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: 52M9Z

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 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 215
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2454068.658151
FMO2-HF: Nuclear repulsion 2370823.731221
FMO2-HF: Total energy -83244.926931
FMO2-MP2: Total energy -83484.254211


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.
-0.5141.439-0.021-0.877-1.0550
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 : -0.033 / q_NPA : -0.030
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].
3A19GLY00.0110.0133.8570.1311.887-0.020-0.858-0.8780.000
4A20ARG10.8960.9376.398-0.238-0.2380.0000.0000.0000.000
5A21GLU-1-0.950-0.9698.8210.1040.1040.0000.0000.0000.000
6A22ALA00.0600.0358.166-0.072-0.0720.0000.0000.0000.000
7A23GLU-1-0.899-0.9466.759-0.271-0.2710.0000.0000.0000.000
8A24ALA0-0.085-0.0413.967-0.0450.0580.000-0.015-0.0880.000
9A25HIS00.0360.0186.121-0.030-0.0300.0000.0000.0000.000
10A26ALA0-0.028-0.0289.042-0.005-0.0050.0000.0000.0000.000
11A27ARG10.8070.87910.3240.2250.2250.0000.0000.0000.000
12A28PRO00.0140.0148.9380.0300.0300.0000.0000.0000.000
13A29TYR00.0520.03611.7400.0320.0320.0000.0000.0000.000
14A30MET0-0.038-0.00414.7820.0170.0170.0000.0000.0000.000
15A31ALA0-0.005-0.00117.1680.0070.0070.0000.0000.0000.000
16A32SER0-0.041-0.04019.899-0.005-0.0050.0000.0000.0000.000
17A33VAL00.0220.00722.8250.0100.0100.0000.0000.0000.000
18A34GLN0-0.023-0.03224.2490.0000.0000.0000.0000.0000.000
19A35LEU00.0640.03728.1460.0050.0050.0000.0000.0000.000
20A36ASN0-0.025-0.03131.8140.0000.0000.0000.0000.0000.000
21A38GLY00.0050.00928.933-0.001-0.0010.0000.0000.0000.000
22A39ALA0-0.0120.01328.475-0.004-0.0040.0000.0000.0000.000
23A40HIS0-0.027-0.00924.4010.0070.0070.0000.0000.0000.000
24A41LEU0-0.0030.01527.602-0.001-0.0010.0000.0000.0000.000
25A42CYS0-0.145-0.07227.634-0.006-0.0060.0000.0000.0000.000
26A43GLY00.0210.02423.5610.0020.0020.0000.0000.0000.000
27A44GLY00.0310.01822.0910.0060.0060.0000.0000.0000.000
28A45VAL0-0.010-0.00518.118-0.010-0.0100.0000.0000.0000.000
29A46LEU0-0.0120.01115.3510.0100.0100.0000.0000.0000.000
30A47VAL00.001-0.00417.675-0.008-0.0080.0000.0000.0000.000
31A48ALA0-0.005-0.00419.2860.0040.0040.0000.0000.0000.000
32A49GLU-1-0.832-0.90817.0060.1590.1590.0000.0000.0000.000
33A50GLN0-0.024-0.01618.9670.0030.0030.0000.0000.0000.000
34A51TRP00.0390.03321.779-0.006-0.0060.0000.0000.0000.000
35A52VAL00.0100.00620.740-0.002-0.0020.0000.0000.0000.000
36A53LEU0-0.034-0.00522.7870.0020.0020.0000.0000.0000.000
37A54SER00.010-0.02124.127-0.007-0.0070.0000.0000.0000.000
38A55ALA00.0260.01026.7460.0010.0010.0000.0000.0000.000
39A56ALA0-0.022-0.01330.2500.0020.0020.0000.0000.0000.000
40A57HIS10.8170.87931.9030.0260.0260.0000.0000.0000.000
41A59LEU0-0.057-0.02831.9160.0010.0010.0000.0000.0000.000
42A60GLU-1-0.864-0.93634.574-0.007-0.0070.0000.0000.0000.000
43A61ASP-1-0.941-0.96637.740-0.004-0.0040.0000.0000.0000.000
44A61ALA00.0070.02036.8630.0000.0000.0000.0000.0000.000
45A61ALA0-0.020-0.01337.7450.0010.0010.0000.0000.0000.000
46A61ASP-1-0.979-1.00739.0590.0120.0120.0000.0000.0000.000
47A62GLY0-0.052-0.02336.6300.0020.0020.0000.0000.0000.000
48A63LYS10.8070.90330.470-0.035-0.0350.0000.0000.0000.000
49A64VAL00.0440.01929.890-0.003-0.0030.0000.0000.0000.000
50A65GLN0-0.097-0.05526.7040.0020.0020.0000.0000.0000.000
51A66VAL00.0110.00621.929-0.008-0.0080.0000.0000.0000.000
52A67LEU0-0.0170.00320.0120.0100.0100.0000.0000.0000.000
53A68LEU0-0.010-0.01416.763-0.012-0.0120.0000.0000.0000.000
54A69GLY00.0720.02513.7010.0100.0100.0000.0000.0000.000
55A70ALA0-0.030-0.00714.244-0.012-0.0120.0000.0000.0000.000
56A71HIS00.0020.00513.464-0.017-0.0170.0000.0000.0000.000
57A72SER0-0.036-0.04115.5350.0090.0090.0000.0000.0000.000
58A73LEU0-0.040-0.01718.6470.0130.0130.0000.0000.0000.000
59A74SER0-0.057-0.05821.6360.0080.0080.0000.0000.0000.000
60A75GLN00.0080.01118.792-0.004-0.0040.0000.0000.0000.000
61A76PRO0-0.0080.00719.1640.0050.0050.0000.0000.0000.000
62A77GLU-1-0.674-0.84014.234-0.124-0.1240.0000.0000.0000.000
63A78PRO00.0120.01611.8220.0190.0190.0000.0000.0000.000
64A79SER0-0.031-0.02411.5000.0300.0300.0000.0000.0000.000
65A80LYS10.7530.89013.5920.0540.0540.0000.0000.0000.000
66A81ARG10.8820.92716.972-0.138-0.1380.0000.0000.0000.000
67A82LEU0-0.022-0.00319.262-0.010-0.0100.0000.0000.0000.000
68A83TYR00.0180.01318.3300.0170.0170.0000.0000.0000.000
69A84ASP-1-0.738-0.86224.0040.0360.0360.0000.0000.0000.000
70A85VAL0-0.001-0.01226.8330.0040.0040.0000.0000.0000.000
71A86LEU0-0.056-0.00128.5740.0000.0000.0000.0000.0000.000
72A87ARG10.8790.92230.400-0.041-0.0410.0000.0000.0000.000
73A88ALA00.0330.01730.5410.0000.0000.0000.0000.0000.000
74A89VAL0-0.028-0.02631.3560.0000.0000.0000.0000.0000.000
75A90PRO00.0680.03832.219-0.002-0.0020.0000.0000.0000.000
76A91HIS00.0090.01133.9260.0020.0020.0000.0000.0000.000
77A92PRO0-0.031-0.01935.3490.0000.0000.0000.0000.0000.000
78A93ASP-1-0.910-0.96638.589-0.001-0.0010.0000.0000.0000.000
79A94SER0-0.099-0.03336.728-0.002-0.0020.0000.0000.0000.000
80A95GLN0-0.002-0.01738.8000.0020.0020.0000.0000.0000.000
81A96PRO00.0460.02440.312-0.002-0.0020.0000.0000.0000.000
82A97ASP-1-1.021-1.00941.365-0.014-0.0140.0000.0000.0000.000
83A98THR0-0.0140.00740.262-0.001-0.0010.0000.0000.0000.000
84A99ILE0-0.015-0.00336.6820.0000.0000.0000.0000.0000.000
85A100ASP-1-0.951-0.97936.683-0.019-0.0190.0000.0000.0000.000
86A101HIS00.0310.00835.1780.0010.0010.0000.0000.0000.000
87A102ASP-1-0.705-0.81633.713-0.017-0.0170.0000.0000.0000.000
88A103LEU0-0.060-0.02528.693-0.003-0.0030.0000.0000.0000.000
89A104LEU00.0020.00529.5440.0040.0040.0000.0000.0000.000
90A105LEU0-0.0220.00326.154-0.002-0.0020.0000.0000.0000.000
91A106LEU00.0030.00526.1960.0030.0030.0000.0000.0000.000
92A107GLN00.0260.02425.761-0.003-0.0030.0000.0000.0000.000
93A108LEU00.020-0.00321.121-0.002-0.0020.0000.0000.0000.000
94A109SER00.033-0.00525.2430.0020.0020.0000.0000.0000.000
95A110GLU-1-0.882-0.93121.9840.1410.1410.0000.0000.0000.000
96A111LYS10.8120.89119.615-0.159-0.1590.0000.0000.0000.000
97A112ALA00.0370.02117.1060.0110.0110.0000.0000.0000.000
98A113THR0-0.033-0.01813.4580.0110.0110.0000.0000.0000.000
99A114LEU0-0.009-0.00211.600-0.023-0.0230.0000.0000.0000.000
100A115GLY0-0.001-0.0138.2850.1170.1170.0000.0000.0000.000
101A118PRO0-0.031-0.0224.738-0.166-0.072-0.001-0.004-0.0890.000
102A119ALA00.0640.0366.588-0.127-0.1270.0000.0000.0000.000
103A120VAL00.0040.0139.910-0.008-0.0080.0000.0000.0000.000
104A121ARG10.9030.9397.749-0.079-0.0790.0000.0000.0000.000
105A122PRO00.0150.00312.112-0.028-0.0280.0000.0000.0000.000
106A123LEU0-0.0020.00513.906-0.012-0.0120.0000.0000.0000.000
107A124PRO0-0.033-0.01614.7090.0120.0120.0000.0000.0000.000
108A124TRP00.0280.01217.946-0.016-0.0160.0000.0000.0000.000
109A125GLN0-0.005-0.00921.4380.0110.0110.0000.0000.0000.000
110A126ARG10.7810.85023.7570.0020.0020.0000.0000.0000.000
111A127VAL0-0.058-0.02726.2390.0040.0040.0000.0000.0000.000
112A128ASP-1-0.779-0.87828.423-0.030-0.0300.0000.0000.0000.000
113A129ARG10.9350.96429.9430.0400.0400.0000.0000.0000.000
114A129ASP-1-0.796-0.85629.739-0.043-0.0430.0000.0000.0000.000
115A130VAL00.0100.00826.091-0.003-0.0030.0000.0000.0000.000
116A131ALA00.004-0.00328.4590.0020.0020.0000.0000.0000.000
117A132PRO00.0460.02129.276-0.005-0.0050.0000.0000.0000.000
118A133GLY0-0.043-0.01930.404-0.001-0.0010.0000.0000.0000.000
119A134THR0-0.056-0.04524.367-0.009-0.0090.0000.0000.0000.000
120A135LEU0-0.026-0.01223.4920.0040.0040.0000.0000.0000.000
121A136CYS0-0.016-0.00520.442-0.015-0.0150.0000.0000.0000.000
122A137ASP-1-0.795-0.86118.052-0.167-0.1670.0000.0000.0000.000
123A138VAL00.0230.02520.4940.0090.0090.0000.0000.0000.000
124A139ALA00.002-0.01118.882-0.009-0.0090.0000.0000.0000.000
125A140GLY00.021-0.00520.8580.0130.0130.0000.0000.0000.000
126A141TRP0-0.079-0.03118.136-0.005-0.0050.0000.0000.0000.000
127A142GLY0-0.010-0.00223.8870.0080.0080.0000.0000.0000.000
128A152PRO00.010-0.00724.5680.0020.0020.0000.0000.0000.000
129A153ASP-1-0.898-0.91122.874-0.080-0.0800.0000.0000.0000.000
130A154SER00.018-0.00218.868-0.005-0.0050.0000.0000.0000.000
131A155LEU0-0.0360.01516.0910.0060.0060.0000.0000.0000.000
132A156GLN0-0.082-0.05118.902-0.018-0.0180.0000.0000.0000.000
133A157HIS0-0.035-0.03717.341-0.011-0.0110.0000.0000.0000.000
134A158VAL0-0.0100.00320.657-0.006-0.0060.0000.0000.0000.000
135A159LEU0-0.0010.00919.3980.0030.0030.0000.0000.0000.000
136A160LEU0-0.007-0.01122.9530.0040.0040.0000.0000.0000.000
137A161PRO0-0.0090.00726.112-0.001-0.0010.0000.0000.0000.000
138A162VAL00.0410.01627.1490.0050.0050.0000.0000.0000.000
139A163LEU0-0.048-0.01529.7990.0000.0000.0000.0000.0000.000
140A164ASP-1-0.789-0.86433.608-0.045-0.0450.0000.0000.0000.000
141A165ARG10.8310.84934.3230.0370.0370.0000.0000.0000.000
142A166ALA00.0080.01837.7890.0020.0020.0000.0000.0000.000
143A167THR0-0.094-0.08638.3470.0020.0020.0000.0000.0000.000
144A168CYS0-0.034-0.02232.4840.0020.0020.0000.0000.0000.000
145A169ASN00.0490.01938.6920.0020.0020.0000.0000.0000.000
146A170ARG10.9340.97441.8060.0380.0380.0000.0000.0000.000
147A170ARG10.7390.83536.2200.0530.0530.0000.0000.0000.000
148A170THR0-0.058-0.02339.559-0.002-0.0020.0000.0000.0000.000
149A171HIS0-0.048-0.03442.2770.0020.0020.0000.0000.0000.000
150A172HIS0-0.051-0.02344.8050.0010.0010.0000.0000.0000.000
151A173ASP-1-0.781-0.89343.623-0.026-0.0260.0000.0000.0000.000
152A174GLY0-0.039-0.01544.3470.0010.0010.0000.0000.0000.000
153A175ALA00.0160.02841.1750.0010.0010.0000.0000.0000.000
154A176ILE0-0.066-0.04036.893-0.001-0.0010.0000.0000.0000.000
155A177THR00.0940.04738.4200.0000.0000.0000.0000.0000.000
156A178GLU-1-0.935-0.97337.052-0.023-0.0230.0000.0000.0000.000
157A179ARG10.9160.94934.5680.0120.0120.0000.0000.0000.000
158A180LEU0-0.0050.01833.432-0.001-0.0010.0000.0000.0000.000
159A181MET00.0000.00427.316-0.001-0.0010.0000.0000.0000.000
160A183ALA00.0500.04228.682-0.003-0.0030.0000.0000.0000.000
161A184GLU-1-0.793-0.86730.691-0.057-0.0570.0000.0000.0000.000
162A185SER0-0.027-0.01530.641-0.001-0.0010.0000.0000.0000.000
163A186ASN0-0.072-0.04130.7090.0070.0070.0000.0000.0000.000
164A187ARG10.8630.91133.8270.0500.0500.0000.0000.0000.000
165A188ARG11.0241.01829.2930.0710.0710.0000.0000.0000.000
166A189ASP-1-0.701-0.84029.284-0.074-0.0740.0000.0000.0000.000
167A190SER0-0.045-0.02031.4200.0040.0040.0000.0000.0000.000
168A191CYS0-0.106-0.06133.7430.0010.0010.0000.0000.0000.000
169A192LYS10.8590.91531.9100.0480.0480.0000.0000.0000.000
170A193GLY00.0150.03028.747-0.003-0.0030.0000.0000.0000.000
171A194ASP-1-0.761-0.86124.895-0.045-0.0450.0000.0000.0000.000
172A195SER00.0670.01727.597-0.001-0.0010.0000.0000.0000.000
173A196GLY00.0570.02627.4170.0040.0040.0000.0000.0000.000
174A197GLY0-0.043-0.00323.9030.0000.0000.0000.0000.0000.000
175A198PRO0-0.0010.00720.1230.0030.0030.0000.0000.0000.000
176A199LEU0-0.027-0.01522.984-0.008-0.0080.0000.0000.0000.000
177A200VAL00.009-0.00716.9960.0070.0070.0000.0000.0000.000
178A202GLY00.0340.01318.4410.0050.0050.0000.0000.0000.000
179A207GLY0-0.026-0.01315.391-0.003-0.0030.0000.0000.0000.000
180A208VAL0-0.0150.00316.1260.0090.0090.0000.0000.0000.000
181A209LEU0-0.023-0.01718.889-0.004-0.0040.0000.0000.0000.000
182A210GLU-1-0.833-0.93220.958-0.051-0.0510.0000.0000.0000.000
183A211GLY00.016-0.00324.3640.0070.0070.0000.0000.0000.000
184A212VAL0-0.0110.00624.813-0.005-0.0050.0000.0000.0000.000
185A213VAL0-0.082-0.01527.0230.0030.0030.0000.0000.0000.000
186A214THR00.0650.01329.2920.0030.0030.0000.0000.0000.000
187A215SER0-0.026-0.01932.3620.0030.0030.0000.0000.0000.000
188A216GLY00.1060.04332.496-0.001-0.0010.0000.0000.0000.000
189A217SER0-0.045-0.01434.6300.0020.0020.0000.0000.0000.000
190A218ARG10.9520.96130.5170.0340.0340.0000.0000.0000.000
191A219VAL0-0.0160.01037.557-0.001-0.0010.0000.0000.0000.000
192A221GLY00.0770.03739.9150.0020.0020.0000.0000.0000.000
193A222ASN00.003-0.00541.108-0.004-0.0040.0000.0000.0000.000
194A223ARG10.9970.98842.4930.0260.0260.0000.0000.0000.000
195A223LYS10.9620.98039.0640.0480.0480.0000.0000.0000.000
196A224LYS10.9310.96337.1850.0420.0420.0000.0000.0000.000
197A225PRO00.0190.01835.236-0.003-0.0030.0000.0000.0000.000
198A226GLY00.0290.03131.6980.0030.0030.0000.0000.0000.000
199A227ILE00.0250.00432.677-0.002-0.0020.0000.0000.0000.000
200A228TYR0-0.006-0.00726.704-0.001-0.0010.0000.0000.0000.000
201A229THR00.0810.03730.3300.0000.0000.0000.0000.0000.000
202A230ARG10.7740.86928.9420.0320.0320.0000.0000.0000.000
203A231VAL00.023-0.00424.4320.0050.0050.0000.0000.0000.000
204A232ALA00.0210.02027.5140.0050.0050.0000.0000.0000.000
205A233SER0-0.0100.01428.6380.0040.0040.0000.0000.0000.000
206A234TYR0-0.060-0.05130.6990.0020.0020.0000.0000.0000.000
207A235ALA00.0360.01428.9360.0040.0040.0000.0000.0000.000
208A236ALA00.0230.01429.9030.0040.0040.0000.0000.0000.000
209A237TRP00.0360.03030.1570.0030.0030.0000.0000.0000.000
210A238ILE00.0650.03725.9070.0040.0040.0000.0000.0000.000
211A239ASP-1-0.776-0.85127.3250.0170.0170.0000.0000.0000.000
212A240SER0-0.131-0.08629.1850.0050.0050.0000.0000.0000.000
213A241VAL0-0.008-0.00629.5630.0040.0040.0000.0000.0000.000
214A242LEU0-0.069-0.03424.1550.0050.0050.0000.0000.0000.000
215A243ALA0-0.058-0.00827.5610.0080.0080.0000.0000.0000.000