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

tag_button

FMODB ID: YZL62

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 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 215
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2455266.451627
FMO2-HF: Nuclear repulsion 2372020.896505
FMO2-HF: Total energy -83245.555122
FMO2-MP2: Total energy -83484.764338


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.
-1.8140.796-0.018-1.222-1.369-0.001
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 : -0.021 / q_NPA : -0.024
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].
3A19GLY00.0220.0203.410-1.0991.218-0.021-1.178-1.118-0.001
4A20ARG10.8900.9455.481-0.377-0.3770.0000.0000.0000.000
5A21GLU-1-0.904-0.9727.9040.2630.2630.0000.0000.0000.000
6A22ALA0-0.0180.0008.137-0.092-0.0920.0000.0000.0000.000
7A23GLU-1-0.867-0.9306.350-0.120-0.1200.0000.0000.0000.000
8A24ALA0-0.061-0.0353.575-0.1030.0700.004-0.037-0.1400.000
9A25HIS00.0040.0015.726-0.084-0.0840.0000.0000.0000.000
10A26ALA0-0.012-0.0199.079-0.001-0.0010.0000.0000.0000.000
11A27ARG10.8210.89710.0760.2100.2100.0000.0000.0000.000
12A28PRO00.0140.0198.7690.0350.0350.0000.0000.0000.000
13A29TYR00.0510.03111.5390.0400.0400.0000.0000.0000.000
14A30MET0-0.047-0.00814.7780.0160.0160.0000.0000.0000.000
15A31ALA0-0.002-0.00317.2030.0110.0110.0000.0000.0000.000
16A32SER0-0.039-0.03219.978-0.007-0.0070.0000.0000.0000.000
17A33VAL00.0300.00722.4710.0120.0120.0000.0000.0000.000
18A34GLN0-0.035-0.03423.884-0.002-0.0020.0000.0000.0000.000
19A35LEU00.0450.02127.7910.0050.0050.0000.0000.0000.000
20A36ASN0-0.017-0.01631.3930.0000.0000.0000.0000.0000.000
21A38GLY00.0220.02428.6360.0000.0000.0000.0000.0000.000
22A39ALA0-0.021-0.00328.363-0.004-0.0040.0000.0000.0000.000
23A40HIS0-0.0100.00324.1850.0080.0080.0000.0000.0000.000
24A41LEU0-0.0160.00827.262-0.002-0.0020.0000.0000.0000.000
25A42CYS0-0.154-0.07027.541-0.007-0.0070.0000.0000.0000.000
26A43GLY00.0150.01023.3440.0030.0030.0000.0000.0000.000
27A44GLY00.0600.03422.0390.0060.0060.0000.0000.0000.000
28A45VAL0-0.035-0.01518.086-0.010-0.0100.0000.0000.0000.000
29A46LEU0-0.0020.00815.4720.0100.0100.0000.0000.0000.000
30A47VAL00.004-0.00518.002-0.009-0.0090.0000.0000.0000.000
31A48ALA00.000-0.00319.4840.0030.0030.0000.0000.0000.000
32A49GLU-1-0.818-0.90417.0210.1920.1920.0000.0000.0000.000
33A50GLN0-0.0130.00818.9270.0070.0070.0000.0000.0000.000
34A51TRP00.0290.02021.528-0.009-0.0090.0000.0000.0000.000
35A52VAL00.0090.00920.791-0.002-0.0020.0000.0000.0000.000
36A53LEU0-0.0160.00122.9060.0010.0010.0000.0000.0000.000
37A54SER00.014-0.02324.024-0.007-0.0070.0000.0000.0000.000
38A55ALA00.0220.01026.7550.0010.0010.0000.0000.0000.000
39A56ALA0-0.0020.00530.3540.0030.0030.0000.0000.0000.000
40A57HIS10.8330.88532.0090.0210.0210.0000.0000.0000.000
41A59LEU0-0.040-0.02732.0110.0020.0020.0000.0000.0000.000
42A60GLU-1-0.881-0.93634.778-0.001-0.0010.0000.0000.0000.000
43A61ASP-1-0.938-0.96437.8100.0010.0010.0000.0000.0000.000
44A61ALA0-0.023-0.01036.8760.0010.0010.0000.0000.0000.000
45A61ALA0-0.021-0.00437.8820.0020.0020.0000.0000.0000.000
46A61ASP-1-0.982-1.00739.4580.0200.0200.0000.0000.0000.000
47A62GLY0-0.0120.01136.4980.0020.0020.0000.0000.0000.000
48A63LYS10.8100.89030.336-0.050-0.0500.0000.0000.0000.000
49A64VAL00.0380.01830.092-0.002-0.0020.0000.0000.0000.000
50A65GLN0-0.101-0.05726.6340.0020.0020.0000.0000.0000.000
51A66VAL00.011-0.00421.951-0.008-0.0080.0000.0000.0000.000
52A67LEU0-0.0240.00419.3860.0120.0120.0000.0000.0000.000
53A68LEU0-0.008-0.00916.665-0.013-0.0130.0000.0000.0000.000
54A69GLY00.0660.02613.3020.0110.0110.0000.0000.0000.000
55A70ALA0-0.028-0.00713.947-0.009-0.0090.0000.0000.0000.000
56A71HIS00.0030.00513.425-0.020-0.0200.0000.0000.0000.000
57A72SER0-0.051-0.05215.4300.0100.0100.0000.0000.0000.000
58A73LEU0-0.019-0.00918.3200.0150.0150.0000.0000.0000.000
59A74SER0-0.052-0.05421.2510.0090.0090.0000.0000.0000.000
60A75GLN00.0300.04218.1980.0010.0010.0000.0000.0000.000
61A76PRO0-0.0040.00018.7870.0090.0090.0000.0000.0000.000
62A77GLU-1-0.698-0.85713.853-0.108-0.1080.0000.0000.0000.000
63A78PRO00.0070.01511.6290.0170.0170.0000.0000.0000.000
64A79SER0-0.034-0.03210.9180.0330.0330.0000.0000.0000.000
65A80LYS10.7650.89512.9650.0330.0330.0000.0000.0000.000
66A81ARG10.8550.91316.419-0.188-0.1880.0000.0000.0000.000
67A82LEU0-0.007-0.00118.825-0.010-0.0100.0000.0000.0000.000
68A83TYR00.0000.00018.1230.0200.0200.0000.0000.0000.000
69A84ASP-1-0.742-0.86323.8240.0500.0500.0000.0000.0000.000
70A85VAL0-0.018-0.02126.4230.0050.0050.0000.0000.0000.000
71A86LEU0-0.045-0.00528.435-0.002-0.0020.0000.0000.0000.000
72A87ARG10.8970.93730.376-0.053-0.0530.0000.0000.0000.000
73A88ALA00.0180.01630.4260.0010.0010.0000.0000.0000.000
74A89VAL0-0.027-0.01531.7430.0000.0000.0000.0000.0000.000
75A90PRO00.0790.03832.294-0.002-0.0020.0000.0000.0000.000
76A91HIS00.0010.00734.2870.0020.0020.0000.0000.0000.000
77A92PRO0-0.027-0.01135.584-0.001-0.0010.0000.0000.0000.000
78A93ASP-1-0.864-0.92939.0530.0020.0020.0000.0000.0000.000
79A94SER0-0.123-0.06936.925-0.002-0.0020.0000.0000.0000.000
80A95GLN0-0.028-0.02639.0180.0020.0020.0000.0000.0000.000
81A96PRO00.0210.00740.697-0.002-0.0020.0000.0000.0000.000
82A97ASP-1-0.977-0.96941.737-0.010-0.0100.0000.0000.0000.000
83A98THR0-0.038-0.01740.294-0.001-0.0010.0000.0000.0000.000
84A99ILE00.0000.00236.5210.0000.0000.0000.0000.0000.000
85A100ASP-1-0.907-0.95436.662-0.016-0.0160.0000.0000.0000.000
86A101HIS00.0300.00635.3000.0010.0010.0000.0000.0000.000
87A102ASP-1-0.722-0.83233.622-0.012-0.0120.0000.0000.0000.000
88A103LEU0-0.079-0.04228.472-0.003-0.0030.0000.0000.0000.000
89A104LEU0-0.0020.00229.5750.0040.0040.0000.0000.0000.000
90A105LEU0-0.0130.00426.282-0.001-0.0010.0000.0000.0000.000
91A106LEU00.003-0.00426.2260.0020.0020.0000.0000.0000.000
92A107GLN00.0260.01525.711-0.003-0.0030.0000.0000.0000.000
93A108LEU00.0300.00220.885-0.001-0.0010.0000.0000.0000.000
94A109SER00.013-0.00624.9160.0010.0010.0000.0000.0000.000
95A110GLU-1-0.866-0.92021.7220.1770.1770.0000.0000.0000.000
96A111LYS10.7910.87919.227-0.195-0.1950.0000.0000.0000.000
97A112ALA00.0460.02416.7670.0160.0160.0000.0000.0000.000
98A113THR0-0.040-0.02513.4990.0120.0120.0000.0000.0000.000
99A114LEU0-0.0050.00111.359-0.008-0.0080.0000.0000.0000.000
100A115GLY00.007-0.0018.2260.1400.1400.0000.0000.0000.000
101A118PRO0-0.034-0.0094.582-0.195-0.075-0.001-0.007-0.1110.000
102A119ALA00.0410.0216.241-0.196-0.1960.0000.0000.0000.000
103A120VAL00.0030.0139.493-0.016-0.0160.0000.0000.0000.000
104A121ARG10.8890.9227.832-0.160-0.1600.0000.0000.0000.000
105A122PRO00.0150.00912.286-0.031-0.0310.0000.0000.0000.000
106A123LEU0-0.0090.00314.010-0.014-0.0140.0000.0000.0000.000
107A124PRO0-0.023-0.01214.9770.0130.0130.0000.0000.0000.000
108A124TRP00.0330.01718.179-0.015-0.0150.0000.0000.0000.000
109A125GLN00.008-0.00321.6250.0110.0110.0000.0000.0000.000
110A126ARG10.7680.83624.085-0.002-0.0020.0000.0000.0000.000
111A127VAL0-0.054-0.02326.9530.0040.0040.0000.0000.0000.000
112A128ASP-1-0.755-0.86029.100-0.027-0.0270.0000.0000.0000.000
113A129ARG10.9420.96930.4300.0380.0380.0000.0000.0000.000
114A129ASP-1-0.801-0.85030.237-0.040-0.0400.0000.0000.0000.000
115A130VAL00.018-0.00126.263-0.003-0.0030.0000.0000.0000.000
116A131ALA00.0150.01028.8180.0030.0030.0000.0000.0000.000
117A132PRO00.0210.00729.692-0.005-0.0050.0000.0000.0000.000
118A133GLY0-0.022-0.00230.711-0.001-0.0010.0000.0000.0000.000
119A134THR0-0.057-0.04624.610-0.008-0.0080.0000.0000.0000.000
120A135LEU0-0.027-0.01123.5200.0040.0040.0000.0000.0000.000
121A136CYS0-0.0270.00020.456-0.016-0.0160.0000.0000.0000.000
122A137ASP-1-0.807-0.87317.870-0.159-0.1590.0000.0000.0000.000
123A138VAL00.0130.01520.6230.0100.0100.0000.0000.0000.000
124A139ALA0-0.002-0.00819.026-0.010-0.0100.0000.0000.0000.000
125A140GLY00.019-0.00220.9980.0130.0130.0000.0000.0000.000
126A141TRP0-0.064-0.03718.081-0.006-0.0060.0000.0000.0000.000
127A142GLY0-0.010-0.00123.9630.0080.0080.0000.0000.0000.000
128A152PRO00.025-0.00124.4300.0020.0020.0000.0000.0000.000
129A153ASP-1-0.911-0.92022.700-0.072-0.0720.0000.0000.0000.000
130A154SER00.0220.01018.672-0.005-0.0050.0000.0000.0000.000
131A155LEU0-0.0350.00715.7450.0030.0030.0000.0000.0000.000
132A156GLN0-0.077-0.04218.752-0.018-0.0180.0000.0000.0000.000
133A157HIS0-0.034-0.04017.487-0.012-0.0120.0000.0000.0000.000
134A158VAL0-0.009-0.00120.669-0.005-0.0050.0000.0000.0000.000
135A159LEU00.0080.01419.4160.0020.0020.0000.0000.0000.000
136A160LEU0-0.018-0.01522.8380.0050.0050.0000.0000.0000.000
137A161PRO0-0.0190.00226.213-0.001-0.0010.0000.0000.0000.000
138A162VAL00.0680.01927.1230.0060.0060.0000.0000.0000.000
139A163LEU0-0.068-0.03129.7370.0000.0000.0000.0000.0000.000
140A164ASP-1-0.783-0.86533.580-0.042-0.0420.0000.0000.0000.000
141A165ARG10.8390.87034.5600.0340.0340.0000.0000.0000.000
142A166ALA00.0040.01837.9610.0020.0020.0000.0000.0000.000
143A167THR0-0.064-0.07938.7180.0020.0020.0000.0000.0000.000
144A168CYS0-0.060-0.02932.3270.0020.0020.0000.0000.0000.000
145A169ASN00.0640.03038.5920.0020.0020.0000.0000.0000.000
146A170ARG10.8670.93741.8910.0380.0380.0000.0000.0000.000
147A170ARG10.7320.82935.9490.0510.0510.0000.0000.0000.000
148A170THR0-0.039-0.03239.768-0.002-0.0020.0000.0000.0000.000
149A171HIS0-0.054-0.04142.4340.0020.0020.0000.0000.0000.000
150A172HIS0-0.019-0.01345.0180.0010.0010.0000.0000.0000.000
151A173ASP-1-0.808-0.88543.541-0.024-0.0240.0000.0000.0000.000
152A174GLY0-0.0190.00644.5800.0020.0020.0000.0000.0000.000
153A175ALA00.0120.01341.3010.0010.0010.0000.0000.0000.000
154A176ILE0-0.054-0.03236.7450.0000.0000.0000.0000.0000.000
155A177THR00.0670.02338.654-0.001-0.0010.0000.0000.0000.000
156A178GLU-1-0.927-0.97137.500-0.020-0.0200.0000.0000.0000.000
157A179ARG10.9150.96334.7560.0070.0070.0000.0000.0000.000
158A180LEU00.0100.02633.431-0.001-0.0010.0000.0000.0000.000
159A181MET00.0000.01027.340-0.001-0.0010.0000.0000.0000.000
160A183ALA00.0480.03628.732-0.003-0.0030.0000.0000.0000.000
161A184GLU-1-0.779-0.86330.589-0.055-0.0550.0000.0000.0000.000
162A185SER0-0.035-0.01330.373-0.001-0.0010.0000.0000.0000.000
163A186ASN0-0.068-0.04031.0040.0070.0070.0000.0000.0000.000
164A187ARG10.8530.91133.9920.0480.0480.0000.0000.0000.000
165A188ARG10.9931.00228.8860.0690.0690.0000.0000.0000.000
166A189ASP-1-0.703-0.84929.337-0.070-0.0700.0000.0000.0000.000
167A190SER0-0.044-0.02131.0910.0050.0050.0000.0000.0000.000
168A191CYS0-0.097-0.03433.7470.0010.0010.0000.0000.0000.000
169A192LYS10.9150.93531.8200.0430.0430.0000.0000.0000.000
170A193GLY00.0410.04028.491-0.003-0.0030.0000.0000.0000.000
171A194ASP-1-0.767-0.85824.972-0.035-0.0350.0000.0000.0000.000
172A195SER00.0240.00627.643-0.001-0.0010.0000.0000.0000.000
173A196GLY00.0680.01727.2950.0040.0040.0000.0000.0000.000
174A197GLY0-0.0350.00123.7750.0000.0000.0000.0000.0000.000
175A198PRO0-0.018-0.00920.2280.0030.0030.0000.0000.0000.000
176A199LEU00.0040.00023.110-0.008-0.0080.0000.0000.0000.000
177A200VAL00.009-0.00317.1180.0070.0070.0000.0000.0000.000
178A202GLY00.0200.00418.5020.0040.0040.0000.0000.0000.000
179A207GLY0-0.0130.00015.588-0.008-0.0080.0000.0000.0000.000
180A208VAL0-0.024-0.00316.2100.0100.0100.0000.0000.0000.000
181A209LEU0-0.018-0.01619.122-0.005-0.0050.0000.0000.0000.000
182A210GLU-1-0.826-0.92321.137-0.047-0.0470.0000.0000.0000.000
183A211GLY00.022-0.00124.5920.0070.0070.0000.0000.0000.000
184A212VAL0-0.0160.00024.902-0.005-0.0050.0000.0000.0000.000
185A213VAL0-0.076-0.01327.0170.0020.0020.0000.0000.0000.000
186A214THR00.0750.01229.2270.0030.0030.0000.0000.0000.000
187A215SER0-0.040-0.01632.4570.0040.0040.0000.0000.0000.000
188A216GLY00.1260.05132.6130.0000.0000.0000.0000.0000.000
189A217SER0-0.037-0.01034.7280.0020.0020.0000.0000.0000.000
190A218ARG10.8920.92730.1060.0290.0290.0000.0000.0000.000
191A219VAL0-0.0010.01437.129-0.001-0.0010.0000.0000.0000.000
192A221GLY00.0760.02939.6840.0020.0020.0000.0000.0000.000
193A222ASN0-0.004-0.00640.867-0.004-0.0040.0000.0000.0000.000
194A223ARG11.0010.99942.2440.0240.0240.0000.0000.0000.000
195A223LYS10.9790.98038.7920.0460.0460.0000.0000.0000.000
196A224LYS10.9140.95537.0470.0400.0400.0000.0000.0000.000
197A225PRO00.0200.01635.206-0.003-0.0030.0000.0000.0000.000
198A226GLY00.0270.04331.4600.0030.0030.0000.0000.0000.000
199A227ILE00.020-0.00732.478-0.002-0.0020.0000.0000.0000.000
200A228TYR00.0030.00826.854-0.001-0.0010.0000.0000.0000.000
201A229THR00.0540.02530.556-0.001-0.0010.0000.0000.0000.000
202A230ARG10.7490.85129.1280.0300.0300.0000.0000.0000.000
203A231VAL00.004-0.00524.5710.0040.0040.0000.0000.0000.000
204A232ALA00.0190.01628.0100.0050.0050.0000.0000.0000.000
205A233SER0-0.038-0.01128.9660.0040.0040.0000.0000.0000.000
206A234TYR0-0.045-0.04030.8070.0020.0020.0000.0000.0000.000
207A235ALA00.0210.01728.9620.0050.0050.0000.0000.0000.000
208A236ALA00.0150.00629.8870.0050.0050.0000.0000.0000.000
209A237TRP00.0030.01330.2870.0030.0030.0000.0000.0000.000
210A238ILE00.0560.03026.1500.0040.0040.0000.0000.0000.000
211A239ASP-1-0.766-0.85427.6650.0250.0250.0000.0000.0000.000
212A240SER0-0.119-0.07029.5890.0060.0060.0000.0000.0000.000
213A241VAL0-0.0070.00229.9210.0030.0030.0000.0000.0000.000
214A242LEU0-0.059-0.03124.3250.0060.0060.0000.0000.0000.000
215A243ALA0-0.066-0.01627.6050.0100.0100.0000.0000.0000.000