ARG10.7730.83623.939-0.035-0.0350.0000.0000.0000.000
111A127VAL0-0.053-0.02026.4350.0020.0020.0000.0000.0000.000
112A128ASP-1-0.807-0.89228.602-0.010-0.0100.0000.0000.0000.000
113A129ARG10.9390.96730.3290.0190.0190.0000.0000.0000.000
114A129ASP-1-0.798-0.85930.092-0.026-0.0260.0000.0000.0000.000
115A130VAL00.0070.01026.431-0.002-0.0020.0000.0000.0000.000
116A131ALA00.000-0.00528.8160.0010.0010.0000.0000.0000.000
117A132PRO00.0470.03429.587-0.005-0.0050.0000.0000.0000.000
118A133GLY0-0.042-0.01830.669-0.002-0.0020.0000.0000.0000.000
119A134THR0-0.064-0.06524.646-0.008-0.0080.0000.0000.0000.000
120A135LEU0-0.025-0.00923.5770.0040.0040.0000.0000.0000.000
121A136CYS0-0.020-0.00520.613-0.015-0.0150.0000.0000.0000.000
122A137ASP-1-0.829-0.89917.476-0.146-0.1460.0000.0000.0000.000
123A138VAL00.0150.02220.5850.0120.0120.0000.0000.0000.000
124A139ALA00.006-0.01018.796-0.011-0.0110.0000.0000.0000.000
125A140GLY00.011-0.01220.7550.0140.0140.0000.0000.0000.000
126A141TRP0-0.066-0.02518.201-0.005-0.0050.0000.0000.0000.000
127A142GLY0-0.017-0.00523.8280.0080.0080.0000.0000.0000.000
128A152PRO00.017-0.00524.9200.0020.0020.0000.0000.0000.000
129A153ASP-1-0.927-0.95023.392-0.086-0.0860.0000.0000.0000.000
130A154SER00.016-0.01718.9080.0020.0020.0000.0000.0000.000
131A155LEU0-0.0460.00916.1430.0070.0070.0000.0000.0000.000
132A156GLN0-0.068-0.03418.972-0.020-0.0200.0000.0000.0000.000
133A157HIS0-0.010-0.01717.210-0.006-0.0060.0000.0000.0000.000
134A158VAL0-0.0130.00220.533-0.009-0.0090.0000.0000.0000.000
135A159LEU00.0080.01319.4670.0050.0050.0000.0000.0000.000
136A160LEU0-0.019-0.01723.0220.0020.0020.0000.0000.0000.000
137A161PRO0-0.0020.01326.2580.0000.0000.0000.0000.0000.000
138A162VAL00.0650.02327.4290.0050.0050.0000.0000.0000.000
139A163LEU0-0.057-0.02130.002-0.001-0.0010.0000.0000.0000.000
140A164ASP-1-0.789-0.84633.810-0.035-0.0350.0000.0000.0000.000
141A165ARG10.8390.84834.5270.0230.0230.0000.0000.0000.000
142A166ALA0-0.0080.01338.0210.0020.0020.0000.0000.0000.000
143A167THR0-0.089-0.10438.5060.0010.0010.0000.0000.0000.000
144A168CYS0-0.027-0.01032.6200.0020.0020.0000.0000.0000.000
145A169ASN00.0740.04738.8450.0020.0020.0000.0000.0000.000
146A170ARG10.9290.97641.9660.0300.0300.0000.0000.0000.000
147A170ARG10.7540.84636.3750.0450.0450.0000.0000.0000.000
148A170THR0-0.060-0.03439.667-0.001-0.0010.0000.0000.0000.000
149A171HIS0-0.030-0.02242.3530.0010.0010.0000.0000.0000.000
150A172HIS0-0.058-0.02244.9040.0020.0020.0000.0000.0000.000
151A173ASP-1-0.816-0.92143.842-0.018-0.0180.0000.0000.0000.000
152A174GLY0-0.057-0.02744.5090.0010.0010.0000.0000.0000.000
153A175ALA00.0350.03841.2150.0010.0010.0000.0000.0000.000
154A176ILE0-0.066-0.04137.2000.0000.0000.0000.0000.0000.000
155A177THR00.0880.04538.5260.0000.0000.0000.0000.0000.000
156A178GLU-1-0.928-0.96637.312-0.009-0.0090.0000.0000.0000.000
157A179ARG10.9040.93134.805-0.004-0.0040.0000.0000.0000.000
158A180LEU00.0000.01933.5990.0000.0000.0000.0000.0000.000
159A181MET0-0.0050.00127.7140.0000.0000.0000.0000.0000.000
160A183ALA00.0540.04428.798-0.002-0.0020.0000.0000.0000.000
161A184GLU-1-0.827-0.89730.799-0.051-0.0510.0000.0000.0000.000
162A185SER00.0420.00930.593-0.001-0.0010.0000.0000.0000.000
163A186ASN0-0.0350.02630.1970.0060.0060.0000.0000.0000.000
164A187ARG10.9440.95633.7600.0460.0460.0000.0000.0000.000
165A188ARG10.9731.00029.5790.0680.0680.0000.0000.0000.000
166A189ASP-1-0.759-0.89328.662-0.065-0.0650.0000.0000.0000.000
167A190SER0-0.035-0.02131.2930.0040.0040.0000.0000.0000.000
168A191CYS0-0.123-0.06833.6030.0010.0010.0000.0000.0000.000
169A192LYS10.8650.91531.4340.0500.0500.0000.0000.0000.000
170A193GLY00.0120.02628.551-0.003-0.0030.0000.0000.0000.000
171A194ASP-1-0.768-0.87524.737-0.031-0.0310.0000.0000.0000.000
172A195SER00.0650.00727.4090.0000.0000.0000.0000.0000.000
173A196GLY00.0670.04427.2730.0040.0040.0000.0000.0000.000
174A197GLY0-0.037-0.00123.8270.0020.0020.0000.0000.0000.000
175A198PRO0-0.007-0.00120.2540.0020.0020.0000.0000.0000.000
176A199LEU0-0.021-0.00423.014-0.010-0.0100.0000.0000.0000.000
177A200VAL00.014-0.00717.2100.0090.0090.0000.0000.0000.000
178A202GLY00.0270.01218.8000.0060.0060.0000.0000.0000.000
179A207GLY0-0.024-0.01315.7360.0010.0010.0000.0000.0000.000
180A208VAL0-0.0070.01116.4430.0160.0160.0000.0000.0000.000
181A209LEU0-0.028-0.02119.195-0.008-0.0080.0000.0000.0000.000
182A210GLU-1-0.842-0.94021.167-0.024-0.0240.0000.0000.0000.000
183A211GLY00.013-0.00824.5250.0050.0050.0000.0000.0000.000
184A212VAL0-0.0100.00824.906-0.003-0.0030.0000.0000.0000.000
185A213VAL0-0.080-0.00827.0740.0010.0010.0000.0000.0000.000
186A214THR00.0640.01529.2930.0030.0030.0000.0000.0000.000
187A215SER0-0.003-0.01632.3390.0020.0020.0000.0000.0000.000
188A216GLY00.1040.04832.392-0.001-0.0010.0000.0000.0000.000
189A217SER0-0.048-0.02034.4900.0010.0010.0000.0000.0000.000
190A218ARG10.9660.97930.6080.0270.0270.0000.0000.0000.000
191A219VAL0-0.0230.01037.343-0.002-0.0020.0000.0000.0000.000
192A221GLY00.0720.03439.7440.0010.0010.0000.0000.0000.000
193A222ASN0-0.073-0.06140.954-0.004-0.0040.0000.0000.0000.000
194A223ARG10.9780.97742.3990.0220.0220.0000.0000.0000.000
195A223LYS10.9800.97738.9000.0450.0450.0000.0000.0000.000
196A224LYS10.9750.99137.6040.0320.0320.0000.0000.0000.000
197A225PRO00.0080.02435.274-0.003-0.0030.0000.0000.0000.000
198A226GLY00.0400.03731.7270.0020.0020.0000.0000.0000.000
199A227ILE00.0320.00832.757-0.001-0.0010.0000.0000.0000.000
200A228TYR0-0.014-0.01526.7090.0000.0000.0000.0000.0000.000
201A229THR00.0740.03130.2720.0000.0000.0000.0000.0000.000
202A230ARG10.7750.86729.0910.0140.0140.0000.0000.0000.000
203A231VAL00.025-0.00124.7200.0040.0040.0000.0000.0000.000
204A232ALA00.0200.01927.8240.0050.0050.0000.0000.0000.000
205A233SER00.0100.02928.8990.0030.0030.0000.0000.0000.000
206A234TYR0-0.073-0.06830.8980.0010.0010.0000.0000.0000.000
207A235ALA00.0420.01628.9670.0040.0040.0000.0000.0000.000
208A236ALA00.0230.01629.8650.0050.0050.0000.0000.0000.000
209A237TRP00.0360.02830.2940.0030.0030.0000.0000.0000.000
210A238ILE00.0720.03925.8770.0040.0040.0000.0000.0000.000
211A239ASP-1-0.771-0.84527.2580.0510.0510.0000.0000.0000.000
212A240SER0-0.141-0.09028.9780.0050.0050.0000.0000.0000.000
213A241VAL0-0.0010.00129.3000.0030.0030.0000.0000.0000.000
214A242LEU0-0.071-0.03623.8790.0050.0050.0000.0000.0000.000
215A243ALA0-0.062-0.00927.1910.0090.0090.0000.0000.0000.000